Author: "Hummer, Gerhard" / Language: undetermined - Searchworks@Jio Institute Digital Library Search Results

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21 results on '"Hummer, Gerhard"'

1. Efficient generation of random rotation matrices in four dimensions

Author: Bullerjahn, Jakob Tómas, Fábián, Balázs, and Hummer, Gerhard
Subjects: FOS: Physical sciences, Computational Physics (physics.comp-ph), Physics - Computational Physics
Abstract: Markov-chain Monte Carlo algorithms rely on trial moves that are either rejected or accepted based on certain criteria. Here, we provide an efficient algorithm to generate random rotation matrices in four dimensions (4D) covering an arbitrary pre-defined range of rotation angles. The matrices can be combined with Monte Carlo methods for the efficient sampling of the SO(4) group of 4D rotations. The matrices are unbiased and constructed such that repeated rotations result in uniform sampling over SO(4). 4D rotations can be used to optimize the mass partitioning for stable time integration in coarse-grained molecular dynamics simulations and should find further applications in the fields of robotics and computer vision., Comment: 9 pages, 2 figures, 1 table
Published: 2023
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2. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level

Author: Zhu, Rong, Canena, Daniel, Sikora, Mateusz, Klausberger, Miriam, Seferovic, Hannah, Mehdipour, Ahmad Reza, Hain, Lisa, Laurent, Elisabeth, Monteil, Vanessa, Wirnsberger, Gerald, Wieneke, Ralph, Tampé, Robert, Kienzl, Nikolaus F., Mach, Lukas, Mirazimi, Ali, Oh, Yoo Jin, Penninger, Josef M., Hummer, Gerhard, and Hinterdorfer, Peter
Subjects: DYNAMICS, Technology and Engineering, Multidisciplinary, SARS-CoV-2, ACE2, PROTEIN, COVID-19, General Physics and Astronomy, Biological Transport, General Chemistry, ADHESION, General Biochemistry, Genetics and Molecular Biology, Atomic force microscopy, Computational biophysics, Single-molecule biophysics, CELLS, Spike Glycoprotein, Coronavirus, SARS-COV-2 SPIKE, Humans, Angiotensin-Converting Enzyme 2, RECEPTOR-BINDING
Abstract: Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.
Published: 2022
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3. AI-based structure prediction empowers integrative structural analysis of human nuclear pores

Author: Mosalaganti, Shyamal, Obarska-Kosinska, Agnieszka, Siggel, Marc, Taniguchi, Reiya, Turoňová, Beata, Zimmerli, Christian E., Buczak, Katarzyna, Schmidt, Florian H., Margiotta, Erica, Mackmull, Marie-Therese, Hagen, Wim J. H., Hummer, Gerhard, Kosinski, Jan, and Beck, Martin
Subjects: Nuclear Pore Complex Proteins, Proteomics, Multidisciplinary, Artificial Intelligence, Cryoelectron Microscopy, Active Transport, Cell Nucleus, Nuclear Pore, Humans, Molecular Dynamics Simulation
Abstract: INTRODUCTION The eukaryotic nucleus protects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the largest protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaffold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conformational breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial challenge for structural biologists. RATIONALE Considerable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integrative modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous structural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaffold is interconnected by a set of intrinsically disordered linker NUPs that are not straightforwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topology and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination. RESULTS In this study, we used artificial intelligence (AI)–based prediction to generate an extensive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharacterized. Benchmarking against previous and unpublished x-ray and cryo–electron microscopy structures revealed unprecedented accuracy. We obtained well-resolved cryo–electron tomographic maps of both the constricted and dilated conformational states of the human NPC. Using integrative modeling, we fitted the structural models of individual NUPs into the cryo–electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaffold. We elucidated in great detail how membrane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane environment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension. CONCLUSION Our 70-MDa atomically resolved model covers >90% of the human NPC scaffold. It captures conformational changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dynamic model of the NPC. Our study exemplifies how AI-based structure prediction may accelerate the elucidation of subcellular architecture at atomic resolution. A 70-MDa model of the human nuclear pore complex scaffold architecture. The structural model of the human NPC scaffold is shown for the constricted state as a cut-away view. High-resolution models are color coded according to nucleoporin subcomplex membership. The nuclear envelope is shown as a gray surface.
Published: 2022
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4. Rebinding kinetics from single-molecule force spectroscopy experiments close to equilibrium

Author: Bullerjahn, Jakob Tómas and Hummer, Gerhard
Subjects: Quantitative Biology::Subcellular Processes, Quantitative Biology - Biomolecules, Statistical Mechanics (cond-mat.stat-mech), Biological Physics (physics.bio-ph), FOS: Biological sciences, FOS: Physical sciences, Biomolecules (q-bio.BM), Physics - Biological Physics, Quantitative Biology - Quantitative Methods, Condensed Matter - Statistical Mechanics, Quantitative Methods (q-bio.QM)
Abstract: Analysis of bond rupture data from single-molecule force spectroscopy experiments commonly relies on the strong assumption that the bond dissociation process is irreversible. However, with increased spatiotemporal resolution of instruments it is now possible to observe multiple unbinding-rebinding events in a single pulling experiment. Here, we augment the theory of force-induced unbinding by explicitly taking into account rebinding kinetics, and provide approximate analytic solutions of the resulting rate equations. Furthermore, we use a short-time expansion of the exact kinetics to construct numerically efficient maximum likelihood estimators for the parameters of the force-dependent unbinding and rebinding rates, which pair well with and complement established methods, such as the analysis of rate maps. We provide an open-source implementation of the theory, evaluated for Bell-like rates, which we apply to synthetic data generated by a Gillespie stochastic simulation algorithm for time-dependent rates., Comment: 14 pages, 5 figures, 1 table. The article has been submitted to Physical Review Research
Published: 2022
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5. Structural basis of polyamine transport by human ATP13A2 (PARK9)

Author: Sim, Sue Im, von Bülow, Sören, Hummer, Gerhard, and Park, Eunyong
Subjects: spermine, Protein Conformation, Parkinson's disease, 1.1 Normal biological development and functioning, Saccharomyces cerevisiae, Spodoptera, Molecular Dynamics Simulation, Medical and Health Sciences, Catalysis, Cytosol, Protein Domains, polyamine, Underpinning research, Polyamines, P-type ATPase, Animals, Humans, membrane protein, Phosphorylation, Cryoelectron Microscopy, Parkinson Disease, Biological Transport, Biological Sciences, Lipids, Proton-Translocating ATPases, transporter, lysosome, cryo-EM, Generic health relevance, Lysosomes, P5B-ATPase, Developmental Biology
Abstract: Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson's disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryoelectron microscopy (cryo-EM) structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand the functions and mechanisms of P5B-ATPases.
Published: 2021

6. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

Author: Klionsky, Daniel J, Abdel-Aziz, Amal Kamal, Abdelfatah, Sara, Abdellatif, Mahmoud, Abdoli, Asghar, Abel, Steffen, Abeliovich, Hagai, Abildgaard, Marie H, Abudu, Yakubu Princely, Acevedo-Arozena, Abraham, Adamopoulos, Iannis E, Adeli, Khosrow, Adolph, Timon E, Adornetto, Annagrazia, Aflaki, Elma, Agam, Galila, Agarwal, Anupam, Aggarwal, Bharat B, Agnello, Maria, Agostinis, Patrizia, Agrewala, Javed N, Agrotis, Alexander, Aguilar, Patricia V, Ahmad, S Tariq, Ahmed, Zubair M, Ahumada-Castro, Ulises, Aits, Sonja, Aizawa, Shu, Akkoc, Yunus, Akoumianaki, Tonia, Akpinar, Hafize Aysin, Al-Abd, Ahmed M, Al-Akra, Lina, Al-Gharaibeh, Abeer, Alaoui-Jamali, Moulay A, Alberti, Simon, Alcocer-Gómez, Elísabet, Alessandri, Cristiano, Ali, Muhammad, Alim Al-Bari, M Abdul, Aliwaini, Saeb, Alizadeh, Javad, Almacellas, Eugènia, Almasan, Alexandru, Alonso, Alicia, Alonso, Guillermo D, Altan-Bonnet, Nihal, Altieri, Dario C, Álvarez, Élida MC, Alves, Sara, Alves Da Costa, Cristine, Alzaharna, Mazen M, Amadio, Marialaura, Amantini, Consuelo, Amaral, Cristina, Ambrosio, Susanna, Amer, Amal O, Ammanathan, Veena, An, Zhenyi, Andersen, Stig U, Andrabi, Shaida A, Andrade-Silva, Magaiver, Andres, Allen M, Angelini, Sabrina, Ann, David, Anozie, Uche C, Ansari, Mohammad Y, Antas, Pedro, Antebi, Adam, Antón, Zuriñe, Anwar, Tahira, Apetoh, Lionel, Apostolova, Nadezda, Araki, Toshiyuki, Araki, Yasuhiro, Arasaki, Kohei, Araújo, Wagner L, Araya, Jun, Arden, Catherine, Arévalo, Maria-Angeles, Arguelles, Sandro, Arias, Esperanza, Arikkath, Jyothi, Arimoto, Hirokazu, Ariosa, Aileen R, Armstrong-James, Darius, Arnauné-Pelloquin, Laetitia, Aroca, Angeles, Arroyo, Daniela S, Arsov, Ivica, Artero, Rubén, Asaro, Dalia Maria Lucia, Aschner, Michael, Ashrafizadeh, Milad, Ashur-Fabian, Osnat, Atanasov, Atanas G, Au, Alicia K, Auberger, Patrick, Auner, Holger W, Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Ávalos, Yenniffer, Aveic, Sanja, Aveleira, Célia Alexandra, Avin-Wittenberg, Tamar, Aydin, Yucel, Ayton, Scott, Ayyadevara, Srinivas, Azzopardi, Maria, Baba, Misuzu, Backer, Jonathan M, Backues, Steven K, Bae, Dong-Hun, Bae, Ok-Nam, Bae, Soo Han, Baehrecke, Eric H, Baek, Ahruem, Baek, Seung-Hoon, Baek, Sung Hee, Bagetta, Giacinto, Bagniewska-Zadworna, Agnieszka, Bai, Hua, Bai, Jie, Bai, Xiyuan, Bai, Yidong, Bairagi, Nandadulal, Baksi, Shounak, Balbi, Teresa, Baldari, Cosima T, Balduini, Walter, Ballabio, Andrea, Ballester, Maria, Balazadeh, Salma, Balzan, Rena, Bandopadhyay, Rina, Banerjee, Sreeparna, Banerjee, Sulagna, Bánréti, Ágnes, Bao, Yan, Baptista, Mauricio S, Baracca, Alessandra, Barbati, Cristiana, Bargiela, Ariadna, Barilà, Daniela, Barlow, Peter G, Barmada, Sami J, Barreiro, Esther, Barreto, George E, Bartek, Jiri, Bartel, Bonnie, Bartolome, Alberto, Barve, Gaurav R, Basagoudanavar, Suresh H, Bassham, Diane C, Bast, Robert C, Basu, Alakananda, Batoko, Henri, Batten, Isabella, Baulieu, Etienne E, Baumgarner, Bradley L, Bayry, Jagadeesh, Beale, Rupert, Beau, Isabelle, Beaumatin, Florian, Bechara, Luiz RG, Beck, George R, Beers, Michael F, Begun, Jakob, Behrends, Christian, Behrens, Georg MN, Bei, Roberto, Bejarano, Eloy, Bel, Shai, Behl, Christian, Belaid, Amine, Belgareh-Touzé, Naïma, Bellarosa, Cristina, Belleudi, Francesca, Belló Pérez, Melissa, Bello-Morales, Raquel, Beltran, Jackeline Soares De Oliveira, Beltran, Sebastián, Benbrook, Doris Mangiaracina, Bendorius, Mykolas, Benitez, Bruno A, Benito-Cuesta, Irene, Bensalem, Julien, Berchtold, Martin W, Berezowska, Sabina, Bergamaschi, Daniele, Bergami, Matteo, Bergmann, Andreas, Berliocchi, Laura, Berlioz-Torrent, Clarisse, Bernard, Amélie, Berthoux, Lionel, Besirli, Cagri G, Besteiro, Sebastien, Betin, Virginie M, Beyaert, Rudi, Bezbradica, Jelena S, Bhaskar, Kiran, Bhatia-Kissova, Ingrid, Bhattacharya, Resham, Bhattacharya, Sujoy, Bhattacharyya, Shalmoli, Bhuiyan, Md Shenuarin, Bhutia, Sujit Kumar, Bi, Lanrong, Bi, Xiaolin, Biden, Trevor J, Bijian, Krikor, Billes, Viktor A, Binart, Nadine, Bincoletto, Claudia, Birgisdottir, Asa B, Bjorkoy, Geir, Blanco, Gonzalo, Blas-Garcia, Ana, Blasiak, Janusz, Blomgran, Robert, Blomgren, Klas, Blum, Janice S, Boada-Romero, Emilio, Boban, Mirta, Boesze-Battaglia, Kathleen, Boeuf, Philippe, Boland, Barry, Bomont, Pascale, Bonaldo, Paolo, Bonam, Srinivasa Reddy, Bonfili, Laura, Bonifacino, Juan S, Boone, Brian A, Bootman, Martin D, Bordi, Matteo, Borner, Christoph, Bornhauser, Beat C, Borthakur, Gautam, Bosch, Jürgen, Bose, Santanu, Botana, Luis M, Botas, Juan, Boulanger, Chantal M, Boulton, Michael E, Bourdenx, Mathieu, Bourgeois, Benjamin, Bourke, Nollaig M, Bousquet, Guilhem, Boya, Patricia, Bozhkov, Peter V, Bozi, Luiz HM, Bozkurt, Tolga O, Brackney, Doug E, Brandts, Christian H, Braun, Ralf J, Braus, Gerhard H, Bravo-Sagua, Roberto, Bravo-San Pedro, José M, Brest, Patrick, Bringer, Marie-Agnès, Briones-Herrera, Alfredo, Broaddus, V Courtney, Brodersen, Peter, Brodsky, Jeffrey L, Brody, Steven L, Bronson, Paola G, Bronstein, Jeff M, Brown, Carolyn N, Brown, Rhoderick E, Brum, Patricia C, Brumell, John H, Brunetti-Pierri, Nicola, Bruno, Daniele, Bryson-Richardson, Robert J, Bucci, Cecilia, Buchrieser, Carmen, Bueno, Marta, Buitrago-Molina, Laura Elisa, Buraschi, Simone, Buch, Shilpa, Buchan, J Ross, Buckingham, Erin M, Budak, Hikmet, Budini, Mauricio, Bultynck, Geert, Burada, Florin, Burgoyne, Joseph R, Burón, M Isabel, Bustos, Victor, Büttner, Sabrina, Butturini, Elena, Byrd, Aaron, Cabas, Isabel, Cabrera-Benitez, Sandra, Cadwell, Ken, Cai, Jingjing, Cai, Lu, Cai, Qian, Cairó, Montserrat, Calbet, Jose A, Caldwell, Guy A, Caldwell, Kim A, Call, Jarrod A, Calvani, Riccardo, Calvo, Ana C, Calvo-Rubio Barrera, Miguel, Camara, Niels Os, Camonis, Jacques H, Camougrand, Nadine, Campanella, Michelangelo, Campbell, Edward M, Campbell-Valois, François-Xavier, Campello, Silvia, Campesi, Ilaria, Campos, Juliane C, Camuzard, Olivier, Cancino, Jorge, Candido De Almeida, Danilo, Canesi, Laura, Caniggia, Isabella, Canonico, Barbara, Cantí, Carles, Cao, Bin, Caraglia, Michele, Caramés, Beatriz, Carchman, Evie H, Cardenal-Muñoz, Elena, Cardenas, Cesar, Cardenas, Luis, Cardoso, Sandra M, Carew, Jennifer S, Carle, Georges F, Carleton, Gillian, Carloni, Silvia, Carmona-Gutierrez, Didac, Carneiro, Leticia A, Carnevali, Oliana, Carosi, Julian M, Carra, Serena, Carrier, Alice, Carrier, Lucie, Carroll, Bernadette, Carter, A Brent, Carvalho, Andreia Neves, Casanova, Magali, Casas, Caty, Casas, Josefina, Cassioli, Chiara, Castillo, Eliseo F, Castillo, Karen, Castillo-Lluva, Sonia, Castoldi, Francesca, Castori, Marco, Castro, Ariel F, Castro-Caldas, Margarida, Castro-Hernandez, Javier, Castro-Obregon, Susana, Catz, Sergio D, Cavadas, Claudia, Cavaliere, Federica, Cavallini, Gabriella, Cavinato, Maria, Cayuela, Maria L, Cebollada Rica, Paula, Cecarini, Valentina, Cecconi, Francesco, Cechowska-Pasko, Marzanna, Cenci, Simone, Ceperuelo-Mallafré, Victòria, Cerqueira, João J, Cerutti, Janete M, Cervia, Davide, Cetintas, Vildan Bozok, Cetrullo, Silvia, Chae, Han-Jung, Chagin, Andrei S, Chai, Chee-Yin, Chakrabarti, Gopal, Chakrabarti, Oishee, Chakraborty, Tapas, Chakraborty, Trinad, Chami, Mounia, Chamilos, Georgios, Chan, David W, Chan, Edmond YW, Chan, Edward D, Chan, HY Edwin, Chan, Helen H, Chan, Hung, Chan, Matthew TV, Chan, Yau Sang, Chandra, Partha K, Chang, Chih-Peng, Chang, Chunmei, Chang, Hao-Chun, Chang, Kai, Chao, Jie, Chapman, Tracey, Charlet-Berguerand, Nicolas, Chatterjee, Samrat, Chaube, Shail K, Chaudhary, Anu, Chauhan, Santosh, Chaum, Edward, Checler, Frédéric, Cheetham, Michael E, Chen, Chang-Shi, Chen, Guang-Chao, Chen, Jian-Fu, Chen, Liam L, Chen, Leilei, Chen, Lin, Chen, Mingliang, Chen, Mu-Kuan, Chen, Ning, Chen, Quan, Chen, Ruey-Hwa, Chen, Shi, Chen, Wei, Chen, Weiqiang, Chen, Xin-Ming, Chen, Xiong-Wen, Chen, Xu, Chen, Yan, Chen, Ye-Guang, Chen, Yingyu, Chen, Yongqiang, Chen, Yu-Jen, Chen, Yue-Qin, Chen, Zhefan Stephen, Chen, Zhi, Chen, Zhi-Hua, Chen, Zhijian J, Chen, Zhixiang, Cheng, Hanhua, Cheng, Jun, Cheng, Shi-Yuan, Cheng, Wei, Cheng, Xiaodong, Cheng, Xiu-Tang, Cheng, Yiyun, Cheng, Zhiyong, Chen, Zhong, Cheong, Heesun, Cheong, Jit Kong, Chernyak, Boris V, Cherry, Sara, Cheung, Chi Fai Randy, Cheung, Chun Hei Antonio, Cheung, King-Ho, Chevet, Eric, Chi, Richard J, Chiang, Alan Kwok Shing, Chiaradonna, Ferdinando, Chiarelli, Roberto, Chiariello, Mario, Chica, Nathalia, Chiocca, Susanna, Chiong, Mario, Chiou, Shih-Hwa, Chiramel, Abhilash I, Chiurchiù, Valerio, Cho, Dong-Hyung, Choe, Seong-Kyu, Choi, Augustine MK, Choi, Mary E, Choudhury, Kamalika Roy, Chow, Norman S, Chu, Charleen T, Chua, Jason P, Chua, John Jia En, Chung, Hyewon, Chung, Kin Pan, Chung, Seockhoon, Chung, So-Hyang, Chung, Yuen-Li, Cianfanelli, Valentina, Ciechomska, Iwona A, Cifuentes, Mariana, Cinque, Laura, Cirak, Sebahattin, Cirone, Mara, Clague, Michael J, Clarke, Robert, Clementi, Emilio, Coccia, Eliana M, Codogno, Patrice, Cohen, Ehud, Cohen, Mickael M, Colasanti, Tania, Colasuonno, Fiorella, Colbert, Robert A, Colell, Anna, Čolić, Miodrag, Coll, Nuria S, Collins, Mark O, Colombo, María I, Colón-Ramos, Daniel A, Combaret, Lydie, Comincini, Sergio, Cominetti, Márcia R, Consiglio, Antonella, Conte, Andrea, Conti, Fabrizio, Contu, Viorica Raluca, Cookson, Mark R, Coombs, Kevin M, Coppens, Isabelle, Corasaniti, Maria Tiziana, Corkery, Dale P, Cordes, Nils, Cortese, Katia, Costa, Maria Do Carmo, Costantino, Sarah, Costelli, Paola, Coto-Montes, Ana, Crack, Peter J, Crespo, Jose L, Criollo, Alfredo, Crippa, Valeria, Cristofani, Riccardo, Csizmadia, Tamas, Cuadrado, Antonio, Cui, Bing, Cui, Jun, Cui, Yixian, Cui, Yong, Culetto, Emmanuel, Cumino, Andrea C, Cybulsky, Andrey V, Czaja, Mark J, Czuczwar, Stanislaw J, D'Adamo, Stefania, D'Amelio, Marcello, D'Arcangelo, Daniela, D'Lugos, Andrew C, D'Orazi, Gabriella, Da Silva, James A, Dafsari, Hormos Salimi, Dagda, Ruben K, Dagdas, Yasin, Daglia, Maria, Dai, Xiaoxia, Dai, Yun, Dai, Yuyuan, Dal Col, Jessica, Dalhaimer, Paul, Dalla Valle, Luisa, Dallenga, Tobias, Dalmasso, Guillaume, Damme, Markus, Dando, Ilaria, Dantuma, Nico P, Darling, April L, Das, Hiranmoy, Dasarathy, Srinivasan, Dasari, Santosh K, Dash, Srikanta, Daumke, Oliver, Dauphinee, Adrian N, Davies, Jeffrey S, Dávila, Valeria A, Davis, Roger J, Davis, Tanja, Dayalan Naidu, Sharadha, De Amicis, Francesca, De Bosscher, Karolien, De Felice, Francesca, De Franceschi, Lucia, De Leonibus, Chiara, De Mattos Barbosa, Mayara G, De Meyer, Guido RY, De Milito, Angelo, De Nunzio, Cosimo, De Palma, Clara, De Santi, Mauro, De Virgilio, Claudio, De Zio, Daniela, Debnath, Jayanta, DeBosch, Brian J, Decuypere, Jean-Paul, Deehan, Mark A, Deflorian, Gianluca, DeGregori, James, Dehay, Benjamin, Del Rio, Gabriel, Delaney, Joe R, Delbridge, Lea MD, Delorme-Axford, Elizabeth, Delpino, M Victoria, Demarchi, Francesca, Dembitz, Vilma, Demers, Nicholas D, Deng, Hongbin, Deng, Zhiqiang, Dengjel, Joern, Dent, Paul, Denton, Donna, DePamphilis, Melvin L, Der, Channing J, Deretic, Vojo, Descoteaux, Albert, Devis, Laura, Devkota, Sushil, Devuyst, Olivier, Dewson, Grant, Dharmasivam, Mahendiran, Dhiman, Rohan, Di Bernardo, Diego, Di Cristina, Manlio, Di Domenico, Fabio, Di Fazio, Pietro, Di Fonzo, Alessio, Di Guardo, Giovanni, Di Guglielmo, Gianni M, Di Leo, Luca, Di Malta, Chiara, Di Nardo, Alessia, Di Rienzo, Martina, Di Sano, Federica, Diallinas, George, Diao, Jiajie, Diaz-Araya, Guillermo, Díaz-Laviada, Inés, Dickinson, Jared M, Diederich, Marc, Dieudé, Mélanie, Dikic, Ivan, Ding, Shiping, Ding, Wen-Xing, Dini, Luciana, Dinić, Jelena, Dinic, Miroslav, Dinkova-Kostova, Albena T, Dionne, Marc S, Distler, Jörg HW, Diwan, Abhinav, Dixon, Ian MC, Djavaheri-Mergny, Mojgan, Dobrinski, Ina, Dobrovinskaya, Oxana, Dobrowolski, Radek, Dobson, Renwick CJ, Đokić, Jelena, Dokmeci Emre, Serap, Donadelli, Massimo, Dong, Bo, Dong, Xiaonan, Dong, Zhiwu, Dorn Ii, Gerald W, Dotsch, Volker, Dou, Huan, Dou, Juan, Dowaidar, Moataz, Dridi, Sami, Drucker, Liat, Du, Ailian, Du, Caigan, Du, Guangwei, Du, Hai-Ning, Du, Li-Lin, Du Toit, André, Duan, Shao-Bin, Duan, Xiaoqiong, Duarte, Sónia P, Dubrovska, Anna, Dunlop, Elaine A, Dupont, Nicolas, Durán, Raúl V, Dwarakanath, Bilikere S, Dyshlovoy, Sergey A, Ebrahimi-Fakhari, Darius, Eckhart, Leopold, Edelstein, Charles L, Efferth, Thomas, Eftekharpour, Eftekhar, Eichinger, Ludwig, Eid, Nabil, Eisenberg, Tobias, Eissa, N Tony, Eissa, Sanaa, Ejarque, Miriam, El Andaloussi, Abdeljabar, El-Hage, Nazira, El-Naggar, Shahenda, Eleuteri, Anna Maria, El-Shafey, Eman S, Elgendy, Mohamed, Eliopoulos, Aristides G, Elizalde, María M, Elks, Philip M, Elsasser, Hans-Peter, Elsherbiny, Eslam S, Emerling, Brooke M, Emre, NC Tolga, Eng, Christina H, Engedal, Nikolai, Engelbrecht, Anna-Mart, Engelsen, Agnete ST, Enserink, Jorrit M, Escalante, Ricardo, Esclatine, Audrey, Escobar-Henriques, Mafalda, Eskelinen, Eeva-Liisa, Espert, Lucile, Eusebio, Makandjou-Ola, Fabrias, Gemma, Fabrizi, Cinzia, Facchiano, Antonio, 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Xin, Werner, Antonia, Weykopf, Beatrice, Wheatley, Sally P, Whitton, J Lindsay, Whitworth, Alexander J, Wiktorska, Katarzyna, Wildenberg, Manon E, Wileman, Tom, Wilkinson, Simon, Willbold, Dieter, Williams, Brett, Williams, Robin SB, Williams, Roger L, Williamson, Peter R, Wilson, Richard A, Winner, Beate, Winsor, Nathaniel J, Witkin, Steven S, Wodrich, Harald, Woehlbier, Ute, Wollert, Thomas, Wong, Esther, Wong, Jack Ho, Wong, Richard W, Wong, Vincent Kam Wai, Wong, W Wei-Lynn, Wu, An-Guo, Wu, Chengbiao, Wu, Jian, Wu, Junfang, Wu, Kenneth K, Wu, Min, Wu, Shan-Ying, Wu, Shengzhou, Wu, Shu-Yan, Wu, Shufang, Wu, William KK, Wu, Xiaohong, Wu, Xiaoqing, Wu, Yao-Wen, Wu, Yihua, Xavier, Ramnik J, Xia, Hongguang, Xia, Lixin, Xia, Zhengyuan, Xiang, Ge, Xiang, Jin, Xiang, Mingliang, Xiang, Wei, Xiao, Bin, Xiao, Guozhi, Xiao, Hengyi, Xiao, Hong-Tao, Xiao, Jian, Xiao, Lan, Xiao, Shi, Xiao, Yin, Xie, Baoming, Xie, Chuan-Ming, Xie, Min, Xie, Yuxiang, Xie, Zhiping, Xie, Zhonglin, Xilouri, Maria, Xu, Congfeng, Xu, En, Xu, Haoxing, Xu, Jing, Xu, JinRong, Xu, Liang, Xu, Wen Wen, Xu, Xiulong, Xue, Yu, Yakhine-Diop, Sokhna MS, Yamaguchi, Masamitsu, Yamaguchi, Osamu, Yamamoto, Ai, Yamashina, Shunhei, Yan, Shengmin, Yan, Shian-Jang, Yan, Zhen, Yanagi, Yasuo, Yang, Chuanbin, Yang, Dun-Sheng, Yang, Huan, Yang, Huang-Tian, Yang, Hui, Yang, Jin-Ming, Yang, Jing, Yang, Jingyu, Yang, Ling, Yang, Liu, Yang, Ming, Yang, Pei-Ming, Yang, Qian, Yang, Seungwon, Yang, Shu, Yang, Shun-Fa, Yang, Wannian, Yang, Wei Yuan, Yang, Xiaoyong, Yang, Xuesong, Yang, Yi, Yang, Ying, Yao, Honghong, Yao, Shenggen, Yao, Xiaoqiang, Yao, Yong-Gang, Yao, Yong-Ming, Yasui, Takahiro, Yazdankhah, Meysam, Yen, Paul M, Yi, Cong, Yin, Xiao-Ming, Yin, Yanhai, Yin, Zhangyuan, Yin, Ziyi, Ying, Meidan, Ying, Zheng, Yip, Calvin K, Yiu, Stephanie Pei Tung, Yoo, Young H, Yoshida, Kiyotsugu, Yoshii, Saori R, Yoshimori, Tamotsu, Yousefi, Bahman, Yu, Boxuan, Yu, Haiyang, Yu, Jun, Yu, Li, Yu, Ming-Lung, Yu, Seong-Woon, Yu, Victor C, Yu, W Haung, Yu, Zhengping, Yu, Zhou, Yuan, Junying, Yuan, Ling-Qing, Yuan, Shilin, Yuan, Shyng-Shiou F, Yuan, Yanggang, Yuan, Zengqiang, Yue, Jianbo, Yue, Zhenyu, Yun, Jeanho, Yung, Raymond L, Zacks, David N, Zaffagnini, Gabriele, Zambelli, Vanessa O, Zanella, Isabella, Zang, Qun S, Zanivan, Sara, Zappavigna, Silvia, Zaragoza, Pilar, Zarbalis, Konstantinos S, Zarebkohan, Amir, Zarrouk, Amira, Zeitlin, Scott O, Zeng, Jialiu, Zeng, Ju-Deng, Žerovnik, Eva, Zhan, Lixuan, Zhang, Bin, Zhang, Donna D, Zhang, Hanlin, Zhang, Hong, Zhang, Honghe, Zhang, Huafeng, Zhang, Huaye, Zhang, Hui, Zhang, Hui-Ling, Zhang, Jianbin, Zhang, Jianhua, Zhang, Jing-Pu, Zhang, Kalin YB, Zhang, Leshuai W, Zhang, Lin, Zhang, Lisheng, Zhang, Lu, Zhang, Luoying, Zhang, Menghuan, Zhang, Peng, Zhang, Sheng, Zhang, Wei, Zhang, Xiangnan, Zhang, Xiao-Wei, Zhang, Xiaolei, Zhang, Xiaoyan, Zhang, Xin, Zhang, Xinxin, Zhang, Xu Dong, Zhang, Yang, Zhang, Yanjin, Zhang, Yi, Zhang, Ying-Dong, Zhang, Yingmei, Zhang, Yuan-Yuan, Zhang, Yuchen, Zhang, Zhe, Zhang, Zhengguang, Zhang, Zhibing, Zhang, Zhihai, Zhang, Zhiyong, Zhang, Zili, Zhao, Haobin, Zhao, Lei, Zhao, Shuang, Zhao, Tongbiao, Zhao, Xiao-Fan, Zhao, Ying, Zhao, Yongchao, Zhao, Yongliang, Zhao, Yuting, Zheng, Guoping, Zheng, Kai, Zheng, Ling, Zheng, Shizhong, Zheng, Xi-Long, Zheng, Yi, Zheng, Zu-Guo, Zhivotovsky, Boris, Zhong, Qing, Zhou, Ao, Zhou, Ben, Zhou, Cefan, Zhou, Gang, Zhou, Hao, Zhou, Hong, Zhou, Hongbo, Zhou, Jie, Zhou, Jing, Zhou, Jiyong, Zhou, Kailiang, Zhou, Rongjia, Zhou, Xu-Jie, Zhou, Yanshuang, Zhou, Yinghong, Zhou, Yubin, Zhou, Zheng-Yu, Zhou, Zhou, Zhu, Binglin, Zhu, Changlian, Zhu, Guo-Qing, Zhu, Haining, Zhu, Hongxin, Zhu, Hua, Zhu, Wei-Guo, Zhu, Yanping, Zhu, Yushan, Zhuang, Haixia, Zhuang, Xiaohong, Zientara-Rytter, Katarzyna, Zimmermann, Christine M, Ziviani, Elena, Zoladek, Teresa, Zong, Wei-Xing, Zorov, Dmitry B, Zorzano, Antonio, Zou, Weiping, Zou, Zhen, Zou, Zhengzhi, Zuryn, Steven, Zwerschke, Werner, Brand-Saberi, Beate, Dong, X Charlie, Kenchappa, Chandra Shekar, Li, Zuguo, Lin, Yong, Oshima, Shigeru, Rong, Yueguang, Sluimer, Judith C, Stallings, Christina L, and Tong, Chun-Kit
Subjects: phagophore, vacuole, Autophagosome, neurodegeneration, Autophagosomes, Autophagy-Related Proteins, flux, macroautophagy, stress, LC3, lysosome, Autophagy, cancer, Animals, Humans, Biological Assay, Lysosomes, Biomarkers
Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
Published: 2021
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7. Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments

Author: Jung, Hendrik, Covino, Roberto, Arjun, A, Bolhuis, Peter G., and Hummer, Gerhard
Subjects: Chemical Physics (physics.chem-ph), Biological Physics (physics.bio-ph), Physics - Chemical Physics, FOS: Physical sciences, Physics - Biological Physics, Computational Physics (physics.comp-ph), Physics - Computational Physics
Abstract: Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Understanding the physical mechanisms that govern the formation of molecular complexes and crystals is key to controlling the assembly of nanomachines and new materials. We present an artificial intelligence (AI) agent that uses deep reinforcement learning and transition path theory to discover the mechanism of molecular self-organization phenomena from computer simulations. The agent adaptively learns how to sample complex molecular events and, on the fly, constructs quantitative mechanistic models. By using the mechanistic understanding for AI-driven sampling, the agent closes the learning cycle and overcomes time-scale gaps of many orders of magnitude. Symbolic regression condenses the mechanism into a human-interpretable form. Applied to ion association in solution, gas-hydrate crystal formation, and membrane-protein assembly, the AI agent identifies the many-body solvent motions governing the assembly process, discovers the variables of classical nucleation theory, and reveals competing assembly pathways. The mechanistic descriptions produced by the agent are predictive and transferable to close thermodynamic states and similar systems. Autonomous AI sampling has the power to discover assembly and reaction mechanisms from materials science to biology.
Published: 2021
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8. Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments

Author: Bullerjahn, Jakob Tómas and Hummer, Gerhard
Subjects: Statistical Mechanics (cond-mat.stat-mech), Biological Physics (physics.bio-ph), FOS: Biological sciences, FOS: Physical sciences, Physics - Biological Physics, Quantitative Biology - Quantitative Methods, Condensed Matter - Statistical Mechanics, Quantitative Methods (q-bio.QM)
Abstract: Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit on mean-square-displacement curves. However, this strategy is suboptimal and prone to errors. Recently, it was shown that the increments between observed positions provide a good estimate for the diffusion coefficient, and their statistics are well-suited for likelihood-based analysis methods. Here, we revisit the problem of extracting diffusion coefficients from single-particle tracking experiments subject to static and dynamic noise using the principle of maximum likelihood. Taking advantage of an efficient real-space formulation, we extend the model to mixtures of subpopulations differing in their diffusion coefficients, which we estimate with the help of the expectation-maximization algorithm. This formulation naturally leads to a probabilistic assignment of trajectories to subpopulations. We employ the theory to analyze experimental tracking data that cannot be explained with a single diffusion coefficient. We test how well a dataset conforms to the assumptions of a diffusion model and determine the optimal number of subpopulations with the help of a quality factor of known analytical distribution. To facilitate use by practitioners, we provide a fast open-source implementation of the theory for the efficient analysis of multiple trajectories in arbitrary dimensions simultaneously., Comment: 19 pages, 8 figures, 1 table. The article has been accepted for publication in The Journal of Chemical Physics
Published: 2020
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9. Artificial Intelligence Assists Discovery of Reaction Coordinates and Mechanisms from Molecular Dynamics Simulations

Author: Jung, Hendrik, Covino, Roberto, and Hummer, Gerhard
Subjects: Chemical Physics (physics.chem-ph), Statistical Mechanics (cond-mat.stat-mech), Physics - Chemical Physics, FOS: Physical sciences, Computational Physics (physics.comp-ph), Physics - Computational Physics, Condensed Matter - Statistical Mechanics
Abstract: Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms, and how to extract them from enormous amounts of data. Both aspects still rely heavily on human experts, which becomes a serious bottleneck when a large number of parallel simulations have to be orchestrated to take full advantage of the available computing power. Here, we use artificial intelligence (AI) both to guide the sampling and to extract the relevant mechanistic information. We combine advanced sampling schemes with statistical inference, artificial neural networks, and deep learning to discover molecular mechanisms from MD simulations. Our framework adaptively and autonomously initializes simulations and learns the sampled mechanism, and is thus suitable for massively parallel computing architectures. We propose practical solutions to make the neural networks interpretable, as illustrated in applications to molecular systems., Comment: 11 pages, 5 figures, supporting information
Published: 2019
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10. Cross-validation tests for cryo-EM maps using an independent particle set

Author: Ortiz, Sebastian, Stanisic, Luka, Rodriguez, Boris A, Rampp, Markus, Hummer, Gerhard, and Cossio, Pilar
Subjects: Quantitative Biology - Biomolecules, Biological Physics (physics.bio-ph), FOS: Biological sciences, FOS: Physical sciences, Biomolecules (q-bio.BM), Physics - Biological Physics
Abstract: Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despite several efforts from the community, it is possible to overfit the reconstructions to noisy data. Here, inspired by modern statistics, we develop a novel methodology that uses a small independent particle set to validate the 3D maps. The main idea is to monitor how the map probability evolves over the control set during the refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and of the refinement iteration. We also compute the similarity between the probability distributions of the two reconstructions. As higher frequencies are added to the maps, more dissimilar are the distributions. We optimized the BioEM software package to perform these calculations, and tested the method on several systems, some which were overfitted. Our results show that our method is able to discriminate the overfitted sets from the non-overfitted ones. We conclude that having a control particle set, not used for the refinement, is essential for cross-validating cryo-EM maps.
Published: 2019
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11. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics

Author: Chang, Chunmei, Young, Lindsey N, Morris, Kyle L, von Bülow, Sören, Schöneberg, Johannes, Yamamoto-Imoto, Hitomi, Oe, Yukako, Yamamoto, Kentaro, Nakamura, Shuhei, Stjepanovic, Goran, Hummer, Gerhard, Yoshimori, Tamotsu, and Hurley, James H
Subjects: Protein Conformation, 1.1 Normal biological development and functioning, Autophagy-Related Proteins, nef Gene Products, Molecular Dynamics Simulation, Medical and Health Sciences, Structure-Activity Relationship, Phosphatidylinositol Phosphates, Autophagy, Humans, Protein Interaction Domains and Motifs, Binding Sites, Cryoelectron Microscopy, Intracellular Signaling Peptides and Proteins, Biological Sciences, Class III Phosphatidylinositol 3-Kinases, Enzyme Activation, HEK293 Cells, Gene Expression Regulation, Generic Health Relevance, Hela Cells, Beclin-1, beta-Strand, Infection, Human Immunodeficiency Virus, Signal Transduction, Protein Binding, Developmental Biology
Abstract: Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes.
Published: 2019

12. Molekulare Mechanismen für die Formung und Qualitätskontrolle von Lipidmembranen

Author: Hummer, Gerhard
Published: 2018
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13. On the free energy of ionic hydration

Author: Hummer, Gerhard, Pratt, Lawrence R., and Garcia, Angel E.
Subjects: Chemical Physics (physics.chem-ph), Physics - Chemical Physics, FOS: Physical sciences
Abstract: The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory. This provides effective methods to calculating free energies from equilibrium computer simulations. The average and the fluctuation of the electrostatic potential at charge sites appear as the first coefficients in a Taylor expansion of the free energy of charging. Combining the data from different charge states allows calculation of free-energy profiles as a function of the ionic charge. The first two Taylor coefficients of the free-energy profiles can be computed accurately from equi- librium simulations; but they are affected by a strong system-size dependence. We apply corrections for these finite-size effects by using Ewald lattice sum- mation and adding the self-interactions consistently. Results are presented for a model ion with methane-like Lennard-Jones parameters in SPC water. We find two very closely quadratic regimes with different parameters for positive and negative ions. We also studied the hydration free energy of potassium, calcium, fluoride, chloride, and bromide ions. We find negative ions to be solvated more strongly compared to positive ions of equal size, in agreement with experimen- tal data. We ascribe this preference of negative ions to their strong interac- tions with water hydrogens, which can penetrate the ionic van der Waals shell without direct energetic penalty in the models used. We also find a positive electrostatic potential at the center of uncharged Lennard-Jones particles in water, which favors negative ions. Regarding finite-system-size effects, we show that even using only 16 water molecules it is possible to calculate accu- rately the hydration free energy of sodium if self-interactions are considered., Comment: 17 pages, 6 Postscript figures, uses revtex.sty
Published: 1995
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14. PHYS 135-Spatial and temporal coarse-graining in simulations of protein dynamics and complex formation

Author: Hummer, Gerhard, Buchete, Nicolae-Viorel, Robert Best, Zheng, Wenjun, Chen, Yng-Gwei, and Kim, Young C.

15. PHYS 197-Are current molecular dynamics force fields too helical?

Author: Robert Best and Hummer, Gerhard

16. The. folding and binding pathway of the transcription factor CREB to CBP

Author: Turjanski, Adrian Gustavo, Best, Robert, Hummer, Gerhard, and J Silvio Gutkind

17. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Author: Klionsky, Daniel J., Abdel-Aziz, Amal Kamal, Abdelfatah, Sara, Abdellatif, Mahmoud, Abdoli, Asghar, Abel, Steffen, Abeliovich, Hagai, Abildgaard, Marie H., Abudu, Yakubu Princely, Acevedo-Arozena, Abraham, Adamopoulos, Iannis E., Adeli, Khosrow, Adolph, Timon E., Adornetto, Annagrazia, Aflaki, Elma, Agam, Galila, Agarwal, Anupam, Aggarwal, Bharat B., Agnello, Maria, Agostinis, Patrizia, Agrewala, Javed N., Agrotis, Alexander, Aguilar, Patricia, V, Ahmad, S. Tariq, Ahmed, Zubair M., Ahumada-Castro, Ulises, Aits, Sonja, Aizawa, Shu, Akkoc, Yunus, Akoumianaki, Tonia, Akpinar, Hafize Aysin, Al-Abd, Ahmed M., Al-Akra, Lina, Al-Gharaibeh, Abeer, Alaoui-Jamali, Moulay A., Alberti, Simon, Alcocer-Gomez, Elisabet, Alessandri, Cristiano, Ali, Muhammad, Al-Bari, M. Abdul Alim, Aliwaini, Saeb, Alizadeh, Javad, Almacellas, Eugenia, Almasan, Alexandru, Alonso, Alicia, Alonso, Guillermo D., Altan-Bonnet, Nihal, Altieri, Dario C., Alves, Sara, da Costa, Cristine Alves, Alzaharna, Mazen M., Amadio, Marialaura, Amantini, Consuelo, Amaral, Cristina, Ambrosio, Susanna, Amer, Amal O., Ammanathan, Veena, An, Zhenyi, Andersen, Stig U., Andrabi, Shaida A., Andrade-Silva, Magaiver, Andres, Allen M., Angelini, Sabrina, Ann, David, Anozie, Uche C., Ansari, Mohammad Y., Antas, Pedro, Antebi, Adam, Anton, Zurine, Anwar, Tahira, Apetoh, Lionel, Apostolova, Nadezda, Araki, Toshiyuki, Araki, Yasuhiro, Arasaki, Kohei, Araujo, Wagner L., Araya, Jun, Arden, Catherine, Arevalo, Maria-Angeles, Arguelles, Sandro, Arias, Esperanza, Arikkath, Jyothi, Arimoto, Hirokazu, Ariosa, Aileen R., Armstrong-James, Darius, Arnaune-Pelloquin, Laetitia, Aroca, Angeles, Arroyo, Daniela S., Arsov, Ivica, Artero, Ruben, Asaro, Dalia Maria Lucia, Aschner, Michael, Ashrafizadeh, Milad, Ashur-Fabian, Osnat, Atanasov, Atanas G., Au, Alicia K., Auberger, Patrick, Auner, Holger W., Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Avalos, Yenniffer, Aveic, Sanja, Aveleira, Celia Alexandra, AvinWittenberg, Tamar, Aydin, Yucel, Ayton, Scott, Ayyadevara, Srinivas, Azzopardi, Maria, Baba, Misuzu, Backer, Jonathan M., Backues, Steven K., Bae, Dong-Hun, Bae, Ok-Nam, Bae, Soo Han, Baehrecke, Eric H., Baek, Ahruem, Baek, Seung-Hoon, Baek, Sung Hee, Bagetta, Giacinto, Bagniewska-Zadworna, Agnieszka, Bai, Hua, Bai, Jie, Bai, Xiyuan, Bai, Yidong, Bairagi, Nandadulal, Baksi, Shounak, Balbi, Teresa, Baldari, Cosima T., Balduini, Walter, Ballabio, Andrea, Ballester, Maria, Balazadeh, Salma, Balzan, Rena, Bandopadhyay, Rina, Banerjee, Sreeparna, Banerjee, Sulagna, Bao, Yan, Baptista, Mauricio S., Baracca, Alessandra, Barbati, Cristiana, Bargiela, Ariadna, Barila, Daniela, Barlow, Peter G., Barmada, Sami J., Barreiro, Esther, Barreto, George E., Bartek, Jiri, Bartel, Bonnie, Bartolome, Alberto, Barve, Gaurav R., Basagoudanavar, Suresh H., Bassham, Diane C., Jr, Robert C. Bast, Basu, Alakananda, Batoko, Henri, Batten, Isabella, Baulieu, Etienne E., Baumgarner, Bradley L., Bayry, Jagadeesh, Beale, Rupert, Beau, Isabelle, Beaumatin, Florian, Bechara, Luiz R. G., Beck, George R., Jr., Beers, Michael F., Begun, Jakob, Behrends, Christian, Behrens, Georg M. N., Bei, Roberto, Bejarano, Eloy, Bel, Shai, Behl, Christian, Belaid, Amine, Belgareh-Touze, Naima, Bellarosa, Cristina, Belleudi, Francesca, Bello Perez, Melissa, Bello-Morales, Raquel, de Oliveira Beltran, Jackeline Soares, Beltran, Sebastian, Benbrook, Doris Mangiaracina, Bendorius, Mykolas, Benitez, Bruno A., Benito-Cuesta, Irene, Bensalem, Julien, Berchtold, Martin W., Berezowska, Sabina, Bergamaschi, Daniele, Bergami, Matteo, Bergmann, Andreas, Berliocchi, Laura, Berlioz-Torrent, Clarisse, Bernard, Amelie, Berthoux, Lionel, Besirli, Cagri G., Besteiro, Sebastien, Betin, Virginie M., Beyaert, Rudi, Bezbradica, Jelena S., Bhaskar, Kiran, Bhatia-Kissova, Ingrid, Bhattacharya, Resham, Bhattacharya, Sujoy, Bhattacharyya, Shalmoli, Bhuiyan, Md Shenuarin, Bhutia, Sujit Kumar, Bi, Lanrong, Bi, Xiaolin, Biden, Trevor J., Bijian, Krikor, Billes, Viktor A., Binart, Nadine, Bincoletto, Claudia, Birgisdottir, Asa B., Bjorkoy, Geir, Blanco, Gonzalo, Blas-Garcia, Ana, Blasiak, Janusz, Blomgran, Robert, Blomgren, Klas, Blum, Janice S., Boada-Romero, Emilio, Boban, Mirta, BoeszeBattaglia, Kathleen, Boeuf, Philippe, Boland, Barry, Bomont, Pascale, Bonaldo, Paolo, Bonam, Srinivasa Reddy, Bonfili, Laura, Bonifacino, Juan S., Boone, Brian A., Bootman, Martin D., Bordi, Matteo, Borner, Christoph, Bornhauser, Beat C., Borthakur, Gautam, Bosch, Jurgen, Bose, Santanu, Botana, Luis M., Botas, Juan, Boulanger, Chantal M., Boulton, Michael E., Bourdenx, Mathieu, Bourgeois, Benjamin, Bourke, Nollaig M., Bousquet, Guilhem, Boya, Patricia, Bozhkov, Peter, V, Bozi, Luiz H. M., Bozkurt, Tolga O., Brackney, Doug E., Brandts, Christian H., Braun, Ralf J., Braus, Gerhard H., Bravo-Sagua, Roberto, Bravo-San Pedro, Jose M., Brest, Patrick, Bringer, Marie-Agnes, Briones-Herrera, Alfredo, Broaddus, V. Courtney, Brodersen, Peter, Alvarez, Elida M. C., Brodsky, Jeffrey L., Brody, Steven L., Bronson, Paola G., Bronstein, Jeff M., Brown, Carolyn N., Brown, Rhoderick E., Brum, Patricia C., Brumell, John H., Brunetti-Pierri, Nicola, Bruno, Daniele, Bryson-Richardson, Robert J., Bucci, Cecilia, Buchrieser, Carmen, Bueno, Marta, Buitrago-Molina, Laura Elisa, Buraschi, Simone, Buch, Shilpa, Buchan, J. Ross, Buckingham, Erin M., Budak, Hikmet, Budini, Mauricio, Bultynck, Geert, Burada, Florin, Burgoyne, Joseph R., Buron, M. Isabel, Bustos, Victor, Buttner, Sabrina, Butturini, Elena, Byrd, Aaron, Cabas, Isabel, Cabrera-Benitez, Sandra, Cadwell, Ken, Cai, Jingjing, Cai, Lu, Cai, Qian, Cairo, Montserrat, Calbet, Jose A., Caldwell, Guy A., Caldwell, Kim A., Call, Jarrod A., Calvani, Riccardo, Calvo, Ana C., Barrera, Miguel Calvo-Rubio, Camara, Niels Os, Camonis, Jacques H., Camougrand, Nadine, Campanella, Michelangelo, Campbell, Edward M., Campbell-Valois, Francois-Xavier, Campello, Silvia, Campesi, Ilaria, Campos, Juliane C., Camuzard, Olivier, Cancino, Jorge, de Almeida, Danilo Candido, Canesi, Laura, Caniggia, Isabella, Canonico, Barbara, Canti, Carles, Cao, Bin, Caraglia, Michele, Carames, Beatriz, Carchman, Evie H., Cardenal-Munoz, Elena, Cardenas, Cesar, Cardenas, Luis, Cardoso, Sandra M., Carew, Jennifer S., Carle, Georges F., Carleton, Gillian, Carloni, Silvia, Carmona-Gutierrez, Didac, Carneiro, Leticia A., Carnevali, Oliana, Carosi, Julian M., Carra, Serena, Carrier, Alice, Carrier, Lucie, Carroll, Bernadette, Carter, A. Brent, Carvalho, Andreia Neves, Casanova, Magali, Casas, Caty, Casas, Josefina, Cassioli, Chiara, Castillo, Eliseo F., Castillo, Karen, Castillo-Lluva, Sonia, Castoldi, Francesca, Castori, Marco, Castro, Ariel F., Castro-Caldas, Margarida, Castro-Hernandez, Javier, Castro-Obregon, Susana, Catz, Sergio D., Cavadas, Claudia, Cavaliere, Federica, Cavallini, Gabriella, Cavinato, Maria, Cayuela, Maria L., Rica, Paula Cebollada, Cecarini, Valentina, Cecconi, Francesco, Cechowska-Pasko, Marzanna, Cenci, Simone, Ceperuelo-Mallafre, Victoria, Cerqueira, Joao J., Cerutti, Janete M., Cervia, Davide, Cetintas, Vildan Bozok, Cetrullo, Silvia, Chae, Han-Jung, Chagin, Andrei S., Chai, Chee-Yin, Chakrabarti, Gopal, Chakrabarti, Oishee, Chakraborty, Tapas, Chakraborty, Trinad, Chami, Mounia, Chamilos, Georgios, Chan, David W., Chan, Edmond Y. W., Chan, Edward D., Chan, H. Y. Edwin, Chan, Helen H., Chan, Hung, Chan, Matthew T., V, Chan, Yau Sang, Chandra, Partha K., Chang, Chih-Peng, Chang, Chunmei, Chang, Hao-Chun, Chang, Kai, Chao, Jie, Chapman, Tracey, Charlet-Berguerand, Nicolas, Chatterjee, Samrat, Chaube, Shail K., Chaudhary, Anu, Chauhan, Santosh, Chaum, Edward, Checler, Frederic, Cheetham, Michael E., Chen, ChangShi, Chen, Guang-Chao, Chen, Jian-Fu, Chen, Liam L., Chen, Leilei, Chen, Lin, Chen, Mingliang, Chen, MuKuan, Chen, Ning, Chen, Quan, Chen, Ruey-Hwa, Chen, Shi, Chen, Wei, Chen, Weiqiang, Chen, XinMing, Chen, Xiong-Wen, Chen, Xu, Chen, Yan, Chen, Ye-Guang, Chen, Yingyu, Chen, Yongqiang, Chen, YuJen, Chen, Yue-Qin, Chen, Zhefan Stephen, Chen, Zhi, Chen, Zhi-Hua, Chen, Zhijian J., Chen, Zhixiang, Cheng, Hanhua, Cheng, Jun, Cheng, Shi-Yuan, Cheng, Wei, Cheng, Xiaodong, Cheng, Xiu-Tang, Cheng, Yiyun, Cheng, Zhiyong, Chen, Zhong, Cheong, Heesun, Cheong, Jit Kong, Chernyak, Boris, V, Cherry, Sara, Cheung, Chi Fai Randy, Cheung, Chun Hei Antonio, Cheung, King-Ho, Chevet, Eric, Chi, Richard J., Chiang, Alan Kwok Shing, Chiaradonna, Ferdinando, Chiarelli, Roberto, Chiariello, Mario, Chica, Nathalia, Chiocca, Susanna, Chiong, Mario, Chiou, Shih-Hwa, Chiramel, Abhilash, I, Chiurchiu, Valerio, Cho, Dong-Hyung, Choe, Seong-Kyu, Choi, Augustine M. K., Choi, Mary E., Choudhury, Kamalika Roy, Chow, Norman S., Chu, Charleen T., Chua, Jason P., Chua, John Jia En, Chung, Hyewon, Chung, Kin Pan, Chung, Seockhoon, Chung, So-Hyang, Chung, Yuen-Li, Cianfanelli, Valentina, Ciechomska, Iwona A., Cifuentes, Mariana, Cinque, Laura, Cirak, Sebahattin, Cirone, Mara, Clague, Michael J., Clarke, Robert, Clementi, Emilio, Coccia, Eliana M., Codogno, Patrice, Cohen, Ehud, Cohen, Mickael M., Colasanti, Tania, Colasuonno, Fiorella, Colbert, Robert A., Colell, Anna, Coll, Nuria S., Collins, Mark O., Colombo, Maria, I, Colon-Ramos, Daniel A., Combaret, Lydie, Comincini, Sergio, Cominetti, Marcia R., Consiglio, Antonella, Conte, Andrea, Conti, Fabrizio, Contu, Viorica Raluca, Cookson, Mark R., Coombs, Kevin M., Coppens, Isabelle, Corasaniti, Maria Tiziana, Corkery, Dale P., Cordes, Nils, Cortese, Katia, Costa, Maria do Carmo, Costantino, Sarah, Costelli, Paola, Coto-Montes, Ana, Crack, Peter J., Crespo, Jose L., Criollo, Alfredo, Crippa, Valeria, Cristofani, Riccardo, Csizmadia, Tamas, Cuadrado, Antonio, Cui, Bing, Cui, Jun, Cui, Yixian, Cui, Yong, Culetto, Emmanuel, Cumino, Andrea C., Cybulsky, Andrey, V, Czaja, Mark J., Czuczwar, Stanislaw J., D'Adamo, Stefania, D'Amelio, Marcello, D'Arcangelo, Daniela, D'Lugos, Andrew C., D'Orazi, Gabriella, da Silva, James A., Dafsari, Hormos Salimi, Dagda, Ruben K., Dagdas, Yasin, Daglia, Maria, Dai, Xiaoxia, Dai, Yun, Dai, Yuyuan, Dal Col, Jessica, Dalhaimer, Paul, Dalla Valle, Luisa, Dallenga, Tobias, Dalmasso, Guillaume, Damme, Markus, Dando, Ilaria, Dantuma, Nico P., Darling, April L., Das, Hiranmoy, Dasarathy, Srinivasan, Dasari, Santosh K., Dash, Srikanta, Daumke, Oliver, Dauphinee, Adrian N., Davies, Jeffrey S., Davila, Valeria A., Davis, Roger J., Davis, Tanja, Naidu, Sharadha Dayalan, De Amicis, Francesca, De Bosscher, Karolien, De Felice, Francesca, De Franceschi, Lucia, De Leonibus, Chiara, de Mattos Barbosa, Mayara G., De Meyer, Guido R. Y., De Milito, Angelo, De Nunzio, Cosimo, De Palma, Clara, De Santi, Mauro, De Virgilio, Claudio, De Zio, Daniela, Debnath, Jayanta, DeBosch, Brian J., Decuypere, JeanPaul, Deehan, Mark A., Deflorian, Gianluca, DeGregori, James, Dehay, Benjamin, Del Rio, Gabriel, Delaney, Joe R., Delbridge, Lea M. D., Delorme-Axford, Elizabeth, Delpino, M. Victoria, Demarchi, Francesca, Dembitz, Vilma, Demers, Nicholas D., Deng, Hongbin, Deng, Zhiqiang, Dengjel, Joern, Dent, Paul, Denton, Donna, DePamphilis, Melvin L., Der, Channing J., Deretic, Vojo, Descoteaux, Albert, Devis, Laura, Devkota, Sushil, Devuyst, Olivier, Dewson, Grant, Dharmasivam, Mahendiran, Dhiman, Rohan, di Bernardo, Diego, Di Cristina, Manlio, Di Domenico, Fabio, Di Fazio, Pietro, Di Fonzo, Alessio, Di Guardo, Giovanni, Di Guglielmo, Gianni M., Di Leo, Luca, Di Malta, Chiara, Di Nardo, Alessia, Di Rienzo, Martina, Di Sano, Federica, Diallinas, George, Diao, Jiajie, Diaz-Araya, Guillermo, Diaz-Laviada, Ines, Dickinson, Jared M., Diederich, Marc, Dieude, Melanie, Dikic, Ivan, Ding, Shiping, Ding, Wen-Xing, Dini, Luciana, Dinic, Miroslav, Dinkova-Kostova, Albena T., Dionne, Marc S., Distler, Jorg H. W., Diwan, Abhinav, Dixon, Ian M. C., Djavaheri-Mergny, Mojgan, Dobrinski, Ina, Dobrovinskaya, Oxana, Dobrowolski, Radek, Dobson, Renwick C. J., Emre, Serap Dokmeci, Donadelli, Massimo, Dong, Bo, Dong, Xiaonan, Dong, Zhiwu, Ii, Gerald W. Dorn, Dotsch, Volker, Dou, Huan, Dou, Juan, Dowaidar, Moataz, Dridi, Sami, Drucker, Liat, Du, Ailian, Du, Caigan, Du, Guangwei, Du, Hai-Ning, Du, Li-Lin, du Toit, Andre, Duan, Shao-Bin, Duan, Xiaoqiong, Duarte, Sonia P., Dubrovska, Anna, Dunlop, Elaine A., Dupont, Nicolas, Duran, Raul, V, Dwarakanath, Bilikere S., Dyshlovoy, Sergey A., Ebrahimi-Fakhari, Darius, Eckhart, Leopold, Edelstein, Charles L., Efferth, Thomas, Eftekharpour, Eftekhar, Eichinger, Ludwig, Eid, Nabil, Eisenberg, Tobias, Eissa, N. Tony, Eissa, Sanaa, Ejarque, Miriam, El Andaloussi, Abdeljabar, El-Hage, Nazira, El-Naggar, Shahenda, Eleuteri, Anna Maria, El-Shafey, Eman S., Elgendy, Mohamed, Eliopoulos, Aristides G., Elizalde, Maria M., Elks, Philip M., Elsasser, Hans-Peter, Elsherbiny, Eslam S., Emerling, Brooke M., Emre, N. C. Tolga, Eng, Christina H., Engedal, Nikolai, Engelbrecht, Anna-Mart, Engelsen, Agnete S. T., Enserink, Jorrit M., Escalante, Ricardo, Esclatine, Audrey, Escobar-Henriques, Mafalda, Eskelinen, Eeva-Liisa, Espert, Lucile, Eusebio, Makandjou-Ola, Fabrias, Gemma, Fabrizi, Cinzia, Facchiano, Antonio, Facchiano, Francesco, Fadeel, Bengt, Fader, Claudio, Faesen, Alex C., Fairlie, W. Douglas, Falco, Alberto, Falkenburger, Bjorn H., Fan, Daping, Fan, Jie, Fan, Yanbo, Fang, Evandro F., Fang, Yanshan, Fang, Yognqi, Fanto, Manolis, Farfel-Becker, Tamar, Faure, Mathias, Fazeli, Gholamreza, Fedele, Anthony O., Feldman, Arthur M., Feng, Du, Feng, Jiachun, Feng, Lifeng, Feng, Yibin, Feng, Yuchen, Feng, Wei, Araujo, Thais Fenz, Ferguson, Thomas A., Fernandez-Checa, Jose C., FernandezVeledo, Sonia, Fernie, Alisdair R., Ferrante, Anthony W., Jr., Ferraresi, Alessandra, Ferrari, Merari F., Ferreira, Julio C. B., Ferro-Novick, Susan, Figueras, Antonio, Filadi, Riccardo, Filigheddu, Nicoletta, FilippiChiela, Eduardo, Filomeni, Giuseppe, Fimia, Gian Maria, Fineschi, Vittorio, Finetti, Francesca, Finkbeiner, Steven, Fisher, Edward A., Fisher, Paul B., Flamigni, Flavio, Fliesler, Steven J., Flo, Trude H., Florance, Ida, Florey, Oliver, Florio, Tullio, Fodor, Erika, Follo, Carlo, Fon, Edward A., Forlino, Antonella, Fornai, Francesco, Fortini, Paola, Fracassi, Anna, Fraldi, Alessandro, Franco, Brunella, Franco, Rodrigo, Franconi, Flavia, Frankel, Lisa B., Friedman, Scott L., Frohlich, Leopold F., Fruhbeck, Gema, Fuentes, Jose M., Fujiki, Yukio, Fujita, Naonobu, Fujiwara, Yuuki, Fukuda, Mitsunori, Fulda, Simone, Furic, Luc, Furuya, Norihiko, Fusco, Carmela, Gack, Michaela U., Gaffke, Lidia, Galadari, Sehamuddin, Galasso, Alessia, Galindo, Maria F., Kankanamalage, Sachith Gallolu, Galluzzi, Lorenzo, Galy, Vincent, Gammoh, Noor, Gan, Boyi, Ganley, Ian G., Gao, Feng, Gao, Hui, Gao, Minghui, Gao, Ping, Gao, Shou-Jiang, Gao, Wentao, Gao, Xiaobo, Garcera, Ana, Garcia, Maria Noe, Garcia, Veronica E., Garcia-Del Portillo, Francisco, Garcia-Escudero, Vega, GarciaGarcia, Aracely, Garcia-Macia, Marina, Garcia-Moreno, Diana, Garcia-Ruiz, Carmen, Garcia-Sanz, Patricia, Garg, Abhishek D., Gargini, Ricardo, Garofalo, Tina, Garry, Robert F., Gassen, Nils C., Gatica, Damian, Ge, Liang, Ge, Wanzhong, Geiss-Friedlander, Ruth, Gelfi, Cecilia, Genschik, Pascal, Gentle, Ian E., Gerbino, Valeria, Gerhardt, Christoph, Germain, Kyla, Germain, Marc, Gewirtz, David A., Afshar, Elham Ghasemipour, Ghavami, Saeid, Ghigo, Alessandra, Ghosh, Manosij, Giamas, Georgios, Giampietri, Claudia, Giatromanolaki, Alexandra, Gibson, Gary E., Gibson, Spencer B., Ginet, Vanessa, Giniger, Edward, Giorgi, Carlotta, Girao, Henrique, Girardin, Stephen E., Giridharan, Mridhula, Giuliano, Sandy, Giulivi, Cecilia, Giuriato, Sylvie, Giustiniani, Julien, Gluschko, Alexander, Goder, Veit, Goginashvili, Alexander, Golab, Jakub, Goldstone, David C., Golebiewska, Anna, Gomes, Luciana R., Gomez, Rodrigo, Gomez-Sanchez, Ruben, Gomez-Puerto, Maria Catalina, Gomez-Sintes, Raquel, Gong, Qingqiu, Goni, Felix M., Gonzalez-Gallego, Javier, Gonzalez-Hernandez, Tomas, Gonzalez-Polo, Rosa A., Gonzalez-Reyes, Jose A., Gonzalez-Rodriguez, Patricia, Goping, Ing Swie, Gorbatyuk, Marina S., Gorbunov, Nikolai, V, Gorojod, Roxana M., Gorski, Sharon M., Goruppi, Sandro, Gotor, Cecilia, Gottlieb, Roberta A., Gozes, Illana, Gozuacik, Devrim, Graef, Martin, Graler, Markus H., Granatiero, Veronica, Grasso, Daniel, Gray, Joshua P., Green, Douglas R., Greenhough, Alexander, Gregory, Stephen L., Griffin, Edward F., Grinstaff, Mark W., Gros, Frederic, Grose, Charles, Gross, Angelina S., Gruber, Florian, Grumati, Paolo, Grune, Tilman, Gu, Xueyan, Guan, Jun-Lin, Guardia, Carlos M., Guda, Kishore, Guerra, Flora, Guerri, Consuelo, Guha, Prasun, Guillen, Carlos, Gujar, Shashi, Gukovskaya, Anna, Gukovsky, Ilya, Gunst, Jan, Gunther, Andreas, Guntur, Anyonya R., Guo, Chuanyong, Guo, Chun, Guo, Hongqing, Guo, Lian-Wang, Guo, Ming, Gupta, Pawan, Fernandez, Alvaro F., Gupta, Shashi Kumar, Gupta, Swapnil, Gupta, Veer Bala, Gupta, Vivek, Gustafsson, Asa B., Gutterman, David D., Ranjitha, H. B., Haapasalo, Annakaisa, Haber, James E., Hadano, Shinji, Hafren, Anders J., Haidar, Mansour, Hall, Belinda S., Hallden, Gunnel, Hamacher-Brady, Anne, Hamann, Andrea, Hamasaki, Maho, Han, Weidong, Hansen, Malene, Hanson, Phyllis, I, Hao, Zijian, Harada, Masaru, Harhaji-Trajkovic, Ljubica, Hariharan, Nirmala, Haroon, Nigil, Harris, James, Hasegawa, Takafumi, Nagoor, Noor Hasima, Haspel, Jeffrey A., Haucke, Volker, Hawkins, Wayne D., Hay, Bruce A., Haynes, Cole M., Hayrabedyan, Soren B., Hays, Thomas S., He, Congcong, He, Qin, He, RongRong, He, You-Wen, He, Yu-Ying, Heakal, Yasser, Heberle, Alexander M., Hejtmancik, J. Fielding, Helgason, Gudmundur Vignir, Henkel, Vanessa, Herb, Marc, Hergovich, Alexander, Herman-Antosiewicz, Anna, Hernandez, Agustin, Hernandez, Carlos, Hernandez-Diaz, Sergio, Hernandez-Gea, Virginia, Herpin, Amaury, Herreros, Judit, Hervas, Javier H., Hesselson, Daniel, Hetz, Claudio, Heussler, Volker T., Higuchi, Yujiro, Hilfiker, Sabine, Hill, Joseph A., Hlavacek, William S., Ho, Emmanuel A., Ho, Idy H. T., Ho, Philip Wing-Lok, Ho, ShuLeong, Ho, Wan Yun, Hobbs, G. Aaron, Hochstrasser, Mark, Hoet, Peter H. M., Hofius, Daniel, Hofman, Paul, Hohn, Annika, Holmberg, Carina, I, Hombrebueno, Jose R., Hong, Chang-Won, Hong, Yi-Ren, Hooper, Lora, V, Hoppe, Thorsten, Horos, Rastislav, Hoshida, Yujin, Hsin, I-Lun, Hsu, Hsin-Yun, Hu, Bing, Hu, Dong, Hu, Li-Fang, Hu, Ming Chang, Hu, Ronggui, Hu, Wei, Hu, Yu-Chen, Hu, Zhuo-Wei, Hua, Fang, Hua, Jinlian, Hua, Yingqi, Huan, Chongmin, Huang, Canhua, Huang, Chuanshu, Huang, Chuanxin, Huang, Chunling, Huang, Haishan, Huang, Kun, Huang, Michael L. H., Huang, Rui, Huang, Shan, Huang, Tianzhi, Huang, Xing, Huang, Yuxiang Jack, Huber, Tobias B., Hubert, Virginie, Hubner, Christian A., Hughes, Stephanie M., Hughes, William E., Humbert, Magali, Hummer, Gerhard, Hurley, James H., Hussain, Sabah, Hussain, Salik, Hussey, Patrick J., Hutabarat, Martina, Hwang, Hui-Yun, Hwang, Seungmin, Ieni, Antonio, Ikeda, Fumiyo, Imagawa, Yusuke, Imai, Yuzuru, Imbriano, Carol, Imoto, Masaya, Inman, Denise M., Inoki, Ken, Iovanna, Juan, Iozzo, Renato, V, Ippolito, Giuseppe, Irazoqui, Javier E., Iribarren, Pablo, Ishaq, Mohd, Ishikawa, Makoto, Ishimwe, Nestor, Isidoro, Ciro, Ismail, Nahed, Issazadeh-Navikas, Shohreh, Itakura, Eisuke, Ito, Daisuke, Ivankovic, Davor, Ivanova, Saska, Iyer, Anand Krishnan, V, Izquierdo, Jose M., Izumi, Masanori, Jaattela, Marja, Jabir, Majid Sakhi, Jackson, William T., Jacobo-Herrera, Nadia, Jacomin, Anne-Claire, Jacquin, Elise, Jadiya, Pooja, Jaeschke, Hartmut, Jagannath, Chinnaswamy, Jakobi, Arjen J., Jakobsson, Johan, Janji, Bassam, JansenDurr, Pidder, Jansson, Patric J., Jantsch, Jonathan, Jassey, Alagie, Jean, Steve, JeltschDavid, Helene, Jendelova, Pavla, Jenny, Andreas, Jensen, Thomas E., Jessen, Niels, Jewell, Jenna L., Ji, Jing, Jia, Lijun, Jia, Rui, Jiang, Liwen, Jiang, Qing, Jiang, Richeng, Jiang, Teng, Jiang, Xuejun, Jiang, Yu, Jimenez-Sanchez, Maria, Jin, Eun-Jung, Jin, Fengyan, Jin, Hongchuan, Jin, Li, Jin, Luqi, Jin, Meiyan, Jin, Si, Jo, Eun-Kyeong, Joffre, Carine, Johansen, Terje, Johnson, Gail V. W., Johnston, Simon A., Jokitalo, Eija, Jolly, Mohit Kumar, Joosten, Leo A. B., Jordan, Joaquin, Joseph, Bertrand, Ju, Dianwen, Ju, Jeong-Sun, Ju, Jingfang, Juarez, Esmeralda, Judith, Delphine, Juhasz, Gabor, Jun, Youngsoo, Jung, Chang Hwa, Jung, SungChul, Jung, Yong Keun, Jungbluth, Heinz, Jungverdorben, Johannes, Just, Steffen, Kaarniranta, Kai, Kaasik, Allen, Kabuta, Tomohiro, Kaganovich, Daniel, Kahana, Alon, Kain, Renate, Kajimura, Shinjo, Kalamvoki, Maria, Kalia, Manjula, Kalinowski, Danuta S., Kaludercic, Nina, Kalvari, Ioanna, Kaminska, Joanna, Kaminskyy, Vitaliy O., Kanamori, Hiromitsu, Kanasaki, Keizo, Kang, Chanhee, Kang, Rui, Kang, Sang Sun, Kaniyappan, Senthilvelrajan, Kanki, Tomotake, Kanneganti, Thirumala-Devi, Kanthasamy, Anumantha G., Kanthasamy, Arthi, Kantorow, Marc, Kapuy, Orsolya, Karamouzis, Michalis, V, Karim, Md Razaul, Karmakar, Parimal, Katare, Rajesh G., Kato, Masaru, Kaufmann, Stefan H. E., Kauppinen, Anu, Kaushal, Gur P., Kaushik, Susmita, Kawasaki, Kiyoshi, Kazan, Kemal, Ke, Po-Yuan, Keating, Damien J., Keber, Ursula, Kehrl, John H., Keller, Kate E., Keller, Christian W., Kemper, Jongsook Kim, Kenific, Candia M., Kepp, Oliver, Kermorgant, Stephanie, Kern, Andreas, Ketteler, Robin, Keulers, Tom G., Khalfin, Boris, Khalil, Hany, Khambu, Bilon, Khan, Shahid Y., Khandelwal, Vinoth Kumar Megraj, Khandia, Rekha, Kho, Widuri, Khobrekar, Noopur, V, Khuansuwan, Sataree, Khundadze, Mukhran, Killackey, Samuel A., Kim, Dasol, Kim, Deok Ryong, Kim, Do-Hyung, Kim, Dong-Eun, Kim, Eun Young, Kim, Eun-Kyoung, Kim, HakRim, Kim, Hee-Sik, Kim, Hyung-Ryong, Kim, Jeong Hun, Kim, Jin Kyung, Kim, Jin-Hoi, Kim, Joungmok, Kim, Ju Hwan, Il Kim, Keun, Kim, Peter K., Kim, Seong-Jun, Kimball, Scot R., Kimchi, Adi, Kimmelman, Alec C., Kimura, Tomonori, King, Matthew A., Kinghorn, Kerri J., Kinsey, Conan G., Kirkin, Vladimir, Kirshenbaum, Lorrie A., Kiselev, Sergey L., Kishi, Shuji, Kitamoto, Katsuhiko, Kitaoka, Yasushi, Kitazato, Kaio, Kitsis, Richard N., Kittler, Josef T., Kjaerulff, Ole, Klein, Peter S., Klopstock, Thomas, Klucken, Jochen, Knovelsrud, Helene, Knorr, Roland L., Ko, Ben C. B., Ko, Fred, Ko, JiunnLiang, Kobayashi, Hotaka, Kobayashi, Satoru, Koch, Ina, Koch, Jan C., Koenig, Ulrich, Kogel, Donat, Koh, Young Ho, Koike, Masato, Kohlwein, Sepp D., Kocaturk, Nur M., Komatsu, Masaaki, Konig, Jeannette, Kono, Toru, Kopp, Benjamin T., Korcsmaros, Tamas, Korkmaz, Gozde, Korolchuk, Viktor, I, Korsnes, Monica Suarez, Koskela, Ali, Kota, Janaiah, Kotake, Yaichiro, Kotler, Monica L., Kou, Yanjun, Koukourakis, Michael, I, Koustas, Evangelos, Kovacs, Attila L., Kovacs, Tibor, Koya, Daisuke, Kozako, Tomohiro, Kraft, Claudine, Krainc, Dimitri, Kramer, Helmut, Krasnodembskaya, Anna D., Kretz-Remy, Carole, Kroemer, Guido, Ktistakis, Nicholas T., Kuchitsu, Kazuyuki, Kuenen, Sabine, Kuerschner, Lars, Kukar, Thomas, Kumar, Ajay, Kumar, Ashok, Kumar, Deepak, Kumar, Dhiraj, Kumar, Sharad, Kume, Shinji, Kumsta, Caroline, Kundu, Chanakya N., Kundu, Mondira, Kunnumakkara, Ajaikumar B., Kurgan, Lukasz, Kutateladze, Tatiana G., Kutlu, Ozlem, Kwak, SeongAe, Kwon, Ho Jeong, Kwon, Taeg Kyu, Kwon, Yong Tae, Kyrmizi, Irene, La Spada, Albert, Labonte, Patrick, Ladoire, Sylvain, Laface, Ilaria, Lafont, Frank, Lagace, Diane C., Lahiri, Vikramjit, Lai, Zhibing, Laird, Angela S., Lakkaraju, Aparna, Lamark, Trond, Lan, Sheng-Hui, Landajuela, Ane, Lane, Darius J. R., Lane, Jon D., Lang, Charles H., Lange, Carsten, Langer, Rupert, Lapaquette, Pierre, Laporte, Jocelyn, LaRusso, Nicholas F., Lastres-Becker, Isabel, Lau, Wilson Chun Yu, Laurie, Gordon W., Lavandero, Sergio, Law, Betty Yuen Kwan, Law, Helen Ka-wai, Layfield, Rob, Le, Weidong, Le Stunff, Herve, Leary, Alexandre Y., Lebrun, Jean-Jacques, Leck, Lionel Y. 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P., Thomas, Sufi Mary, Thomes, Paul G., Thorburn, Andrew, Thukral, Lipi, Thum, Thomas, Thumm, Michael, Tian, Ling, Tichy, Ales, Till, Andreas, Timmerman, Vincent, Titorenko, Vladimir, I, Todi, Sokol, V, Todorova, Krassimira, Toivonen, Janne M., Tomaipitinca, Luana, Tomar, Dhanendra, Tomas-Zapico, Cristina, Tong, Benjamin Chun-Kit, Tong, Chao, Tong, Xin, Tooze, Sharon A., Torgersen, Maria L., Torii, Satoru, Torres-Lopez, Liliana, Torriglia, Alicia, Towers, Christina G., Towns, Roberto, Toyokuni, Shinya, Trajkovic, Vladimir, Tramontano, Donatella, Tran, QuynhGiao, Travassos, Leonardo H., Trelford, Charles B., Tremel, Shirley, Trougakos, Ioannis P., Tsao, Betty P., Tschan, Mario P., Tse, Hung-Fat, Tse, Tak Fu, Tsugawa, Hitoshi, Tsvetkov, Andrey S., Tumbarello, David A., Tumtas, Yasin, Tunon, Maria J., Turcotte, Sandra, Turk, Boris, Turk, Vito, Turner, Bradley J., Tuxworth, Richard, I, Tyler, Jessica K., Tyutereva, Elena, V, Uchiyama, Yasuo, UgunKlusek, Aslihan, Uhlig, Holm H., Ulasov, Ilya, V, Umekawa, Midori, Ungermann, Christian, Unno, Rei, Urbe, Sylvie, Uribe-Carretero, Elisabet, Ustun, Suayib, Uversky, Vladimir N., Vaccari, Thomas, Vaccaro, Maria, I, Vahsen, Bjorn F., Vakifahmetoglu-Norberg, Helin, Valdor, Rut, Valente, Maria J., Valko, Ayelen, Vallee, Richard B., Valverde, Angela M., Van den Berghe, Greet, van Der Veen, Stijn, Van Kaer, Luc, van Loosdregt, Jorg, van Wijk, Sjoerd J. L., Vandenberghe, Wim, Vanhorebeek, Ilse, Vannier-Santos, Marcos A., Vannini, Nicola, Vanrell, M. Cristina, Vantaggiato, Chiara, Varano, Gabriele, Varela-Nieto, Isabel, Varga, Mate, Vasconcelos, M. 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Lindsay, Whitworth, Alexander J., Wiktorska, Katarzyna, Wildenberg, Manon E., Wileman, Tom, Wilkinson, Simon, Willbold, Dieter, Williams, Brett, Williams, Robin S. B., Williams, Roger L., Williamson, Peter R., Wilson, Richard A., Winner, Beate, Winsor, Nathaniel J., Witkin, Steven S., Wodrich, Harald, Woehlbier, Ute, Wollert, Thomas, Wong, Esther, Wong, Jack Ho, Wong, Richard W., Wong, Vincent Kam Wai, Wong, W. Wei-Lynn, Wu, An-Guo, Wu, Chengbiao, Wu, Jian, Wu, Junfang, Wu, Kenneth K., Wu, Min, Wu, Shan-Ying, Wu, Shengzhou, Wu, ShuYan, Wu, Shufang, Wu, William K. K., Wu, Xiaohong, Wu, Xiaoqing, Wu, Yao-Wen, Wu, Yihua, Xavier, Ramnik J., Xia, Hongguang, Xia, Lixin, Xia, Zhengyuan, Xiang, Ge, Xiang, Jin, Xiang, Mingliang, Xiang, Wei, Xiao, Bin, Xiao, Guozhi, Xiao, Hengyi, Xiao, Hong-tao, Xiao, Jian, Xiao, Lan, Xiao, Shi, Xiao, Yin, Xie, Baoming, Xie, Chuan-Ming, Xie, Min, Xie, Yuxiang, Xie, Zhiping, Xie, Zhonglin, Xilouri, Maria, Xu, Congfeng, Xu, En, Xu, Haoxing, Xu, Jing, Xu, JinRong, Xu, Liang, Xu, Wen Wen, Xu, Xiulong, Xue, Yu, Yakhine-Diop, Sokhna M. S., Yamaguchi, Masamitsu, Yamaguchi, Osamu, Yamamoto, Ai, Yamashina, Shunhei, Yan, Shengmin, Yan, Shian-Jang, Yan, Zhen, Yanagi, Yasuo, Yang, Chuanbin, Yang, Dun-Sheng, Yang, Huan, Yang, Huang-Tian, Yang, Hui, Yang, Jin-Ming, Yang, Jing, Yang, Jingyu, Yang, Ling, Yang, Liu, Yang, Ming, Yang, Pei-Ming, Yang, Qian, Yang, Seungwon, Yang, Shu, Yang, Shun-Fa, Yang, Wannian, Yang, Wei Yuan, Yang, Xiaoyong, Yang, Xuesong, Yang, Yi, Yang, Ying, Yao, Honghong, Yao, Shenggen, Yao, Xiaoqiang, Yao, Yong-Gang, Yao, Yong-Ming, Yasui, Takahiro, Yazdankhah, Meysam, Yen, Paul M., Yi, Cong, Yin, Xiao-Ming, Yin, Yanhai, Yin, Zhangyuan, Yin, Ziyi, Ying, Meidan, Ying, Zheng, Yip, Calvin K., Yiu, Stephanie Pei Tung, Yoo, Young H., Yoshida, Kiyotsugu, Yoshii, Saori R., Yoshimori, Tamotsu, Yousefi, Bahman, Yu, Boxuan, Yu, Haiyang, Yu, Jun, Yu, Li, Yu, Ming-Lung, Yu, Seong-Woon, Yu, Victor C., Yu, W. Haung, Yu, Zhengping, Yu, Zhou, Yuan, Junying, Yuan, Ling-Qing, Yuan, Shilin, Yuan, Shyng-Shiou F., Yuan, Yanggang, Yuan, Zengqiang, Yue, Jianbo, Yue, Zhenyu, Yun, Jeanho, Yung, Raymond L., Zacks, David N., Zaffagnini, Gabriele, Zambelli, Vanessa O., Zanella, Isabella, Zang, Qun S., Zanivan, Sara, Zappavigna, Silvia, Zaragoza, Pilar, Zarbalis, Konstantinos S., Zarebkohan, Amir, Zarrouk, Amira, Zeitlin, Scott O., Zeng, Jialiu, Zeng, Ju-deng, Zerovnik, Eva, Zhan, Lixuan, Zhang, Bin, Zhang, Donna D., Zhang, Hanlin, Zhang, Hong, Zhang, Honghe, Zhang, Huafeng, Zhang, Huaye, Zhang, Hui, Zhang, Hui-Ling, Zhang, Jianbin, Zhang, Jianhua, Zhang, Jing-Pu, Zhang, Kalin Y. B., Zhang, Leshuai W., Zhang, Lin, Zhang, Lisheng, Zhang, Lu, Zhang, Luoying, Zhang, Menghuan, Zhang, Peng, Zhang, Sheng, Zhang, Wei, Zhang, Xiangnan, Zhang, Xiao-Wei, Zhang, Xiaolei, Zhang, Xiaoyan, Zhang, Xin, Zhang, Xinxin, Zhang, Xu Dong, Zhang, Yang, Zhang, Yanjin, Zhang, Yi, Zhang, Ying-Dong, Zhang, Yingmei, Zhang, Yuan-Yuan, Zhang, Yuchen, Zhang, Zhe, Zhang, Zhengguang, Zhang, Zhibing, Zhang, Zhihai, Zhang, Zhiyong, Zhang, Zili, Zhao, Haobin, Zhao, Lei, Zhao, Shuang, Zhao, Tongbiao, Zhao, Xiao-Fan, Zhao, Ying, Zhao, Yongchao, Zhao, Yongliang, Zhao, Yuting, Zheng, Guoping, Zheng, Kai, Zheng, Ling, Zheng, Shizhong, Zheng, Xi-Long, Zheng, Yi, Zheng, Zu-Guo, Zhivotovsky, Boris, Zhong, Qing, Zhou, Ao, Zhou, Ben, Zhou, Cefan, Zhou, Gang, Zhou, Hao, Zhou, Hong, Zhou, Hongbo, Zhou, Jie, Zhou, Jing, Zhou, Jiyong, Zhou, Kailiang, Zhou, Rongjia, Zhou, Xu-Jie, Zhou, Yanshuang, Zhou, Yinghong, Zhou, Yubin, Zhou, Zheng-Yu, Zhou, Zhou, Zhu, Binglin, Zhu, Changlian, Zhu, Guo-Qing, Zhu, Haining, Zhu, Hongxin, Zhu, Hua, Zhu, WeiGuo, Zhu, Yanping, Zhu, Yushan, Zhuang, Haixia, Zhuang, Xiaohong, Zientara-Rytter, Katarzyna, Zimmermann, Christine M., Ziviani, Elena, Zoladek, Teresa, Zong, Wei-Xing, Zorov, Dmitry B., Zorzano, Antonio, Zou, Weiping, Zou, Zhen, Zou, Zhengzhi, Zuryn, Steven, Zwerschke, Werner, Brand-Saberi, Beate, Dong, X. Charlie, Kenchappa, Chandra Shekar, Li, Zuguo, Lin, Yong, Oshima, Shigeru, Rong, Yueguang, Sluimer, Judith C., Stallings, Christina L., and Tong, Chun-Kit
Subjects: phagophore, endoplasmic-reticulum stress, vacuole, breast-cancer cells, life-span extension, amyotrophic-lateral-sclerosis, autophagosome, neurodegeneration, activated protein-kinase, starvation-induced autophagy, flux, macroautophagy, stress, lc3, nf-kappa-b, lysosome, genome-wide association, cancer, chaperone-mediated autophagy, programmed cell-death
Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

18. Exploring the structural stability and the mechanism of dissociation of Alzheimer's amyloid fibrils

Author: Nicolae-Viorel Buchete and Hummer, Gerhard

19. CHEMISTRY Methods for computational chemistry

Author: Walter Thiel and Hummer, Gerhard

20. Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

Author: Markus Zweckstetter, Gerhard Hummer, J. S. Oroz, Lukas S. Stelzl, J. Köfinger, M. Sikora, Benjamin Schuler, Lisa M. Pietrek, A. Holla, German Research Foundation, Max Planck Society, Swiss National Science Foundation, European Commission, Austrian Science Fund, Stelzl, Lukas S., Pietrek, Lisa M., Sikora, Mateusz, Köfinger, Jürgen, Schuler, Benjamin, Zweckstetter, Markus, Hummer, Gerhard, and University of Zurich
Subjects: Tau protein, Population, 610 Medicine & health, Molecular dynamics, Exponential growth, 10019 Department of Biochemistry, Molecule, education, Physics, education.field_of_study, biology, Molecular dynamics simulations, SAXS, Alzheimer's disease, NMR, Tauopathy, Förster resonance energy transfer, Intrinsically disordered protein, RHCG, Chemical physics, ddc:540, FRET, biology.protein, 570 Life sciences, Tau, Importance sampling
Abstract: 14 pags., 5 figs., The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the balance between functional and disease-associated conformational states, we build a structural ensemble of the tau K18 fragment containing the four pseudorepeat domains involved in both microtubule binding and amyloid fibril formation. We assemble 129-residue-long tau K18 chains with atomic detail from an extensive fragment library constructed with molecular dynamics simulations. We introduce a reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on the local structure into the assembly process in a systematic manner. By combining Bayesian ensemble refinement with importance sampling, we obtain well-defined ensembles and overcome the problem of exponentially varying weights in the integrative modeling of long-chain polymeric molecules. The resulting tau K18 ensembles capture nuclear magnetic resonance (NMR) chemical shift and J-coupling measurements. Without further fitting, we achieve very good agreement with measurements of NMR residual dipolar couplings. The good agreement with experimental measures of global structure such as single-molecule Förster resonance energy transfer (FRET) efficiencies is improved further by ensemble refinement. By comparing wild-type and mutant ensembles, we show that pathogenic single-point P301L, P301S, and P301T mutations shift the population from the turn-like conformations of the functional microtubule-bound state to the extended conformations of disease-associated tau fibrils. RHCG thus provides us with an atomically detailed view of the population equilibrium between functional and aggregation-prone states of tau K18, and demonstrates that global structural characteristics of this intrinsically disordered protein emerge from its local structure., We acknowledge financial support from the German Research Foundation (CRC902: Molecular Principles of RNA Based Regulation), the Max Planck Society, and the Swiss National Science Foundation. M.Z. was supported by the European Research Council (ERC) under the EU Horizon 2020 research and innovation program (grant agreement No. 787679). L.S.S. thanks ReALity (Resilience, Adaptation and Longevity), M3ODEL (Mainz Institute of Multiscale Modeling) and Forschungsinitiative des Landes Rheinland-Pfalz for their support M.S. was supported by the FWF Schrödinger fellowship J4332-B28.
Published: 2022
Full Text: View/download PDF

21. Co-translational assembly orchestrates competing biogenesis pathways

Author: Maximilian Seidel, Anja Becker, Filipa Pereira, Jonathan J. M. Landry, Nayara Trevisan Doimo de Azevedo, Claudia M. Fusco, Eva Kaindl, Natalie Romanov, Janina Baumbach, Julian D. Langer, Erin M. Schuman, Kiran Raosaheb Patil, Gerhard Hummer, Vladimir Benes, Martin Beck, Seidel, Maximilian [0000-0003-1615-3549], Fusco, Claudia M [0000-0002-9812-2203], Langer, Julian D [0000-0002-5190-577X], Schuman, Erin M [0000-0001-7505-1855], Hummer, Gerhard [0000-0001-7768-746X], Benes, Vladimir [0000-0002-0352-2547], Beck, Martin [0000-0002-7397-1321], and Apollo - University of Cambridge Repository
Subjects: Multidisciplinary, 82/58, 631/45/500, article, General Physics and Astronomy, 38/90, Proteins, General Chemistry, General Biochemistry, Genetics and Molecular Biology, 38/91, Protein Domains, Protein Biosynthesis, 38/88, 631/80/389/2029, 631/337/574, 631/1647/514/1949, Ribosomes
Abstract: Funder: Max-Planck-Gesellschaft (Max Planck Society); doi: https://doi.org/10.13039/501100004189, During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.
Published: 2021

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21 results on '"Hummer, Gerhard"'

1. Efficient generation of random rotation matrices in four dimensions

2. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level

3. AI-based structure prediction empowers integrative structural analysis of human nuclear pores

4. Rebinding kinetics from single-molecule force spectroscopy experiments close to equilibrium

5. Structural basis of polyamine transport by human ATP13A2 (PARK9)

6. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

7. Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments

8. Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments

9. Artificial Intelligence Assists Discovery of Reaction Coordinates and Mechanisms from Molecular Dynamics Simulations

10. Cross-validation tests for cryo-EM maps using an independent particle set

11. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics

12. Molekulare Mechanismen für die Formung und Qualitätskontrolle von Lipidmembranen

13. On the free energy of ionic hydration

14. PHYS 135-Spatial and temporal coarse-graining in simulations of protein dynamics and complex formation

15. PHYS 197-Are current molecular dynamics force fields too helical?

16. The. folding and binding pathway of the transcription factor CREB to CBP

17. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

18. Exploring the structural stability and the mechanism of dissociation of Alzheimer's amyloid fibrils

19. CHEMISTRY Methods for computational chemistry

20. Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

21. Co-translational assembly orchestrates competing biogenesis pathways

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