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14 results on '"Pekka Mark"'

1. Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucanendo-transglycosylase

Author

Qiong Zhang, Pekka Mark, Mirjam Czjzek, Hans Ågren, and Harry Brumer

Subjects
biology, Chemistry, Stereochemistry, Hydrogen bond, Ligand, General Chemical Engineering, Beta sheet, Active site, Protonation, General Chemistry, Condensed Matter Physics, Xyloglucan, chemistry.chemical_compound, Deprotonation, Nucleophile, Modeling and Simulation, biology.protein, General Materials Science, Information Systems
Abstract

Molecular dynamics simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analysed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called ‘helper residue’ aspartate 87 (Asp87), which lies between the catalytic nucleophile [glutamate 85 (Glu85)] and general acid/base (Glu89) residues on the same beta strand, had a significant effect on PttXET16-34 active site structure. When Asp87 was deprotonated, electrostatic repulsion forced the nucleophile away from C1 of the sugar ring in subsite − 1 and the proton–donating ability of Glu89 was also weakened due to the formation of a hydrogen bond with Asp87, whereas the protonation of Asp87 resulted in the formation of a hydrogen bond with the catalytic nucleophile and correct positioning of the catalytic machinery. The results suggest that catalysis in glycoside hydrolase family 16, and by extension clan GH-B e...

Published
2011
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2. Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Author

Pekka Mark, Aatto Laaksonen, and Henrik Rundgren

Subjects
Alanine, Stereochemistry, Chemistry, Hydrogen bond, Tryptophan, Condensed Matter Physics, Biochemistry, Folding (chemistry), Molecular dynamics, chemistry.chemical_compound, Intramolecular force, Aromatic amino acids, Organic chemistry, Physical and Theoretical Chemistry, Hox gene
Abstract

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.

Published
2007
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3. Molecular dynamics simulations of conserved Hox protein hexapeptides II. Folded structures in water solution

Author

Henrik Rundgren, Pekka Mark, and Aatto Laaksonen

Subjects
Alanine, Methionine, Stereochemistry, Hydrogen bond, Tryptophan, Phenylalanine, Condensed Matter Physics, Biochemistry, Molecular dynamics, chemistry.chemical_compound, chemistry, Side chain, Physical and Theoretical Chemistry, Hox gene
Abstract

MD simulations of Hox protein N-terminal hexapeptides TFDWMK (Hox B1) and LFPWMR (Hox B8) are performed in water solution and complemented with simulations where the aromatic residues phenylalanine (F) and tryptophan (W) are successively replaced by alanine (A). Results from this study give support that different hexapeptides can form similar folded structures in water, stabilized mainly by internal hydrogen bonding where the arrangement of the aromatic side chains together with the methionine (M) side chain forming a hydrophobic core covers and protects the internal hydrogen bonds from water. Replacement of the aromatic side chains with Alanine did not lead to unfolding, but rather the hexapeptides were slightly changing their conformations where the Methionine side chain together with the peptide backbone protected the internal hydrogen bonds and the hexapeptides remain folded. Our results give support that these hexapeptides are able to remain folded to some extent even without the aromatic side chains.

Published
2007
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4. Recipe of Polarized One-Electron Potential Optimization for Development of Polarizable Force Fields

Author

Setsuko Nakagawa, Hans Ågren, and Pekka Mark

Subjects
Physics, Polarization (waves), Computer Science Applications, Partial charge, Dipole, Chemical bond, Polarizability, Intramolecular force, Physics::Atomic and Molecular Clusters, Physics::Atomic Physics, Electric potential, Physics::Chemical Physics, Physical and Theoretical Chemistry, Test particle, Atomic physics
Abstract

Polarized one-electron potential (POP) optimization is a powerful and practical method to determine multicenter dipole polarizabilities that can be used for constructing polarizable force fields. The POP optimization is similar to the widely used electrostatic potential (ESP) optimization to determine the partial charges of molecules. However, while the ESP optimization targets the electrostatic potentials on a molecular surface, the POP optimization targets the change of electrostatic potentials on molecular surfaces which are induced by the field of a test charge on the molecular surface. Since only additional one-electron integrals for the test charge are required for the estimation of the surface potentials, the change of electrostatic potentials has been named "polarized one-electron potentials". We show that in the POP optimization, both an explicitly interacting polarizability model and an implicitly interacting polarizability model can be used for the determination of the multicenter polarizabilities. In the explicitly interacting model, intramolecular induced dipole-induced dipole interaction is mutually included in the process of the POP optimization, but the interaction is not included in the implicitly interacting model. In the implicitly interacting polarizability model, a combined model of isotropic atom polarization and anisotropic bond polarization is shown to provide the best fitting results for nucleic acid bases which show large polarization anisotropy. A simple scaling model to the chemical bond has been newly proposed for the explicitly interacting polarizability model. We show that the simple model can be applied to molecular simulations without any damping of exponential type in the intramolecular induced dipole interaction. A detailed procedure for determination of the multicenter dipole polarizability by the POP optimization is also presented.

Published
2015

5. A Molecular Dynamics Study of Tryptophan in Water

Author

Pekka Mark and Lennart Nilsson

Subjects
Quantitative Biology::Biomolecules, Chemistry, Tryptophan, Thermodynamics, Nanosecond, Electrostatics, Surfaces, Coatings and Films, Viscosity, Molecular dynamics, Dipole, Computational chemistry, Materials Chemistry, Water model, Periodic boundary conditions, Physical and Theoretical Chemistry
Abstract

Molecular dynamics simulations of a single tryptophan amino acid in water were performed with the CHARMM molecular mechanics program using the modified TIP3P, the refined SPC, and the original SPC/E water models. All these empirical water models are similar in nature, but small differences give significant differences in their properties for liquid water. Nanosecond molecular dynamics simulations were carried out in the NVT, NVE, or NPT ensembles using a cubic simulation cell furnished with periodic boundary conditions. The calculations of long-range interactions were performed with two different methods, the atom-based spherical cutoff method with force shifting, where the nonbonded interactions were smoothly shifted to zero at the cutoff distance, and the particle-mesh Ewald technique. Transition dipole autocorrelation functions and reorientation times of tryptophan were calculated and compared to experimental values. Tryptophan hydration was affected by the water model and the treatment of long-range electrostatic interactions. The reorientation time of tryptophan depended strongly on the water model used, and the viscosity of the model liquid was found to correlate with the tryptophan translational and rotational dynamics in water. Statistical accuracy and errors in the analyses are discussed.

Published
2002
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6. Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

Author

Pekka Mark and Lennart Nilsson

Subjects
Computational Mathematics, Molecular dynamics, Temperature control, Chemistry, Truncation, Water model, Cutoff, General Chemistry, Radius, Statistical physics, Radial distribution function, Ewald summation
Abstract

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods—the Ewald summation technique, and three different spherical truncation methods—for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (gOO), the distance dependent Kirkwood G-factor [Gk(r)] and the intermolecular potential energy (Epot) were determined from the different trajectories and compared with the experimental data. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1211–1219, 2002

Published
2002
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7. Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

Author

Pekka Mark and and Lennart Nilsson

Subjects
Molecular dynamics, Chemistry, Significant difference, Dynamics (mechanics), Water model, Structure (category theory), Molecule, Periodic boundary conditions, Shake, Statistical physics, Physical and Theoretical Chemistry
Abstract

Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were carried out in the microcanonical NVE ensemble, using 901 water molecules in a cubic simulation cell furnished with periodic boundary conditions at 298 K. The SHAKE algorithm was used to keep water molecules rigid. Nanosecond trajectories were calculated with all water models for high statistical accuracy. The characteristic self-diffusion coefficients D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data. The effects of velocity rescaling on the self-diffusion coefficient D were examined. All these empirical water models used in this study are similar by having three interaction sites, but the small differences in their pair potentials composed of Lennard-Jones (LJ) and Coulombic terms give significant difference...

Published
2001
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8. Molecular Dynamics Simulations of the Ala-Pro Dipeptide in Water: Conformational Dynamics of Trans and Cis Isomers Using Different Water Models

Author

Lennart Nilsson and Pekka Mark

Subjects
Dipeptide, Hydrogen bond, Stereochemistry, Chemistry, Surfaces, Coatings and Films, Molecular dynamics, chemistry.chemical_compound, Computational chemistry, Intramolecular force, Intermolecular potential, Materials Chemistry, Water model, Molecule, Physical and Theoretical Chemistry, Cis–trans isomerism
Abstract

Molecular dynamics simulations of a single dipeptide (Ala-Pro) molecule in water were carried out using different water models, the modified TIP3P (transferable intermolecular potential 3P), the refined SPC (simple point charge), and the original SPC/E (extended simple point charge). Both trans and cis isomers of the dipeptide were simulated, and conformations from simulations with the different water models were compared. Both isomers have several conformations, but the total conformational space is limited. Two experimentally obtained subconformations of the cis isomer were found in simulations with the different water models. The bioactive conformation, which is binding to Cyclophilin A, was the major cis conformation, and the conformation with an intramolecular hydrogen bond between the N-terminal and the C-terminal was found to exist as the minor cis conformation. The hydration of the dipeptide was found to depend both on its conformation and on the water model.

Published
2001
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9. Contributory presentations/posters

Author

N. Manoj, V. R. Srinivas, A. Surolia, M. Vijayan, K. Suguna, R. Ravishankar, R. Schwarzenbacher, K. Zeth, null Diederichs, G. M. Kostner, A. Gries, P. Laggner, R. Prassl, null Madhusudan, Pearl Akamine, Nguyen-huu Xuong, Susan S. Taylor, M. Bidva Sagar, K. Saikrishnan, S. Roy, K. Purnapatre, P. Handa, U. Varshney, B. K. Biswal, N. Sukumar, J. K. Mohana Rao, A. Johnson, Vasantha Pattabhi, S. Sri Krishna, Mira Sastri, H. S. Savithri, M. R. N. Murthy, Bindu Pillai, null Kannan, M. V. Hosur, Mukesh Kumar, Swati Patwardhan, K. K. Kannan, B. Padmanabhaa, S. Sasaki-Sugio, M. Nukaga, T. Matsuzaki, S. Karthikevan, S. Sharma, A. K. Sharma, M. Paramasivam, P. Kumar, J. A. Khan, S. Yadav, A. Srinivasan, T. P. Singh, S. Gourinath, Neelima Alam, A. Srintvasan, Vikas Chandra, Punit Kaur, Ch. Betzel, S. Ghosh, A. K. Bera, S. Bhattacharya, S. Chakraborty, A. K. Pal, B. P. Mukhopadhyay, I. Dey, U. Haldar, Asok Baneriee, Jozef Sevcik, Adriana Solovicova, K. Sekar, M. Sundaralingam, N. Genov, Dong-cai Liang, Tao Jiang, Ji-ping Zhang, Wen-rui Chang, Wolfgang Jahnke, Marcel Blommers, S. C. Panchal, R. V. Hosur, Bindu Pillay, Puniti Mathur, S. Srivatsun, Ratan Mani Joshi, N. R. Jaganathan, V. S. Chauhan, H. S. Atreya, S. C. Sahu, K. V. R. Chary, Girjesh Govil, Elisabeth Adjadj, Éric Quinjou, Nadia Izadi-Pruneyre, Yves Blouquit, Joël Mispelter, Bernadette Heyd, Guilhem Lerat, Philippe Milnard, Michel Desmadreil, Y. Lin, B. D. Nageswara Rao, Vidva Raghunathan, Mei H. Chau, Prashant Pesais, Sudha Srivastava, Evans Coutinho, Anil Saran, Leizl F. Sapico, Jayson Gesme, Herbert Lijima, Raymond Paxton, Thamarapu Srikrishnan, C. R. Grace, G. Nagenagowda, A. M. Lynn, Sudha M. Cowsik, Sarata C. Sahu, S. Chauhan, A. Bhattacharya, G. Govil, Anil Kumar, Maurizio Pellecchia, Erik R. P. Zuiderweg, Keiichi Kawano, Tomoyasu Aizawa, Naoki Fujitani, Yoichi Hayakawa, Atsushi Ohnishi, Tadayasu Ohkubo, Yasuhiro Kumaki, Kunio Hikichi, Katsutoshi Nitta, V. Rani Parvathy, R. M. Kini, Takumi Koshiba, Yoshihiro Kobashigawa, Min Yao, Makoto Demura, Astushi Nakagawa, Isao Tanaka, Kunihiro Kuwajima, Jens Linge, Seán O. Donoghue, Michael Nilges, G. Chakshusmathi, Girish S. Ratnaparkhi, P. K. Madhu, R. Varadarajan, C. Tetreau, M. Tourbez, D. Lavalette, M. Manno, P. L. San Biagio, V. Martorana, A. Emanuele, S. M. Vaiana, D. Bulone, M. B. Palma-Vittorelli, M. U. Palma, V. D. Trivedi, S. F. Cheng, W. J. Chien, S. H. Yang, S. Francis, D. K. Chang, Renn Batra, Michael A. Geeves, Dietmar J. Manstein, Joanna Trvlska, Pawel Grochowski, Maciej Geller, K. Ginalski, P. Grochowski, B. Lesyng, P. Lavalette, Y. Blouquit, D. Roccatano, A. Amadei, A. Di Nola, H. J. C. Berendsen, Bosco Ho, P. M. G. Curmi, H. Berry, D. Lairez, E. Pauthe, J. Pelta, V. Kothekar, Shakti Sahi, M. Srinivasan, Anil K. Singh, Kartha S. Madhusudnan, Fateh S. Nandel, Harpreet Kaur, Balwinder Singh, D. V. S. Jain, K. Anton Feenstra, Herman J. C. Berendsen, F. Tama, Y. -H. Sanejouand, N. Go, Deepak Sharma, Sunita Sharma, Santosh Pasha, Samir K. Brahmachari, R. Viiavaraghavan, Jyoti Makker, Sharmisllia Dey, S. Kumar, G. S. Lakshmikanth, G. Krishnamoorthy, V. M. Mazhul, E. M. Zaitseva, Borys Kierdaszuk, J. Widengren, B. Terry, Ü. Mets, R. Rigler, R. Swaminathan, S. Thamotharan, N. Yathindra, Y. Shibata, H. Chosrowjan, N. Mataga, I. Morisima, Tania Chakraharty, Ming Xiao, Roger Cooke, Paul Selvin, C. Branca, A. Faraone, S. Magazù, G. Maisano, P. Migliardo, V. Villari, Digambar V. Behere, M. Sharique Zahida Waheed Deva, M. Brunori, F. Cutruzzolà, Q. H. Gibson, C. Savino, C. Travaglini-Allocatelli, B. Vallone, Swati Prasad, Shyamalava Mazumdar, Samaresh Mitra, P. Soto, R. Fayad, I. E. Sukovataya, N. A. Tyulkova, Sh. V. Mamedov, B. Aktas, M. Canturk, B. Aksakal, R. Yilgin, K. I. Bogutska, N. S. Miroshnichenko, S. Chacko, M. DiSanto, J. A. Hypolite, Y-M. Zheng, A. J. Wein, M. Wojciechowski, T. Grycuk, J. Antosiewicz, Marc A. Ceruso, Alfredo Di Nola, Subhasis Bandvopadhvay, Bishnu P. Chatterjee, Devapriva Choudhury, Andrew Thompson, Vivian Stojanoff, Jerome Pinkner, Scott Hultgren, Stefan Khight, Delphine Flatters, Julia Goodfellow, Fumi Takazawatt, Minoru Kanehisa, Masaki Sasai, Hironori Nakamura, Wang Bao Han, Yuan Zheng, Wang Zhi Xin, Pan xin Min, Vlnod Bhakuni, Sangeeta Kulkarni, Atta Ahmad, Koodathingal Prakash, Shashi Prajapati, Alexey Surin, Tomoharu Matsumoto, Li Yang, Yuki Nakagawa, Kazumoto Kimura, Yoshiyuki Amemiya, Gennady V. Semisotnov, Hiroshi Kihara, Saad Tayyab, Salman Muzammil, Yogesh Kumar, Vinod Bhakuni, Monica Sundd, Suman Kundu, M. V. Jagannadham, Medicherla V. Jagannadham, Bina Chandani, Ruby Dhar, Lalankumar Sinha, Deepti Warrier, Sonam Mehrotra, Purnima Khandelwal, Subhendu Seth, Y. U. Sasidhar, C. Ratna Prabha, Arun Gidwani, K. P. Madhusudan, Akira R. Kinjo, Ken Nishikawa, Suvobrata Chakravarty, Raghavan Varadarajan, K. Noyelle, P. Haezebrouck, M. Joniau, H. Van Dael, Sheffali Dash, Indra Brata Jha, Rajiv Bhat, Prasanna Mohanty, A. K. Bandyopadhyay, H. M. Sonawat, Ch. Mohan Rao, Siddhartha Datta, K. Rajaraman, B. Raman, T. Ramakrishna, A. Pande, J. Pande, S. Betts, N. Asherie, O. Ogun, J. King, G. Benedek, I. V. Sokolova, G. S. Kalacheva, Masashi Sonoyama, Yasunori Yokoyama, Kunihiro Taira, Shigeki Mitaku, Chicko Nakazawal, Takanori Sasakil, Yuri Mukai, Naoki Kamo, Seema Dalal, Lynne Regan, Shigeki Mituku, Mihir Roychoudhury, Devesh Kumar, Dénes Lőrinczv, Franciska Könczöl, László Farkas, Joseph Belagyi, Christoph Schick, Christy A. Thomson, Vettai S. Ananthanarayanan, E. G. Alirzayeva, S. N. Baba-Zade, M. Michael Gromiha, M. Oobatake, H. Kono, J. An, H. Uedaira, A. Sarai, Kazufumi Takano, Yuriko Yamagata, Katsuhide Yutani, Gouri S. Jas, Victor Muñoz, James Hofrichter, William A. Eaton, Jonathan Penoyar, Philip T. Lo Verde, J. Kardos, Á. Bódi, I. Venekei, P. Závodszky, L. Gráf, András Szilágyi, Péter Závodszky, R. D. Allan, J. Walshaw, D. N. Woolfson, Jun Funahashi, Savan Gupta, M. Mangoni, P. Roccatano, Gosu Ramachandraiah, Nagasuma R. Chandra, Barbara Ciani, Derek N. Woolfson, Usha B. Nair, Kanwal J. Kaur, Dinakar M. Salunke, Chittoor P. Swaminathan, Avadhesha Surolia, A. Pramanik, P. Jonasson, G. Kratz, O. T. Jansson, P. -Å. Nygren, S. Ståhl, K. Ekberg, B. -L. Johansson, S. Uhlén, M. Uhlén, H. Jörnvall, J. Wahren, Karin Welfle, Rolf Misselwitz, Wolfgang Höhne, Heinz Welfle, L. G. Mitskevich, N. V. Fedurkina, B. I. Kurganov, Gotam K. Jarori, Haripada Maity, J. Guharay, B. Sengupta, P. K. Sengupta, K. Sridevi, S. R. Kasturi, S. P. Gupta, Gunjan Agarwal, Suzanne Kwong, Robin W. Briehl, O. I. Ismailova, N, A. Tyulkova, C. Hariharan, D. Pines, E. Pines, M. Zamai, R. Cohen-Luria, A. Yayon, A. H. Parola, M. J. Padya, G. A. Spooner, D. N. Woolfeon, Panchan Bakshi, D. K. Bharadwaj, U. Sharma, N. Srivastava, R. Barthwal, N. R. Jagannathan, Keiko Matsuda, Takaaki Nishioka, Nobuhiro Go, T. Aita, S. Urata, Y. Husimi, Mainak Majumder, Nicola G. A. Abrescia, Lucy Malinina, Juan A. Subirana, Juan Aymami, Ramón Eritxa, Miquel Coll, B. J. Premraj, R. Thenmalarchelvi, P. Satheesh Kumar, N. Gautham, Lou -Sing Kan, null Ming-Hou, Shwu-Bin Lin, Tapas Sana, Kanal B. Roy, N. Bruant, D. Flatters, R. Lavery, D. Genest, Remo Rons, Heinz Sklenar, Richard Lavery, Sudip Kundu, Dhananjay Bhattacharyya, Debashree Bandyopadhyay, Ashoke Ranjan Thakur, Rabi Majumdar, F. Barceló, J. Portugal, Sunita Ramanathan, B. J. Rao, Mahua Gliosli, N. Vinay Kumar, Umesh Varshney, Shashank S. Pataskar, R. Sarojini, S. Selvasekarapandian, P. Kolandaivel, S. Sukumar, P. Kolmdaivel, Motilal Maiti, Anjana Sen, Suman Das, Elisa Del Terra, Chiara Suraci, Silvia Diviacco, Franco Quadrifoglio, Luigi Xodo, Arghya Ray, G. Karthikeyan, Kandala V. R. Chary, Basuthkar J. Rao, Anwer Mujeeb, Thomas L. James, N. Kasyanenko, E. E. F. Haya, A. Bogdanov, A. Zanina, M. R. Bugs, M. L. Cornélio, M. Ye. Tolstorukov, Nitish K. Sanval, S. N. Tiwari, Nitish K. Sanyal, Mihir Roy Choudhury, P. K. Patel, Neel S. Bhavesh, Anna Gabrielian, Stefan Wennmalm, Lars Edman, Rudolf Rigler, B. Constantinescu, L. Radu, I. Radulcscu, D. Gazdaru, Sebastian Wärmländer, Mikael Leijon, Setsuyuki Aoki, Takao Kondo, Masahiro Ishiura, V. A. Pashinskaya, M. V. Kosevich, V. S. Shelkovsky, Yu. P. Blagoy, Ji-hua Wang, R. Malathi, K. Chandrasekhar, E. R. Kandimalla, S. Agrawal, V. K. Rastogi, M. Alcolea Palafox, Chatar Singh, A. D. Beniaminov, S. A. Bondarenko, E. M. Zdobnov, E. E. Minyat, N. B. Ulyanov, V. I. Ivanov, J. S. Singh, Kailas D. Sonawane, Henri Grosjean, Ravindra Tewari, Uddhavesh B. Sonavane, Annie Morin, Elizabeth A. Doherty, Jennifer A. Doudna, H. Tochio, S. Sato, H. Matsuo, M. Shirakawa, Y. Kyogoku, B. Javaram, Surjit B. Dixit, Piyush Shukla, Parul Kalra, Achintya Das, Kevin McConnell, David L. Beveridge, W. H. Sawyer, R. Y. S. Chan, J. F. Eccelston, Yuling Yan, B. E. Davidson, Eimer Tuite, Bengt Norden, Peter Nielsen, Masayuki Takahashi, Anirban Ghosh, Manju Bansal, Frauke Christ, Hubert Thole, Wolfgang Wende, Alfred Pingoud, Vera Pingoud, Pratibha Mehta Luthra, Ramesh Chandra, Ranjan Sen, Rodney King, Robert Weisberg, Olaf F. A. Larsen, Jos Berends, Hans A. Heus, Cornelis W. Hilbers, Ivo H. M. van Stokkum, Bas Gobets, Rienk van Grondelle, Herbert van Amerongen, HE. Sngrvan, Yu. S. Babayan, N. V. Khudaverdian, M. Gromiha, F. Pichierri, M. Aida, P. Prabakaran, K. Sayano, Saulius Serva, Eglė Merkienė, Giedrius Vilkaitis, Elmar Weinhold, Saulius Klimašauskas, Eleonora Marsich, Antonella Bandiera, Giorgio Manzini, G. Potikyan, V. Arakelyan, Yu. Babayan, Alex Ninaber, Julia M. Goodfellow, Yoichiro Ito, Shigeru Ohta, Yuzuru Husimi, J. Usukura, H. Tagami, H. Aiba, Mougli Suarez, Elia Nunes, Deborah Keszenman, E. Carmen Candreva, Per Thyberg, Zeno Földes-Papp, Amita Joshi, Dinesh Singh, M. R. Rajeswari, null Ira, M. Pregetter, H. Amenitsch, J. Chapman, B. N. Pandev, K. P. Mishra, E. E. Pohl, J. Sun, I. I. Agapov, A. G. Tonevitsky, P. Pohl, S. M. Dennison, G. P. Gorbeako, T. S. Dynbko, N. Pappavee, A. K. Mishra, Prieto Manuel, Almeida Rodrigo, Loura Luis, L. Ya. Gendel, S. Przestalski, J. Kuczera, H. Kleszczyńska, T. Kral, E. A. Chernitsky, O. A. Senkovich, V. V. Rosin, Y. M. Allakhverdieva, G. C. Papageorgiou, R. A. Gasanov, Calin Apetrei, Tudor Savopol, Marius Balea, D. Cucu, D. Mihailescu, K. V. Ramanathan, Goran Bačić, Nicolas Sajot, Norbert Garnier, Serge Crouzy, Monique Genest, Z. S. Várkonyi, O. Zsiros, T. Farkas, Z. Combos, Sophie Cribier, I. F. Fraceto, S. Schreier, A. Spisni, F. de Paula, F. Sevšek, G. Gomišček, V. Arrigler, S. Svetina, B. Žekš, Fumimasa Nomura, Miki Nagata, Kingo Takiguchi, Hirokazu Hotani, Lata Panicker, P. S. Parvathanathan, A. Ishino, A. Saitoh, H. Hotani, K. Takiguchi, S. Afonin, A. Takahashi, Y. Nakato, T. Takizawa, Dipti Marathe, Kent Jørgensen, Satinder S. Rawat, R. Rukmini, Amitabha Chattopadhyay, M. Šentiurc, J. Štrancar, Z. Stolič, K. Filipin, S. Pečar, S. C. Biswas, Satyen Sana, Anunay Samanta, Koji Kinoshita, Masahito Yamazaki, Tetsuhiko Ohba, Tai Kiuchi, null Yoshitoshi, null Kamakura, Akira Goto, Takaaki Kumeta, Kazuo Ohki, I. P. Sugar, T. E. Thompson, K. K. Thompson, R. L. Biltonen, Y. Suezaki, H. Ichinose, M. Akivama, S. Matuoka, K. Tsuchihashi, S. Gasa, P. Mattjus, J. G. Molotkovsky, H. M. Pike, R. E. Brown, Ashish Arora, Jörg H. Kleinschmidt, Lukas K. Tamm, O. G. Luneva, K. E. Kruglyakova, V. A. Fedin, O. S. Kuptsoya, J. W. Borst, N. V. Visser, A. J. W. G. Visser, T. S. Dyubko, Toshihiko Ogihara, Kiyoshi Mishima, A. L. Shvaleva, N. Č. Radenović, P. M. Minić, M. G. Jeremić, Č. N. Radenović, T. F. Aripov, E. T. Tadjibaeva, O. N. Vagina, M. V. Zamaraeva, B. A. Salakhutdinov, A. Cole, M. Poppofl, C. Naylor, R. Titball, A. K. Basak, J. T. Eaton, C. E. Naylor, N. Justin, D. S. Moss, R. W. Titball, F. Nomura, M. Nagata, S. Ishjkawa, S. Takahashi, Kaoru Obuchi, Erich Staudegger, Manfred Kriechbaum, Robert I. Lehrer, Alan J. Waring, Karl Lohner, Susanne Gangl, Bernd Mayer, Gottfried Köhler, J. Shobini, Z. Guttenberg, B. Lortz, B. Hu, E. Sackmann, N. M. Kozlova, L. M. Lukyanenko, A. N. Antonovich, E. I. Slobozhanina, Andrey V. Krylov, Yuri N. Antonenko, Elena A. Kotova, Alexander A. Yaroslavov, Subhendu Ghosh, Amal K. Bera, Sudipto Das, Eva Urbánková, Masood Jelokhani-Niaraki, Karl Freeman, Petr Jezek, P. B. Usmanov, A. Ongarbaev, A. K. Tonkikh, Peter Pohl, Sapar M. Saparov, P. Harikumar, J. P. Reeves, S. Rao, S. K. Sikdar, A. S. Ghatpande, C. Corsso, A. C. Campos de Carvalho, W. A. Varanda, C. ElHamel, E. Dé, N. Saint, G. Molle, Anurae Varshney, M. K. Mathew, E. Loots, E. Y. Isacoff, Michiki Kasai, Naohiro Yamaguchi, Paramita Ghosh, Joseph Tigyi, Gabor Tigyi, Karoly Liliom, Ricardo Miledi, Maja R. Djurisic, Pavle R. Andjus, Indira H. Shrivastava, M. S. P. Sansom, C. Barrias, P. F. Oliveira, A. C. Mauricio, A. M. Rebelo da Costa, I. A. Lopes, S. V. Fedorovich, V. S. Chubanov, M. V. Sholukh, S. V. Konev, N. Fedirko, V. Manko, M. Klevets, N. Shvinka, B. S. Prabhananda, Mamata H. Kombrabail, S. Aravamudhan, Berenice Venegas-Cotero, Ivan Ortega Blake, Zhi-hong Zhang, Xiao-jian Hu, Han-qing Zhou, Wei-ying Cheng, Hang-fang Feng, L. O. Dubitsky, L. S. Vovkanvch, I. A. Zalyvsky, E. Savio-Galimberti, P. Bonazzola, J. E. Ponce-Homos, Mario Parisi, Claudia Capurro, Roxana Toriano, Laxma G. Ready, Larry R. Jones, David D. Thomas, B. A. Tashmukhamedov, B. T. Sagdullaev, D. Heitzmann, R. Warth, M. Bleich, R. Greger, K. T. G. Ferreira, H. G. Ferreira, Orna Zagoory, Essa Alfahel, Abraham H. Parola, Zvi Priel, H. Hama-Inaba, R. Wang, K. Choi, T. Nakajima, K. Haginoya, M. Mori, H. Ohyama, O. Yukawa, I. Hayata, Nanda B. Joshi, Sridhar K. Kannurpatti, Preeti G. Joshi, Mau Sinha, Xun Shen, Tianhui Hu, Ling Bei, Menno L. W. Knetsch, Nicole Schäfers, John Sandblom, Juris Galvanovskis, Roxana Pologea-Moraru, Eugenia Kovacs, Alexandra Dinu, S. H. Sanghvi, V. Jazbinšek, G. Thiel, W. Müller, G. Wübeller, Z. Tronteli, Leš Fajmut, Marko Marhl, Milan Brumen, I. D. Volotovski, S. G. Sokolovski, M. R. Knight, Alexei N. Vasil’ev, Alexander V. Chalyi, P. Sharma, P. J. Steinbach, M. Sharma, N. D. Amin, J. Barchir, R. W. Albers, H. C. Pant, M. Balasubramanyam, M. Condrescu, J. P. Gardner, Shamci Monajembashi, Gotz Pilarczyk, K. O. Greulich, F. M. El-Refaei, M. M. Talaat, A. I. El-Awadi, F. M. Ali, Ivan Tahradník, Jana Pavelková, Alexandra Zahradniková, Boris S. Zhorov, Vettai S. Ananthanaravanan, M. Ch. Michailov, E. Neu, W. Seidenbusch, E. Gornik, D. Martin, U. Welscher, D. G. Weiss, B. R. Pattnaik, A. Jellali, V. Forster, D. Hicks, J. Sahel, H. Dreyfus, S. Picaud, Hong-Wei Wang, Sen-fang Sui, Pradeep K. Luther, John Barry, Ed Morris, John Squire, C. Sivakama Sundari, D. Balasubramanian, K. Veluraia, T. Hema Thanka Christlet, M. Xavier Suresh, V. Laretta-Garde, Dubravka Krilov, Nataša Stojanović, Janko N. Herak, Ravi Jasuja, Maria Ivanova, Rossen Mirchev, Frank A. Ferrone, David Stopar, Ruud B. Spruijt, Cor J. A. M. Wolfs, Marcus A. Hemminga, G. Arcovito, M. De Spirito, Rajendra K. Agrawal, Amy B. Heagle, Pawel Penczek, Robert Grassucci, Joachim Frank, Manjuli R. Sharma, Loice H. Jeyakumar, Sidney Fleischer, Terence Wagenknecht, Carlo Knupp, Peter M. G. Munro, Eric Ezra, John M. Squire, Koji Ichihara, Hidefumi Kitazawa, Yusuke Iguchi, Tomohiko J. Itoh, Greta Pifat, Marina Kveder, Slavko Pečar, Milan Schara, Deepak Nair, Kavita Singh, Kanury V. S. Rao, Kanwaljeet Kaur, Deepti Jain, B. Sundaravadivel, Manisha Goel, D. M. Salunke, E. I. Kovalenko, G. N. Semenkova, S. N. Cherenkevich, T. Lakshmanan, D. Sriram, S. Srinivasan, D. Loganathan, T. S. Ramalingam, J. A. Lebrón, P. J. Bjorkman, A. K. Singh, T. N. Gayatri, Ernesto R. Caffarena, J. Raul Grigera, Paulo M. Bisch, V. Kiessling, P. Fromherz, K. N. Rao, S. M. Gaikwad, M. I. Khan, C. G. Suresh, P. Kaliannan, M. Elanthiraiyan, K. Chadha, J. Payne, J. L. Ambrus, M. P. N. Nair, Madhavan P. N. Nair, S. Mahajan, K. C. Chadha, R. Hewitt, S. A. Schwartz, J. Bourguignon, M. Faure, C. Cohen-Addad, M. Neuburger, R. Ober, L. Sieker, D. Macherel, R. Douce, D. S. Gurumurthy, S. Velmurugan, Z. Lobo, Ratna S. Phadke, Prashant Desai, I. M. Guseinova, S. Yu. Suleimanov, I. S. Zulfugarov, S. N. Novruzova, J. A. Aliev, M. A. Ismayilov, T. V. Savchenko, D. R. Alieva, Petr Ilík, Roman Kouřil, Hana Bartošková, Jan Nauš, Jvoti U. Gaikwad, Sarah Thomas, P. B. Vidyasagar, G. Garab, I. Simidjiev, S. Rajagopal, Zs. Várkonyi, S. Stoylova, Z. Cseh, E. Papp, L. Mustárdy, A. Holzenburg, R. Bruder, U. K. Genick, T. T. Woo, D. P. Millar, K. Gerwert, E. D. Getzoff, Tamás Jávorfí, Győző Garab, K. Razi Naqvi, Md. Kalimullah, Jyoti Gaikwad, Manoj Semwal, Roman Kouril, Petr Ilik, Man Naus, István Pomozi, Gábor Horváth, Rüdiger Wehner, Gary D. Bernard, Ana Damjanović, Thorsten Ritz, Klaus Schulten, Wang Jushuo, Shan Jixiu, Gong Yandao, Kuang Tingyun, Zhao Nanming, Arvi Freiberg, Kõu Timpmann, Rein Ruus, Neal W. Woodbury, E. V. Nemtseva, N. S. Kudryasheva, A. G. Sizykh, V. N. Shikhov, T. V. Nesterenko, A. A. Tikhomirov, Giorgio Forti, Giovanni Finazzi, Alberto Furia, Romina Paola Barbagallo, S. Iskenderova, R. Agalarov, R. Gasanov, Miyashita Osamu, G. O. Nobuhiro, R. K. Soni, M. Ramrakhiani, Hiromasa Yagi, Kacko Tozawa, Nobuaki Sekino, Tomoyuki Iwabuchi, Masasuke Yoshida, Hideo Akutsu, A. V. Avetisyan, A. D. Kaulen, V. P. Skulachev, B. A. Feniouk, Cécile Breyton, Werner Kühlbrandt, Maria Assarsson, Astrid Gräslund, G. Horváth, B. Libisch, Z. Gombos, N. V. Budagovskaya, N. Kudryasheva, Erisa Harada, Yuki Fukuoka, Tomoaki Ohmura, Arima Fukunishi, Gota Kawai, Kimitsuna Watanabe, Jure Derganc, Bojan Božič, Saša Svetina, Boštjan Žekš, J. F. Y. Hoh, Z. B. Li, G. H. Rossmanith, E. L. de Beer, B. W. Treijtel, P. L. T. M. Frederix, T. Blangè, S. Hénon, F. Galtet, V. Laurent, E. Planus, D. Isabey, L. S. Rath, P. K. Dash, M. K. Raval, C. Ramakrishnan, R. Balaram, Milan Randic, Subhash C. Basak, Marjan Vracko, Ashesh Nandy, Dragan Amic, Drago Beslo, Sonja Nikolic, Nenad Trinajstic, J. Walahaw, Marc F. J. Lensink, Boojala V. B. Reddy, Ilya N. Shindylov, Philip E. Bourne, M. C. Donnamaria, J. de Xammar Oro, J. R. Grigera, Monica Neagu, Adrian Neagu, Matej Praprotnik, Dušanka Janežič, Pekka Mark, Lennart Nilsson, L. La Fata, Laurent E. Dardenne, Araken S. Werneck, Marçal de O. Neto, N. Kannan, S. Vishveshwara, K. Veluraja, Gregory D. Grunwald, Alexandra T. Balaban, Kanika Basak, Brian D. Gute, Denise Mills, David Opitz, Krishnan Balasubramanian, G. I. Mihalas, Diana Lungeanu, G. Macovievici, Raluca Gruia, C. Cortez-Maghelly, B. Dalcin, E. P. Passos, S. Blesic, M. Ljubisavljevic, S. Milosevic, D. J. Stratimirovic, Nandita Bachhawat, Shekhar C. Mande, A. Nandy, Ayumu Saito, Koichi Nishigaki, Mohammed Naimuddin, Takatsugu Hirokawa, Mitsuo Ono, Hirotomo Takaesu, M. I. El Gohary, Abdalla S. Ahmed, A. M. Eissa, Hiroshi Nakashima, G. P. S. Raghava, N. Kurgalvuk, O. Goryn, Bernard S. Gerstman, E. V. Gritsenko, N. N. Remmel, O. M. Maznyak, V. A. Kratasyuk, E. N. Esimbekova, D. Tchitchkan, S. Koulchitsky, A. Tikhonov, A. German, Y. Pesotskaya, S. Pashkevich, S. Pletnev, V. Kulchitsky, Umamaheswar Duvvuri, Sridhar Charagundla, Rahim Rizi, John S. Leigh, Ravinder Reddy, Mahesh Kumar, O. Coshic, P. K. Julka, O. K. Rath, NR. Jagannathan, Karina Roxana Iliescu, Maria Sajin, Nicolcta Moisoi, Ileana Petcu, A. I. Kuzmenko, R. P. Morozova, I. A. Nikolenko, G. V. Donchenko, M. K. Rahman, M. M. Ahmed, Takehiro Watanabe, Y. Rubin, H. Gilboa, R. Sharony, R. Ammar, G. Uretzky, M. Khubchandani, H. N. Mallick, V. Mohan Kumar, Arijitt Borthakur, Erik M. Shapiro, M. Gulnaz Begum, Mahaveer N. Degaonkar, S. Govindasamy, Ivan Dimitrov, T. A. Kumosani, W. Bild, I. Stefanescu, G. Titescu, R. Iliescu, C. Lupusoru, V. Nastasa, I. Haulica, Gopal Khetawat, N. Faraday, M. Nealen, S. Noga, P. F. Bray, T. V. Ananieva, E. A. Lycholat, MV. Kosevich, S. G. Stepanyan, S. V. Antonyuk, R. Khachatryan, H. Arakelian, A. Kumar, S. Ayrapetyan, V. Mkheyan, S. Agadjanyan, A. Khachatryan, S. S. Rajan, V. Kabaleeswaran, Geetha Gopalakrishnan, T. R. Govindachari, Meera Ramrakhiani, Phillip Lowe, Andrew Badley, David C. Cullen, H. Hermel, W. Schmahl, H. Möhwald, Nirmalya Majumdar, Joydip Das, András Dér, Loránd Kelemen, László Oroszi, András Hámori, Jeremy J. Ramsden, Pál Ormos, D. Savitri, Chanchal K. Mitra, Toshio Yanagida, Seiji Esaki, Yuji Kimura, Tomoyuki Nishida, Yosiyuki Sowa, M. Radu, V. K. Koltover, Ya. I. Estrin, L. A. Kasumova, V. P. Bubnov, E. E. Laukhina, Rajiv Dotta, M. Degaonkar, P. Raghunathan, Rama Jayasundar, Pavel Novák, Milan Marko, Ivan Zahradník, Hiroaki Hirata, Hidetake Miyata, J. Balaji, P. Sengupta, S. Maiti, M. Gonsalves, A. L. Barker, J. V. Macpherson, D. O’Hare, C. P. Winlove, P. R. Unwin, R. Phillip, S. Banerjee, G. Ravindra Kumar, K. Nagayaka, R. Danev, S. Sugitani, K. Murata, Michael Gősch, H. Blom, P. Thyberg, Z. Földes-Papp, G. Björk, J. Holm, T. Heino, Masashi Yokochi, Fuyuhiko Inagaki, Masami Kusunoki, E. K. Matthews, J. Pines, Yu. P. Chukova, Vitaly K. Koltover, Geetanjali Bansal, Uma Singh, M. P. Bansal, Kotoko Nakata, Tastuya Nakano, Tsuguchika Kaminuma, B. P. S. Kang, U. Singh, Bonn Kirn, Neja Potocnik, Vito Stare, Latal Shukla, V. Natarajan, T. P. A. Devasagayam, M. D. Sastry, P. C. Kesavan, R. Sayfutdinov, V. V. Adamovich, D. Yu. Rogozin, A. G. Degermendzhy, C. L. Khetrapal, G. A. Nagana Gowda, Kedar Nath Ghimire, Ishida Masaru, H. Fujita, S. Ishiwata, Y. Kishimoto, S. Kawahara, M. Suzuki, H. Mori, M. Mishina, Y. Kirino, H. Ohshima, A. S. Dukhin, V. N. Shilov, P. J. Goetz, and R. K. Mishra

Subjects
0303 health sciences, biology, General Medicine, 010402 general chemistry, 01 natural sciences, Horseradish peroxidase, General Biochemistry, Genetics and Molecular Biology, 0104 chemical sciences, 03 medical and health sciences, Biochemistry, Manganese porphyrin, biology.protein, Enzyme reconstitution, General Agricultural and Biological Sciences, 030304 developmental biology
Published
1999
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10. The MIPS mammalian protein–protein interaction database

Author

Volker Stümpflen, Corinna Montrone, Hans-Werner Mewes, Dmitrij Frishman, Barbara Brauner, Philipp Pagel, Goar Frishman, Stefan Kovac, Matthias Oesterheld, Irmtraud Dunger-Kaltenbach, Pekka Mark, and Andreas Ruepp

Subjects
Mammals, Statistics and Probability, Internet, Database, Computer science, Information Storage and Retrieval, Documentation, computer.software_genre, Biochemistry, Computer Science Applications, Protein–protein interaction, User-Computer Interface, Computational Mathematics, ComputingMethodologies_PATTERNRECOGNITION, Vocabulary, Controlled, Computational Theory and Mathematics, Protein Interaction Mapping, Animals, Database Management Systems, Periodicals as Topic, Databases, Protein, Molecular Biology, computer, Software, Natural Language Processing
Abstract

Summary: The MIPS mammalian protein–protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements. Availability: The MPPI database is located at http://mips.gsf.de/proj/ppi/ Contact: d.frishman@wzw.tum.de

Published
2004
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11. Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases

Author

Jens M. Eklöf, Åsa M. Kallas, Gurvan Michel, Mirjam Czjzek, Tuula T. Teeri, Harry Brumer, Fredrika Gullfot, Martin J. Baumann, and Pekka Mark

Subjects
Models, Molecular, Nasturtium, Glycoside Hydrolases, Protein Conformation, Molecular Sequence Data, Crystallography, X-Ray, Biochemistry, Pichia, Substrate Specificity, chemistry.chemical_compound, Protein structure, Structural Biology, Catalytic Domain, Hydrolase, Glycoside hydrolase, Computer Simulation, Amino Acid Sequence, Glycosyl donor, Molecular Biology, Glucans, Plant Proteins, biology, Glycosyl acceptor, Tryptophan, Active site, Glycosyltransferases, biology.organism_classification, Xyloglucan, Crystallography, chemistry, biology.protein, Xylans, Sequence Alignment
Abstract

Reorganization and degradation of the wall crosslinking and seed storage polysaccharide xyloglucan by glycoside hydrolase family 16 (GH16) endo-transglycosylases and hydrolases are crucial to the growth of the majority of land plants, affecting processes as diverse as germination, morphogenesis, and fruit ripening. A high-resolution, three-dimensional structure of a nasturtium (Tropaeolum majus) endo-xyloglucanase loop mutant, TmNXG1-DeltaYNIIG, with an oligosaccharide product bound in the negative active-site subsites, has been solved by X-ray crystallography. Comparison of this novel complex to that of the strict xyloglucan endo-transglycosylase PttXET16-34 from hybrid aspen (Populus tremula x tremuloides), previously solved with a xylogluco-oligosaccharide bound in the positive subsites, highlighted key protein structures that affect the disparate catalytic activities displayed by these closely related enzymes. Combination of these "partial" active-site complexes through molecular dynamics simulations in water allowed modeling of wild-type TmNXG1, TmNXG1-DeltaYNIIG, and wild-type PttXET16-34 in complex with a xyloglucan octadecasaccharide spanning the entire catalytic cleft. A comprehensive analysis of these full-length complexes underscored the importance of various loops lining the active site. Subtle differences leading to a tighter hydrogen bonding pattern on the negative (glycosyl donor) binding subsites, together with loop flexibility on the positive (glycosyl acceptor) binding subsites appear to favor hydrolysis over transglycosylation in GH16 xyloglucan-active enzymes.

Published
2008

12. A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide

Author

Pekka Mark and Lennart Nilsson

Subjects
Models, Molecular, Stereochemistry, Protein Conformation, Biophysics, Membrane biology, Isomerase, Molecular dynamics, Cyclophilin A, chemistry.chemical_compound, polycyclic compounds, Computer Simulation, Cyclophilin, Dipeptide, Binding Sites, biology, Active site, Water, General Medicine, Dipeptides, enzymes and coenzymes (carbohydrates), Kinetics, chemistry, Models, Chemical, biology.protein, Isomerization, Protein Binding
Abstract

Six different molecular dynamics simulations of Cyclophilin A, three with the protein free in water and three with the Ala-Pro dipeptide bound to the protein, have been performed, and analysed with respect to structure and hydration of the active site. The water structure in the binding pocket of the free Cyclophilin A was found to mimic the experimentally obtained binding cis conformation of the dipeptide. Cyclophilin A is a peptidyl–prolyl cis–trans isomerase (PPIase), but the mechanism of the cis/trans isomerization is not exactly clear. This study was performed to understand better the binding between dipeptide and Cyclophilin A, but also two previously proposed isomerization mechanisms are discussed.

Published
2006

13. Solvent effects on biomolecular dynamics simulations: A comparison between TIP3P, SPC and SPC/E water models acting on the Glucocorticoid receptor DNA-binding domain

Author

Pekka Mark, Johan Bredenberg, and Lennart Nilsson

Subjects
Solvent, Molecular dynamics, Computational chemistry, Chemistry, Solvent models, Protein dynamics, Thermal fluctuations, Thermodynamics, DNA-binding domain, Solvent effects, Entropy (order and disorder)
Abstract

Three widely used solvent models (TIP3P, SPC and SPC/E) have been compared in the context of molecular dynamics simulations performed on the Glucocorticoid receptor DNA-binding domain (GR DBD), using eight different initial coordinate sets. The analysis involved hydration properties, protein dynamics, entropy, order parameters, reorientational diffusion times and thermal fluctuations of non-hydrogen protein atoms. The three latter admit a direct comparison with experimental observations. It was found that only reorientation times showed significant solvent dependence.

Published
2006
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14. List of Contributors

Author

Shinji Amari, J.F.R. Archilla, David N. Beratan, F. Matthias Bickelhaupt, Johan Bredenberg, Ralf Bulla, Arrigo Calzolari, Hiroshi Chuman, Peter Claiden, Daniel L. Cox, Tobias Cramer, Jane Crawshaw, Gianaurelio Cuniberti, Martin Dahlberg, Owen R. Davies, James Elliott, Robert G. Endres, Dmitri G. Fedorov, Rosa Di Felice, B. Fischer, Kaori Fukuzawa, Yi Qin Gao, Heather L. Gordon, Hitoshi Goto, Célia Fonseca Guerra, Rafael Gutierrez, Michiaki Hamada, D. Hennig, Arnd Hübsch, Yuichi Inadomi, Yuichiro Inagaki, John E. Inglesfield, Masakatsu Ito, Toshiyuki Kamakura, Martin Karplus, Kazuo Kitaura, Thorsten Koslowski, Petras J. Kundrotas, Noriyuki Kurita, Aatto Laaksonen, Victor D. Lakhno, K.H. Lee, J.P. Lewis, Jianping Lin, Raimo A. Lohikoski, Pekka Mark, R. Marsh, H. Merlitz, Yuji Mochizuki, Umpei Nagashima, Yoshihiro Nakajima, Tatsuya Nakano, Naofumi Nakayama, Takayuki Natsume, Lennart Nilsson, Takeshi Nishikawa, Sigeaki Obata, Miroslav Pinak, Dragan M. Popovic, Jason Quenneville, Aina Quintilla, R.A. Römer, Stuart M. Rothstein, Mitsuhisa Sato, Matthias Schmitz, A. Schug, Yasuo Sengoku, Rajiv R.P. Singh, Spiros S. Skourtis, Evgeni B. Starikov, Alexei A. Stuchebrukhov, Shigenori Tanaka, Paul Tavan, Nadine Utz, A. Verma, Alexander A. Voityuk, H. Wang, Toshio Watanabe, Wolfgang Wenzel, Alan Windle, and Wei Yang

Published
2006
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