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6. Contributory presentations/posters

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

Published
1999
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10. Theoretical Study of Nanostructured Biopolymers Using Molecular Dynamics Simulations: A Practical Introduction.

Author

Avouris, Phaedon, Bhushan, Bharat, Bimberg, Dieter, von Klitzing, Klaus, Sakaki, Hiroyuki, Wiesendanger, Roland, Zvelindovsky, Andrei V., and Roccatano, Danilo

Abstract

The study of the properties of nanostructured biopolymers (namely natural and synthetic polymers constituted of amino acids, carbohydrates and nucleic acids) can benefit from theoretical investigations of their mechanical properties at the atomic scale. In fact, this information can be used to understand the properties of these substances and to provide the foundation for engineering new materials with enhanced properties. For this purpose, MD simulation techniques offer a very powerful method to analyze these materials at different time and space scales. Several comprehensive reviews [1-4] and textbooks [5-8] have been published on this topic. Therefore, the aim of this chapter is to provide a short and concise guide to molecular dynamics simulation. It is intended for those just entering the field to acquire this technique. The chapter is organized as follows. In the first part, a basic introduction to the force fields is reported; together with an overview of currently available libraries of parameters. This is followed by a short description of the basic algorithms and techniques used to model molecular systems. A list of the most commonly used packages for MD simulation is provided with information concerning the techniques that are included. In the second part of the chapter, some examples of application to molecular systems will be given to familiarize the readers with the results that can be obtained from the simulation of complex molecular systems. Finally, in the Perspective section, an outline of the future development of this technique is reported. [ABSTRACT FROM AUTHOR]

Published
2007
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11. Unraveling Binding Effects of Cobalt(II) Sepulchrate with the Monooxygenase P450 BM-3 Heme Domain Using Molecular Dynamics Simulations

Author

Verma, Rajni, Schwaneberg, Ulrich, Holtmann, Dirk, and Roccatano, Danilo

Abstract

One of the major limitations to exploit enzymes in industrial processes is their dependence on expensive reduction equivalents like NADPH to drive their catalytic cycle. Soluble electron-transfer (ET) mediators like cobalt(II) sepulchrate have been proposed as a cost-effective alternative to shuttle electrons between an inexpensive electron source and an enzyme’s redox center. The interactions of these molecules with enzymes have not yet been elucidated at the molecular level. Herein, molecular dynamics simulations are performed to understand the binding and ET mechanism of the cobalt(II) sepulchrate with the heme domain of cytochrome P450 BM-3. The study provides a detailed map of ET mediator binding sites on the protein surface that are prevalently composed of Asp and Glu amino acids. The cobalt(II) sepulchrate does not show a preferential binding to these sites. However, among the observed binding sites, only few of them provide efficient ET pathways to heme iron. The results of this study can be used to improve the ET mediator efficiency of the enzyme for possible biotechnological applications.

Published
2016
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13. Contributory presentations/posters

Author

Manoj, N., Srinivas, V., Surolia, A., Vijayan, M., Suguna, K., Ravishankar, R., Suguna, K., Surolia, A., Vijayan, M., Schwarzenbacher, R., Zeth, K., Diederichs, Kostner, G., Gries, A., Laggner, P., Prassl, R., Madhusudan, Akamine, Pearl, Xuong, Nguyen-huu, Taylor, Susan, Sagar, M., Ravishankar, R., Saikrishnan, K., Roy, S., Purnapatre, K., Handa, P., Varshney, U., Vijayan, M., Biswal, B., Sukumar, N., Vijayan, M., Rao, J., Johnson, A., Pattabhi, Vasantha, Krishna, S., Sastri, Mira, Savithri, H., Murthy, M., Pillai, Bindu, Kannan, Hosur, M., Kumar, Mukesh, Patwardhan, Swati, Kannan, K., Hosur, M., Padmanabhaa, B., Sasaki-Sugio, S., Nukaga, M., Matsuzaki, T., Karthikevan, S., Sharma, S., Sharma, A., Paramasivam, M., Kumar, P., Khan, J., Yadav, S., Srinivasan, A., Singh, T., Gourinath, S., Alam, Neelima, Srintvasan, A., Singh, T., Chandra, Vikas, Kaur, Punit, Betzel, Ch., Singh, T., Ghosh, S., Bera, A., Bhattacharya, S., Chakraborty, S., Pal, A., Mukhopadhyay, B., Dey, I., Haldar, U., Baneriee, Asok, Sevcik, Jozef, Solovicova, Adriana, Sekar, K., Sundaralingam, M., Betzel, Ch., Genov, N., Singh, T., Liang, Dong-cai, Jiang, Tao, Zhang, Ji-ping, Chang, Wen-rui, Jahnke, Wolfgang, Blommers, Marcel, Panchal, S., Hosur, R., Pillay, Bindu, Hosur, M., Mathur, Puniti, Srivatsun, S., Joshi, Ratan, Jaganathan, N., Chauhan, V., Atreya, H., Sahu, S., Chary, K., Govil, Girjesh, Adjadj, Elisabeth, Quinjou, Éric, Izadi-Pruneyre, Nadia, Blouquit, Yves, Mispelter, Joël, Heyd, Bernadette, Lerat, Guilhem, Milnard, Philippe, Desmadreil, Michel, Lin, Y., Rao, B., Raghunathan, Vidva, Chau, Mei, Rao, B., Pesais, Prashant, Srivastava, Sudha, Coutinho, Evans, Saran, Anil, Sapico, Leizl, Gesme, Jayson, Lijima, Herbert, Paxton, Raymond, Srikrishnan, Thamarapu, Grace, C., Nagenagowda, G., Lynn, A., Cowsik, Sudha, Sahu, Sarata, Chauhan, S., Bhattacharya, A., Chary, K., Govil, G., Kumar, Anil, Pellecchia, Maurizio, Zuiderweg, Erik, Kawano, Keiichi, Aizawa, Tomoyasu, Fujitani, Naoki, Hayakawa, Yoichi, Ohnishi, Atsushi, Ohkubo, Tadayasu, Kumaki, Yasuhiro, Hikichi, Kunio, Nitta, Katsutoshi, Rani Parvathy, V., Chary, K., Kini, R., Govil, G., Koshiba, Takumi, Kobashigawa, Yoshihiro, Yao, Min, Demura, Makoto, Nakagawa, Astushi, Tanaka, Isao, Kuwajima, Kunihiro, Nitta, Katsutoshi, Linge, Jens, Donoghue, Seán, Nilges, Michael, Chakshusmathi, G., Ratnaparkhi, Girish, Madhu, P., Varadarajan, R., Tetreau, C., Tourbez, M., Lavalette, D., Manno, M., Biagio, P., Martorana, V., Emanuele, A., Vaiana, S., Bulone, D., Palma-Vittorelli, M., Palma, M., Trivedi, V., Cheng, S., Chien, W., Yang, S., Francis, S., Chang, D., Batra, Renn, Geeves, Michael, Manstein, Dietmar, Trvlska, Joanna, Grochowski, Pawel, Geller, Maciej, Ginalski, K., Grochowski, P., Lesyng, B., Lavalette, P., Tetreau, C., Tourbez, M., Blouquit, Y., Roccatano, D., Amadei, A., Nola, A., Berendsen, H., Ho, Bosco, Curmi, P., Berry, H., Lairez, D., Pauthe, E., Pelta, J., Kothekar, V., Sahi, Shakti, Srinivasan, M., Singh, Anil, Madhusudnan, Kartha, Nandel, Fateh, Kaur, Harpreet, Nandel, Fateh, Singh, Balwinder, Jain, D., Feenstra, K., Berendsen, Herman, Tama, F., Sanejouand, Y., Go, N., Sharma, Deepak, Sharma, Sunita, Pasha, Santosh, Brahmachari, Samir, Viiavaraghavan, R., Makker, Jyoti, Dey, Sharmisllia, Kumar, S., Singh, T., Lakshmikanth, G., Krishnamoorthy, G., Mazhul, V., Zaitseva, E., Kierdaszuk, Borys, Widengren, J., Terry, B., Mets, Ü., Rigler, R., Swaminathan, R., Thamotharan, S., Yathindra, N., Shibata, Y., Chosrowjan, H., Mataga, N., Morisima, I., Chakraharty, Tania, Xiao, Ming, Cooke, Roger, Selvin, Paul, Branca, C., Faraone, A., Magazù, S., Maisano, G., Migliardo, P., Villari, V., Behere, Digambar, Deva, M., Brunori, M., Cutruzzolà, F., Gibson, Q., Savino, C., Travaglini-Allocatelli, C., Vallone, B., Prasad, Swati, Mazumdar, Shyamalava, Mitra, Samaresh, Soto, P., Fayad, R., Sukovataya, I., Tyulkova, N., Mamedov, Sh., Aktas, B., Canturk, M., Aksakal, B., Yilgin, R., Bogutska, K., Miroshnichenko, N., Chacko, S., DiSanto, M., Hypolite, J., Zheng, Y-M., Wein, A., Wojciechowski, M., Grycuk, T., Antosiewicz, J., Lesyng, B., Ceruso, Marc, Nola, Alfredo, Bandvopadhvay, Subhasis, Chatterjee, Bishnu, Choudhury, Devapriva, Thompson, Andrew, Stojanoff, Vivian, Pinkner, Jerome, Hultgren, Scott, Khight, Stefan, Flatters, Delphine, Goodfellow, Julia, Takazawatt, Fumi, Kanehisa, Minoru, Sasai, Masaki, Nakamura, Hironori, Sasai, Masaki, Han, Wang, Zheng, Yuan, Xin, Wang, Min, Pan, Bhakuni, Vlnod, Kulkarni, Sangeeta, Ahmad, Atta, Prakash, Koodathingal, Prajapati, Shashi, Surin, Alexey, Matsumoto, Tomoharu, Yang, Li, Nakagawa, Yuki, Kimura, Kazumoto, Amemiya, Yoshiyuki, Semisotnov, Gennady, Kihara, Hiroshi, Tayyab, Saad, Muzammil, Salman, Kumar, Yogesh, Kulkarni, Sangeeta, Prajapati, Shashi, Prakash, Koodathingal, Ahmad, Atta, Bhakuni, Vinod, Sundd, Monica, Kundu, Suman, Jagannadham, M., Kundu, Suman, Sundd, Monica, Jagannadham, Medicherla, Chandani, Bina, Dhar, Ruby, Sinha, Lalankumar, Warrier, Deepti, Mehrotra, Sonam, Khandelwal, Purnima, Seth, Subhendu, Hosur, R., Sasidhar, Y., Prabha, C., Gidwani, Arun, Ahmad, Atta, Kulkarni, Sangeeta, Madhusudan, K., Bhakuni, Vinod, Kinjo, Akira, Nishikawa, Ken, Chakravarty, Suvobrata, Varadarajan, Raghavan, Noyelle, K., Haezebrouck, P., Joniau, M., Dael, H., Dash, Sheffali, Jha, Indra, Bhat, Rajiv, Mohanty, Prasanna, Bandyopadhyay, A., Sonawat, H., Rao, Ch., Datta, Siddhartha, Rajaraman, K., Raman, B., Ramakrishna, T., Rao, Ch., Pande, A., Pande, J., Betts, S., Asherie, N., Ogun, O., King, J., Benedek, G., Sokolova, I., Tyulkova, N., Kalacheva, G., Sonoyama, Masashi, Yokoyama, Yasunori, Taira, Kunihiro, Mitaku, Shigeki, Nakazawal, Chicko, Sasakil, Takanori, Mukai, Yuri, Kamo, Naoki, Sonoyama, Masashi, Mitaku, Shigeki, Dalal, Seema, Regan, Lynne, Mukai, Yuri, Kamo, Naoki, Mituku, Shigeki, Roychoudhury, Mihir, Kumar, Devesh, Lőrinczv, Dénes, Könczöl, Franciska, Farkas, László, Belagyi, Joseph, Schick, Christoph, Thomson, Christy, Ananthanarayanan, Vettai, Alirzayeva, E., Baba-Zade, S., Gromiha, M., Oobatake, M., Kono, H., An, J., Uedaira, H., Sarai, A., Takano, Kazufumi, Yamagata, Yuriko, Yutani, Katsuhide, Jas, Gouri, Muñoz, Victor, Hofrichter, James, Eaton, William, Penoyar, Jonathan, Srikrishnan, Thamarapu, Lo Verde, Philip, Kardos, J., Bódi, Á., Venekei, I., Závodszky, P., Gráf, L., Szilágyi, András, Závodszky, Péter, Allan, R., Walshaw, J., Woolfson, D., Funahashi, Jun, Takano, Kazufumi, Yamagata, Yuriko, Yutani, Katsuhide, Gupta, Savan, Mazumdar, Shyamalava, Di Nola, A., Mangoni, M., Roccatano, P., Ramachandraiah, Gosu, Chandra, Nagasuma, Kothekar, V., Srinivasan, M., Sahi, Shakti, Chakraborty, S., Bhattacharya, S., Bera, A., Ghosh, S., Pal, A., Haldar, U., Mukhopadhyay, B., Baneriee, Asok, Ciani, Barbara, Woolfson, Derek, Nair, Usha, Kaur, Kanwal, Salunke, Dinakar, Swaminathan, Chittoor, Surolia, Avadhesha, Rigler, R., Pramanik, A., Jonasson, P., Kratz, G., Jansson, O., Nygren, P., Ståhl, S., Ekberg, K., Johansson, B., Uhlén, S., Uhlén, M., Jörnvall, H., Wahren, J., Welfle, Karin, Misselwitz, Rolf, Höhne, Wolfgang, Welfle, Heinz, Mazhul, V., Zaitseva, E., Mitskevich, L., Fedurkina, N., Kurganov, B., Jarori, Gotam, Maity, Haripada, Guharay, J., Sengupta, B., Sengupta, P., Sridevi, K., Kasturi, S., Gupta, S., Agarwal, Gunjan, Kwong, Suzanne, Briehl, Robin, Ismailova, O., N, Tyulkova, Hariharan, C., Pines, D., Pines, E., Zamai, M., Cohen-Luria, R., Yayon, A., Parola, A., Padya, M., Spooner, G., Woolfeon, D., Bakshi, Panchan, Sharma, Deepak, Sharma, Sunita, Bharadwaj, D., Pasha, Santosh, Sharma, U., Srivastava, N., Barthwal, R., Jagannathan, N., Matsuda, Keiko, Nishioka, Takaaki, Go, Nobuhiro, Aita, T., Urata, S., Husimi, Y., Majumder, Mainak, Chatterjee, Bishnu, Abrescia, Nicola, Malinina, Lucy, Subirana, Juan, Aymami, Juan, Eritxa, Ramón, Coll, Miquel, Premraj, B., Yathindra, N., Thenmalarchelvi, R., Yathindra, N., Kumar, P., Gautham, N., Kan, Lou, Ming-Hou, Lin, Shwu-Bin, Sana, Tapas, Roy, Kanal, Bruant, N., Flatters, D., Lavery, R., Genest, D., Rons, Remo, Sklenar, Heinz, Lavery, Richard, Kundu, Sudip, Bhattacharyya, Dhananjay, Bandyopadhyay, Debashree, Thakur, Ashoke, Majumdar, Rabi, Barceló, F., Portugal, J., Ramanathan, Sunita, Chary, K., Rao, B., Gliosli, Mahua, Kumar, N., Varshney, Umesh, Chary, K., Pataskar, Shashank, Brahmachari, Samir, Sarojini, R., Selvasekarapandian, S., Kolandaivel, P., Sukumar, S., Selvasekarapandian, S., Sarojini, R., Kolmdaivel, P., Sukumar, S., Sarojini, R., Selvasekarapandian, S., Kolandaivel, P., Sukumar, S., Selvasekarapandian, S., Sarojini, R., Kolandaivel, P., Sukumar, S., Maiti, Motilal, Sen, Anjana, Das, Suman, Terra, Elisa, Suraci, Chiara, Diviacco, Silvia, Quadrifoglio, Franco, Xodo, Luigi, Bandyopadhyay, Debashree, Bhattacharyya, Dhananjay, Kundu, Sudip, Thakur, Ashoke, Das, Suman, Ray, Arghya, Maiti, Motilal, Karthikeyan, G., Chary, Kandala, Rao, Basuthkar, Mujeeb, Anwer, James, Thomas, Kasyanenko, N., Haya, E., Bogdanov, A., Zanina, A., Bugs, M., Cornélio, M., Srikrishnan, Thamarapu, Tolstorukov, M., Sanval, Nitish, Tiwari, S., Tiwari, S., Sanyal, Nitish, Choudhury, Mihir, Kumar, Devesh, Sanyal, Nitish, Patel, P., Bhavesh, Neel, Hosur, R., Gabrielian, Anna, Wennmalm, Stefan, Edman, Lars, Rigler, Rudolf, Constantinescu, B., Radu, L., Radulcscu, I., Gazdaru, D., Wärmländer, Sebastian, Leijon, Mikael, Aoki, Setsuyuki, Kondo, Takao, Ishiura, Masahiro, Pashinskaya, V., Kosevich, M., Shelkovsky, V., Blagoy, Yu., Wang, Ji-hua, Malathi, R., Chandrasekhar, K., Premraj, B., Patel, P., Kandimalla, E., Agrawal, S., Hosur, R., Yathindra, N., Rastogi, V., Palafox, M., Singh, Chatar, Beniaminov, A., Bondarenko, S., Zdobnov, E., Minyat, E., Ulyanov, N., Ivanov, V., Singh, J., Sonawane, Kailas, Grosjean, Henri, Tewari, Ravindra, Sonavane, Uddhavesh, Morin, Annie, Grosjean, Henri, Tewari, Ravindra, Doherty, Elizabeth, Doudna, Jennifer, Tochio, H., Sato, S., Matsuo, H., Shirakawa, M., Kyogoku, Y., Javaram, B., Dixit, 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S., Sikdar, S., Ghatpande, A., Rao, S., Sikdar, S., Corsso, C., Campos de Carvalho, A., Varanda, W., ElHamel, C., Dé, E., Saint, N., Molle, G., Varshney, Anurae, Mathew, M., Loots, E., Isacoff, E., Kasai, Michiki, Yamaguchi, Naohiro, Ghosh, Paramita, Ghosh, Subhendu, Tigyi, Joseph, Tigyi, Gabor, Liliom, Karoly, Miledi, Ricardo, Djurisic, Maja, Andjus, Pavle, Shrivastava, Indira, Sansom, M., Barrias, C., Oliveira, P., Mauricio, A., Rebelo da Costa, A., Lopes, I., Barrias, C., Fedorovich, S., Chubanov, V., Sholukh, M., Konev, S., Fedirko, N., Manko, V., Klevets, M., Shvinka, N., Prabhananda, B., Kombrabail, Mamata, Aravamudhan, S., Venegas-Cotero, Berenice, Blake, Ivan, Zhang, Zhi-hong, Hu, Xiao-jian, Zhou, Han-qing, Cheng, Wei-ying, Feng, Hang-fang, Dubitsky, L., Vovkanvch, L., Zalyvsky, I., Savio-Galimberti, E., Bonazzola, P., Ponce-Homos, J., Parisi, Mario, Capurro, Claudia, Toriano, Roxana, Ready, Laxma, Jones, Larry, Thomas, David, Tashmukhamedov, B., Sagdullaev, B., Usmanov, P., 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F., Tahradník, Ivan, Pavelková, Jana, Zahradniková, Alexandra, Zhorov, Boris, Ananthanaravanan, Vettai, Michailov, M., Neu, E., Seidenbusch, W., Gornik, E., Martin, D., Welscher, U., Weiss, D., Pattnaik, B., Jellali, A., Forster, V., Hicks, D., Sahel, J., Dreyfus, H., Picaud, S., Wang, Hong-Wei, Sui, Sen-fang, Luther, Pradeep, Barry, John, Morris, Ed, Squire, John, Sundari, C., Balasubramanian, D., Veluraia, K., Christlet, T., Suresh, M., Berry, H., Pelta, J., Lairez, D., Laretta-Garde, V., Krilov, Dubravka, Stojanović, Nataša, Herak, Janko, Jasuja, Ravi, Ivanova, Maria, Mirchev, Rossen, Ferrone, Frank, Stopar, David, Spruijt, Ruud, Wolfs, Cor, Hemminga, Marcus, Arcovito, G., Spirito, M., Sui, Sen-fang, Wang, Hong-Wei, Agrawal, Rajendra, Heagle, Amy, Penczek, Pawel, Grassucci, Robert, Frank, Joachim, Sharma, Manjuli, Jeyakumar, Loice, Fleischer, Sidney, Wagenknecht, Terence, Knupp, Carlo, Munro, Peter, Luther, Pradeep, Ezra, Eric, Squire, John, Ichihara, Koji, Kitazawa, Hidefumi, Iguchi, Yusuke, Hotani, Hirokazu, Itoh, Tomohiko, Pifat, Greta, Kveder, Marina, Pečar, Slavko, Schara, Milan, Nair, Deepak, Singh, Kavita, Rao, Kanury, Salunke, Dinakar, Kaur, Kanwaljeet, Jain, Deepti, Sundaravadivel, B., Goel, Manisha, Salunke, D., Kovalenko, E., Semenkova, G., Cherenkevich, S., Lakshmanan, T., Sriram, D., Srinivasan, S., Loganathan, D., Ramalingam, T., Lebrón, J., Bjorkman, P., Singh, A., Gayatri, T., Jain, Deepti, Kaur, Kanwaljeet, Sundaravadivel, B., Salunke, Dinakar, Caffarena, Ernesto, Grigera, J., Bisch, Paulo, Kiessling, V., Fromherz, P., Rao, K., Gaikwad, S., Khan, M., Suresh, C., Kaliannan, P., Gromiha, M., Elanthiraiyan, M., Chadha, K., Payne, J., Ambrus, J., Nair, M., Nair, Madhavan, Mahajan, S., Chadha, K., Hewitt, R., Schwartz, S., Bourguignon, J., Faure, M., Cohen-Addad, C., Neuburger, M., Ober, R., Sieker, L., Macherel, D., Douce, R., Gurumurthy, D., Velmurugan, S., Lobo, Z., Srivastava, Sudha, Phadke, Ratna, Govil, Girjesh, Desai, Prashant, Coutinho, Evans, Guseinova, I., Suleimanov, S., Zulfugarov, I., Novruzova, S., Aliev, J., Ismayilov, M., Savchenko, T., Alieva, D., Ilík, Petr, Kouřil, Roman, Bartošková, Hana, Nauš, Jan, Gaikwad, Jvoti, Thomas, Sarah, Vidyasagar, P., Garab, G., Simidjiev, I., Rajagopal, S., Várkonyi, Zs., Stoylova, S., Cseh, Z., Papp, E., Mustárdy, L., Holzenburg, A., Bruder, R., Genick, U., Woo, T., Millar, D., Gerwert, K., Getzoff, E., Jávorfí, Tamás, Garab, Győző, Naqvi, K., Kalimullah, Md., Gaikwad, Jyoti, Thomas, Sarah, Semwal, Manoj, Vidyasagar, P., Kouril, Roman, Ilik, Petr, Naus, Man, Pomozi, István, Horváth, Gábor, Wehner, Rüdiger, Bernard, Gary, Damjanović, Ana, Ritz, Thorsten, Schulten, Klaus, Jushuo, Wang, Jixiu, Shan, Yandao, Gong, Tingyun, Kuang, Nanming, Zhao, Freiberg, Arvi, Timpmann, Kõu, Ruus, Rein, Woodbury, Neal, Nemtseva, E., Kudryasheva, N., Sizykh, A., Shikhov, V., Nesterenko, T., Tikhomirov, A., Forti, Giorgio, Finazzi, Giovanni, Furia, Alberto, Barbagallo, Romina, Forti, Giorgio, Iskenderova, S., Agalarov, R., Gasanov, R., Osamu, Miyashita, Nobuhiro, G., Soni, R., Ramrakhiani, M., Yagi, Hiromasa, Tozawa, Kacko, Sekino, Nobuaki, Iwabuchi, Tomoyuki, Yoshida, Masasuke, Akutsu, Hideo, Avetisyan, A., Kaulen, A., Skulachev, V., Feniouk, B., Breyton, Cécile, Kühlbrandt, Werner, Assarsson, Maria, Gräslund, Astrid, Zsiros, O., Horváth, G., Mustárdy, L., Libisch, B., Gombos, Z., Budagovskaya, N., Kudryasheva, N., Harada, Erisa, Fukuoka, Yuki, Ohmura, Tomoaki, Fukunishi, Arima, Kawai, Gota, Watanabe, Kimitsuna, Akutsu, Hideo, Derganc, Jure, Božič, Bojan, Svetina, Saša, Žekš, Boštjan, Hoh, J., Li, Z., Rossmanith, G., Beer, E., Treijtel, B., Frederix, P., Blangè, T., Hénon, S., Galtet, F., Laurent, V., Planus, E., Isabey, D., Rath, L., Dash, P., Raval, M., Ramakrishnan, C., Balaram, R., Randic, Milan, Basak, Subhash, Vracko, Marjan, Nandy, Ashesh, Amic, Dragan, Beslo, Drago, Nikolic, Sonja, Trinajstic, Nenad, Walahaw, J., Woolfson, D., Lensink, Marc, Berendsen, Herman, Reddy, Boojala, Shindylov, Ilya, Bourne, Philip, Donnamaria, M., Xammar Oro, J., Grigera, J., Neagu, Monica, Neagu, Adrian, Praprotnik, Matej, Janežič, Dušanka, Mark, Pekka, Nilsson, Lennart, Martorana, V., Bulone, D., Fata, L., Manno, M., Biagio, P., Dardenne, Laurent, Werneck, Araken, Neto, Marçal, Bisch, Paulo, Kannan, N., Vishveshwara, S., Christlet, T., Veluraja, K., Grunwald, Gregory, Balaban, Alexandra, Basak, Kanika, Gute, Brian, Mills, Denise, Opitz, David, Balasubramanian, Krishnan, Mihalas, G., Lungeanu, Diana, Macovievici, G., Gruia, Raluca, Neagu, Monica, Cortez-Maghelly, C., Dalcin, B., Passos, E., Blesic, S., Ljubisavljevic, M., Milosevic, S., Stratimirovic, D., Bachhawat, Nandita, Mande, Shekhar, Ghosh, S., Nandy, A., Saito, Ayumu, Nishigaki, Koichi, Nishigaki, Koichi, Naimuddin, Mohammed, Mitaku, Shigeki, Hirokawa, Takatsugu, Ono, Mitsuo, Takaesu, Hirotomo, El Gohary, M., Ahmed, Abdalla, Eissa, A., Nakashima, Hiroshi, Nishikawa, Ken, Neagu, Monica, Neagu, Adrian, 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A., Macpherson, J., O’Hare, D., Winlove, C., Unwin, P., Sengupta, P., Phillip, R., Banerjee, S., Kumar, G., Maiti, S., Nagayaka, K., Danev, R., Sugitani, S., Murata, K., Gősch, Michael, Blom, H., Thyberg, P., Földes-Papp, Z., Björk, G., Holm, J., Heino, T., Rigler, Rudolf, Yokochi, Masashi, Inagaki, Fuyuhiko, Kusunoki, Masami, Matthews, E., Pines, J., Chukova, Yu., Koltover, Vitaly, Bansal, Geetanjali, Singh, Uma, Bansal, M., Nakata, Kotoko, Nakano, Tastuya, Kaminuma, Tsuguchika, Kang, B., Singh, U., Kirn, Bonn, Potocnik, Neja, Stare, Vito, Shukla, Latal, Natarajan, V., Devasagayam, T., Sastry, M., Kesavan, P., Sayfutdinov, R., Adamovich, V., Rogozin, D., Degermendzhy, A., Khetrapal, C., Ramanathan, K., Gowda, G., Ghimire, Kedar, Masaru, Ishida, Fujita, H., Ishiwata, S., Kishimoto, Y., Kawahara, S., Suzuki, M., Mori, H., Mishina, M., Kirino, Y., Ohshima, H., Dukhin, A., Shilov, V., Goetz, P., Sengupta, B., Guharay, J., Sengupta, P., and Mishra, R.

Published
1999
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21. Coating Mechanisms of Single-Walled Carbon Nanotube by Linear Polyether Surfactants: Insights from Computer Simulations

Author

Sarukhanyan, Edita, Milano, Giuseppe, and Roccatano, Danilo

Abstract

The noncovalent coating of carbon-based nanomaterials, such as carbon nanotubes, has important applications in nanotechnology and nanomedicine. The molecular modeling of this process can clarify its mechanism and provide a tool for the design of novel materials. In this paper, the coating mechanism of single-walled carbon nanotubes (SWCNT) in aqueous solutions by 1,2-dimethoxyethane oxide (DME), 1,2-dimethoxypropane oxide (DMP), poly(ethylene oxide) (PEO), poly(propylene oxide) (PPO) pentamers, and L64 triblock copolymer chains have been studied using molecular dynamics (MD) simulations. The results suggest a preferential binding to the SWCNT surface of the DMP molecules with respect to DME mainly driven by their difference in hydrophobicity. For the longer pentamers, it depends by the chain conformation. PPO isomers with radius of gyration larger than PEO pentamers bind more tightly than those with more compact conformation. In the case of the L64 triblock copolymer, the coating of the SWCNT surface produces a shell of PPO blocks with the PEO chains protruding into bulk water as expected from the so-called nonwrapping binding mechanism of SWCNT. In addition, the polymer coating, in qualitative agreement with experimental evidence on the poor capability of the L64 to disperse SWCNT, do not prevent the formation of CNT aggregates.

Published
2014
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22. Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3

Author

Verma, Rajni, Schwaneberg, Ulrich, and Roccatano, Danilo

Abstract

In the cytochrome P450BM-3, the flavin mononucleotide (FMN) binding domain is an intermediate electron donor between the flavin adenine dinucleotide (FAD) binding domain and the HEME domain. Experimental evidence has shown that different redox states of FMN cofactor were found to induce conformational changes in the FMN domain. Herein, molecular dynamics (MD) simulation is used to gain insight into the latter phenomenon at the atomistic level. We have studied the effect of FMN cofactor and its redox states (oxidized and reduced) on the structure and dynamics of the FMN domain. The results of our study show significant differences in the atomic fluctuation amplitude of the FMN domain in both holo- and apoprotein. The change in the protonation state of FMN cofactor mostly affects its binding in holo-protein. In particular, the loops involved in the binding of the isoalloxazine ring (Lβ4) and ribityl side chain (Lβ1) adopt different conformations in both reduced and oxidized states. In addition, the reduced FMN cofactor mainly induces a conformational change in Trp574 residue (Lβ4) that is essential for controlling electron transfer (ET) within P450BM-3 domains. The structure of the apoprotein in solution remains mostly unchanged with respect to the crystal structure of the holo-protein. However, FMN binding loops were more flexible in apoprotein that might favor the rebinding of FMN cofactor. In the holo-protein simulation, the largest conformational changes in FMN cofactor are caused by the ribityl side chain. The isoalloxazine ring of FMN cofactor remains almost planar (∼177°) in the oxidized state and bends along the N5–N10 axis at an angle of ∼160° in the reduced state. The collective modes of the isoalloxazine ring were identical in both protonation states of FMN cofactor except the first eigenvector. In the reduced state, the isoalloxazine ring attains the butterfly motion as a dominant collective motion in the first eigenvector due to the bending along the N5–N10 axis.

Published
2013
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23. Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

Author

De Nicola, Antonio, Zhao, Ying, Kawakatsu, Toshihiro, Roccatano, Danilo, and Milano, Giuseppe

Abstract

In the framework of a recently developed scheme for a hybrid particle-field simulation technique where self-consistent field theory (SCF) and molecular dynamics (MD) are combined [J. Chem. Phys.2009, 130, 214106], specific coarse-grained models for phospholipids and water have been developed. We optimized the model parameters, which are necessary in evaluating the interactions between the particles and the density fields, so that the coarse-grained model can reproduce the structural properties of the reference particle–particle simulations. The development of these specific coarse-grained models suitable for hybrid particle-field simulations opens the way toward simulations of large-scale systems employing models with chemical specificity, especially for biological systems.

Published
2011
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24. Molecular Dynamics Simulation Study of Chlorophyll a in Different Organic Solvents

Author

Karki, Khadga and Roccatano, Danilo

Abstract

Herein, we present a new model of chlorophyll a for molecular dynamics simulations based on the optimized potentials for liquid simulations force field. The new model was used to study the structural and dynamic properties of the molecule in three different solvents: water, methanol, and benzene. The results of the simulations show that structural and dynamic properties of the chlorin ring are similar in both methanol and benzene. In methanol and water, the magnesium in the chlorin ring binds the oxygen of the solvent molecules with residence times of 2566 and 1300 ps, respectively. In both methanol and benzene, the phytol tail shows a worm-like chain distribution with a larger persistence length for the molecule in benzene. On the contrary, chlorophyll a in water adopts a more compact structure with the phytol chain folded onto the chlorin ring. This conformation is consistent with the expected conformation of the aggregates of chlorophyll a in aqueous environments. Finally, the rotational time constants obtained with our model from the simulations in methanol (125 ps) and benzene (192 ps) are in good agreement with the value extrapolated from the experimental data.

Published
2011
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25. Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions

Author

Roccatano, Danilo

Abstract

Pure organic solvents or mixtures with water are very common environments for studying protein and peptide in solution. These milieu conditions are used either for improving the catalytic performance of enzymes or for studying the effect of solvent on the protein stability and hence gaining insight into the protein folding mechanism. The atomic details of these processes are mainly addressed using computer simulation approaches. In particular, Molecular Dynamics simulation represents the most powerful and versatile tool to investigate the details of solvation processes at atomic level. In the last few years, the number of publications peptide and protein simulations in non-natural environments has proliferated. These studies are providing important contributions to shed light on the nature of non-aqueous solvent effects. In this review, the achievements and the future prospects in this field of computational biochemistry are reviewed by summarizing the most important theoretical results published in the last 10 years.

Published
2008

26. Sensitive Assay for Laboratory Evolution of Hydroxylases toward Aromatic and Heterocyclic Compounds

Author

Wong, T. S., Wu, N., Roccatano, D., Zacharias, M., and Schwaneberg, U.

Abstract

Powerful directed evolution methods have been developed for tailoring proteins to our needs in industrial applications. Here, the authors report a medium-throughput assay system designed for screening mutant libraries of oxygenases capable of inserting a hydroxyl group into a C-H bond of aromatic or O-heterocyclic compounds and for exploring the substrate profile of oxygenases. The assay system is based on 4-aminoantipyrine (4-AAP), a colorimetric phenol detection reagent. By using 2 detection wavelengths (509 nm and 600 nm), the authors achieved a linear response from 50 to 800 μM phenol and standard deviations below 11% in 96-well plate assays. The monooxygenase P450 BM-3 and its F87A mutant were used as a model system for medium-throughput assay development, identification of novel substrates (e.g., phenoxytoluene, phenylallyether, and coumarone), and discovery of P450 BM-3 F87A mutants with 8-fold improvement in 3-phenoxytoluene hydroxylation activity. This activity increase was achieved by screening a saturation mutagenesis library of amino acid position Y51 using the 4-AAP protocol in the 96-well format.

Published
2005
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27. Sensitive Assay for Laboratory Evolution of Hydroxylases toward Aromatic and Heterocyclic Compounds

Author

Wong, T.S., Wu, N., Roccatano, D., Zacharias, M., and Schwaneberg, U.

Abstract

Powerful directed evolution methods have been developed for tailoring proteins to our needs in industrial applications. Here, the authors report a medium-throughput assay system designed for screening mutant libraries of oxygenases capable of inserting a hydroxyl group into a C-H bond of aromatic or O-heterocyclic compounds and for exploring the substrate profile of oxygenases. The assay system is based on 4-aminoantipyrine (4-AAP), a colorimetric phenol detection reagent. By using 2 detection wavelengths (509 nm and 600 nm), the authors achieved a linear response from 50 to 800 μM phenol and standard deviations below 11% in 96-well plate assays. The monooxygenase P450 BM-3 and its F87A mutant were used as a model system for medium-throughput assay development, identification of novel substrates (e.g., phenoxytoluene, phenylallyether, and coumarone), and discovery of P450 BM-3 F87A mutants with 8-fold improvement in 3-phenoxytoluene hydroxylation activity. This activity increase was achieved by screening a saturation mutagenesis library of amino acid position Y51 using the 4-AAP protocol in the 96-well format. (Journal of Biomolecular Screening2005:246-252)

Published
2005
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28. Extended Molecular Dynamics Simulation of the Carbon Monoxide Migration in Sperm Whale Myoglobin

Author

Bossa, Cecilia, Anselmi, Massimiliano, Roccatano, Danilo, Amadei, Andrea, Vallone, Beatrice, Brunori, Maurizio, and Di Nola, Alfredo

Abstract

We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, CO, after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the CO motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of CO in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins.

Published
2004
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29. Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c

Author

Daidone, Isabella, Amadei, Andrea, Roccatano, Danilo, and Nola, Alfredo Di

Abstract

A new method for simulating the folding process of a protein is reported. The method is based on the essential dynamics sampling technique. In essential dynamics sampling, a usual molecular dynamics simulation is performed, but only those steps, not increasing the distance from a target structure, are accepted. The distance is calculated in a configurational subspace defined by a set of generalized coordinates obtained by an essential dynamics analysis of an equilibrated trajectory. The method was applied to the folding process of horse heart cytochrome c, a protein with ∼3000° of freedom. Starting from structures, with a root-mean-square deviation of ∼20Å from the crystal structure, the correct folding was obtained, by utilizing only 106 generalized degrees of freedom, chosen among those accounting for the backbone carbon atoms motions, hence not containing any information on the side chains. The folding pathways found are in agreement with experimental data on the same molecule.

Published
2003
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30. Molecular Dynamics Simulations of Lignin Peroxidase in Solution

Author

Francesca Gerini, M., Roccatano, Danilo, Baciocchi, Enrico, and Nola, Alfredo Di

Abstract

The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel.

Published
2003
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31. Selective Excitation of Native Fluctuations during Thermal Unfolding Simulations: Horse Heart Cytochrome c as a Case Study

Author

Roccatano, Danilo, Daidone, Isabella, Ceruso, Marc-Antoine, Bossa, Cecilia, and Nola, Alfredo Di

Abstract

The effect of temperature on the activation of native fluctuation motions during molecular dynamics unfolding simulations of horse heart cytochrome c has been studied. Essential dynamics analysis has been used to analyze the preferred directions of motion along the unfolding trajectories obtained by high temperature simulations. The results of this study have evidenced a clear correlation between the directions of the deformation motions that occur in the first stage of the unfolding process and few specific essential motions characterizing the 300K dynamics of the protein. In particular, one of those collective motions, involved in the fluctuation of a loop region, is specifically excited in the thermal denaturation process, becoming progressively dominant during the first 500ps of the unfolding simulations. As further evidence, the essential dynamics sampling performed along this collective motion has shown a tendency of the protein to promptly unfold. According to these results, the mechanism of thermal induced denaturation process involves the selective excitation of one or few specific equilibrium collective motions.

Published
2003
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32. Folding and stability of the three‐stranded β‐sheet peptide Betanova: Insights from molecular dynamics simulations

Author

Colombo, Giorgio, Roccatano, Danilo, and Mark, Alan E.

Abstract

The dynamics of the three‐stranded β‐sheet peptide Betanova has been studied at four different temperatures (280, 300, 350, and 450 K by molecular dynamics simulation techniques, in explicit water. Two 20‐ns simulations at 280 K indicate that the peptide remains very flexible under “folding” conditions sampling a range of conformations that together satisfy the nuclear magnetic resonance (NMR)‐derived experimental constraints. Two simulations at 300 K (above the experimental folding temperature) of 20 ns each show partial formation of “native”‐like structure, which also satisfies most of the NOE constraints at 280 K. At higher temperature, the presence of compact states, in which a series of hydrophobic contacts remain present, are observed. This is consistent with experimental observations regarding the role of hydrophobic contacts in determining the peptide's stability and in initiating the formation of turns and loops. A set of different structures is shown to satisfy NMR‐derived distance restraints and a possible mechanism for the folding of the peptide into the NMR‐determined structure is proposed. Proteins 2002;46:380–392. © 2002 Wiley‐Liss, Inc.

Published
2002
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33. Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S3and S′3subsites in the interaction with a phosphonate inhibitor

Author

Aschi, Massimiliano, Roccatano, Danilo, Di Nola, Alfredo, Gallina, Carlo, Gavuzzo, Enrico, Pochetti, Giorgio, Pieper, Michael, Tschesche, Harald, and Mazza, Fernando

Abstract

Human neutrophil collagenase (HNC, MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S′-side of the enzyme active site occupying the S′1primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic domain of MMP-8 and Pro-Leu-l-TrpP(OH)2(PLTP) showed that this phosphonate inhibitor binds in the S side of the active site. This finding was unexpected since it represents the first example of accommodation of the bulky Trp indolyl chain in the S1rather than in the S′1subsite. Dynamical and structural factors favouring this uncommon mode of binding were therefore investigated. MD simulations performed on the uncomplexed enzyme show that its structure in aqueous solution is only slightly different from the crystal structure found in the complex with PLTP. ED analysis of the MD simulations, performed on PLTP alternatively interacting with the S- or S′-side of the active site, shows that the enzyme fluctuation increases in both cases. The main contribution to the overall enzyme fluctuation is given by the loop 164–173. The fluctuation of this loop is spread over more degrees of freedom when PLTP interacts with the S-side. This dynamical factor can enhance the preference of PLTP for the S subsites of MMP-8. MD simulations also show that ligation of PLTP in the S subsites is further favoured by better zinc chelation, a cation-π interaction at the S3subsite and unstrained binding conformations. The role of the S3, S′3and S′1subsites in determining the inhibitor binding is discussed.

Published
2002
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34. Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics Simulations

Author

Fioroni, M., Burger, K., Mark, A. E., and Roccatano, D.

Abstract

An all-atom model of 1,1,1,3,3,3-hexafluoro-propan-2-ol (HFIP) for use in molecular dynamics simulation studies is proposed. The model was parametrized by fitting to the experimental density, pressure, and enthalpy of vaporization of the pure liquid at 298 K. The model was then tested by comparison against other experimental thermodynamic and kinetic properties of the pure liquid. Mixtures with SPC water were also investigated. Overall, reasonable agreement with the available experimental data for the neat liquid and for mixtures with SPC water was found. A tendency for HFIP to cluster in SPC water was observed in qualitative agreement with experimental observations. The effect of HFIP on the secondary structure of peptides was also studied. Two simulations of the peptide Melittin, in pure water and in 30% v/v HFIP, demonstrate the helix stabilizing effect of HFIP.

Published
2001

35. Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation11Edited by R. Huber

Author

Roccatano, Danilo, Mark, Alan E., and Hayward, Steven

Abstract

Six, 2 ns molecular dynamics simulations have been performed on the homodimeric enzyme citrate synthase. In three, both monomers were started from the open, unliganded X-ray conformation. In the remaining three, both monomers started from a closed, liganded X-ray conformation, with the ligands removed. Projecting the motion from the simulations onto the experimental domain motion revealed that the free-energy profile is rather flat around the open conformation, with steep sides. The most closed conformations correspond to hinge-bending angles of 12–14 ° compared to the 20 ° that occurs upon the binding of oxaloacetate. It is also found that the open, unliganded X-ray conformation is situated at the edge of the steep rise in free energy, although conformations that are about 5 ° more open were sampled. A rigid-body essential dynamics analysis of the combined open trajectories has shown that domain motions in the direction of the closed X-ray conformation are compatible with the natural domain motion of the unliganded protein, which has just two main degrees of freedom. The simulations starting from the closed conformation suggest a free-energy profile with a small barrier in going from the closed to open conformation. A combined essential dynamics and hinge-bending analysis of a trajectory that spontaneously converts from the closed to open state shows an almost exact correspondence to the experimental transition that occurs upon ligand binding. The simulations support the conclusion from an earlier analysis of the experimental transition that the β-hairpin acts as a mechanical hinge by attaching the small domain to the large domain through a conserved main-chain hydrogen bond and salt-bridges, and allowing rotation to occur via its two flexible termini. The results point to a mechanism of domain closure in citrate synthase that has analogy to the process of closing a door.

Published
2001
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36. A New 2,2,2-Trifluoroethanol Model for Molecular Dynamics Simulations

Author

Fioroni, M., Burger, K., Mark, A. E., and Roccatano, D.

Abstract

A new model for 2,2,2-trifluoroethanol is proposed. It is a 7-atom model with the methylene group treated as an united atom. The model was optimized to reproduce the physicochemical properties of the pure liquid. The properties of the new model were compared with the available experimental data over a range of temperatures. Furthermore, mixtures with the SPC water model were simulated to assess the ability to reproduce available thermodynamic and kinetic data as well as dielectric properties. The model provides a good agreement with experimental data for the neat liquid and for mixtures with water.

Published
2000

38. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

Author

Mangoni, Massimiliano, Roccatano, Danilo, and Di Nola, Alfredo

Abstract

In this paper, a method of simulating the docking of small flexible ligands to flexible receptors in water is reported. The method is based on molecular dynamics simulations and is an extension of an algorithm previously reported by Di Nola et al. (Di Nola et al., Proteins 1994;19:174–182). The method allows a fast exploration of the receptor surface, using a high temperature of the center of mass translational motion, while the ligand internal motions, the solvent, and the receptor are simulated at room temperature. In addition, the method allows a fast center of mass motion of the ligand, even in solution. The dampening effect of the solvent can be overcome by applying different weights to the interactions between system subsets (solvent, receptor, and ligand). Specific ligand–receptor distances have been used to compare the results of the simulations with the crystal structure. The method is applied, as a test system, to the docking of the phosphocholine to the immunoglobulin McPC603. The results show the similarity of structure between the complex in solution and in the crystal. Proteins 1999;35:153–162. © 1999 Wiley‐Liss, Inc.

Published
1999
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39. Development of a parallel molecular dynamics code on SIMD computers: Algorithm for use of pair list criterion

Author

Roccatano, D., Bizzarri, R., Chillemi, G., Sanna, N., and Di Nola, A.

Abstract

In recent years several implementations of molecular dynamics (MD) codes have been reported on multiple instruction multiple data (MIMD) machines. However, very few implementations of MD codes on single instruction multiple data (SIMD) machines have been reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD codes for SIMD machines, such that, generally, the full connectivity computation has been used. We present an algorithm, the global cut‐off algorithm (GCA), which permits the use of pair lists on SIMD machines. GCA is based on a probabilistic approach and requires the cut‐off condition to be simultaneously verified on all nodes of the machine. The MD code used was taken from the GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded interactions were rewritten for a parallel architecture. The remaining calculations were performed on the host computer. The algorithm has been tested on Quadrics computers for configurations of 32, 128, and 512 processors and for systems of 4000, 8000, 15,000, and 30,000 particles. Quadrics was developed by Istituto Nazionale di Fisica Nucleare (INFN) and marketed by Alenia Spazio. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 685–694, 1998

Published
1998
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