Computer graphics presentations and analysis of hydrogen bonds from molecular dynamics simulation |
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| Institution: | 1. Faculty of Natural Sciences and Institute for Science & Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK;2. Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38000 Grenoble, France;3. Wits Research Institute for Malaria (WRIM), Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa;4. Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France;5. CNRS, IBS, F-38044 Grenoble, France;6. CEA, DSV, IBS, F-38044 Grenoble, France;7. ESRF, 71 avenue des Martyrs, CS 40220, 38043 Grenoble Cedex 9, France;1. Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia;2. Department of Microbiology, Monash University, Clayton 3168, Australia;3. NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India;4. Garvan Institute of Medical Research, Darlinghurst 2010, Australia;5. National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights 2234, Australia;6. Centre for Biomedical Research, The Burnet Institute, Melbourne 3004, Australia;7. Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia |
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| Abstract: | To obtain better insights into the dynamic nature of hydrogen bonding, computer graphics representations were introduced as an aid for the analysis of molecular dynamics trajectories. A schematic representation of hydrogen bonding patterns is generated to reflect the frequency and the type of hydrogen bonding occurring during the simulation period. Various trajectory plots for monitoring geometrical parameters and for analyzing three-center hydrogen bonding were also generated. The methods proposed are applicable to a variety of biopolymers. In this study, hydrogen bonding in the d(G) · d(C)6 system was examined. For the nucleic acid fragments examined, three-center hydrogen bonds can be classified as in-plane and major or minor groove types. The in-plane three-center hydrogen bond represents a stable state in which both bonds simultaneously satisfy the relaxed hydrogen bonding criteria for a measurable period. On the other hand, groove three-center hydrogen bonds behave as a transient intermediate state in a flip-flop hydrogen bonding system. |
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