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| Journal Article | FZJ-2015-03607 |
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2012
Cuyahoga Falls, Ohio
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Please use a persistent id in citations: http://hdl.handle.net/2128/8783 doi:10.1155/2012/709085
Abstract: The dauntingly complex functioning of human cells is often the outcome of several molecular processes. Understanding such processes is crucial for modern drug discovery, defining interaction cascades, assessing the effects of mutations changes in local concentrations of ligands, and so forth. Computational methods, from systems biology to bioinformatics and molecular simulation, allow to access features difficult or impossible to be measured. Models (if properly validated against experimental data) help understand the intricate molecular mechanisms of life processes. Bolstering the predictive power of these models calls upon the computational biologist to improve algorithms and methods. This issue reports on procedures and on applications facing current challenges in computational biology.Modern biological sciences are becoming more and more multidisciplinary. At the same time, theoretical and computational approaches gain in reliability and their field of application widens. O. Fisette at al. discuss recent advances in the areas of solution nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations that were made possible by the synergistic combination of both methods.Interaction of proteins is of vital importance for many cellular processes and when altered may cause significant health problems, thus the availability of reliable tools to predict and study the determinants of protein-protein interactions is needed. In this regard, X. -Y. Meng et al. present a newly adapted, computationally efficient Brownian Dynamics- (BD-) based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. A shell-based grid force field represents the receptor protein and solvation effects, partially considering protein flexibility.Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are routinely used to study quantum mechanical processes in biological systems. J. Kang et al. present a review paper describing an UNIX shell-based interface program connecting two widely used QM and MM calculation engines, GAMESS and AMBER. The tool was used to investigate a metalloenzyme, azurin, and PU.1-DNA complex and mechanisms of hydrolysis (editing reaction) in leucyl-tRNA synthetase complexed with the mis-aminoacylated tRNALeu. The authors investigate the influence of environmental effects on the electronic structure.Electron transfer in proteins constitutes key steps in several biological processes, ranging from photosynthesis to aerobic respiration. T. Hayashi and A. Stuchebrukhov investigate electron tunneling in NADH : ubiquinone oxidoreductase (Complex I), a key enzyme in cellular respiration as an entry point of the electron transport chain of mitochondria and bacteria, by evaluating the transition flux between donor and acceptor at atomistic resolution. The study suggests that the diffusion of internal water molecules dynamically controls tunneling efficiency.
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