Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields
作者： P. Faccioli , S. a Beccara
DOI: 10.1016/J.BPC.2015.06.014
关键词:
摘要: The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development this method. Next, we discuss its validation against results plain MD protein folding simulations performed DE-Shaw group Anton supercomputer. Finally, a few representative applications DRP approach study reactions are far too complex and rare investigated MD, even on machine.
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sci-hub.se 参考文章(28)
William R. Taylor, A deeply knotted protein structure and how it might fold Nature. ,vol. 406, pp. 916- 919 ,(2000) , 10.1038/35022623
Peter Eastman, Niels Grønbech-Jensen, Sebastian Doniach, Simulation of protein folding by reaction path annealing Journal of Chemical Physics. ,vol. 114, pp. 3823- 3841 ,(2001) , 10.1063/1.1342162
R. B. Best, G. Hummer, Coordinate-dependent diffusion in protein folding. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 107, pp. 1088- 1093 ,(2010) , 10.1073/PNAS.0910390107
Roberto Covino, Tatjana Škrbić, Silvio Beccara, Pietro Faccioli, Cristian Micheletti, The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations Biomolecules. ,vol. 4, pp. 1- 19 ,(2013) , 10.3390/BIOM4010001
Peter Hägglöf, Fredrik Bergström, Malgorzata Wilczynska, Lennart B.-Å Johansson, Tor Ny, The reactive-center loop of active PAI-1 is folded close to the protein core and can be partially inserted Journal of Molecular Biology. ,vol. 335, pp. 823- 832 ,(2004) , 10.1016/J.JMB.2003.11.005
Marc L. Mansfield, Fit to be tied. Nature Structural & Molecular Biology. ,vol. 4, pp. 166- 167 ,(1997) , 10.1038/NSB0397-166
Carlo Camilloni, Ricardo A. Broglia, Guido Tiana, Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations. Journal of Chemical Physics. ,vol. 134, pp. 045105- 045105 ,(2011) , 10.1063/1.3523345
S. a Beccara, T. Skrbic, R. Covino, P. Faccioli, Dominant folding pathways of a WW domain Proceedings of the National Academy of Sciences of the United States of America. ,vol. 109, pp. 2330- 2335 ,(2012) , 10.1073/PNAS.1111796109
G. Cazzolli, F. Wang, S. a Beccara, A. Gershenson, P. Faccioli, P. L. Wintrode, Serpin latency transition at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 15414- 15419 ,(2014) , 10.1073/PNAS.1407528111
Emanuele Paci, Martin Karplus, Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. Journal of Molecular Biology. ,vol. 288, pp. 441- 459 ,(1999) , 10.1006/JMBI.1999.2670