Mode Localization in the Cooperative Dynamics of Protein Recognition

Autor:	Copperman, J., Guenza, M. G.
Rok vydání:	2015
Předmět:	Physics - Biological Physics Condensed Matter - Soft Condensed Matter Quantitative Biology - Biomolecules
Druh dokumentu:	Working Paper
DOI:	10.1016/j.bpj.2015.11.356
Popis:	The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. Local fluctuations are known to initiate biologically relevant pathways as they cooperatively enhance the dynamics in specific regions in the protein. Those biologically active regions provide energetically-comparable conformational states that can be trapped by a reacting partner. We analyze this mechanism as we calculate the dynamics of monomeric and dimerized HIV protease, and free Insulin Growth Factor II Receptor (IGF2R) domain 11 and its IGF2R:IGF2 complex. We adopt a newly developed coarse-grained model, the Langevin Equation for Protein Dynamics (LE4PD), which predicts dynamical relevant mechanisms with high accuracy. Both simulation-derived and experimental NMR conformers are the input structural ensembles for the LE4PD. The use of the experimental NMR conformers requires minimal computational resources. Comment: arXiv admin note: text overlap with arXiv:1509.08551
Databáze:	arXiv
Externí odkaz:	http://arxiv.org/abs/1509.08913 Zobrazit plný text záznamu View this record from Arxiv