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Applications of the molecular dynamics flexible fitting method.

Abstract：

:In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to landmark advances in experimental and computational techniques, resulting in sub-nanometer resolution structures being obtained routinely. The remaining gap between these data and revealing the mechanisms of molecular function can be closed through hybrid modeling tools that incorporate known atomic structures into the cryo-EM data. One such tool, molecular dynamics flexible fitting (MDFF), uses molecular dynamics simulations to combine structures from X-ray crystallography with cryo-EM density maps to derive atomic models of large biomolecular complexes. The structures furnished by MDFF can be used subsequently in computational investigations aimed at revealing the dynamics of the complexes under study. In the present work, recent applications of MDFF are presented, including the interpretation of cryo-EM data of the ribosome at different stages of translation and the structure of a membrane-curvature-inducing photosynthetic complex.

journal_name

J Struct Biol

journal_title

Journal of structural biology

authors

Trabuco LG,Schreiner E,Gumbart J,Hsin J,Villa E,Schulten K

doi

10.1016/j.jsb.2010.09.024

subject

Has Abstract

pub_date

2011-03-01 00:00:00

pages

420-7

issue

3

eissn

1047-8477

issn

1095-8657

pii

S1047-8477(10)00293-5

journal_volume

173

pub_type

杂志文章

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