TCB Publications - Abstract

Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, and Klaus Schulten. xMDFF: Molecular dynamics flexible fitting of low-resolution X-Ray structures. Acta Crystallographica D, 70:2344-2355, 2014. (PMC: PMC4157446)

MCGR2014 X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, availability of only medium to low-resolution diffraction data often limits the determination of all-atom details. We have developed a new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as is tested with synthetic low-resolution maps of D ribose binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that were already submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Åresolution, xMDFF refinements together with electrophysiology experiments confirmed the first all-atom structure of a voltage sensing protein Ci-VSP.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: PDF ( 1.8MB), Supplemental Material (483.6KB), Journal