Cited by 20Protein Structure and DynamicsEnzyme Structure and FunctionAdvanced Physical and Chemical Molecular Interactions

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

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Wen, Bin, Peng, Junhui, Zuo, Xiaobing, Gong, Qingguo, Zhang, Zhiyong·2014·Biophysical Journal

Abstract

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations.

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Crossref · 10.1016/j.bpj.2014.07.005

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Authors
Wen, B., Peng, J., Zuo, X., Gong, Q., & Zhang, Z.
Affiliations
  • University of Science and Technology of China (CN)
  • Argonne National Laboratory (US)
Corresponding author
Zhang, Zhiyong
Venue
Biophysical Journal
Publisher
Elsevier BV
Published
2014-08
Volume
107
Issue
4
Pages
956-964
ISSN
0006-3495 (ISSN-L)
OpenAlex
W2071623887
Cited by
20
References
59
Citations by year
2024: 1 · 2023: 1 · 2022: 2 · 2021: 3 · 2020: 1 · 2019: 3 · 2018: 1 · 2017: 4 · 2016: 1 · 2015: 3
FWCI
1.09
Type
journal article
Language
en
Open access
Locations
  • Biophysical Journal (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords
protein flexibility, multidomain proteins, small-angle X-ray scattering, conformational sampling, bacteriophage T4 lysozyme, WW domain, protein conformational space
MeSH terms
Carrier Proteins, Computer Simulation, Elasticity, Models, Molecular, Motion, Muramidase, Nuclear Proteins, Protein Conformation, Proteins, X-Ray Diffraction, RNA-Binding Proteins, Bacteriophage T4, Scattering, Small Angle, Molecular Dynamics Simulation

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