SAXS-Oriented Ensemble Refinement of Flexible Biomolecules

Peng Cheng; Junhui Peng; Zhiyong Zhang

doi:10.1016/j.bpj.2017.02.024

SAXS-Oriented Ensemble Refinement of Flexible Biomolecules

Biophys J. 2017 Apr 11;112(7):1295-1301. doi: 10.1016/j.bpj.2017.02.024.

Authors

Peng Cheng¹, Junhui Peng¹, Zhiyong Zhang²

Affiliations

¹ Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
² Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China. Electronic address: zzyzhang@ustc.edu.cn.

Abstract

The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well. The tool has been validated with a protein and an RNA system, i.e., the tandem WW domains of formin-binding protein 21 and the aptamer domain of SAM-1 riboswitch, respectively. These Python scripts are user-friendly and can be easily modified if a different simulation engine is preferred.

MeSH terms

Carrier Proteins / chemistry
Carrier Proteins / metabolism*
Protein Domains
Riboswitch
S-Adenosylmethionine / metabolism
Scattering, Small Angle*
X-Ray Diffraction*

Substances

Carrier Proteins
Riboswitch
S-Adenosylmethionine