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Review
. 2021 Dec 24:8:765562.
doi: 10.3389/fmolb.2021.765562. eCollection 2021.

Recent Developments in Data-Assisted Modeling of Flexible Proteins

Cezary Czaplewski  1 , Zhou Gong  2 , Emilia A Lubecka  3 , Kai Xue  4 , Chun Tang  4 , Adam Liwo  1
Affiliations
Review

Recent Developments in Data-Assisted Modeling of Flexible Proteins

Cezary Czaplewski et al. Front Mol Biosci. .

Abstract

Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.

Keywords: chemical cross-linking coupled with mass spectroscopy; coarse graining; conformational ensembles; data-assisted modeling; molecular dynamics; nuclear magnetic resonance; proteins; small-angle X-ray scattering.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
A scheme of methods for the determination of conformational ensembles of flexible proteins.
See this image and copyright information in PMC

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