Literature DB >> 29172147

Interpreting solution X-ray scattering data using molecular simulations.

Jochen S Hub1.   

Abstract

Small-angle and wide-angle X-ray scattering in solution (SAXS, WAXS, SWAXS) is an increasingly accurate method for obtaining information on biomolecular structures, ensembles, and time-resolved dynamics at near-native conditions. However, the interpretation of the solution scattering data by computational methods is complicated by the low information content of the data, by scattering contributions from the hydration layer, and by unknown systematic errors. In the light of available computational methods, we first review the main computational challenges with the interpretation of SWAXS data. Molecular dynamics (MD) simulations may help to overcome these challenges and guide the interpretation of SWAXS in multiple ways. The physical information in atomistic force fields complements the low-information SWAXS data; explicit-solvent MD may be used to predict solvent scattering, and the MD-related sampling methods may guide the structure refinement against SWAXS data.
Copyright © 2017 Elsevier Ltd. All rights reserved.

Mesh:

Substances:

Year:  2017        PMID: 29172147     DOI: 10.1016/j.sbi.2017.11.002

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  22 in total

1.  BEES: Bayesian Ensemble Estimation from SAS.

Authors:  Samuel Bowerman; Joseph E Curtis; Joseph Clayton; Emre H Brookes; Jeff Wereszczynski
Journal:  Biophys J       Date:  2019-07-18       Impact factor: 4.033

2.  Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data.

Authors:  Maud Chan-Yao-Chong; Célia Deville; Louise Pinet; Carine van Heijenoort; Dominique Durand; Tâp Ha-Duong
Journal:  Biophys J       Date:  2019-02-26       Impact factor: 4.033

3.  An Extended Guinier Analysis for Intrinsically Disordered Proteins.

Authors:  Wenwei Zheng; Robert B Best
Journal:  J Mol Biol       Date:  2018-03-21       Impact factor: 5.469

4.  Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Authors:  Utsab R Shrestha; Puneet Juneja; Qiu Zhang; Viswanathan Gurumoorthy; Jose M Borreguero; Volker Urban; Xiaolin Cheng; Sai Venkatesh Pingali; Jeremy C Smith; Hugh M O'Neill; Loukas Petridis
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

5.  Salt Dependence of A-Form RNA Duplexes: Structures and Implications.

Authors:  Yen-Lin Chen; Lois Pollack
Journal:  J Phys Chem B       Date:  2019-11-11       Impact factor: 2.991

6.  Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data.

Authors:  Francesco Pesce; Kresten Lindorff-Larsen
Journal:  Biophys J       Date:  2021-10-08       Impact factor: 4.033

7.  New Light on the Mechanism of Phototransduction in Phototropin.

Authors:  L Henry; O Berntsson; M R Panman; A Cellini; A J Hughes; I Kosheleva; R Henning; S Westenhoff
Journal:  Biochemistry       Date:  2020-08-25       Impact factor: 3.162

8.  Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods.

Authors:  Mustapha Carab Ahmed; Line K Skaanning; Alexander Jussupow; Estella A Newcombe; Birthe B Kragelund; Carlo Camilloni; Annette E Langkilde; Kresten Lindorff-Larsen
Journal:  Front Mol Biosci       Date:  2021-04-22

Review 9.  Time-resolved X-ray scattering studies of proteins.

Authors:  Hyun Sun Cho; Friedrich Schotte; Valentyn Stadnytskyi; Philip Anfinrud
Journal:  Curr Opin Struct Biol       Date:  2021-06-25       Impact factor: 7.786

10.  Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs.

Authors:  Elena Papaleo; Carlo Camilloni; Kaare Teilum; Michele Vendruscolo; Kresten Lindorff-Larsen
Journal:  PeerJ       Date:  2018-07-04       Impact factor: 2.984

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.