Literature DB >> 23767571

Atomic-resolution structural information from scattering experiments on macromolecules in solution.

Jürgen Köfinger1, Gerhard Hummer.   

Abstract

The pair-distance distribution function (PDDF) contains all structural information probed in an elastic scattering experiment of macromolecular solutions. However, in small-angle x-ray scattering (SAXS) or small-angle neutron scattering (SANS) experiments only their Fourier transform is measured over a restricted range of scattering angles. We therefore developed a mathematically simple and computationally efficient method to calculate the PDDFs as well as accurate scattering intensities from molecular dynamics simulations. The calculated solution scattering intensities are in excellent agreement with SAXS and wide-angle x-ray scattering (WAXS) experiments for a series of proteins. The corresponding PDDFs are remarkably rich in features reporting on the detailed protein structure. Using an inverse Fourier transform method, most of these features can be recovered if scattering intensities are measured up to a momentum transfer of q≈2-3Å(-1). Our results establish that high-precision solution scattering experiments utilizing x-ray free-electron lasers and third generation synchrotron sources can resolve subnanometer structural detail, well beyond size, shape, and fold.

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Year:  2013        PMID: 23767571     DOI: 10.1103/PhysRevE.87.052712

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  16 in total

1.  Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics.

Authors:  Po-Chia Chen; Jochen S Hub
Journal:  Biophys J       Date:  2015-05-19       Impact factor: 4.033

2.  Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures.

Authors:  Dudu Tong; Sichun Yang; Lanyuan Lu
Journal:  J Appl Crystallogr       Date:  2016-06-20       Impact factor: 3.304

Review 3.  Hybrid methods for combined experimental and computational determination of protein structure.

Authors:  Justin T Seffernick; Steffen Lindert
Journal:  J Chem Phys       Date:  2020-12-28       Impact factor: 3.488

4.  Reduction of small-angle scattering profiles to finite sets of structural invariants.

Authors:  Jérôme Houdayer; Frédéric Poitevin
Journal:  Acta Crystallogr A Found Adv       Date:  2017-06-09       Impact factor: 2.290

5.  Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data.

Authors:  Po-Chia Chen; Jochen S Hub
Journal:  Biophys J       Date:  2014-07-15       Impact factor: 4.033

6.  Extracting water and ion distributions from solution x-ray scattering experiments.

Authors:  Hung T Nguyen; Suzette A Pabit; Lois Pollack; David A Case
Journal:  J Chem Phys       Date:  2016-06-07       Impact factor: 3.488

7.  Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.

Authors:  Wenwei Zheng; Alessandro Borgia; Karin Buholzer; Alexander Grishaev; Benjamin Schuler; Robert B Best
Journal:  J Am Chem Soc       Date:  2016-09-01       Impact factor: 15.419

8.  WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics.

Authors:  Christopher J Knight; Jochen S Hub
Journal:  Nucleic Acids Res       Date:  2015-04-08       Impact factor: 16.971

9.  Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations.

Authors:  Samuel Bowerman; Ambar S J B Rana; Amy Rice; Grace H Pham; Eric R Strieter; Jeff Wereszczynski
Journal:  J Chem Theory Comput       Date:  2017-05-17       Impact factor: 6.006

10.  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

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