Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

Stephen J. Perkins, David W. Wright, Hailiang Zhang, Emre H. Brookes, Jianhan Chen, Thomas C. Irving, Susan Krueger, David J. Barlow, Karen J. Edler, David J. Scott, Nicholas J. Terrill, Stephen M. King, Paul D. Butler, Joseph E. Curtis

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.

Original languageEnglish
Pages (from-to)1861-1875
JournalJournal of Applied Crystallography
Volume49
Issue number6
DOIs
Publication statusPublished - 1 Dec 2016

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Small Angle Scattering
Scattering
Software
Mannose-Binding Protein-Associated Serine Proteases
Computing Methodologies
Physical Chemistry
Crystallography
Workflow
Physics
Molecular Dynamics Simulation
Ubiquitin
Running
Computer Simulation
Immunoglobulin A
HIV-1
Electron Microscopy
Polymers
Immunoglobulin G
Physical chemistry
Molecular modeling

Keywords

  • Molecular dynamics (MD)
  • Molecular modelling
  • Scattering curve fits
  • Small-angle-neutron scattering (SANS)
  • Small-angle-X-ray scattering (SAXS)

Cite this

Perkins, S. J., Wright, D. W., Zhang, H., Brookes, E. H., Chen, J., Irving, T. C., ... Curtis, J. E. (2016). Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Journal of Applied Crystallography, 49(6), 1861-1875. https://doi.org/10.1107/S160057671601517X

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). / Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang; Brookes, Emre H.; Chen, Jianhan; Irving, Thomas C.; Krueger, Susan; Barlow, David J.; Edler, Karen J.; Scott, David J.; Terrill, Nicholas J.; King, Stephen M.; Butler, Paul D.; Curtis, Joseph E.

In: Journal of Applied Crystallography, Vol. 49, No. 6, 01.12.2016, p. 1861-1875.

Research output: Contribution to journalArticle

Perkins, SJ, Wright, DW, Zhang, H, Brookes, EH, Chen, J, Irving, TC, Krueger, S, Barlow, DJ, Edler, KJ, Scott, DJ, Terrill, NJ, King, SM, Butler, PD & Curtis, JE 2016, 'Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)', Journal of Applied Crystallography, vol. 49, no. 6, pp. 1861-1875. https://doi.org/10.1107/S160057671601517X
Perkins, Stephen J. ; Wright, David W. ; Zhang, Hailiang ; Brookes, Emre H. ; Chen, Jianhan ; Irving, Thomas C. ; Krueger, Susan ; Barlow, David J. ; Edler, Karen J. ; Scott, David J. ; Terrill, Nicholas J. ; King, Stephen M. ; Butler, Paul D. ; Curtis, Joseph E. / Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). In: Journal of Applied Crystallography. 2016 ; Vol. 49, No. 6. pp. 1861-1875.
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