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Cited by 23Protein Structure and DynamicsEnzyme Structure and FunctionAdvanced Physical and Chemical Molecular Interactions

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Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations

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Ballabio, Federico, Paissoni, Cristina, Bollati, Michela, de Rosa, Matteo, Capelli, Riccardo, Camilloni, Carlo·2023·Journal of Chemical Theory and Computation
DOI 10.1021/acs.jctc.3c00864PMC PMC10687869

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Abstract

Small-angle X-ray and neutron scattering (SAXS/SANS) provide valuable insights into the structure and dynamics of biomolecules in solution, complementing a wide range of structural techniques, including molecular dynamics simulations. As contrast-based methods, they are sensitive not only to structural properties but also to solvent-solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. In this work, we demonstrate the feasibility of calculating SAXS and SANS intensities using a coarse-grained representation consisting of one bead per amino acid and three beads per nucleic acid, with form factors that can be corrected on the fly to account for solvation effects at no additional computational cost. By coupling this forward model with molecular dynamics simulations restrained with SAS data, it is possible to determine conformational ensembles or refine the structure and dynamics of proteins and nucleic acids in agreement with the experimental results. To assess the robustness of this approach, we applied it to gelsolin, for which we acquired SAXS data on its closed state, and to a UP1-microRNA complex, for which we used previously collected measurements. Our hybrid-resolution small-angle scattering (hySAS) implementation, being distributed in PLUMED, can be used with atomistic and coarse-grained simulations using diverse restraining strategies.

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  1. 10.1107/S2052252517008740 · DOI
  2. 10.1017/S0033583503003871 · DOI
  3. 10.1016/j.febslet.2015.08.027 · DOI
  4. 10.1021/jacs.1c06264 · DOI
  5. 10.1021/jacsau.1c00536 · DOI
  6. 10.1073/pnas.1607193113 · DOI
  7. 10.1016/j.sbi.2017.11.002 · DOI
  8. 10.1107/S0365110X6500018X · DOI
  9. Brown P. J., 2006, International Tables for Crystallography, 554, 10.1107/97809553602060000600 · DOI
  10. 10.1107/S0021889878014296 · DOI
  11. Feigin L. A., 2013, Structure Analysis by Small-Angle X-ray and Neutron Scattering
  12. 10.1080/10448639208218770 · DOI
  13. 10.1107/S0907444910017658 · DOI
  14. 10.1073/pnas.95.5.2267 · DOI
  15. 10.1016/S0301-4622(01)00216-2 · DOI
  16. 10.1101/2023.06.13.544709 · DOI
  17. 10.1073/pnas.082335099 · DOI
  18. 10.1016/j.bpj.2014.06.006 · DOI
  19. 10.1093/nar/gkv309 · DOI
  20. 10.1103/PhysRevE.87.052712 · DOI
  21. 10.1107/S1600576717007786 · DOI
  22. 10.1093/nar/gkq461 · DOI
  23. 10.1107/S2059798317005745 · DOI
  24. 10.1063/1.4960175 · DOI
  25. 10.1063/1.4824627 · DOI
  26. 10.1140/epjb/s10051-021-00186-9 · DOI
  27. 10.1107/S0021889895007047 · DOI
  28. 10.1016/j.bpj.2009.03.036 · DOI
  29. 10.1063/1.4774148 · DOI
  30. 10.1186/1471-2105-11-429 · DOI
  31. 10.1016/j.bpj.2011.11.003 · DOI
  32. 10.1107/S1600576714009959 · DOI
  33. 10.1039/c3cs60093a · DOI
  34. 10.1107/S1600576719002450 · DOI
  35. 10.1126/sciadv.abc3786 · DOI
  36. 10.1021/acs.jctc.9b01181 · DOI
  37. 10.1016/j.jmb.2021.167119 · DOI
  38. 10.3389/fmolb.2021.694130 · DOI
  39. 10.3389/fmolb.2021.654333 · DOI
  40. 10.1002/cm.21117 · DOI
  41. 10.1038/281583a0 · DOI
  42. 10.1074/jbc.274.47.33179 · DOI
  43. 10.3390/ijms19092516 · DOI
  44. 10.3109/10409238.2012.661401 · DOI
  45. 10.1002/med.20231 · DOI
  46. 10.1074/jbc.M702446200 · DOI
  47. 10.1073/pnas.0812374106 · DOI
  48. 10.1073/pnas.1902189116 · DOI
  49. 10.1007/s00249-019-01409-9 · DOI
  50. 10.1016/j.csbj.2021.11.025 · DOI
  51. 10.1093/bioinformatics/btx529 · DOI
  52. 10.1016/j.cpc.2013.09.018 · DOI
  53. 10.1038/s41592-019-0506-8 · DOI
  54. 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A · DOI
  55. 10.1021/acs.chemrev.7b00427 · DOI
  56. 10.1093/nar/gkn260 · DOI
  57. 10.1261/rna.2543711 · DOI
  58. 10.1007/s10822-013-9644-8 · DOI
  59. 10.1021/jp508971m · DOI
  60. 10.1126/sciadv.1501177 · DOI
  61. 10.1021/acs.jctc.5b00255 · DOI
  62. 10.1038/nmeth.3658 · DOI
  63. 10.1063/1.445869 · DOI
  64. 10.1038/s41467-018-04871-9 · DOI
  65. 10.1016/j.softx.2015.06.001 · DOI · Paper page
  66. 10.1109/MCSE.2007.55 · DOI · Paper page
  67. 10.1016/0263-7855(96)00018-5 · DOI · Paper page
  68. Ballabio, F.; Capelli, R.; Camilloni, C. Supporting data for: ″An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations.”. Zenodo: 2023. · DOI · Paper page
  69. 10.1016/j.bbadis.2019.01.010 · DOI
  70. 10.1107/S1600577520009960 · DOI
  71. 10.1093/nar/gku1047 · DOI
  72. 10.1021/acs.jpcb.1c01694 · DOI
  73. 10.1002/jcc.540160303 · DOI
  74. 10.1007/s10974-019-09571-5 · DOI
  75. 10.1016/j.bbrc.2019.08.013 · DOI
  76. 10.1073/pnas.0832273100 · DOI
  77. 10.1016/j.sbi.2016.12.004 · DOI
  78. 10.1016/bs.pmbts.2019.12.006 · DOI
  79. 10.1515/hsz-2023-0145 · DOI
  80. 10.1063/1.4937786 · DOI
  81. 10.1021/acs.jctc.8b00738 · DOI
  82. 10.1063/1.4793625 · DOI
  83. 10.1021/acs.jctc.6b00944 · DOI
  84. 10.1063/1.5030339 · DOI
  85. 10.1073/pnas.202427399 · DOI · Paper page
  86. 10.1016/0021-9991(77)90121-8 · DOI · Paper page

Metadata

Authors
Ballabio, F., Paissoni, C., Bollati, M., de Rosa, M., Capelli, R., & Camilloni, C.
Affiliations
University of Milan (IT)
Corresponding author
  • de Rosa, Matteo
  • Capelli, Riccardo
  • Camilloni, Carlo
ORCID
Venue
Journal of Chemical Theory and Computation
Publisher
American Chemical Society (ACS)
Published
2023-11-03
Volume
19
Issue
22
Pages
8401-8413
ISSN
  • 1549-9618 (ISSN-L)
  • 1549-9626
DOI
10.1021/acs.jctc.3c00864
PMC
PMC10687869
OpenAlex
W4388314297
Cited by
23
References
1
Citations by year
2026: 7 · 2025: 11 · 2024: 4 · 2023: 1
FWCI
2.05
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Chemical Theory and Computation (publishedVersion, cc-by)
  • ChemRxiv (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
Funders
Diamond Light Source
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords
small-angle X-ray scattering, small-angle neutron scattering, forward scattering model, coarse-grained representation, PLUMED, molecular dynamics simulation, gelsolin, protein structure refinement, solute-solvent interactions
MeSH terms
Protein Conformation, Proteins, X-Ray Diffraction, Scattering, Small Angle, Molecular Dynamics Simulation

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