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Cited by 90Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsDiffusion and Search Dynamics

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Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations

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Saglam, Ali S., Chong, Lillian T.·2019·Chemical Science
DOI 10.1039/c8sc04811hPMC PMC6385678

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Abstract

The weighted ensemble (WE) strategy enables direct simulation of atomistic, fully-continuous protein–protein binding pathways in explicit solvent, yielding rigorous kinetics.

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Research works printed but not linked: 50

  1. A. C. Pan , D.Jacobson , K.Yatsenko , D.Sritharan , T. M.Weinreich and D. E.Shaw , bioRxiv, 2018 , 303370
  2. Plattner, 2017, Nat. Chem., 9, 1005, 10.1038/nchem.2785 · DOI
  3. Chong, 2017, Curr. Opin. Struct. Biol., 43, 88, 10.1016/j.sbi.2016.11.019 · DOI
  4. Huber, 1996, Biophys. J., 70, 97, 10.1016/S0006-3495(96)79552-8 · DOI
  5. Zwier, 2016, J. Phys. Chem. Lett., 7, 3440, 10.1021/acs.jpclett.6b01502 · DOI
  6. Suarez, 2014, J. Chem. Theory Comput., 10, 2658, 10.1021/ct401065r · DOI
  7. Zwier, 2015, J. Chem. Theory Comput., 11, 800, 10.1021/ct5010615 · DOI
  8. Zuckerman, 2017, Annu. Rev. Biophys., 46, 43, 10.1146/annurev-biophys-070816-033834 · DOI
  9. Suarez, 2016, Protein Sci., 25, 67, 10.1002/pro.2738 · DOI
  10. Hess, 2008, J. Chem. Theory Comput., 4, 435, 10.1021/ct700301q · DOI
  11. Case, 2005, J. Comput. Chem., 26, 1668, 10.1002/jcc.20290 · DOI · Paper page
  12. Zhang, 2010, J. Chem. Phys., 132, 054107, 10.1063/1.3306345 · DOI
  13. DeGrave, 2018, Nat. Commun., 9, 1013, 10.1038/s41467-018-03228-6 · DOI
  14. Zwier, 2011, J. Chem. Theory Comput., 7, 1189, 10.1021/ct100626x · DOI
  15. Saglam, 2016, J. Phys. Chem. B, 120, 117, 10.1021/acs.jpcb.5b10747 · DOI
  16. Adelman, 2013, J. Chem. Phys., 138, 044105, 10.1063/1.4773892 · DOI
  17. Adelman, 2015, J. Chem. Theory Comput., 11, 1907, 10.1021/ct501134s · DOI
  18. Schreiber, 1996, Nat. Struct. Biol., 3, 427, 10.1038/nsb0596-427 · DOI
  19. Gabdoulline, 1997, Biophys. J., 72, 1917, 10.1016/S0006-3495(97)78838-6 · DOI
  20. Buckle, 1994, Biochemistry, 33, 8878, 10.1021/bi00196a004 · DOI
  21. Best, 2009, J. Phys. Chem. B, 113, 9004, 10.1021/jp901540t · DOI
  22. Jorgensen, 1983, J. Chem. Phys., 79, 926, 10.1063/1.445869 · DOI
  23. Bussi, 2007, J. Chem. Phys., 126, 014101, 10.1063/1.2408420 · DOI
  24. Berendsen, 1984, J. Chem. Phys., 81, 3684, 10.1063/1.448118 · DOI
  25. Hess, 1997, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H · DOI
  26. Essmann, 1995, J. Chem. Phys., 103, 8577, 10.1063/1.470117 · DOI
  27. Saglam, 2017, J. Phys. Chem. B, 121, 10046, 10.1021/acs.jpcb.7b08486 · DOI
  28. Dickson, 2016, J. Phys. Chem. B, 120, 5377, 10.1021/acs.jpcb.6b04012 · DOI
  29. Jacomy, 2014, PLoS One, 9, e98679, 10.1371/journal.pone.0098679 · DOI · Paper page
  30. M. Bastian , S.Heymann and M.Jacomy , International AAAI Conference on Weblogs and Social Media , North America , 2009
  31. Shrake, 1973, J. Mol. Biol., 79, 351, 10.1016/0022-2836(73)90011-9 · DOI
  32. McGibbon, 2015, Biophys. J., 109, 1528, 10.1016/j.bpj.2015.08.015 · DOI
  33. Michaud-Agrawal, 2011, J. Comput. Chem., 32, 2319, 10.1002/jcc.21787 · DOI
  34. Schreiber, 2009, Chem. Rev., 109, 839, 10.1021/cr800373w · DOI
  35. Miller, 2002, Protein Sci., 6, 2166, 10.1002/pro.5560061011 · DOI · Paper page
  36. Zhang, 1999, Proteins, 34, 255, 10.1002/(SICI)1097-0134(19990201)34:2<255::AID-PROT10>3.0.CO;2-O · DOI
  37. Tovchigrechko, 2001, Protein Sci., 10, 1572, 10.1110/ps.8701 · DOI
  38. Selzer, 2001, Proteins, 45, 190, 10.1002/prot.1139 · DOI
  39. Northrup, 1992, Proc. Natl. Acad. Sci. U. S. A., 89, 3338, 10.1073/pnas.89.8.3338 · DOI
  40. Panteva, 2011, Biophys. J., 100, L50, 10.1016/j.bpj.2011.03.035 · DOI
  41. Zhang, 2016, Biophys. J., 110, 877, 10.1016/j.bpj.2015.12.036 · DOI
  42. Lindorff-Larsen, 2010, Proteins, 78, 1950, 10.1002/prot.22711 · DOI
  43. Martin, 1999, Acta Crystallogr., Sect. D: Biol. Crystallogr., 55, 386, 10.1107/S0907444998010865 · DOI
  44. Ratnaparkhi, 1998, Biochemistry, 37, 6958, 10.1021/bi972857n · DOI
  45. Zhuravleva, 2007, J. Mol. Biol., 367, 1079, 10.1016/j.jmb.2007.01.051 · DOI
  46. Spaar, 2006, Biophys. J., 90, 1913, 10.1529/biophysj.105.075507 · DOI
  47. Schreiber, 1993, Biochemistry, 32, 5145, 10.1021/bi00070a025 · DOI
  48. Frisch, 2001, J. Mol. Biol., 308, 69, 10.1006/jmbi.2001.4577 · DOI
  49. Rajamani, 2004, Proc. Natl. Acad. Sci. U. S. A., 101, 11287, 10.1073/pnas.0401942101 · DOI
  50. Mauguen, 1982, Nature, 297, 162, 10.1038/297162a0 · DOI

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Metadata

Authors
Saglam, A. S., & Chong, L. T.
Affiliations
University of Pittsburgh (US)
Corresponding author
Chong, Lillian T.
ORCID
Venue
Chemical Science
Publisher
Royal Society of Chemistry (RSC)
Published
2019
Volume
10
Issue
8
Pages
2360-2372
ISSN
  • 2041-6520 (ISSN-L)
  • 2041-6539
DOI
10.1039/c8sc04811h
PMC
PMC6385678
OpenAlex
W2898094195
Cited by
90
References
4
Citations by year
2026: 6 · 2025: 9 · 2024: 15 · 2023: 12 · 2022: 19 · 2021: 15 · 2020: 10 · 2019: 4
FWCI
2.67
Type
journal article
Language
en
Open access
Licence
Locations
  • Chemical Science (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Science Foundation (MCB-0845216)
  • National Institutes of Health (1R01GM115805-01)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
Keywords
protein-protein binding, barnase, barstar, binding kinetics, rate constants, electrostatic steering, encounter complex, hydrogen bonding, atomistic simulation, explicit solvent

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