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Protein Folding: Molecular Dynamics Simulations

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References

  • Bartlett AI, Radford SE (2009) An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 16:582–588

    Article  CAS  PubMed  Google Scholar 

  • Brodie NI, Konstantin I, Petrochenko EV, Dokholyan NV, Brochers CH (2017) Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. Sci Adv 3:e1700479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caflisch A, Paci E (2005) Molecular dynamics simulations to study protein folding and unfolding. In: Buchner J, Kiefhaber T (eds) Protein folding handbook. Wiley-VCH, Weinheim, pp 1143–1169

    Chapter  Google Scholar 

  • Childers MC, Towse CL, Daggett V (2016) The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design. Protein Eng Des Sel 29:271–280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daggett V (2006) Protein folding – simulation. Chem Rev 106:1898–1916

    Article  CAS  PubMed  Google Scholar 

  • Daggett V, Levitt M (1993) Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol 232:600–619

    Article  CAS  PubMed  Google Scholar 

  • Day R, Daggett V (2005) Ensemble versus single-molecule protein unfolding. Proc Natl Acad Sci U S A 102:13445–13450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Day R, Daggett V (2007) Direct observation of microscopic reversibility of single-molecule protein folding. J Mol Biol 366:677–686

    Article  CAS  PubMed  Google Scholar 

  • Day R, Bennion B, Ham S, Daggett V (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J Mol Biol 322:189–203

    Article  CAS  PubMed  Google Scholar 

  • Dellago C, Bolhuis PG, Geissler PL (2006) Transiton path sampling methods. Lect Notes Phys 703:349–391

    Article  CAS  Google Scholar 

  • Ding F, Tsao D, Nie H, Dokholyan NV (2008) Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure 16:1010–1018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dokhoylan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (1998) Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 3:577–587

    Google Scholar 

  • Doshi U, Hamelberg D (2015) Towards fast, rigorous and efficient conformational sampling of biomolecules: advances in accelerated molecular dynamics. Biochim Biophys Acta 1850:878–888

    Article  CAS  PubMed  Google Scholar 

  • Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282:740–744

    Article  CAS  PubMed  Google Scholar 

  • Fersht AR, Daggett V (2002) Protein folding and unfolding at atomic resolution. Cell 108:573–582

    Article  CAS  PubMed  Google Scholar 

  • Forman JR, Clarke J (2007) Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol 17:58–66

    Article  CAS  PubMed  Google Scholar 

  • Galera-Prat A, Gomez-Sicilia A, Oberhauser AF, Cieplak M, Carrion-Vazquez M (2010) Understanding biology by stretching proteins: recent progress. Curr Opin Struct Biol 20:63–69

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys 120:11919–11929

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13:1011–1021

    Article  CAS  Google Scholar 

  • Leach AR (2001) Molecular modelling: principles and applications, 2nd edn. Pearson Education, Harlow

    Google Scholar 

  • Levitt M, Warshel A (1975) Computer simulation of protein folding. Nature 253:694–698

    Article  CAS  PubMed  Google Scholar 

  • Li A, Daggett V (1994) Characterization of the transition state of protein unfolding using molecular dynamics: chymotrypsin inhibitor 2. Proc Natl Acad Sci U S A 91:10430–10434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) How fast-folding proteins fold. Science 334:517–520

    Article  CAS  PubMed  Google Scholar 

  • McCammon A, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267:585–590

    Article  CAS  PubMed  Google Scholar 

  • Miao Y, Feixas F, Eun C, McCammon JA (2015) Accelerate molecular dynamics simulations of protein folding. J Comput Chem 36:1536–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pande VS, Sorin EJ, Snow CD, Rhee YM (2008) Computer simulations of protein folding. In: Muñoz V (ed) Protein folding, misfolding and aggregation: classical themes and novel approaches, 1st edn. Royal Society of Chemistry, Cambridge, pp 161–169

    Chapter  Google Scholar 

  • Ponder JW, Case DA (2003) Force field for protein simulations. Adv Protein Chem 66:27–86

    Article  CAS  PubMed  Google Scholar 

  • Proctor EA, Dokholyan NV (2016) Applications of discrete molecular dynamics in biology and medicine. Curr Opin Struct Biol 37:9–13

    Article  CAS  PubMed  Google Scholar 

  • Proctor EA, Ding F, Dokholyan NV (2011) Discrete molecular dynamics. WIREs Comput Mol Sci 1:80–92

    Article  CAS  Google Scholar 

  • Schaeffer RD, Jonsson AL, Simms AM, Daggett V (2011) Generation of a consensus protein domain dictionary. Bioinformatics 27:46–54

    Article  CAS  PubMed  Google Scholar 

  • Schlick T (2009) Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules. F1000 Biol Rep 1:51

    PubMed  PubMed Central  Google Scholar 

  • Schlick T (2010) Molecular modelling and simulation: an interdisciplinary approach, 2nd edn. Springer, New York

    Book  Google Scholar 

  • Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan YB, Wriggers W (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341–346

    Article  CAS  PubMed  Google Scholar 

  • Sheinerman FB, Brooks CL III (1998) Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol 278:439–456

    Article  CAS  PubMed  Google Scholar 

  • Towse CL, Rysavy SJ, Vulovic IM, Daggett V (2016a) New dynamic rotamer libraries: data-driven analysis of side-chain conformational propensities. Structure 24(1):187–199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Towse CL, Vymetal J, Vondrasek J, Daggett V (2016b) Insights into unfolded proteins from the intrinsic Ï•/ψ propensities of the AAXAA host-guest series. Biophys J 110(2):348–361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Towse CL, Akke M, Daggett V (2017) The dynameomics entropy dictionary: a large-scale assessment of conformational entropy across protein fold space. J Phys Chem B 121:3933–3945

    Article  CAS  PubMed  Google Scholar 

  • Tozzini V (2005) Coarse-grained models for proteins. Curr Opin Struct Biol 15:144–150

    Article  CAS  PubMed  Google Scholar 

  • Van der Kamp MW, Schaeffer RD, Jonsson AL, Scouras AD, Simms AM, Toofanny RD, Benson NC, Anderson PC, Merkley ED, Rysavy S, Bromley D, Beck DA, Daggett V (2010) Dynameomics: a comprehensive database of protein dynamics. Structure 18:423–435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vendruscolo M, Dobson CM (2011) Protein dynamics: Moore’s law in molecular biology. Curr Biol 21:R68–R70

    Article  CAS  PubMed  Google Scholar 

  • Voter AF (1997) Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys Rev Lett 78:3908–3911

    Article  CAS  Google Scholar 

  • Wang Y, McCammon JA (2012) Accelerated molecular dynamics: theory, implementation and applications. AIP Conf Proc 1456:165–172

    Article  CAS  Google Scholar 

  • Wolynes PG (2008) The protein folding energy landscape: a primer. In: Muñoz V (ed) Protein folding, misfolding and aggregation: classical themes and novel approaches, 1st edn. Royal Society of Chemistry, Cambridge, pp 49–69

    Chapter  Google Scholar 

  • Zamora RJ, Uberuaga BP, Perez D, Voter AF (2016) The modern temperature-accelerated dynamics approach. Annu Rev Chem Biomol Eng 7:87–110

    Article  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Chemistry and Biosciences, University of Bradford, Bradford, UK

    Clare-Louise Towse

  2. Department of Bioengineering, University of Washington, Seattle, WA, USA

    Valerie Daggett

Authors
  1. Clare-Louise Towse
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  2. Valerie Daggett
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Corresponding author

Correspondence to Clare-Louise Towse .

Editor information

Editors and Affiliations

  1. University Leicester MRC Centre, Leicester, United Kingdom

    Gordon Roberts

  2. Dept Biochemistry, University of Oxford, Oxford, United Kingdom

    Anthony Watts

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© 2018 European Biophysical Societies' Association (EBSA)

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Towse, CL., Daggett, V. (2018). Protein Folding: Molecular Dynamics Simulations. In: Roberts, G., Watts, A. (eds) Encyclopedia of Biophysics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35943-9_607-1

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  • DOI: https://doi.org/10.1007/978-3-642-35943-9_607-1

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  • Print ISBN: 978-3-642-35943-9

  • Online ISBN: 978-3-642-35943-9

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