Understanding Protein Folding Using Markov State Models

  • Vijay S. PandeEmail author
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 797)


Understanding how proteins assemble into their final shapes (or “fold”) has been a grand challenge of computational biology for decades. MSM methods have allowed, for the first time, the direct simulation of how proteins fold on the microsecond to 10’s of millisecond timescale, yielding novel insight into the process.


Beta Sheet Markov State Model Simulate Protein Folding Slow Timescale Millisecond Timescale 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Beauchamp KA, Lin YS, Das R, Pande VS (2012) Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. J Chem Theory Comput 8(4):1409–1414 PubMedCrossRefGoogle Scholar
  2. 2.
    Beauchamp KA, McGibbon R, Lin YS, Pande VS (2012) Simple few-state models reveal hidden complexity in protein folding. Proc Natl Acad Sci USA 109(44):17,807–17,813 CrossRefGoogle Scholar
  3. 3.
    Bowman GR, Beauchamp KA, Boxer G, Pande VS (2009) Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 131(12):124,101 CrossRefGoogle Scholar
  4. 4.
    Bowman GR, Pande VS (2010) Protein folded states are kinetic hubs. Proc Natl Acad Sci USA 107(24):10,890–10,895 CrossRefGoogle Scholar
  5. 5.
    Bowman GR, Voelz VA, Pande VS (2011) Atomistic folding simulations of the five-helix bundle protein (685). J Am Chem Soc 133(4):664–667 PubMedCrossRefGoogle Scholar
  6. 6.
    Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS (2011) Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. J Am Chem Soc 133(45):18,413–18,419 CrossRefGoogle Scholar
  7. 7.
    Morcos F, Chatterjee S, McClendon CL, Brenner PR, Lopez-Rendon R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA (2010) Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Comput Biol 6(12):e1001, 015 CrossRefGoogle Scholar
  8. 8.
    Noe F, Schutte C, Vanden-Eijnden E, Reich L, Weikl TR (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci USA 106(45):19,011–19,016 CrossRefGoogle Scholar
  9. 9.
    Voelz VA, Bowman GR, Beauchamp K, Pande VS (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc 132(5):1526–1528 PubMedCrossRefGoogle Scholar
  10. 10.
    Voelz VA, Jager M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS (2012) Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. J Am Chem Soc 134(30):12,565–12,577 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Stanford UniversityStanfordUSA

Personalised recommendations