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Sampling Kinetic Protein Folding Pathways using All-Atom Models

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Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1

Part of the book series: Lecture Notes in Physics ((LNP,volume 703))

Abstract

This chapter summarizes several computational strategies to study the kinetics of two-state protein folding using all atom models. After explaining the background of two state folding using energy landscapes I introduce common protein models and computational tools to study folding thermodynamics and kinetics. Free energy landscapes are able to capture the thermodynamics of two-state protein folding, and several methods for efficient sampling of these landscapes are presented. An accurate estimate of folding kinetics, the main topic of this chapter, is more difficult to achieve. I argue that path sampling methods are well suited to overcome the problems connected to the sampling of folding kinetics. Some of the major issues are illustrated in the case study on the folding of the GB1 hairpin.

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  1. van ’t Ho. Institute for Molecular Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands

    P.G. Bolhuis

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  1. Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi, 213/A, 41100, Modena, Italy

    Mauro Ferrario Professor

  2. Dipartimento di Fisica, INFN, Università di Roma La Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy

    Giovanni Ciccotti Professor

  3. Institut für Physik, Universität Mainz, Staudinger Weg 7, 55128, Mainz, Germany

    Kurt Binder Professor

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Bolhuis, P. (2006). Sampling Kinetic Protein Folding Pathways using All-Atom Models. In: Ferrario, M., Ciccotti, G., Binder, K. (eds) Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Lecture Notes in Physics, vol 703. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-35273-2_11

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