Organisers

• Emanuele Paci (University of Leeds)
• Michele Vendruscolo (University of Cambridge)

Supports

 SimBioMa

 CECAM

Description

Proteins are biological macromolecules that have evolved to perform nearly all the important tasks in the cell, such as enzymatic activity, transmission of signals, control of trafficking, etc [1]. In order to carry out these functions, proteins usually undergo a spontaneous process of folding in which they self-organize into specific structures [2]. The energy landscape picture of protein folding [3] has helped enormously to understand the determinants of the behaviour of proteins. The possibility to extend our knowledge to the nonnative sections of the energy landscape is now a challenge that can result in a general theory for protein folding and misfolding. It is also increasingly evident that an important biological role is played by non-native conformations of proteins, which include those populated by intrinsically unfolded peptides and proteins, as well as denatured states, molten globules and other partially unfolded conformations. Such conformations have a fundamental interest because provides snapshots along the folding and misfolding reaction pathways and are thus crucial to benchmark folding theories and simulations. Moreover, such conformations have a direct biological and medical interest as they may also act as precursors for aggregation processes that can give rise to species that are non-functional and may be toxic. Recent advances in experimental techniques, including protein engineering and NMR, have made it possible to obtain information at the atomic level about the nature of these partially folded states. Several recent applications (see e.g. [4, 5, 6, 7]) have demonstrated that such a wealth of experimental information can be converted into structural data, although this remain challenging because of the heterogeneous nature of the partially folded states and because of the difficulty in translating the measured quantities in microscopic terms. Other innovative biochemical and spectroscopic methods, such as single molecule fluorescence [8, 9, 10], atomic force microscopy [11] and optical tweezers [12] have recently provided information on the folding and unfolding of individual molecules, thus providing crucial information to benchmark simulation, mainly through unfolding simulations, since timescales for folding are still exceedingly large for present computers. Further, application of novel spectroscopic techniques to peptides has provided previously unavailable measurement of the dynamics of peptides, such as the rate of contact formation which occurs on the timescale of nanoseconds [13, 14]. These measurements allow for the first time the direct comparison of "brute force" or "distributed computing" simulations with the experiment. The quality of force fields, as well as the importance of an explicit treatment of the solvent can now be assessed with high accuracy.

Scientific Objectives

We aim at bringing together the leading experimentalist and theoreticians to discuss about recent developments in both experimental and computational protein science and the further progress that can be envisaged if the cooperation becomes stronger [15, 16]. The central theme that we intend to develop is to identify common goals and a unified picture of the folding and misfolding mechanisms, as well to identify fields in which only a stronger interaction between experiment and simulation can provide a real advancement. A clear example, which relates to the main topic of research of the organizers in the past few years, is the description of partially folded, misfolded and unfolded states where experimental (mainly NMR) measurements can be used as experimental restraints or as validation of the results of simulations. As more experimental information become available, the efficiency and the resolution of the picture increases and allow the reliable prediction of independent experimental observable [17]. Another example is that of using single molecule experiments to benchmark molecular models and simplified approaches to folding, such as those involving structure-based models, or of using simulation to test hypotheses based solely on the analysis of the experimental results (see e.g., Ref [11] and [18]). This proposal aims at establishing guidelines about relevant topics, and we will encourage the participants to bring new cases based on their most recent experimental and simulation results. The proposed workshop is a follow-up of a successful workshop we organized in Lyon in 2003. The previous "Protein folding: Bringing theory and experiment closer together" workshop was aimed at creating an environment to facilitate the debate on protein folding between two communities that use different tools and languages to address the problem of understanding the mechanisms by which certain amino acid sequences fold to a unique functional structure or, failing to do so, give rise to ordered aggregates. In the past two years the field has enormously advanced, and many of the participants of the workshop that we organised in 2003 played a major role in these developments. By considering the way in which the field of protein science has developed in the last two years we now aim in particular at analysing critically new approaches in experimental and theoretical studies on protein misfolding and on the structure and dynamics of non-native states of proteins.

The principal goal of the workshop is to bring together the leading experts in computational studies and in experimental techniques in protein folding and misfolding. We aim at stimulating a debate among the participants on new approaches for probing the dynamical properties of peptides and proteins, and the structures that they populate under non-native conditions, or off-equilibrium. We particularly aim at exploring circumstances in which computer simulations can provide information not accessible to experiments. Computational issues Computational studies of protein behaviour represent a formidable challenge on two major fronts. Firstly, macromolecular systems of biological interest are extremely large (thousands or even millions of atoms) and the interesting events take place on very long timescales (millisecond and beyond). Secondly, force fields are needed that are capable of reproducing the stable states of the systems of interest as local minima. Many of the theoreticians that we invited have played a central role in developing methods to deal with these issues. In addition, we have selected experimentalists that have shown particular interest in engaging in technical debates about the improvement of computational methods, e.g., for the determination of both native and non-native protein structures from spectroscopic data. We believe that this type of meeting will generate new insights into the way to make significant advances in computational methods for studying protein structure and dynamics.

References

[1] Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K, and Walter, P. 2002. Molecular Biology of the Cell. (Garland Publishing, New York).
[2] Fersht, A. R. 1999. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. (W. H. Freeman & Co., New York, USA).
[3] Wolynes, P. G, Onuchic, J. N, and Thirumalai, D. 1995. Navigating the folding routes Science 267:1619­1620.
[4] Vendruscolo, M, Paci, E, Dobson, C. M, and Karplus, M. 2001. Three key residues form a critical contact network in a protein folding transition state Nature 409:641­645.
[5] Choy, W. Y and Forman-Kay, J. D. 2001. Calculation of ensembles of structures representing the unfolded state of an SH3 domain J. Mol. Biol. 308:1011­1032.
[6] Vendruscolo, M, Paci, E, Karplus, M, and Dobson, C. M. 2003. Structures and relative free energies of partially folded states of proteins Proc. Natl. Acad. Sci. USA 100:14817­14821.
[7] Paci, E, Lindorff-Larsen, K, Karplus, M, Dobson, C. M, and Vendruscolo, M. 2005. Transition state contact orders correlate with protein folding rates J. Mol. Biol. 352:495­500.
[8] Schuler, B, Lipman, E. A, and Eaton, W. A. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy Nature 419:743­747.
[9] Lipman, E. A, Schuler, B, Bakajin, O, and Eaton, W. A. 2003. Single-molecule measurement of protein folding kinetics Science 301:1233­1235.
[10] Rhoades, E, Cohen, M, Schuler, B, and Haran, G. 2004. Two-state folding observed in individual protein molecules J. Am. Chem. Soc. 126:14686­14687.
[11] Fernandez, J. M and Li, H. 2004. Force-clamp spectroscopy monitors the folding trajectory of a single protein Science 303:1674­1678.
[12] Cecconi, C, Shank, E. A, Bustamante, C, and Marqusee, S. 2005. Direct observation of the three-state folding of a single protein molecule Science 309:2057­2060.
[13] Krieger, F, Fierz, B, Bieri, O, Drewello, M, and Kiefhaber, T. 2003. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding J. Mol. Biol. 332:265­274.
[14] Krieger, F, Moglich, A, and Kiefhaber, T. 2005. Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains J. Am. Chem. Soc. 127:3346­ 3352.
[15] Fersht, A. R and Daggett, V. 2002. Protein folding and unfolding at atomic resolution Cell 108:573­582.
[16] Vendruscolo, M and Paci, E. 2003. Protein folding: Bringing theory and experiment closer together Curr. Opin. Struct. Biol. 13:82­87.
[17] Lindorff-Larsen, K, Best, R. B, Depristo, M. A, Dobson, C. M, and Vendruscolo, M. 2005. Simultaneous determination of protein structure and dynamics Nature 433:128­132.
[18] Best, R. B and Hummer, G. 2005. Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein" Science 308:498.