Institute for Complex Systems - Sapienza - CNR

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ISC Sapienza Physics of Biopolymers Protein functional dynamics

Protein functional dynamics

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All those movements and structural rearrangements which proteins undergo in their active state are generally referred to as functional dynamics since they are believed to be dependent on protein physiological functions. A quantitative characterization of mechanisms intertwining structure, chemistry, and dynamics with functions represent a challenge in molecular biology. For this reason normal mode analysis (NMA) has been a widely applied technique for reconstructing conformational changes of proteins from the knowledge of native structures.

Our activity aims to investigate the predictability of normal modes on the salient features of the dynamics even in regimes near folding transitions with the purpose to understand whether physiological-temperature NMA is justified at least in proteins with cooperative folding. We suggest how to identify several modes in order to eliminate the unpredictable temperature dependence of single-mode contributions to protein fluctuations.

PDZ domains are suitable candidates to test functional dynamics as they are typical examples of binding motifs mediating the formation of protein-protein assemblies in cells. Their main function is to bind C-terminals of selected proteins that are recognized through specific sequence in their carboxyl end.

PDZ binding is associated with a deformation of the native structure and is responsible for dynamical changes in regions not in direct contact with the target. PDZ domain and its target peptide (blu)

We investigate how this deformation is related to the harmonic dynamics of the PDZ structure and show that one low-frequency collective normal mode, characterized by the concerted movements of different secondary structures, is involved in the binding process. Our results suggest that even minimal structural changes are responsible for communication between distant regions of the protein, in agreement with recent NMR experiments.
This a clear example of how collective normal modes are able to characterize the relation between function and dynamics of proteins, but also provide indications on the precursors of binding/unbinding events.

The influence of native state topology on thermodynamics and dissociation kinetics for a PDZ/peptide complex can be studied via molecular dynamics simulations based on a coarse-grained description of PDZ domains. Our native-centric approach neglects chemical details but incorporates the basic structural information to reproduce the coupling between protein dynamics and binding. The interest outcome is that, at physiological temperatures, the unbinding of a peptide from the PDZ domain becomes increasingly diffusive rather than thermally activated as a consequence of the significant reduction of the free energy barrier with temperature. In turn, this results in a significant slowing down of the process of 2 orders of magnitude with respect to the conventional Arrhenius extrapolation from low-temperature calculations.

These methods allow a detailed analysis of a typical unbinding event based on the rupture times of single peptide-PDZ contacts and shed further light on the dissociation mechanism providing a coherent picture of the relation between function and dynamics in PDZ and other small binding domains.


[1] R. Burioni, D. Cassi, F. Cecconi and A. Vulpiani, "Topological Thermal Instability and Length of Proteins", Proteins: Struct. Funct. Bioinf. 55 529 (2004).

[2] P. De-Los-Rios, F. Cecconi, A. Grignoli-Pretre, G. Dietler, O. Michielin, F. Piazza and B. Juanico,
"Functional Dynamics of PDZ Binding Domains: A Normal-Mode Analysis" Biophys. J. 89, 14 (2005).

[3] F. Cecconi, F. Piazza and P. De-Los-Rios, "Diffusion-limited unbinding of small peptides" J. Phys. Chem B 111, 11057 (2007).