engleski

Computational biophysics of macromolecules: protein-protein interactions in a crowded cell

Computational modeling of biomolecular structure and dynamics has become an indispensible aid in our efforts to understand biological events on the molecular level. In this talk, I will focus on several aspects of using computational approaches to study protein-protein interactions. Direct non-covalent protein-protein interactions underlie most of biological functional activity on the molecular level. A binding event between two proteins typically consists of two stages: 1) a diffusional, non-specific search of the binding partners for each other, and 2) specific recognition of the compatible contact surfaces followed by complex-formation. Despite significant progress in studying these processes, a number of open questions remain. What are the exact mechanisms of the specific recognition of binding surfaces? How do the partners find each other in the crowded and interaction-rich cellular environment? What is the role of co-localization in binding and what are the mechanisms that lead to it? In this talk, I will present several recent results obtained using structural modeling, molecular dynamics simulations and advanced computational techniques to address these questions. In particular, I will focus on: 1) the question of binding specificity in protein-protein interactions [1], and 2) the role of specific and non-specific aspects, most notably protein surface hydrophilicity, in protein localization [2, 3]. [1] Wlodarski T & Zagrovic B (2010) PNAS 106, 46, 19346-19351 [2] Hlevnjak M, Zitkovic G & Zagrovic B (2010) PLoS ONE, 5, 6, e11169 [3] Awile O, Krisko A, Sbalzarini IF & Zagrovic B (2010) PloS Computational Biology, in press

protein-protein interactions; molecular dynamics; hydrophilicity

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