engleski

Studying protein‐protein interactions using computer simulations: from specific effects to protein ecology

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. How do the partners find each other in the crowded and interaction‐rich cellular environment? What is the role of colocalization in binding and what are the mechanisms that lead to it? What are the exact mechanisms of the specific recognition of binding surfaces? In this talk, I will present several recent results obtained using structural modeling, molecular dynamics simulations and advanced computational techniques such as distributed computing on the world‐wide‐web to address these questions. In particular, I will focus on: 1) the question of binding specificity in ubiquitin binding, and 2) the role of intrinsically unstructured regions in polypeptides in protein localization.

protein-protein interactions; simulations

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