Computational studies in protein folding and enzymes engineering involved in bioethanol production

Abstract

This project aims to continue the research that has been developed at IBILCE in the area of theoretical models in molecular biological physics, with emphasis on computational methods. Problems in the area of molecular biological physics have great complexity, and simplified models play an important role in understanding these systems. Such models have served as fundamental tools, from which more elaborate issues can be developed. In this project, the problems to be addressed through simplified models can be divided into three areas: (1) Protein folding, focusing on fundamental questions in the area. The topics covered are: understanding of the diffusion coefficient in the representation of folding, the effects of frustration, hydrophobicity and topology in the folding process, and visualization of the folding funnel. (2) Study of the enzymes involved in the production of bioethanol, in a theoretical and experimental collaboration. We use coarse-grained models in the study of the mechanisms of thermophilic enzymes 1XXN, 1IGO and 2JEN. We will optimize the thermostability of these enzymes {\sl in silico}, we will suggest site-directed mutations to be tested experimentally. We also use simplified models to investigate enzyme activity variations due to conformational changes in the protein domains. (3) Other topics in biological physics involving external collaborators. These include: statistical mechanics applications in bioinformatics and information processing, and the study of ribosome dynamics. (AU)