Computational studies on protein folding and applications in the study of enzymes involved in bioethanol production

Abstract

This project aims to continue the research being developed at IBILCE in the area of theoretical molecular biological physics, with emphasis on computational methods. The problems in the area of molecular biological physics have great complexity. History shows that minimalist models play an important role in understanding these complex systems. Such models have served as fundamental tools, from which more elaborate issues could 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 in one and two dimensions, the effects of frustration, hydrophobicity and topology in folding process, and visualization and quantitative descriptors of the folding funnel. (2) Study of the enzymes involved in the production of bioethanol, in a collaboration between theoretical and experimental groups. More specifically, we study the mechanisms associated with two thermophilic enzymes (xynalase and laminarinase). We also use coarse-grained models in combination with SAXS data to investigate the modulation of enzymatic activity by conformational changes of protein domains. (3) Other topics in biological physics involving external collaborators. These include: electron transfer in proteins, statistical mechanics applications in bioinformatics and chemometrics studies. Computational resources are requested, especially a computer cluster, and means (transportation and per diem) to carry out research with external collaborators of the group. (AU)