BCB faculty member in Biochemistry, Biophysics and Molecular Biology Department
- Email: email@example.com
- 3116 Molecular Biology Building
Expertise: Solution NMR of proteins
The research projects in my group are focused on the study of protein folding, design and evolution using solution Nuclear Magnetic Resonance spectroscopy and a variety of complementary biophysical methods. How does a protein fold into it specific tridimensional structure and evolve to perform a given biological function remain key questions in most modern day diseases. Especially when combined with high-pressure perturbation, NMR spectroscopy offers the opportunity to characterize protein free-energy landscapes at an atomic resolution.
Related projects include the study of intrinsically disordered proteins, the characterization of amyloid-type peptides and the development of coarse-grained methods for protein folding simulations.
Veterinary Microbiology and Preventive Medicine Department
2118 Vet Med
Research Focus & Interests
I am interested in the large scale analyses of proteins, genomes and metagenomes.
Metagenomics is the study of genomic material extracted directly from the environment. New sequencing technologies have enabled the study of whole populations of genomes taken from microbial communities in the field, as opposed to single species clonal cultures in the lab. Metagenomics offers a way to study how genomes evolve to cope with the microbial biotic and abiotic environments. Our lab helped developed a method to study the correlation between the human gut microbiota and gut gene expression. We are applying this method towards studying infant gut development the effect of gut microbes on human health and wellness.
Bacterial Genome Evolution: Gene blocks are a common occurrence in bacteria: these are genes which lie close together on the chromosome, and may participate in a common cellular or biochemical function. Operons are gene blocks whose member genes are co-transcribed. We have developed a new method to describe the evolution of operons and gene blocks in bacteria. We describe a small set of evolutionary events that can take place in gene block evolution, and count these events to create a new type of molecular clock that tells us how fast or how slow certain gene blocks may have evolved. We hope to learn how new funcitons are acquired by ensembles of genes such as these.
Function Prediction: genomics, proteomics and various other ``-omics'' inundate us with sequence and structure information, but the biological functions of those proteins in many cases still eludes us. Computational prediction of protein and gene function is a rapidly growing research field in bioinformatics . I am the co-organizer of the automated computational protein function prediction meetings: AFP. The AFP meetings bring together researchers to discuss various methods for protein function prediction. My personal interest in function prediction lies in predicting function from protein structure . We have recently started work on predicting gene function based on its genomic context in bacteria, using both genomic and metagenomic data towards that end.
For professional opportunities, and for more information, see my website.
Biochemistry, Biophysics and Molecular Biolgy
Topics of interest: Molecular models, Nucleic acids, Small molecules, Structures of proteins
Computational studies on the structures of proteins, nucleic acids, and small molecules, and their interactions. Overall the direction of his research has been to push toward the comprehension of the functions of large structures. Applications are sometimes made to develop molecular models and to select new drugs.
Protein Datamining is used to assess protein structures and their folding patterns. We have evaluated interactions from available structures and other experimental data. We developed a standard way to view interaction energies between residues, based on sets of protein structures. This approach led to useful ways to incorporate structural and hydrophobicity information into simulations.
Conformation Generation. We developed a new approach to enumerate protein lattice conformations with full efficiency. This is particularly important for determining native protein conformations, where the problem is akin to searching for a needle in a haystack, and random searches are largely ineffective. This new approach opens the way for the computer generation of much larger numbers of protein conformations.
Elastic models of Proteins. Large-domain motions of proteins are computed with simple inter-connected elastic models. These highly cohesive, cooperative models are most appropriate for considering the largest functional motions of proteins, which are necessarily independent of the structural details. Functional mechanisms for processing proteins or for protein machines can be developed. The methods lend themselves in straightforward ways to the investigation of the motions of extremely large biomolecular assemblages of more than 100,000 residues.