1) The problem of protein folding: The second genetic code is a code of the production of protein structure in which genetic information is expressed during the process of building complex and precise molecular structures. Deciphering the code involves studying the process of protein folding. Our research focuses on identification of intermediate situations of the folding process with an integrated approach based on genetic engineering, protein chemistry, and physical measurements using laser systems.
We study the role of nonlocal interactions in the control of the folding pathways in an ensemble of refolding protein molecules. Our current emphasis is on the study of the role of very effective nonlocal interactions in the early phases of the refolding transition.
We search for specific clusters of residues that form essential nonlocal interactions in order to create, in the long run, a typing of the sequence messages that appear in protein molecules and that are involved in the control of the folding pathways.
We study many other aspects of the protein-folding problem, such as: the effect of crowding, the order of appearance of secondary structure elements, the question of downhill versus barrier-crossing mechanisms, residual structures in the unfolded state, etc.
2) Dynamic mechanisms of structure and enzyme activity: I view enzyme molecules as 'nano-machines' which operate in the DH-DS plane in the direction of the chemical potential gradient. We are studying the rate of motion of chain elements, the correlation of such motions, effect of mutations, effect of ligand binding, crowding, and others. The research methods are based on various spectroscopic methods (CD, CPL, and ultra-fast fluorescence measurement).
3) Studies of the phenomenon of intrinsically unfolded proteins: Many proteins appear to have no well-defined native structure. Some of these are involved in neurodegenerative diseases. We are studying the problem of intrinsically unfolded proteins (IUPs) as models of partially unfolded protein molecules with the working hypothesis that these proteins are indeed folded, but with much flexibility. Our model is human a-synuclein and we are also studying it initial change of conformation upon transition to dimers or small oligomers, prior to fibrilization.
4) We are studying the conformational change of insulin upon binding to its receptor.
5) We are studying DNA bending in relation to specific sequences and to protein binding (collaboration with Prof. Mike Weiss of Case U.)
6) We have developed ultrafast time-resolved FRET methods which enable us to attack the above problems. We are now developing new instruments for measurements of 'double kinetics' using stopped flow system (ms resolution), laser T-jump system (ns time resolution), and P-jump (ms time resolution), as well as single-molecule fluorescence detection.