The Computational Biophysics Section studies problems of biological significance using several theoretical techniques: molecular dynamics, molecular mechanics, modeling, ab initio analysis of small molecule structure, and molecular graphics. These techniques are applied to a wide variety of macromolecular systems.? ? Dr. Larkin's research involves the application of Quantum Mechanical/Molecular Modeling(QM/MM) and Molecular Dynamics simulation techniques to enzymatic reaction pathways. Specifically, Dr. Larkin is investigating reaction mechanisms of boronic acid inhibitors of Beta Lactamase enzymes that are responsible for increased resistance to penicillin antibiotics.? ? Dr. Woodcocks research, in collaboration with Membrane Biophysics Section, involves high level ab initio computations in vacuum and with the IEFPCM implicit solvent modelon 5-hydroxy-methyl-tetrahydropyran to investigate the effects of water on the exocyclic torsional surface. Rotamer populations evaluated from the omega (C-C-C-O), theta (C-C-C-O) solvent surface agree almost quantitatively with experimental values for the closely related methyl-alpha-D-4-deoxyglucopyranoside. Potentials of mean force obtained from the two surfaces show substantial solvent stabilization of the TG (omega = 180 plus or minus 60 degrees) rotamer and the barriers at omega = 120 and 240 degrees, but solvent destabilization at the cis barrier (omega = 0 degrees). Natural bond orbital analyses indicate that energetics of these effects are largely explained by overstabilization of the vacuum GT (omega = 60 plus or minus 60 degrees) and GG (omega = 300 plus or minus 60 degrees) rotomers. Solvent stabilization of theta conformations provides entropic stabilization.? ? Dr. Woodcock and Edward O'Brien have been working on a comprehensive study to identify the strengths and weaknesses with advanced sampling techniques for simulations. More specifically, they are using standard Replica Exchange (REX) methodology in combination with multiplexed REX (MREX) to examine the effectiveness of self-guided Langevin dynamics (SGLD). This work is being carried out on both all-atom systems (i.e. a model beta-hairpin peptide) and a coarse grain representation of the ACBP protein. Preliminary results are very encouraging and should allow us to define a new paradigm for performing enhanced sampling simulations. ? ? Dr. Damjanovic is studying the structural consequences of ionization of internal groups in proteins. The work is performed in collaboration with experimental group of Prof. Bertrand Garcia-Moreno (JHU). Through experiments it is known that some variants of staphylococcal nuclease (SN) in which an ionizable group is buried in the protein interior exhibit conformational rearrangements triggered by pH induced ionization of internal groups. Through a relatively novel technique for advanced sampling, i.e., Self-Guided Langevin Dynamics (SGLD) simulation method, changes in secondary structure that are consistent with experimental findings are found. The simulations suggest that ionization of internal groups enhances water penentration which, in certain cases, can lead to unfolding of the protein core.? ? Dr. Damjanovic is also studying the regulatory interactions in nitrogen regulatory protein C (NtrC). NtrC can exist in two conformations: inactive and active. Binding of a phosphate group stabilizes the active form. SGLD simulations of this protein indicate large conformational heterogeneity in the region involved in structural transition, and suggest that the transition pathway involves partial unfolding. Continuum electrostatics calculations and SGLD simulations suggest that phosphorylation may result in charging of a nearby His residue, which in turn may further modulate the conformation of a key helix.? ? Dr. Okurs research involves examining the structural and energetic basis for diabetes. In collaboration with Professor Michael Weiss of Case Western Reserve University School of Medicine, NMR experiments on a single chain insulin analog (SCI-57, wild type insulin chains A and B linked with a 6-residue connecting peptide, PDB_ID: 2JZQ) were investigated and we observed a significant increase in stability with respect to wild type insulin. We speculate that the connecting peptide has a dampening effect on the fluctuations between the two chains. We have been investigating this stabilizing effect via molecular dynamics simulations of wild type and single chain insulin using CHARMM. Initial results are consistent with the hypothesis that the single chain analog has more defined structure than the wild type insulin. Detailed analysis of the fluctuations as a probable cause for increased stability is still ongoing.? ? Mr. O'Brien's research has focused on the development and application of the Molecular Transfer Model (MTM). The MTM is a statistical mechanical method for accurately predicting osmolyte, denaturant, and pH effects on a protein's thermodynamic properties by combining ergodic molecular simulations with experimentally measured, or theoretically computed, transfer free energies of individual amino acids. The MTM has been shown to be in quantitative agreement with a number of published experiments. The MTM is the first, and only example in which molecular simulations have been capable of studying equilibrium folding and unfolding as a function of osmolyte type, osmolyte concentration, and pH. All previous computational studies used temperature to examine folding/unfolding. For this reason the MTM is useful because it can predict quantities that can be directly compared to experiment and it offers a molecular level interpretation of these phenomena based on the simulation structures it utilizes.? ? We have applied the MTM to understand protein denatured state properties under varying solution conditions. We found that denatured state collapse occurs as urea concentration decreases and that residual secondary structure persists even at high denaturant concentrations. We also applied the MTM to examine how accurate FRET (Forestor resonance energy transfer) inferred denatured state properties are. Using measurements of the FRET efficiency as a function of denaturant concentration, in conjunction with simple polymer models (such as the Gaussian chain model), a number of experimental research groups have inferred denatured properties such as the radius-of-gyration and persistance length. Using the MTM, we found that error associated with these inferred properties can be as large as 25%, suggesting that this approach results only in qualitative estimates of denatured state properties.? ? Another area of research Mr. O'Brien is focused on is confinement effects on protein folding, due to its relevance to a number of problems in biology and biotechnology. We have examined the stability of different helix-forming sequences upon confinement to a carbon nanotube. We showed that the interplay of several factors that include sequence, solvent conditions, the strength of nanotube-peptide interactions, and the nanotube diameter determines confinement-induced stability of helicies. Our results provide a framework for interpreting a number of experiments involving the structure formation of peptides in the ribosome tunnel as well as transport of biopolymers across nanotubes.
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