Molecular Dynamics Simulations Of Biological Macromolecu

Heart, Lung, And Blood Institute

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Abstract

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. Specific projects applied to molecules of biomedical interest uses molecular dynamics simulations to predict function or structures of peptides and proteins. Such projects include: - Molecular dynamics of native and mutant vnd/NK-2 homeodomain--DNA complexes - Protein structure stabilization and activity in human rhinovirus - Modeling of Acanthamoeba Myosin II wildtype leucine zipper segment - The study of the catalytic mechanism of D5-3-Ketosteroid Isomerase using QM/MM methods - The study of the catalytic mechanism of N-acetyltransferase using QM/MM methods - The study of the catalytic mechanism of Chorismate Mutase using QM/MM methods - Tracing the catalytic pathway of b-lactam hydrolysis Basic research is underway to provide a better understanding of macromolecular systems. The projects include studies of: - Examining chaperonin-mediated protein folding - NMR Shielding Tensor calculations - Lipid bilayer gel phase simulations - Investigating the environmental dependence of nucleic acid structure - Free energy calculations on the leucine zipper domain of yeast transcription factor GCN4 - Simulations of myoglobin and lysozyme crystals and solutions - Protein folding simulation studies - Solvation Free energy force of protein systems - Ligand binding dynamics - Microscopic details of rotational diffusion of perylene in organic solvents The annealing action of the GroEL/GroES chaperonin system is the result of changes in the microenvironment felt by substrate proteins. We analyzed the GroEL structural transformations during the cycle by examining known structures of GroEL (T state), GroEL-7ATP (R) and GroEL-GroES-7ADP (R"). We find that large structural changes occur even prior to GroES binding, and are associated mostly with residues in the apical domain. Multiple sequence alignments show a strong conservation of the chemical character, rather than the residue type, of residues important for the chaperonin functions. We predict that mutations in several strongly conserved charged residues (Lys 262, Gly 252, and Asp 253) lead to reduced efficiency of the annealing action. Molecular dynamics simulations of a solvated apical domain, liganded to a 12-mer polypeptide or unliganded, yield information about the solvent effects and the chaperonin structural dynamics. Upon polypeptide binding, water is completely removed from the peptide binding site. The apical domain manifests a high flexibility at a pair of parallel helices, which execute a transverse translation to accommodate the peptide. Protein folding mediated by chaperonin molecules is studied using computer simulations. Our focus is on the GroEL-GroES chaperonin complex of the Escherichia coli, for which the associated structures are known. High-performance scientific computing methods are used, such as coarse-grained and all-atom descriptions of proteins in conjunction with the state-of-the-art CHARMM simulation program. These studies elucidate the effect of chaperones on the protein structure, the mechanism of the chaperonin system, and the timescales in the chaperonin cycle. Ab initio calculations of NMR shielding tensors were performed for comparison with experimental studies for 1H and 15N nuclei. There was little correlation between calculated and experimental values for amide 1H, and role of factors such as basis set, and isotope effect were investigated as potential causes for the discrepancy. An 15N study is currently underway, using the 1H results as a starting point. Free energy calculations on the leucine zipper domain (GCN4-p1) of the yeast transcription factor GCN4 using Molecular Dynamics (MD) under physiological conditions and continuum models. The leucine zipper motif is a parallel left-handed supercoil composed of two a-helices. It is estimated that the native (parallel) alignment is energetically more stable than the non-native antiparallel alignment where electrostatic energies contribute significantly in the overall energetic picture of both orientation as well as to the preference of the parallel vs the antiparallel orientation. Modeling of Acanthamoeba Myosin II wildtype leucine zipper segment using molecular dynamics. This type of analysis has been extended to the modeling of acanthamoeba myosin II wildtype leucine zipper segment using molecular dynamics which examines free energy of solvation and helical packing, while evaluating different alignments of the myosin II wildtype leucine zipper segment. The results suggest likely mechanism for previously unexplained protein mutation behavior. Protein mechanisms are studied by examining different possible pathways in which the mechanism can proceed. This employs quantum mechanical/molecular mechanical techniques using our double link atom method with gaussian blur of MM charges. We have carried out QM/MM simulations N-acetyltransferase to determine whether a proton of the primary amine of serotonin is transferred via a water channel or His120 during catalysis. Similarly, we have examined D5-3-Ketosteroid Isomerase. This enzyme catalyzes the isomerization of the 5,6 double bond of D5-3-ketosteroid isomerase to the 4,5 position. In particular, examine h-bonding interactions between substrate D5-3-ketosteroid and the key residues, Tyr14 and Asp99 at both QM/MM and MM level. Studying protein folding mechanism through SGMD simulation with all-atom model and explicit water. We have successfully observed two-state protein folding phenomena. This method have proved useful in the rapid exploration of conformational space without resorting to higher temperature simulations, or other forcing potentials.