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: - 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 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 - 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 GroEL/GroES chaperonin system facilitates protein folding through a complex cycle involving the capture and encapsulation of substrate proteins. We study the change in the microenvironment felt by substrate proteins as a result of GroEL structural transformations and the effect of peptide binding on the GroEL apical domain binding site and on the peptide. Microenvironment changes due to GroEL structural transformations during the cycle are studied 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. This flexibility is reduced upon peptide binding, as shown by the reduced capacity of these two helices to establish hydrogen bonds with water. Charged residues at both ends of these helices, Lys 242, Glu 257, and Arg 268, are likely to play a significant role in peptide unbinding. Their destabilizing effect on the peptide-chaperonin interaction is shown by the reduced hydration compared to the unbound state and the formation of unstable hydrogen bonds to the peptide. These observations are supported by the reduction in surface area of Lys 242 and Glu 257 during the chaperonin cycle. The peptide, which is in a random coil conformation in solution, is forced to adopt a hairpin structure upon binding to apical domain. 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. The beta-hairpin fold mechanism of a 9-residue peptide is studied through direct folding simulations in explicit water at native folding conditions. Self-guided molecular dynamics (SGMD) simulations have revealed a series of beta-hairpin folding events. For the first time, we successfully observed two-state protein folding phenomena. During these simulations, the peptide folds repeatedly into a major cluster of b-hairpin structures, which agree well with NMR experimental observations. These direct observation of the peptide folding at atomic detail provide us many clues of protein folding mechanism. We find hydration interaction plays a signigicant role in mediating protein folding. It is hydration confinement makes b-hairpin the only energetically favored structure for this peptide to fold.