We have made significant progress in several areas related to protein dynamics, folding, and function. In a series of molecular dynamics simulations, we explored the structure and stability of Alzheimer's Abeta amyloid fibrils. Fibrils of Alzheimers amyloid-beta peptides are the major component of Alzheimers disease plaques. In our simulations, we found that fibril structures with different molecular topology consistently exhibit interdigitated side-chain packing, and present water channels solvating the interior D23/K28 salt bridges. At elevated temperatures, we observe the early phases of fibril dissociation as a loss of order in the hydrophilic loops connecting the hydrophobic beta-strands, and in the solvent-exposed N-terminal beta-sheets. The high stability of the C-terminal beta-sheets in the hydrophobic core of the fibrils indicates that they are are crucial to the dissociation/elongation of Abeta fibrils (Buchete and Hummer, Biophys. J., 2007).? ? By developing and applying a new method to study large-scale conformational changes, we gained important new insights into the structural dynamics of calmodulin (Chen and Hummer, J. Am. Chem. Soc. 2007). Calmodulin (CaM) is a calcium-sensing protein whose physiological function in gene regulation, cytoskeletal organization, muscle contraction, signal transduction, etc., requires large-scale conformational changes. Upon Ca2+ binding, the structures of the CaM domains change from a relatively compact, closed apo conformation to a more open holo conformation that partially exposes the hydrophobic interior of the protein. From our simulations emerged a three-state picture that reconciled a number of contradictory experimental findings: the three states include a folded state with apo structures (closed), an unfolded state, and a hololike state (open) which is rather floppy without bound Ca2+ and structurally less defined. An emerging question is whether this unfolded apo state has direct functional relevance, for example, in target peptide binding or as an intermediate in the Ca2+- induced apo-to-holo transition.? ? By adapting this methodology to coarse network representations of proteins, we were also able to gain insights into the conformational transitions of large motor proteins. In a collaboration with the group of Dr Brooks (NHLBI, NIH), we explored the conformational changes of kinesin and myosin (Zheng, Brooks, and Hummer, Proteins 2007) as they undergo the powerstroke transition. By following the transition path from a pre-powerstroke to a post-powerstroke state, we could identify the key residue contact formation and breaking events.? ? In collaboration with Dr Hurley (LMB, NIDDK, NIH), we studied the molecular machinery involved in endosomal protein sorting. The yeast Vps27/Hse1 complex and the homologous mammalian Hrs/STAM complex deliver ubiquitinated transmembrane proteins to the ESCRT endosomal-sorting pathway. The Vps27/Hse1 complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. The struxtures of the various components were solved by our experimental collaborators. We developed a computational formalism and energy functions to assemble the component structures into the full Vps27/Hse1 complex. Our coarse-grained Monte Carlo simulations of the Vps27/Hse1 complex on a membrane show how the complex binds cooperatively to lipids and ubiquitinated membrane proteins and acts as a scaffold for ubiquitination reactions (Prag et al, Dev. Cell 2007).? ? In collaboration with the group of Dr Tabak (NIDDK and NIDCR), we studied the dynamics involved in the transfer of N-acetylgalactosamine (GalNAc) from a nucleotide-sugar donor (UDP-GalNAc) to Ser/Thr residues of an acceptor substrate, as catalyzed by the protein ppGalNAcT-2 (Milac et al., J. Mol. Biol. 2007). Glycosyltransferases are a large family of enzymes involved in the biosynthesis of oligosaccharides, polysaccharides, and glycoconjugates. Our simulations accurately identified dynamically active regions of the protein ppGalNAcT-2, as previously revealed by the x-ray structures, and permitted a detailed, atomistic description of the conformational changes of loops near the active site and the characterization of the ensemble of structures adopted by the transferase complex on the transition pathway between the ligand-bound and ligand-free states.

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Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard (2009) Thermostat artifacts in replica exchange molecular dynamics simulations. J Chem Theory Comput 5:1393-1399
Best, Robert B; Hummer, Gerhard (2009) Biochemistry. Unfolding the secrets of calmodulin. Science 323:593-4
Kim, Young C; Hummer, Gerhard (2008) Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol 375:1416-33
Canagarajah, Bertram J; Hummer, Gerhard; Prinz, William A et al. (2008) Dynamics of cholesterol exchange in the oxysterol binding protein family. J Mol Biol 378:737-48
Tikhonova, Irina G; Best, Robert B; Engel, Stanislav et al. (2008) Atomistic insights into rhodopsin activation from a dynamic model. J Am Chem Soc 130:10141-9
Turjanski, Adrian Gustavo; Gutkind, J Silvio; Best, Robert B et al. (2008) Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol 4:e1000060
Kim, Young C; Tang, Chun; Clore, G Marius et al. (2008) Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci U S A 105:12855-60
Best, Robert B; Buchete, Nicolae-Viorel; Hummer, Gerhard (2008) Are current molecular dynamics force fields too helical? Biophys J 95:L07-9
Buchete, Nicolae-Viorel; Hummer, Gerhard (2008) Peptide folding kinetics from replica exchange molecular dynamics. Phys Rev E Stat Nonlin Soft Matter Phys 77:030902
Buchete, Nicolae-Viorel; Hummer, Gerhard (2008) Coarse master equations for peptide folding dynamics. J Phys Chem B 112:6057-69

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