Search Results - "Scheraga, H. A."

Dynamic and conformational switching in proteins by Scheraga, H.A., Rackovsky, S.

“…Using bioinformatic methods for treating protein dynamics, developed in earlier work, we study the relationship between sequence mobility and dynamics in…”
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A third blind test of crystal structure prediction by Day, G. M., Motherwell, W. D. S., Ammon, H. L., Boerrigter, S. X. M., Della Valle, R. G., Venuti, E., Dzyabchenko, A., Dunitz, J. D., Schweizer, B., Van Eijck, B. P., Erk, P., Facelli, J. C., Bazterra, V. E., Ferraro, M. B., Hofmann, D. W. M., Leusen, F. J. J., Liang, C., Pantelides, C. C., Karamertzanis, P. G., Price, S. L., Lewis, T. C., Nowell, H., Torrisi, A., Scheraga, H. A., Arnautova, Y. A., Schmidt, M. U., Verwer, P.

“…Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project…”
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Tracking the Mechanism of Fibril Assembly by Simulated Two-Dimensional Ultraviolet Spectroscopy by Lam, A. R, Rodriguez, J. J, Rojas, A, Scheraga, H. A, Mukamel, S

“…Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by the accumulation of plaque deposits in the human brain. The main component of these…”
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Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests by Ołdziej, S., Czaplewski, C., Liwo, A., Chinchio, M., Nanias, M., Vila, J. A., Khalili, M., Arnautova, Y. A., Jagielska, A., Makowski, M., Schafroth, H. D., Kaźmierkiewicz, R., Ripoll, D. R., Pillardy, J., Saunders, J. A., Kang, Y. K., Gibson, K. D., Scheraga, H. A.

“…Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The…”
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Sequence‐specific dynamic information in proteins by Scheraga, H. A., Rackovsky, S.

“…We examine the local and global properties of the average B‐factor, 〈B〉, as a residue‐specific indicator of protein dynamic characteristics. It has been shown…”
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Physical Reasons for the Unusual α -Helix Stabilization Afforded by Charged or Neutral Polar Residues in Alanine-Rich Peptides by Vila, Jorge A., Ripoll, Daniel R., Scheraga, H. A.

“…We have carried out conformational energy calculations on alanine-based copolymers with the sequence Ac-AAAAAXAAAA-NH2in water, where X stands for lysine or…”
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field by Chinchio, M, Czaplewski, C, Liwo, A, Ołdziej, S, Scheraga, H. A

“…Many proteins contain disulfide bonds that are usually essential for maintaining function and a stable structure. Several algorithms attempt to predict the…”
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Oxidative Folding of Proteins by Narayan, Mahesh, Welker, Ervin, Wedemeyer, William J, Scheraga, Harold A

“…The oxidative folding of proteins is reviewed and illustrated with bovine pancreatic ribonuclease A (RNase A). The mutual effects of conformational folding and…”
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Monte Carlo-Minimization Approach to the Multiple-Minima Problem in Protein Folding by Li, Zhenqin, Scheraga, Harold A.

“…A Monte Carlo-minimization method has been developed to overcome the multiple-minima problem. The Metropolis Monte Carlo sampling, assisted by energy…”
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The protein folding problem: global optimization of the force fields by Scheraga, H A, Liwo, A, Oldziej, S, Czaplewski, C, Pillardy, J, Ripoll, D R, Vila, J A, Kazmierkiewicz, R, Saunders, J A, Arnautova, Y A, Jagielska, A, Chinchio, M, Nanias, M

“…The evolutionary development of a theoretical approach to the protein folding problem, in our laboratory, is traced. The theoretical foundations and the…”
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Coupling of Conformational Folding and Disulfide-Bond Reactions in Oxidative Folding of Proteins by Welker, Ervin, Wedemeyer, William J, Narayan, Mahesh, Scheraga, Harold A

“…The oxidative folding of proteins consists of conformational folding and disulfide-bond reactions. These two processes are coupled significantly in…”
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Accessible Surface Areas as a Measure of the Thermodynamic Parameters of Hydration of Peptides by Ooi, Tatsuo, Oobatake, Motohisa, Nemethy, George, Scheraga, Harold A.

“…A method is described for the inclusion of the effects of hydration in empirical conformational energy computations on polypeptides. The free energy of…”
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Structural Determinants of Oxidative Folding in Proteins by Welker, Ervin, Narayan, Mahesh, Wedemeyer, William J., Scheraga, Harold A.

“…A method for determining the kinetic fate of structured disulfide species (i.e., whether they are preferentially oxidized or reshuffle back to an unstructured…”
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Distributions of Intramolecular Distances in the Reduced and Denatured States of Bovine Pancreatic Ribonuclease A. Folding Initiation Structures in the C-Terminal Portions of the Reduced Protein by Navon, Amiel, Ittah, Varda, Landsman, Pavel, Scheraga, Harold A, Haas, Elisha

“…The purpose of this investigation is to characterize the reduced state of RNase A (r-RNase A) in terms of (i) intramolecular distances, (ii) the sequence of…”
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Global Optimization of Clusters, Crystals, and Biomolecules by Wales, David J., Scheraga, Harold A.

“…Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design…”
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United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials by Liwo, A., Kaźmierkiewicz, R., Czaplewski, C., Groth, M., Ołdziej, S., Wawak, R. J., Rackovsky, S., Pincus, M. R., Scheraga, H. A.

“…Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci., 2, 1697 (1993)], a cumulant expansion of the average free…”
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A Role for Intermolecular Disulfide Bonds in Prion Diseases? by Welker, Ervin, Wedemeyer, William J., Scheraga, Harold A.

“…The key event in prion diseases seems to be the conversion of the prion protein PrP from its normal cellular isoform (PrPC) to an aberrant "scrapie" isoform…”
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Proline Isomerization in Bovine Pancreatic Ribonuclease A. 1. Unfolding Conditions by Juminaga, D, Wedemeyer, W. J, Scheraga, H. A

“…The slow fluorescence unfolding phase of bovine pancreatic ribonuclease A is studied by stopped-flow kinetics and site-directed mutagenesis of tyrosines to…”
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Molecular simulation study of cooperativity in hydrophobic association by CZAPLEWSKI, CEZARY, RODZIEWICZ-MOTOWIDŁO, SYLWIA, LIWO, ADAM, RIPOLL, DANIEL R., WAWAK, RYSZARD J., SCHERAGA, HAROLD A.

“…To investigate the cooperativity of hydrophobic interactions, the potential of mean force of two- and three-molecule methane clusters in water was determined…”
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Tyrosyl Interactions in the Folding and Unfolding of Bovine Pancreatic Ribonuclease A:  A Study of Tyrosine-to-Phenylalanine Mutants by Juminaga, D, Wedemeyer, W. J, Garduño-Júarez, R, McDonald, M. A, Scheraga, H. A

“…Three tyrosine-to-phenylalanine mutants of ribonuclease A (Y25F, Y92F, and Y97F) are investigated for their enzymatic activities, molecular stabilities, and…”
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