George RoseSummaryAffiliation: Johns Hopkins University Country: USA Publications
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A backbone-based theory of protein foldingGeorge D Rose
T C Jenkins Department of Biophysics, The Johns Hopkins University, Jenkins Hall, 3400 North Charles Street, Baltimore, MD 21218, USA
Proc Natl Acad Sci U S A 103:16623-33. 2006..Then, under folding conditions, the resultant fold is selected from a limited repertoire of structural possibilities, each corresponding to a distinct hydrogen-bonded arrangement of alpha-helices and/or strands of beta-sheet...
Are proteins made from a limited parts list?Nicholas C Fitzkee
Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
Trends Biochem Sci 30:73-80. 2005..Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture?..- Assessing the solvent-dependent surface area of unfolded proteins using an ensemble modelHaipeng Gong
T C Jenkins Department of Biophysics, The Johns Hopkins University, Jenkins Hall, 3400 North Charles Street, Baltimore, MD 21218, USA
Proc Natl Acad Sci U S A 105:3321-6. 2008.... - Physical-chemical determinants of turn conformations in globular proteinsTimothy O Street
T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
Protein Sci 16:1720-7. 2007..These results provide a molecular explanation for the observation that reverse turns between elements of regular secondary can be classified into a small number of discrete conformations... - Sterics and solvation winnow accessible conformational space for unfolded proteinsNicholas C Fitzkee
T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
J Mol Biol 353:873-87. 2005..These disfavored conformations are usually absent from the coil library, and exceptions can be uniformly rationalized... - Secondary structure determines protein topologyPatrick J Fleming
TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
Protein Sci 15:1829-34. 2006..For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them... - A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA)Patrick J Fleming
Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
Protein Sci 14:111-8. 2005..We dedicate this paper to Frederic M. Richards... - Reassessing random-coil statistics in unfolded proteinsNicholas C Fitzkee
T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
Proc Natl Acad Sci U S A 101:12497-502. 2004..Despite this extreme degree of imposed internal structure, these ensembles have end-to-end distances and mean radii of gyration that agree well with random-coil expectations in all but two cases... - Recursive domains in proteinsTeresa Przytycka
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Protein Sci 11:409-17. 2002..The existence of a protein grammar has potential implications for both the mechanism of folding and the evolution of domains... - Building native protein conformation from highly approximate backbone torsion anglesHaipeng Gong
T. C. Jenkins Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
Proc Natl Acad Sci U S A 102:16227-32. 2005..Among these, the native topology is found with high frequency and can be identified as the cluster with the most favorable energy... - Hydrogen-bonded turns in proteins: the case for a recountNick Panasik
Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
Protein Sci 14:2910-4. 2005..Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure... - A molecular mechanism for osmolyte-induced protein stabilityTimothy O Street
T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Jenkins Hall, 3400 North Charles Street, Baltimore, MD 21218, USA
Proc Natl Acad Sci U S A 103:13997-4002. 2006..Taken together, these model-based results rationalize the dominant interactions observed in experimental studies of osmolyte-induced protein stabilization and denaturation... - Structures, basins, and energies: a deconstruction of the Protein Coil LibraryLauren L Perskie
TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
Protein Sci 17:1151-61. 2008..These three motifs in conjunction with alpha-helices, strands of beta-sheet, canonical beta-turns, and polyproline II conformers comprise approximately 90% of all protein structure... - Does secondary structure determine tertiary structure in proteins?Haipeng Gong
Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 2608, USA
Proteins 61:338-43. 2005..These linear strings can then be aligned and assessed by conventional sequence-comparison methods. We report that the mesostate sequence is sufficient to recognize a protein's family, superfamily, and fold with good fidelity... - Physical-chemical determinants of coil conformations in globular proteinsLauren L Perskie
T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
Protein Sci 19:1127-36. 2010..Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue... - The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDBNicholas C Fitzkee
T. C. Jenkins Department of Biophysics, Johns Hopkins Univeristy, Baltimore, Maryland 21218-2608, USA
Proteins 58:852-4. 2005..Additionally, several popular searches are stored and updated for immediate access. The library is a useful tool for exploring conformational propensities, turn motifs, and a recent model of the unfolded state... - Ab initio prediction of protein structure using LINUSRajgopal Srinivasan
Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
Proteins 47:489-95. 2002..llnl.gov). It should be emphasized that our use of the descriptor "ab initio" is unequivocal: the sole input into these simulations is the amino acid sequence... - Ab initio protein folding using LINUSRajgopal Srinivasan
Jenkins Deparment of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
Methods Enzymol 383:48-66. 2004 - Steric restrictions in protein folding: an alpha-helix cannot be followed by a contiguous beta-strandNicholas C Fitzkee
T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
Protein Sci 13:633-9. 2004..This straightforward conformational constraint has far-reaching consequences in organizing unfolded proteins and limiting the number of possible protein domains... - Local secondary structure content predicts folding rates for simple, two-state proteinsHaipeng Gong
Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
J Mol Biol 327:1149-54. 2003..Accordingly, it should be possible to utilize secondary structure prediction methods to predict folding rates from sequence alone... - Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assemblyHaipeng Gong
T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
Protein Sci 16:1515-21. 2007..Currently, the method has been applied successfully to five small proteins with simple topology. Although still under development, this approach offers promise for high-throughput NMR structure determination... - Methinks it is like a folding curveRajgopal Srinivasan
Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
Biophys Chem 101:167-71. 2002..Natl. Acad. Sci. USA 96 (1999) 14258-14263], and it is found in recent studies of both proteins and peptides. The imposition of even a modest bias would transform our assessment of the folding problem... - Do all backbone polar groups in proteins form hydrogen bonds?Patrick J Fleming
T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
Protein Sci 14:1911-7. 2005..Accordingly, the likelihood of finding an unsatisfied hydrogen bond in a protein is insignificant. This realization establishes a powerful rule for evaluating protein conformations... - Polyproline II structure in a sequence of seven alanine residuesZhengshuang Shi
Department of Chemistry, New York University, New York, NY 10003, USA
Proc Natl Acad Sci U S A 99:9190-5. 2002..New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue... - Polyproline II helix is the preferred conformation for unfolded polyalanine in waterMihaly Mezei
Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA
Proteins 55:502-7. 2004..The use of explicit water allows us to capture and characterize these dynamic water bridges that form and dissolve during our simulations... 
Structure and energetics of the hydrogen-bonded backbone in protein foldingD Wayne Bolen
Department of Biochemistry and Molecular Biology and The Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, TX 77555 1052, USA
Annu Rev Biochem 77:339-62. 2008..This reciprocal relationship establishes the essential link between protein thermodynamics and the protein's hydrogen-bonded backbone structure...- Lifting the lid on helix-cappingGeorge D Rose
Nat Chem Biol 2:123-4. 2006 - Getting to know uGeorge D Rose
Adv Protein Chem 62:xv-xxi. 2002
Research Grants
- SELF RECOGNITION IN GLOBULAR PROTEINSGeorge Rose; Fiscal Year: 2001..The chain is represented by simplified geometry and folds under the influence of an extremely simple energy function. Current results are encouraging. ..