References for Research Highlights

Hierarchy

• George D. Rose (1979) Hierarchic Organization of Domains in Globular Proteins. J. Mol. Biol. 134: 447-470.
• Arthur M. Lesk and George D. Rose (1981) Folding Units in Globular Proteins. Proc. Nat. Acad. Sci. USA 78: 4304-4308.
• Thomas J. Yuschok and George D. Rose (1983) Hierarchic Organization of Globular Proteins: A Control Study. Int. J. Peptide Protein Res. 21: 479-484.
• George D. Rose (1985) Automatic Identification of Domains in Globular Proteins. Methods in Enzymology, Academic Press, New York. 115: 430-440.
• Robert L. Baldwin and George D. Rose (1999) Is protein folding hierarchic? II. Folding Intermediates and Transition States. Tibs 24: 77-83.
• Robert L. Baldwin and George D. Rose (1999) Is protein folding hierarchic? I. Local Structure and Peptide Folding. Tibs 24: 26-33.
• Nicholas C. Fitzkee, Patrick J. Fleming, Haipeng Gong, Nicholas Panasik Jr, Timothy O. Street and George D. Rose (2005) Are proteins made from a limited parts list? TiBS 30:73-80.
• George D. Rose, Patrick J. Fleming, Jayanth R. Banavar and Amos Maritan (2006) A backbone-based theory of protein folding. Proc. Nat. Acad. Sci. 103:16623-16633.

Hydrogen-bonding

• Michael J. Behe, Eaton E. Lattman and George D. Rose (1991) Protein folding: the native fold determines packing, but does packing determine the native fold? Proc. Nat. Acad. Sci., 88: 4195-4199.
• Douglas F. Stickle, Leonard G. Presta, Ken A. Dill and George D. Rose (1992) Hydrogen bonding in globular proteins. J. Mol. Biol. 226: 1143-1159.
• George D. Rose and Richard Wolfenden (1993) Hydrogen bonding, the hydrophobic effect, packing, and protein folding. Ann. Rev. Biophysics and Biological Structure 22: 381-415.
• Nick Panasik Jr., Patrick J. Fleming and George D. Rose (2005) Hydrogen-bonded turns in proteins: The case for a recount. Protein Science 14:2910-2914.
• Patrick J. Fleming and George D. Rose (2005) Do all backbone polar groups in proteins form hydrogen bonds? Protein Science 14:1911-1917.
• Haipeng Gong, Patrick J. Fleming and George D. Rose (2005) Building native protein conformation from highly approximate backbone torsion angles. Proc. Nat. Acad. Sci. 102:16227-16232.
• George D. Rose, Patrick J. Fleming, Jayanth R. Banavar and Amos Maritan (2006) A backbone-based theory of protein folding. Proc. Nat. Acad. Sci. 103:16623-16633.
• Timothy O. Street, D. Wayne Bolen and George D. Rose (2006) A molecular mechanism for osmolyte-induced protein stability. Proc Nat. Acad. Sci. 103: 13997-14002.
• D. Wayne Bolen and George D. Rose (2008) Structure and energetics of the hydrogen-bonded backbone in protein folding. Annu. Rev. Biochem. 77:339-362.

Hydrophobicity

• George D. Rose (1978) Prediction of Chain Turns in Globular Proteins on a Hydrophobic Basis. Nature 272: 586-590.
• George D. Rose and Siddhartha Roy (1980) The Hydrophobic Basis of Packing in Folded Proteins. Proc. Nat. Acad. Sci. USA 77: 4643-4647.
• George D. Rose, Lila Gierasch and John A. Smith (1985) Turns in Peptides and Proteins. Advances in Protein Chemistry, Academic Press, New York. 37: 1-109.
• George D. Rose, Ari R. Geselowitz, Glenn J. Lesser, Richard H. Lee and Micheal H. Zehfus (1985) Hydrophobicity of Amino Acid Residues in Globular Proteins. Science 229: 834-838.
• George D. Rose (1987) Protein Hydrophobicity: Is It The Sum of Its Parts? PROTEINS: Structure, Function, and Genetics 2: 79-80.
• George D. Rose (1988) Hydrophobicity Profiles, Computational Molecular Biology, ed. A.M. Lesk, 198-204, Oxford University Press, Oxford.
• George D. Rose and Jonathan E. Dworkin (1989) The Hydrophobicity Profile in Prediction of Protein Structure and the Principles of Protein Conformation, ed. G. Fasman, 625-633, Plenum Pub. Corp., New York.
• Glenn J. Lesser and George D. Rose (1990) Hydrophobicity of amino acid subgroups in proteins. PROTEINS: Structure, Function, and Genetics 8: 6-13.
• Patrick J. Fleming, Nicholas C. Fitzkee, Mihaly Mezei, Rajgopal Srinivasan and George D. Rose (2005) A novel method reveals that solvent water favors polyproline II over β-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). Protein Science 14: 111-118.

The Ω-Loop

• Jacquelyn Leszczynski and George D. Rose (1986) Loops in Globular Proteins. Science 234: 849-855.
• Micheal H. Zehfus and George D. Rose (1986) Compact Units in Proteins. Biochemistry 25: 5759-5765.
• Jacquelyn Fetrow, Micheal H. Zehfus and George D. Rose (1988) Protein Folding: New Twists. Bio/Technology 6: 167-171.

Helix capping

• Leonard G. Presta and George D. Rose (1988) Helix Signals in Proteins. Science, 240: 1632-1641.
• Edwin T. Harper and George D. Rose (1993) Helix stop signals in proteins and peptides: the capping box. Biochemistry 32: 7605-7609.
• Jeffrey W. Seale, Rajgopal Srinivasan, and George D. Rose (1994) Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices. Protein Science 3: 1741-1745.
• Rajeev Aurora, Rajgopal Srinivasan and George D. Rose (1994) Rules for α-helix termination by glycine. Science 264: 1126-1130.
• George D. Rose, Rajeev Aurora and Rajgopal Srinivasan (1995) Possible exceptions to rules for α-helix termination by glycine. Science 269: 1451-1452. [Technical Comments]
• Rajeev Aurora, Trevor P. Creamer, Rajgopal Srinivasan, and George D. Rose (1997) Local interactions in protein folding: lessons from the α-helix J. Biol. Chem. 272: 1413-1416.
• Rajeev Aurora and George D. Rose (1998) Helix capping, Protein Science 7: 21-38.

Turns in proteins

• George D. Rose and Jack Seltzer (1977) A New Algorithm for Finding the Peptide Chain Turns in a Globular Protein. J. Mol. Biol. 113: 153-164.
• George D. Rose (1978) Prediction of Chain Turns in Globular Proteins on a Hydrophobic Basis. Nature 274: 586-590.
• George D. Rose, William B. Young and Lila M. Gierasch (1983) Interior Turns in Globular Proteins. Nature 304: 654-657.
• George D. Rose, Lila Gierasch and John A. Smith (1985) Turns in Peptides and Proteins. Advances in Protein Chemistry, Academic Press, New York. 37: 1-109.
• Nick Panasik Jr., Patrick J. Fleming and George D. Rose (2005) Hydrogen-bonded turns in proteins: The case for a recount. Protein Science 14:2910-2914.
• Timothy O. Street, Nicholas C. Fitzkee, Lauren L. Perskie and George D. Rose (2007) Physical-chemical determinants of turn conformations in globular proteins. Protein Science 16:1720-1727.

Secondary structure determines tertiary structure

• Teresa Przytycka, Rajeev Aurora, George D. Rose (1999) A Protein Taxonomy Based on Secondary Structure. Nature Structural Biology 6: 672-682.
• Haipeng Gong and George D. Rose (2005) Does secondary structure determine tertiary structure in proteins? Proteins 61:338-34
• Haipeng Gong, Patrick J. Fleming and George D. Rose (2005) Building native protein conformation from highly approximate backbone torsion angles. Proc. Nat. Acad. Sci. 102:16227-16232.
• Patrick J. Fleming, Haipeng Gong and George D. Rose (2006) Secondary structure determines protein topology. Protein Science 15:1828-1834.
• Haipeng Gong, Yang Shen and George D. Rose (2007) Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly. Protein Science 16:1515-1521.

Unfolded state

• Trevor P. Creamer, Rajgopal Srinivasan and George D. Rose (1995) Modeling unfolded states of peptides and proteins. Biochemistry 34: 16245-16250.
• Trevor P. Creamer, Rajgopal Srinivasan and George D. Rose (1997) Modeling unfolded states of peptides and proteins. II. Backbone solvent accessibility. Biochemistry 36: 2832-2835.
• Rohit V. Pappu, Rajgopal Srinivasan and George D. Rose (2000) The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc Nat. Acad. Sci. 97: 12565-12570.
• George D. Rose (2002) Getting to know U, in Unfolded Proteins, Advances in Protein Chemistry (G. Rose, ed.) 62:xv-xxi.
• Zhengshuang Shi, C. Anders Olson, George D. Rose, Robert L. Baldwin, and Neville R. Kallenbach (2002) Polyproline II structure in a sequence of seven alanine residues, Proc. Nat. Acad. Sci.i 99: 9190-9195.
• Rohit V. Pappu and George D. Rose (2002) A simple model for poly-proline II structure in unfolded states of alanine-based peptides. Protein Science 11: 2437-2455.
• Haipeng Gong, Daniel G. Isom, Ragjopal Srinivasan and George D. Rose (2003) Local secondary structure content predicts folding rates for simple two-state proteins. J. Mol. Biol. 327: 1150-1157.
• Nicholas C. Fitzkee and George D. Rose (2004) Steric restrictions in protein folding: an α-helix cannot be followed by a contiguous β-strand. Protein Science 13: 633-639.
• Mihaly Mezei, Patrick J. Fleming, Rajgopal Srinivasan and George D. Rose (2004) Polyproline II helix is the preferred conformation for unfolded polyalanine in water Proteins: Structure, Function and Bioinformatics 55: 502-507.
• Nicholas C. Fitzkee and George D. Rose (2004) Reassessing random-coil statistics in unfolded proteins. Proc. Nat. Acad. Sci. 101:12497-12502.
• Nicholas C. Fitzkee, Patrick J. Fleming, Haipeng Gong, Nicholas Panasik Jr, Timothy O. Street and George D. Rose (2005) Are proteins made from a limited parts list? TiBS 30:73-80.
• Patrick J. Fleming and George D. Rose (2005) Do all backbone polar groups in proteins form hydrogen bonds? Protein Science 14:1911-1917.
• Nicholas C. Fitzkee and George D. Rose (2005) Sterics and solvation winnow accessible conformational space for unfolded proteins. J. Mol. Biol. 353:873-887.
• George D. Rose, Patrick J. Fleming, Jayanth R. Banavar and Amos Maritan (2006) A backbone-based theory of protein folding. Proc. Nat. Acad. Sci. 103:16623-16633.
• Lauren L. Perskie, Timothy O. Street and George D. Rose (2008) Structures, basins and energies: A deconstruction of the Protein Coil Library. Protein Science 17:1151-1161.

Conformational entropy

• Trevor P. Creamer and George D. Rose (1992) Sidechain entropy opposes α-helix formation but rationalizes experimentally-determined helix-forming propensities. Proc. Nat. Acad. Sci.,U.S.A. 89: 5937-5941.
• Trevor P. Creamer and George D. Rose (1994) α-helix-forming propensities in proteins and peptides. Proteins: Structure, Function, and Genetics 19: 85-97.
• Rohit V. Pappu, Rajgopal Srinivasan and George D. Rose (2000) The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc Nat. Acad. Sci. 97: 12565-12570.
• Rajgopal Srinivasan and George D. Rose (2002) Methinks it like a folding curve, Biophysical Chemistry 101-102:167-171.
• Rohit V. Pappu and George D. Rose (2002) A simple model for poly-proline II structure in unfolded states of alanine-based peptides. Protein Science 11: 2437-2455.
• Nicholas C. Fitzkee and George D. Rose (2004) Reassessing random-coil statistics in unfolded proteins. Proc. Nat. Acad. Sci. 101:12497-12502.

Physical Basis of Secondary Structure

• Rajgopal Srinivasan and George D. Rose (1999) The physical basis of secondary structure in globular proteins. Proc Nat. Acad. Sci. 96: 14258-14263.
• Teresa Przytycka, Rajeev Aurora, George D. Rose (1999) A Protein Taxonomy Based on Secondary Structure, Nature Structural Biology 6: 672-682.
• Patrick J. Fleming, Nicholas C. Fitzkee, Mihaly Mezei, Rajgopal Srinivasan and George D. Rose (2005) A novel method reveals that solvent water favors polyproline II over β-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). Protein Science 14:111-118.
• Patrick J. Fleming and George D. Rose (2005) Do all backbone polar groups in proteins form hydrogen bonds? Protein Science 14:1911-1917.

LINUS

• Rajgopal Srinivasan and George D. Rose (1995) LINUS - A hierarchic procedure to predict the fold of a protein. Proteins: Structure, Function, and Genetics 22: 81-99.
• Rajgopal Srinivasan and George D. Rose (1999) The physical basis of secondary structure in globular proteins. Proc Nat. Acad. Sci. 96: 14258-14263.
• Rajgopal Srinivasan and George D. Rose (2002) Ab initio prediction of protein structure using LINUS, Proteins 47: 489-495.
• Rajgopal Srinivasan, Patrick J. Fleming and George D. Rose (2004) Ab initio protein folding using LINUS. Methods Enzymol. 383:48-66.

Polyproline II

• Rohit V. Pappu and George D. Rose (2002) A simple model for poly-proline II structure in unfolded states of alanine-based peptides. Protein Science 11: 2437-2455.
• Zhengshuang Shi, C. Anders Olson, George D. Rose, Robert L. Baldwin, and Neville R. Kallenbach (2002) Polyproline II structure in a sequence of seven alanine residues, Proc. Nat. Acad. Sci.i 99: 9190-9195.
• Mihaly Mezei, Patrick J. Fleming, Rajgopal Srinivasan and George D. Rose (2004) Polyproline II helix is the preferred conformation for unfolded polyalanine in water Proteins: Structure, Function and Bioinformatics 55: 502-507.
• Patrick J. Fleming, Nicholas C. Fitzkee, Mihaly Mezei, Rajgopal Srinivasan and George D. Rose (2005) A novel method reveals that solvent water favors polyproline II over β-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). Protein Science 14: 111-118.

RNA

• Venkatesh L. Murthy, Rajgopal Srinivasan, David E. Draper and George D. Rose (1999) A complete conformational map for RNA. J. Mol. Biol. 291: 313-327.
• Venkatesh L. Murthy and George D. Rose (2000) Is counterion delocalization responsible for collapse in RNA folding? Biochemistry 39: 14365-14370.
• Venkatesh L. Murthy and George D. Rose (2003) RNABase: an annotated database of RNA structures. Nucleic Acids Research 31: 502-504.