Alanine-based peptides containing polar residues presumably favour α-helical structure entropically

References

• Ingwall , R.T. , Scheraga , H.A. , Lotan , N. , Berger , A. and Katchalski , E. 1968 . Conformational studies of poly-l-alanine in water . Biopolymers , 6 : 331 – 368 .
   PubMed Web of Science ®Google Scholar
• Marqusee , S. , Robbins , V.H. and Baldwin , R.T. 1989 . Unusually stable helix formation in short alanine-based peptides . Proc. Natl Acad. Sci. USA , 86 : 5286 – 5290 .
   PubMed Web of Science ®Google Scholar
• Sugiyama , H. and Noda , H. 1970 . Stability of the helical conformation of random l-alanine-l-lysine copolymers in aqueous solution . Biopolymers , 9 : 459 – 469 .
   Google Scholar
• Song , K. , Stewart , J.M. , Fesinmeyer , M. , Andersen , N.H. and Simmerling , C. 2008 . Structural insights for designed alanine-rich helices: Comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation . Biopolymers , 89 : 747 – 760 .
   PubMed Web of Science ®Google Scholar
• Vila , J.A. , Ripoll , D.R. and Scheraga , H.A. 2000 . Physical reasons for the unusual α-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides . Proc. Natl Acad. Sci. USA , 97 : 13075 – 13079 .
   PubMed Web of Science ®Google Scholar
• García , A.E. and Sanbonmatsu , K.Y. 2002 . α-Helical stabilization by side chain shielding of backbone hydrogen bonds . Proc. Natl Acad. Sci. USA , 99 : 2782 – 2787 .
   PubMed Web of Science ®Google Scholar
• O'Neil , K.T. and DeGrado , W.F. 1990 . A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids . Science , 250 : 646 – 651 .
   PubMed Web of Science ®Google Scholar
• Lyu , P.C. , Liff , M.I. , Marky , L.A. and Kallenbach , N.R. 1990 . Side chain contributions to the stability of alpha-helical structure in peptides . Science , 250 : 669 – 673 .
   PubMed Web of Science ®Google Scholar
• Creamer , T.P. and Rose , G.D. 1992 . Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities . Proc. Natl Acad. Sci. USA , 89 : 5927 – 5941 .
   Google Scholar
• Creamer , T.P. and Rose , G.D. 1994 . α-Helix-forming propensities in peptides and proteins . Proteins , 19 : 85 – 97 .
   PubMed Web of Science ®Google Scholar
• Marqusee , S. and Baldwin , R.L. 1987 . Helix stabilization by Glu− ···Lys+ salt bridges in short peptides of de novo design . Proc. Natl Acad. Sci. USA , 84 : 8898 – 8902 .
   PubMed Web of Science ®Google Scholar
• Shoemaker , K.R. , Fairman , R. , Schultz , D.A. , Robertson , A.D. , York , E.J. , Stewart , J.M. and Baldwin , R.L. 1989 . Side-chain interactions in the C-peptide helix: Phe 8···His 12+ . Biopolymers , 29 : 1 – 11 .
   Google Scholar
• Merutka , G. and Stellwagen , E. 1991 . Effect of amino acid ion pairs on peptide helicity . Biochemistry , 30 : 1591 – 1594 .
   Google Scholar
• Lopez , M.M. , Chin , D.-H. , Baldwin , R.L. and Makhatadze , G.I. 2002 . The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation . Proc. Natl Acad. Sci. USA , 99 : 1298 – 1302 .
   Google Scholar
• Padmanabhan , S. , Marqusee , S. , Ridgeway , T. , Laue , T.M. and Baldwin , R.L. 1990 . Relative helix-forming tendencies of nonpolar amino acids . Nature , 344 : 268 – 270 .
   PubMed Web of Science ®Google Scholar
• Luo , P. and Baldwin , R.L. 1999 . Interaction between water and polar groups of the helix backbone: An important determinant of helix propensities . Proc. Natl Acad. Sci. USA , 96 : 4930 – 4935 .
   PubMed Web of Science ®Google Scholar
• Ando , T. , Meguro , T. and Yamato , I. 2002 . Development of an atomistic Brownian dynamics algorithm with implicit solvent model for long time simulation . J. Comput. Chem. Jpn , 1 : 115 – 122 .
   Google Scholar
• Ando , T. , Meguro , T. and Yamato , I. 2003 . Multiple time step Brownian dynamics for long time simulation of biomolecules . Mol. Simulat. , 29 : 471 – 478 .
   Web of Science ®Google Scholar
• Ando , T. , Meguro , T. and Yamato , I. 2004 . A new implicit solvent model for Brownian dynamics simulation: Solvent-accessible surface area dependent effective charge model . J. Comput. Chem. Jpn , 3 : 129 – 136 .
   Google Scholar
• Ando , T. and Yamato , I. 2005 . Free energy landscapes of two model peptides: α-helical and β-hairpin peptides explored with Brownian dynamics simulation . Mol. Simulat. , 31 : 683 – 693 .
   Web of Science ®Google Scholar
• Kim , W. , Itoh , T. , Yamato , I. and Ando , T. 2007 . Development of an implicit membrane model for Brownian dynamics simulation . J. Comput. Chem. Jpn , 6 : 253 – 262 .
   Google Scholar
• Torrie , G.M. and Valleau , J.P. 1977 . Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling . J. Comput. Phys. , 23 : 187 – 199 .
   Web of Science ®Google Scholar
• Roux , B. 1995 . The calculation of the potential of mean force using computer simulations . Comput. Phys. Commun. , 91 : 275 – 282 .
   Web of Science ®Google Scholar
• Duan , Y. , Wu , C. , Chowdhury , S. , Lee , M.C. , Xiong , G.M. , Zhang , W. , Yang , R. , Cieplak , P. , Luo , R. , Lee , T. , Caldwell , J. , Wang , J.M. and Kollman , P. 2003 . A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations . J. Comput. Chem. , 24 : 1999 – 2012 .
   PubMed Web of Science ®Google Scholar
• Weiner , S.J. , Kollman , P.A. , Case , D.A. , Singh , U.C. , Ghio , C. , Alagona , G. , Profeta , S. Jr and Weiner , P. 1984 . A new force field for molecular mechanical simulation of nucleic acids and proteins . J. Am. Chem. Soc. , 106 : 765 – 784 .
   Web of Science ®Google Scholar
• Eisenberg , D. and McLachlan , A.D. 1986 . Solvation energy in protein folding and binding . Nature , 319 : 199 – 203 .
   PubMed Web of Science ®Google Scholar
• Hasel , W. , Hendrickson , T.F. and Still , W.C. 1988 . A rapid approximation to the solvent accessible surface areas of atoms . Tetrahed. Comput. Methodol. , 1 : 103 – 116 .
   Web of Science ®Google Scholar
• Wesson , L. and Eisenberg , D. 1992 . Atomic solvation parameters applied to molecular dynamics of proteins in solution . Protein Sci. , 1 : 227 – 235 .
   PubMed Web of Science ®Google Scholar
• Gelin , B.R. and Karplus , M. 1979 . Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment . Biochemistry , 18 : 1256 – 1268 .
   PubMed Web of Science ®Google Scholar
• Kabsch , W. and Sander , C. 1983 . Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features . Biopolymers , 22 : 2577 – 2637 .
   PubMed Web of Science ®Google Scholar
• Taylor , J.W. , Greenfield , N.J. , Wu , B. and Privalov , P.L. 1999 . A calorimetric study of the folding-unfolding of an α-helix with covalently closed N and C-terminal loops . J. Mol. Biol. , 291 : 965 – 967 .
   Google Scholar
• Richardson , J.M. , McMahon , K.W. , MacDonald , C.C. and Makhatadze , G.I. 1999 . MEARA sequence repeat of human CstF-64 polyadenylation factor is helical in solution. A spectroscopic and calorimetric study . Biochemistry , 38 : 12869 – 12875 .
   PubMedGoogle Scholar
• Scholtz , J.M. , Marqusee , S. , Baldwin , R.L. , York , E.J. , Stewart , J.M. , Santoro , M. and Bolen , D.W. 1991 . Calorimetric determination of the enthalpy change for the α-helix to coil transition of an alanine peptide in water . Proc. Natl Acad. Sci. USA , 88 : 2854 – 2858 .
   Google Scholar
• Chou , P.Y. and Scheraga , H.A. 1970 . Calorimetric measurement of enthalpy change in the isothermal helix-coil transition of poly-l-lysine in aqueous solution . Biopolymers , 10 : 657 – 680 .
   Google Scholar
• Jas , G.S. and Kuczera , K. 2004 . Equilibrium structure and folding of a helix-forming peptide: Circular dichroism measurements and replica-exchange molecular dynamics simulations . Biophys. J. , 87 : 3786 – 3798 .
   PubMed Web of Science ®Google Scholar
• Platzer , K.E.B. , Ananthanarayanan , V.S. , Andreatta , R.H. and Scheraga , H.A. 1972 . Helix-coil stability constants for the naturally occurring amino acids in water. IV. Alanine parameters from random poly(hydroxypropylglutamine-co-l-alanine) . Macromolecules , 5 : 177 – 187 .
   Web of Science ®Google Scholar
• Nymeyer , H. and García , A.E. 2003 . Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent . Proc Natl Acad. Sci. USA , 100 : 13934 – 13939 .
   PubMed Web of Science ®Google Scholar
• Yang , A.S. and Honig , B. 1995 . Free energy determinants of secondary structure formation: I. α-Helices . J. Mol. Biol. , 252 : 351 – 365 .
   PubMed Web of Science ®Google Scholar