title: Context-independent, temperature-dependent helical propensities for amino acid residues.
abstract: Assigned from data sets measured in water at 2, 25, and 60 degrees C containing (13)C=O NMR chemical shifts and [theta](222) ellipticities, helical propensities are reported for the 20 genetically coded amino acids, as well as for norvaline and norleucine. These have been introduced by chemical synthesis at central sites within length-optimized, spaced, solubilized Ala(19) hosts. The resulting polyalanine-derived, quantitative propensity sets express for each residue its temperature-dependent but context-independent tendency to forego a coil state and join a preexisting helical conformation. At 2 degrees C their rank ordering is: P << G < H < C, T, N < S < Y, F, W < V, D < K < Q < I < R, M < L < E < A; at 60 degrees C the rank becomes: H, P < G < C < R, K < T, Y, F < N, V < S < Q < W, D < I, M < E < A < L. The DeltaDeltaG values, kcal/mol, relative to alanine, for the cluster T, N, S, Y, F, W, V, D, Q, imply that at 2 degrees C all are strong breakers: DeltaDeltaG(mean) = +0.63 +/- 0.11, but at 60 degrees C their breaking tendencies are dramatically attenuated and converge toward the mean: DeltaDeltaG(mean) = +0.25 +/- 0.07. Accurate modeling of helix-rich proteins found in thermophiles, mesophiles, and organisms that flourish near 0 degrees C thus requires appropriately matched propensity sets. Comparisons are offered between the temperature-dependent propensity assignments of this study and those previously assigned by the Scheraga group; the special problems that attend propensity assignments for charged residues are illustrated by lysine guest data; and comparisons of errors in helicity assignments from shifts and ellipticity data show that the former provide superior precision and accuracy.
authors.affiliation: Department of Chemistry, Room 6-433, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Moreau
authors.forename: Christian R
authors.initials: CR
authors.lastname: Schubert
authors.forename: Khaled A
authors.initials: KA
authors.lastname: Nasr
authors.forename: Marianna
authors.initials: M
authors.lastname: Török
authors.forename: Justin S
authors.initials: JS
authors.lastname: Miller
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Kennedy
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Kemp
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013696:Temperature
chemical_list: D000596:Amino Acids; D010455:Peptides; C019529:polyalanine
references.citation: J Am Chem Soc. 2005 Feb 16;127(6):1690-704
references.pmid: 15701003
references.citation: Protein Sci. 1994 May;3(5):843-52
references.pmid: 8061613
references.citation: Biochemistry. 1994 Jul 19;33(28):8604-9
references.pmid: 8031795
references.citation: Biochemistry. 2002 Jun 25;41(25):8152-61
references.pmid: 12069608
references.citation: J Mol Biol. 1998 Nov 20;284(1):173-91
references.pmid: 9811549
references.citation: Biophys Chem. 2002 Dec 10;101-102:255-65
references.pmid: 12488006
references.citation: Adv Protein Chem. 2005;72:199-226
references.pmid: 16581378
references.citation: J Mol Biol. 1995 Jan 20;245(3):297-308
references.pmid: 7844818
references.citation: J Mol Biol. 1991 May 20;219(2):135-7
references.pmid: 2038048
references.citation: Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7821-5
references.pmid: 1502201
references.citation: J Am Chem Soc. 2005 Dec 7;127(48):16961-8
references.pmid: 16316242
references.citation: J Am Chem Soc. 2001 Oct 24;123(42):10245-54
references.pmid: 11603974
references.citation: Protein Sci. 1996 Dec;5(12):2623-37
references.pmid: 8976571
references.citation: Protein Sci. 1995 Jul;4(7):1305-14
references.pmid: 7670373
references.citation: J Am Chem Soc. 2003 Feb 5;125(5):1203-20
references.pmid: 12553823
references.citation: J Mol Biol. 1994 Jan 14;235(2):600-24
references.pmid: 8289284
references.citation: Biochemistry. 1990 Aug 7;29(31):7133-55
references.pmid: 2207096
references.citation: Fold Des. 1997;2(1):23-33
references.pmid: 9080196
references.citation: J Am Chem Soc. 2002 Feb 13;124(6):945-62
references.pmid: 11829602
references.citation: Biopolymers. 1990;30(1-2):107-20
references.pmid: 2224046
references.citation: Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4930-5
references.pmid: 10220396
references.citation: Macromolecules. 1974 Jul;7(4):459-67
references.pmid: 4418767
references.citation: Biopolymers. 1992 Dec;32(12):1675-7
references.pmid: 1472650
references.citation: Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11337-40
references.pmid: 8248249
references.citation: Biopolymers. 2001;60(5):366-80
references.pmid: 12115147
references.citation: J Am Chem Soc. 2006 Jun 28;128(25):8227-33
references.pmid: 16787087
references.citation: Proc Natl Acad Sci U S A. 1991 Jun 15;88(12):5317-20
references.pmid: 2052608
references.citation: Nature. 1990 Mar 15;344(6263):268-70
references.pmid: 2314462
references.citation: Biochemistry. 1993 Jul 13;32(27):7048-53
references.pmid: 8334134
references.citation: Science. 1990 Nov 2;250(4981):669-73
references.pmid: 2237416
references.citation: Biophys Chem. 2002 Dec 10;101-102:281-93
references.pmid: 12488008
references.citation: Trends Biochem Sci. 1999 Feb;24(2):77-83
references.pmid: 10098403
references.citation: Methods Enzymol. 1994;239:363-92
references.pmid: 7830591
references.citation: PLoS Comput Biol. 2007 Mar 23;3(3):e52
references.pmid: 17381236
references.citation: J Mol Biol. 1991 Nov 20;222(2):311-33
references.pmid: 1960729
references.citation: OMICS. 2005 Winter;9(4):391-9
references.pmid: 16402896
references.citation: Biopolymers. 1997 Apr 15;41(5):495-509
references.pmid: 9095674
references.citation: Methods Enzymol. 1998;295:26-41
references.pmid: 9750212
references.citation: Protein Sci. 1993 Oct;2(10):1604-11
references.pmid: 8251935
references.citation: Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):2026-30
references.pmid: 2000410
references.citation: Biochemistry. 1997 Sep 9;36(36):10923-9
references.pmid: 9283083
references.citation: Curr Opin Struct Biol. 1998 Feb;8(1):101-6
references.pmid: 9519302
references.citation: J Am Chem Soc. 2002 Feb 13;124(6):934-44
references.pmid: 11829601
references.citation: Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):10962-6
references.pmid: 7902575
references.citation: Biochemistry. 2001 Jan 16;40(2):305-9
references.pmid: 11148022
references.citation: Proc Natl Acad Sci U S A. 1989 Jul;86(14):5286-90
references.pmid: 2748584
references.citation: Science. 1990 Nov 2;250(4981):646-51
references.pmid: 2237415
references.citation: Biopolymers. 2009 May;91(5):311-20
references.pmid: 19117030