Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions

Protein Science

Volumn 3, Issue 5, 1994, Pages 843-852

  Chakrabartty, Avijit ^a   Kortemme, Tanja ^a,b   Baldwin, Robert L ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

alanine based peptides; helix capping; helix propensities; helix stability; modified Lifson Roig theory; peptide helices; protein folding

Indexed keywords

ALANINE; AMINO ACID; SYNTHETIC PEPTIDE;

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CIRCULAR DICHROISM; COMPUTER PROGRAM; ENTROPY; HYDROGEN BOND; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY;

ALANINE; AMINO ACID SEQUENCE; AMINO ACIDS; CIRCULAR DICHROISM; COMPARATIVE STUDY; DRUG DESIGN; DRUG STABILITY; HYDROGEN BONDING; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0028222235     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.5560030514     Document Type: Article

References (55)

1. Helix‐coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamine‐co‐L‐proline)
2. Charged histidine affects alpha‐helix stability at all positions in the helix by interacting with backbone charges
3. Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59
4. The role of hydrogen bonds in protein folding and protein association
5. Structural basis of amino acid alpha helix propensity
6. Derivative spectroscopy applied to tyrosyl chromophores. Studies on ribonuclease, lima bean inhibitor, and pancreatic trypsin inhibitor
7. Helix‐coil transition of the isolated amino terminus of ribonuclease
8. Side chain‐backbone hydrogen bonding contributes to helix stability in peptides derived from an alpha‐helical region of carboxypeptidase A
9. Comparison of amino acid helix propensities (s‐values) measured in different experimental systems
10. Helix capping propensities in peptides parallel those found in proteins
11. Aromatic side‐chain contribution to far‐ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities
12. Large differences in the helix propensities of alanine and glycine
13. Side‐chain entropy opposes alpha‐helix formation but rationalizes experimentally determined helix‐forming propensities
14. Determination of free energies of N‐capping in alpha‐helices by modification of the Lifson‐Roig helix‐coil theory to include N‐ and C‐capping
15. Defining solution conformations of small linear peptides
16. Stabilization of alpha‐helical structures in short peptides via end capping
17. The helix‐coil transition in heterogeneous peptides with specific side‐chain interactions: Theory and comparison with CD spectral data
18. Differential helix propensity of small apolar side chains studied by molecular dynamics simulations
19. Alpha‐helix stability in proteins. II. Factors that influence stability at an internal position
20. Probing the stability of a partly folded apomyoglobin intermediate by site‐directed mutagenesis
21. The effect of a single aspartate on helix stability at different positions in a neutral alanine‐based peptide
22. CD and 1H‐NMR studies on the conformational properties of peptide fragments from the C‐terminal domain of thermolysin
23. The helical s constant for alanine in water derived from template‐nucleated helices
24. Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size
25. On the theory of helix‐coil transitions in biopolymers
26. Alpha helix stability and the native state of myoglobin
27. Crystal structure of a synthetic triple‐stranded alpha‐helical bundle
28. Side chain contributions to the stability of alpha‐helical structure in peptides
29. Capping interactions in isolated alpha helices: Position‐dependent substitution effects and structure of a serine‐capped peptide helix
30. Unusually stable helix formation in short alanine‐based peptides
31. Effect of central‐residue replacements on the helical stability of a monomeric peptide
32. A thermodynamic scale for the helix‐forming tendencies of the commonly occurring amino acids
33. Relative helix‐forming tendencies of nonpolar amino acids
34. Residue helix parameters obtained from dichroic analysis of peptides of defined sequence
35. Modulation of the helical stability of a model peptide by ionic residues
36. Effect of alanine substitution on the stability of myoglobin
37. Helix signals in proteins
38. Thermodynamic parameters of helix‐coil transitions in polypeptide chains
39. Helix‐coil theories: A comparative study of finite length polypeptides
40. Solvents, interfaces and protein structure
41. Amino acid preferences for specific locations at the ends of alpha helices
42. Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson‐Roig equation
43. An N‐terminal fragment of barnase has residual helical structure similar to that in a refolding intermediate
44. Effect of alanine versus glycine in alpha‐helices on protein stability
45. Alpha‐helix stability in proteins. I. Empirical correlations concerning substitution of side‐chains at the N and C‐caps and the replacement of alanine by glycine or serine at solvent‐exposed surfaces
46. The mechanism of alpha‐helix formation by peptides
47. Calorimetric determination of the enthalpy change for the alpha‐helix to coil transition of an alanine‐peptide in water
48. The energetics of ion‐pair and hydrogen‐bonding interactions in a helical peptide
49. Parameters of helix‐coil transition theory for alanine‐based peptides of varying chain lengths in water
50. The contribution of residue ion pairs to the helical stability of a model peptide
51. Helix‐coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly[(hydroxybutyl)glutamine‐co‐L‐histidine]
52. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation
53. Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G‐ and H‐helices of myoglobin
54. Theory of the phase transition between helix and random coil in polypeptide chains
55. A single‐stranded amphipathic alpha‐helix in aqueous solution: Design, structural characterization, and its application for determining alpha‐helical propensities of amino acids