A helix initiation motif, XLLRA, is stabilized by hydrogen bond, hydrophobic and van der Waals interactions

Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology

Volumn 1478, Issue 1, 2000, Pages 39-50

  Chang, Ding Kwo ^a   Cheng, Shu Fang ^a   Yang, Shyh Haur ^a  

^a INSTITUTE OF CHEMISTRY   (Taiwan)

Author keywords

Helix initiation; Hydrogen bond; N capping; Van der Waals interaction

Indexed keywords

SYNTHETIC PEPTIDE;

ARTICLE; CIRCULAR DICHROISM; HYDROGEN BOND; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ARGININE; ASPARAGINE; CIRCULAR DICHROISM; HIV ENVELOPE PROTEIN GP41; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OLIGOPEPTIDES; SOLUTIONS;

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 0034673621     PISSN: 01674838     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4838(99)00286-1     Document Type: Article

References (41)

1. Ptitsyn O.B., Rashin A.A. A model of myoglobin self-organization. Biophys. Chem. 3:1975;1-20.
2. Richards F.M. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6:1977;151-176.
3. Richardson J.S. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34:1981;167-339.
4. Zimm B.H., Bragg J.K. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 11:1959;526-535.
5. Lifson R., Roig A. On the theory of helix-coil transitions in biopolymers. J. Chem. Phys. 34:1961;1963-1974.
6. Sueki M., Lee S., Powers S.P., Denton J.B., Konishi Y., Scheraga H.A. Helix-coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly(hydroxybutyl)glutamine-co-L-histidine. Macromolecules. 17:1984;148-155.
7. Brown J.E., Klee W.A. Helix-coil transition of the isolated amino terminus of ribonuclease. Biochemistry. 10:1971;470-476.
8. Waltho J.P., Feher V.A., Merutka G., Dyson H.J., Wright P.E. Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. Biochemistry. 32:1993;6337-6347.
9. Finkelstein A.V., Badretdinov A.Y., Ptitsyn O.B. Physical reasons for secondary structure stability: α-helices in short peptides. Proteins. 10:1991;287-299.
10. Doig A.J., Chakrabartty A., Klingler T.M., Baldwin R.L. Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil therapy to include N- and C-capping. Biochemistry. 33:1994;3396-3403.
11. + salt bridge in short peptides of de novo design. Proc. Natl. Acad. Sci. USA. 84:1987;8898-8902.
12. Merutka G., Shalongo W., Stellwagen E. The effect of amino-acid ion-pairs on peptide helicity. Biochemistry. 30:1991;4245-4248.
13. Gans P.J., Lyu P.C., Manning M.C., Woody R.W., Kallenbach N.L. The helix-coil transition in heterogeneous peptides with specific side-chain interactions: theory and comparison with CD spectral data. Biopolymers. 31:1991;1605-1614.
14. Scholtz J.M., Qian H., Robbins V.H., Baldwin R.L. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry. 32:1993;9668-9676.
15. Stapley B.J., Doig A.J. Hydrogen bonding interactions between glutamine and asparagine in α-helical peptides. J. Mol. Biol. 272:1997;465-479.
16. Huyghuee-Despointes B.M., Klingler T.M., Baldwin R.L. Measuring the strength of side chain hydrogen bonds in peptide helices: the Gln·Asp (i,i+4) interaction. Biochemistry. 34:1995;13267-13271.
17. Stapley B.J., Rohl C.A., Doig A.J. Addition of side chain-side chain interactions to modified Lifson-Roig theory: application to energetics of phenylalanine-methionine interactions. Protein Sci. 4:1995;2383-2391.
18. Viguera A.R., Serrano L. Side-chain interactions between sulfur containing amino acids and phenylalanine in α-helices. Biochemistry. 34:1995;8771-8779.
19. Padmanabhan S., Baldwin R.L. A helix-stabilizing interaction between tyrosine and leucine or valine when the spacing is i, i+4. J. Mol. Biol. 241:1994;706-713.
20. Creamer T.P., Rose G.D. Interactions between hydrophobic side-chains within α-helices. Protein Sci. 4:1995;1305-1314.
21. Park S.H., Shalongo W., Stellwagen E. Residue helix parameters obtained from dichroic analysis of peptides of defined sequence. Biochemistry. 32:1993;7048-7053.
22. Gilmanshin R., Williams S., Callender R.H., Woodruff W.H., Dyer R.B. Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Proc. Natl. Acad. Sci. USA. 94:1997;3709-3713.
23. Chang D.K., Cheng S.F., Chien W.J. The amino-terminal fusion domain peptide of gp41 of HIV-1 inserts into sodium dodecyl sulfate micelle primarily as a helix with a conserved glycine at the micellar-aqueous interface. J. Virol. 71:1997;6593-6602.
24. Goodman M., Listowsky I. Conformational aspects of synthetic polypeptides. VI. Hypochromic spectral studies of oligo-γ-methyl-L-glutamate peptides. J. Am. Chem. Soc. 84:1962;3770-3771.
25. Luo P., Baldwin R.L. Mechanism of helix induction by trifluoroethanol: a framework for extrapolating helix-forming properties of peptide from trifluoroethanol/water mixtures back to water. Biochemistry. 36:1997;8413-8421.
26. Bartels C., Xia T.H., Billeter M., Güntert P., Wüthrich K. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR. 6:1995;1-10.
27. Hennessey J.P. Jr., Johnson W.C. Jr. Information content in the circular dichroism of proteins. Biochemistry. 20:1981;1085-1094.
28. Douglas N.W., Munro G.H., Daniels R.S. HIV/SIV glycoproteins: structure-function relationships. J. Mol. Biol. 273:1997;122-149.
29. Chakrabartty A., Kortemme T., Baldwin R.I. Helix propensity of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:1994;843-852.
30. Doig A.J., MacArthur M.W., Stapley B.J., Thornton J.M. Structures of N-termini of helices in proteins. Protein Sci. 6:1997;147-155.
31. Muñoz V., Serrano L. Development of the multiple sequence approximation within the Agadir model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers. 41:1997;495-509.
32. Lyu P.C., Zhou H.X., Jelveh N., Wemmer D.E., Kallenbach N.R. Position-dependent stabilizing effects in α-helices: N-terminal capping in synthetic model peptides. J. Am. Chem. Soc. 114:1992;6560-6562.
33. Nicholson H., Bechtel W.J., Matthews B.W. Enhanced protein thermostability from designed mutations that interact with alpha-helix dipoles. Nature. 336:1988;651-656.
34. Poumbourios P., el Ahmar W., McPhee D.A., Kemp B.E. Determinants of human immunodeficiency virus type 1 envelope glycoprotein oligomeric structure. J. Virol. 69:1995;1209-1218.
35. Cao J., Bergeron L., Helseth E., Thali M., Repke H., Sodroski J. Effects of amino acid changes in the extracellular domain of the human immunodeficiency virus type 1 gp41 envelope glycoprotein. J. Virol. 67:1993;2747-2755.
36. Seale J.W., Srinivasan R., Rose G.D. Sequence determinants of the capping box, a stabilizing motif of the N-termini of α-helices. Protein Sci. 3:1994;1741-1745.
37. Forood B., Feliciano E.J., Nambiar K.P. Stabilization of α-helical structures in short peptides via end capping. Proc. Natl. Acad. Sci. USA. 90:1993;838-842.
38. Aceto A., Dragani B., Melino S., Allocati N., Masulli M., Di Ilio C., Petruzzelli R. Identification of an N-capping box that affects the alpha 6-helix propensity in glutathione S-transferase superfamily proteins: a role for an invariant aspartic residue. Biochem. J. 322:1997;229-234.
39. Lacroix E., Viguera A.R., Serrano L. Elucidating the folding problem of α-helices: Local motifs, long-range electrostatics, ionic strength dependence and prediction of NMR parameters. J. Mol. Biol. 284:1998;173-191.
40. Presnell S.R., Cohen B.I., Cohen F.E. A segment-based approach to protein secondary structure prediction. Biochemistry. 31:1992;983-993.
41. Aurora R., Creamer T.P., Srinivasan R., Rose G.D. Local interactions in protein folding: lessons from the α-helix. J. Biol. Chem. 272:1997;1413-1416.