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PMID: 10595534 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.

Protein science : a publication of the Protein Society ·Vol. 8 ·No. 11 ·1999-11-00 ·Pages 2312-29

Wagschal K, Tripet B, Lavigne P, Mant C, Hodges RS

Abstract

We describe here a systematic investigation into the role of position a in the hydrophobic core of a model coiled-coil protein in determining coiled-coil stability and oligomerization state. We employed a model coiled coil that allowed the formation of an extended three-stranded trimeric oligomerization state for some of the analogs; however, due to the presence of a Cys-Gly-Gly linker, unfolding occurred from the same two-stranded monomeric oligomerization state for all of the analogs. Denaturation from a two-stranded state allowed us to measure the relative contribution of 20 different amino acid side chains to coiled-coil stability from chemical denaturation profiles. In addition, the relative hydrophobicity of the substituted amino acid side chains was assessed by reversed-phase high-performance liquid chromatography and found to correlate very highly (R = 0.95) with coiled-coil stability. We also determined the effect of position a in specifying the oligomerization state using ultracentrifugation as well as high-performance size-exclusion chromatography. We found that nine of the analogs populated one oligomerization state exclusively at peptide concentrations of 50 microM under benign buffer conditions. The Leu-, Tyr-, Gln-, and His-substituted analogs were found to be exclusively three-stranded trimers, while the Asn-, Lys-, Orn-, Arg-, and Trp-substituted analogs formed exclusively two-stranded monomers. Modeling results for the Leu-substituted analog showed that a three-stranded oligomerization state is preferred due to increased side-chain burial, while a two-stranded oligomerization state was observed for the Trp analog due to unfavorable cavity formation in the three-stranded state.

MeSH Terms
Amino Acid Sequence Circular Dichroism Disulfides Drug Stability Guanidine Macromolecular Substances Models, Molecular Molecular Sequence Data Peptides/chemical synthesis,chemistry Protein Denaturation Protein Structure, Secondary Proteins/chemistry Regression Analysis Thermodynamics Urea
Chemicals
Disulfides Macromolecular Substances Peptides Proteins Urea Guanidine
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Wagschal K
Department of Biochemistry and the Medical Research Council Group in Protein Structure and Function, University of Alberta, Edmonton, Canada.
Tripet B
Lavigne P
Mant C
Hodges R S
References (75)
75 references, click to expand
  1. The structure of the N-terminus of striated muscle alpha-tropomyosin in a chimeric peptide: nuclear magnetic resonance structure and circular dichroism studies.
    Biochemistry. 1998 May 26;37(21):7834-43 PMID: 9601044
  2. Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism.
    Nat Struct Biol. 1996 Dec;3(12):1002-9 PMID: 8946853
  3. Effect of chain length on the formation and stability of synthetic alpha-helical coiled coils.
    Biochemistry. 1994 Dec 27;33(51):15501-10 PMID: 7803412
  4. Induced conformational states of amphipathic peptides in aqueous/lipid environments.
    Biophys J. 1995 Jan;68(1):351-9 PMID: 7711261
  5. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA.
    Nature. 1995 Jan 19;373(6511):257-61 PMID: 7816143
  6. Demonstration of coiled-coil interactions within the kinesin neck region using synthetic peptides. Implications for motor activity.
    J Biol Chem. 1997 Apr 4;272(14):8946-56 PMID: 9083016
  7. Native-like and structurally characterized designed alpha-helical bundles.
    Curr Opin Struct Biol. 1995 Aug;5(4):457-63 PMID: 8528761
  8. Guanidine hydrochloride stabilization of a partially unfolded intermediate during the reversible denaturation of protein disulfide isomerase.
    Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2107-11 PMID: 8460117
  9. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.
    Proteins. 1991;11(4):281-96 PMID: 1758883
  10. Predicting coiled coils by use of pairwise residue correlations.
    Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8259-63 PMID: 7667278
  11. Predicting oligomerization states of coiled coils.
    Protein Sci. 1995 Aug;4(8):1596-607 PMID: 8520486
  12. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation.
    Proteins. 1994 Sep;20(1):68-84 PMID: 7824524
  13. Packing and hydrophobicity effects on protein folding and stability: effects of beta-branched amino acids, valine and isoleucine, on the formation and stability of two-stranded alpha-helical coiled coils/leucine zippers.
    Protein Sci. 1993 Mar;2(3):383-94 PMID: 8453376
  14. Interactions of coiled coils in transcription factors: where is the specificity?
    Curr Opin Genet Dev. 1993 Apr;3(2):278-85 PMID: 8504253
  15. Alpha-helical coiled coils and bundles: how to design an alpha-helical protein.
    Proteins. 1990;7(1):1-15 PMID: 2184436
  16. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding.
    Protein Sci. 1995 Oct;4(10):2138-48 PMID: 8535251
  17. Evidence that the leucine zipper is a coiled coil.
    Science. 1989 Jan 27;243(4890):538-42 PMID: 2911757
  18. Synthetic model proteins: contribution of hydrophobic residues and disulfide bonds to protein stability.
    Pept Res. 1990 May-Jun;3(3):123-37 PMID: 2134057
  19. The effect of conformation on the CD of interacting helices: a theoretical study of tropomyosin.
    Biopolymers. 1990;30(7-8):657-76 PMID: 2275971
  20. Coiled coils: new structures and new functions.
    Trends Biochem Sci. 1996 Oct;21(10):375-82 PMID: 8918191
  21. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
    Science. 1991 Oct 25;254(5031):539-44 PMID: 1948029
  22. Tenascin-C hexabrachion assembly is a sequential two-step process initiated by coiled-coil alpha-helices.
    J Biol Chem. 1998 Apr 24;273(17):10602-8 PMID: 9553121
  23. Insights into the mechanism of heterodimerization from the 1H-NMR solution structure of the c-Myc-Max heterodimeric leucine zipper.
    J Mol Biol. 1998 Aug 7;281(1):165-81 PMID: 9680483
  24. Oligomerization properties of GCN4 leucine zipper e and g position mutants.
    Protein Sci. 1997 Oct;6(10):2218-26 PMID: 9336844
  25. An analysis of packing in the protein folding problem.
    Q Rev Biophys. 1993 Nov;26(4):423-98 PMID: 8058892
  26. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants.
    Science. 1993 Nov 26;262(5138):1401-7 PMID: 8248779
  27. Buried polar residues and structural specificity in the GCN4 leucine zipper.
    Nat Struct Biol. 1996 Dec;3(12):1011-8 PMID: 8946854
  28. Predicting coiled-coil regions in proteins.
    Curr Opin Struct Biol. 1997 Jun;7(3):388-93 PMID: 9204281
  29. Synthesis of a model protein of defined secondary and quaternary structure. Effect of chain length on the stabilization and formation of two-stranded alpha-helical coiled-coils.
    J Biol Chem. 1984 Nov 10;259(21):13253-61 PMID: 6490655
  30. Protein denaturation with guanidine hydrochloride or urea provides a different estimate of stability depending on the contributions of electrostatic interactions.
    Protein Sci. 1994 Nov;3(11):1984-91 PMID: 7703845
  31. The stability of tropomyosin, a two-stranded coiled-coil protein, is primarily a function of the hydrophobicity of residues at the helix-helix interface.
    Biochemistry. 1995 Dec 26;34(51):16797-805 PMID: 8527455
  32. MultiCoil: a program for predicting two- and three-stranded coiled coils.
    Protein Sci. 1997 Jun;6(6):1179-89 PMID: 9194178
  33. Electrostatic interactions control the parallel and antiparallel orientation of alpha-helical chains in two-stranded alpha-helical coiled-coils.
    Biochemistry. 1994 Apr 5;33(13):3862-71 PMID: 8142389
  34. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect.
    Science. 1992 Jan 10;255(5041):178-83 PMID: 1553543
  35. Determination of the helix and beta form of proteins in aqueous solution by circular dichroism.
    Biochemistry. 1974 Jul 30;13(16):3350-9 PMID: 4366945
  36. Comparison of antiparallel and parallel two-stranded alpha-helical coiled-coils. Design, synthesis, and characterization.
    J Biol Chem. 1993 Sep 15;268(26):19218-27 PMID: 8366074
  37. Relationship of sidechain hydrophobicity and alpha-helical propensity on the stability of the single-stranded amphipathic alpha-helix.
    J Pept Sci. 1995 Sep-Oct;1(5):319-29 PMID: 9223011
  38. Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle.
    EMBO J. 1993 Aug;12(8):3227-36 PMID: 8344260
  39. Principles of protein folding--a perspective from simple exact models.
    Protein Sci. 1995 Apr;4(4):561-602 PMID: 7613459
  40. The relative positions of alanine residues in the hydrophobic core control the formation of two-stranded or four-stranded alpha-helical coiled-coils.
    Protein Eng. 1996 Apr;9(4):353-63 PMID: 8738211
  41. Effect of preferred binding domains on peptide retention behavior in reversed-phase chromatography: amphipathic alpha-helices.
    Pept Res. 1990 Jan-Feb;3(1):8-20 PMID: 2134049
  42. Alpha-helical coiled-coil oligomerization domains in extracellular proteins.
    Matrix Biol. 1997 Mar;15(8-9):555-65; discussion 567-8 PMID: 9138288
  43. Synthetic model for two-stranded alpha-helical coiled-coils. Design, synthesis, and characterization of an 86-residue analog of tropomyosin.
    J Biol Chem. 1981 Feb 10;256(3):1214-24 PMID: 7451500
  44. Protein destabilization by electrostatic repulsions in the two-stranded alpha-helical coiled-coil/leucine zipper.
    Protein Sci. 1995 Feb;4(2):237-50 PMID: 7757012
  45. Local versus nonlocal interactions in protein folding and stability--an experimentalist's point of view.
    Fold Des. 1996;1(4):R71-7 PMID: 9079385
  46. Solvation energy in protein folding and binding.
    Nature. 1986 Jan 16-22;319(6050):199-203 PMID: 3945310
  47. Nuclear magnetic resonance characterization of the Jun leucine zipper domain: unusual properties of coiled-coil interfacial polar residues.
    Biochemistry. 1995 May 9;34(18):6164-74 PMID: 7742321
  48. Alpha-helical protein assembly motifs.
    J Biol Chem. 1997 Jan 31;272(5):2583-6 PMID: 9053397
  49. Structure, function and application of the coiled-coil protein folding motif.
    Curr Opin Biotechnol. 1993 Aug;4(4):428-37 PMID: 7763973
  50. Crystal structure of a synthetic triple-stranded alpha-helical bundle.
    Science. 1993 Feb 26;259(5099):1288-93 PMID: 8446897
  51. Leucine is the most stabilizing aliphatic amino acid in the d position of a dimeric leucine zipper coiled coil.
    Biochemistry. 1997 Oct 14;36(41):12567-73 PMID: 9376362
  52. Boehringer Mannheim award lecture 1995. La conference Boehringer Mannheim 1995. De novo design of alpha-helical proteins: basic research to medical applications.
    Biochem Cell Biol. 1996;74(2):133-54 PMID: 9213423
  53. Unzipping the secrets of coiled-coils.
    Curr Biol. 1992 Mar;2(3):122-4 PMID: 15335985
  54. Structure of the leucine zipper.
    Curr Opin Genet Dev. 1992 Apr;2(2):205-10 PMID: 1638114
  55. Effect of trifluoroethanol on protein secondary structure: an NMR and CD study using a synthetic actin peptide.
    Biochemistry. 1992 Sep 22;31(37):8790-8 PMID: 1390666
  56. Structural and genetic analysis of protein stability.
    Annu Rev Biochem. 1993;62:139-60 PMID: 8352587
  57. Synthetic model proteins. Positional effects of interchain hydrophobic interactions on stability of two-stranded alpha-helical coiled-coils.
    J Biol Chem. 1992 Feb 5;267(4):2664-70 PMID: 1733963
  58. Surface electrostatic interactions contribute little of stability of barnase.
    J Mol Biol. 1991 Aug 5;220(3):779-88 PMID: 1870131
  59. Circular dichroic analysis of protein conformation: inclusion of the beta-turns.
    Anal Biochem. 1978 Nov;91(1):13-31 PMID: 9762080
  60. Analysis of data from the analytical ultracentrifuge by nonlinear least-squares techniques.
    Biophys J. 1981 Dec;36(3):575-88 PMID: 7326325
  61. Atomic structure of the ectodomain from HIV-1 gp41.
    Nature. 1997 May 22;387(6631):426-30 PMID: 9163431
  62. Preferential heterodimeric parallel coiled-coil formation by synthetic Max and c-Myc leucine zippers: a description of putative electrostatic interactions responsible for the specificity of heterodimerization.
    J Mol Biol. 1995 Dec 1;254(3):505-20 PMID: 7490766
  63. Use of a heterodimeric coiled-coil system for biosensor application and affinity purification.
    J Chromatogr B Biomed Sci Appl. 1998 Sep 11;715(1):307-29 PMID: 9792518
  64. An engineered allosteric switch in leucine-zipper oligomerization.
    Nat Struct Biol. 1996 Jun;3(6):510-5 PMID: 8646536
  65. De novo design of a model peptide sequence to examine the effects of single amino acid substitutions in the hydrophobic core on both stability and oligomerization state of coiled-coils.
    J Mol Biol. 1999 Jan 15;285(2):785-803 PMID: 9878444
  66. Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4.
    Biochemistry. 1993 Jun 1;32(21):5491-6 PMID: 8504069
  67. Synthetic model proteins: the relative contribution of leucine residues at the nonequivalent positions of the 3-4 hydrophobic repeat to the stability of the two-stranded alpha-helical coiled-coil.
    Biochemistry. 1992 Jun 30;31(25):5739-46 PMID: 1610823
  68. SEQSEE: a comprehensive program suite for protein sequence analysis.
    Comput Appl Biosci. 1994 Apr;10(2):121-32 PMID: 8019859
  69. Orientation, positional, additivity, and oligomerization-state effects of interhelical ion pairs in alpha-helical coiled-coils.
    J Mol Biol. 1998 Nov 13;283(5):993-1012 PMID: 9799639
  70. The dimerization stability of the HLH-LZ transcription protein family is modulated by the leucine zippers: a CD and NMR study of TFEB and c-Myc.
    Biochemistry. 1994 Sep 20;33(37):11296-306 PMID: 7727380
  71. Proximity of sulfhydryl groups to the sites of interaction between components of the troponin complex from rabbit skeletal muscle.
    J Biol Chem. 1982 Mar 10;257(5):2549-55 PMID: 7061438
  72. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil.
    Biochemistry. 1995 Jul 11;34(27):8642-8 PMID: 7612604
  73. Determination and analysis of urea and guanidine hydrochloride denaturation curves.
    Methods Enzymol. 1986;131:266-80 PMID: 3773761
  74. A single amino acid can switch the oligomerization state of the alpha-helical coiled-coil domain of cartilage matrix protein.
    EMBO J. 1997 Jul 1;16(13):3767-77 PMID: 9233786
  75. Predicting coiled coils from protein sequences.
    Science. 1991 May 24;252(5009):1162-4 PMID: 2031185
Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
0961-8368
DOI
10.1110/ps.8.11.2312
Published
1999-11-00
Pages
2312-29
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2144206
Subset
IM
External Links
PubMed source DOI: 10.1110/ps.8.11.2312 PMC Full Text View journal details
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