Rational design of a three‐heptad coiled‐coil protein and comparison by molecular dynamics simulation with the GCN4 coiled coil: Presence of interior three‐center hydrogen bonds

Protein Science

Volumn 3, Issue 2, 1994, Pages 345-355

  Rozzelle, James E ^a   Tropsha, Alexander ^a   Erickson, Bruce W ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

3 center hydrogen bonds; coiled coils; GCN4; molecular dynamics; protein folding; rational protein design

Indexed keywords

AMINO ACID; DISULFIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER MODEL; CROSS LINKING; CRYSTAL STRUCTURE; DISULFIDE BOND; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; SIMULATION;

AMINO ACID SEQUENCE; COMPARATIVE STUDY; COMPUTER SIMULATION; CRYSTALLIZATION; DISULFIDES; DRUG DESIGN; FUNGAL PROTEINS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN FOLDING; PROTEIN KINASES; PROTEIN STRUCTURE, SECONDARY; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, P.H.S.; TRANSCRIPTION FACTORS;

EID: 0028280457     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.5560030217     Document Type: Article

References (44)

1. Principles that govern the folding of protein chains
2. Hydrogen bonding in globular proteins
3. Interaction models for water in relation to protein hydration
4. Solvent‐induced distortions and the curvature of α‐helices
5. Weakly polar interactions in proteins
6. The molecular dynamics workshop laboratory
7. α‐Helical coiled coils — A widespread motif in proteins
8. α‐Helical coiled coils: How to design an α‐helical protein
9. The packing of α‐helices: Simple coiled‐coils
10. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices: Crystal structure of the protein‐DNA complex
11. Designed coiled‐coil proteins: Synthesis and spectroscopy of two 78‐residue α‐helical dimers
12. Energy minimizations of rubredoxin
13. Periodicity of amide proton exchange rates in a coiled‐coil leucine zipper peptide
14. The amide hydrogen bond in energy functions for peptides and proteins
15. Synthetic model for two‐stranded α‐helical coiled‐coils: Design, synthesis, and characterization of an 86‐residue analog of tropomyosin
16. Protein design using model synthetic peptides
17. Synthetic model proteins: Contribution of hydrophobic residues and disulfide bonds to protein stability
18. Sequence requirements for coiled‐coils: Analysis with 1 repressor‐GCN4 leucine zipper fusions
19. The leucine zipper: A hypothetical structure common to a new class of DNA binding proteins
20. Synthesis of a model protein of defined secondary and quaternary structure: Effect of chain length on the stabilization and formation of two‐stranded α‐helical coiled‐coils
21. Predicting coiled coils from protein sequences
22. The double helix coiled coil structure of murein lipoprotein from Escherichia coli
23. Tropomyosin coiled‐coil interactions: Evidence for an unstaggered structure
24. A second righthanded helical structure with the parameters of the Pauling‐Corey α‐helix
25. Automated modeling of coiled coils: Application to the GCN4 dimerization region
26. Secondary structure of a leucine zipper determined by nuclear magnetic resonance spectroscopy
27. A thermodynamic scale for the helix‐forming tendencies of the commonly occurring amino acids
28. X‐ray structure of the GCN4 leucine zipper, a two‐stranded, parallel coiled coil
29. Intrachain potential energy of the α‐helix and of a coiled coil strand
30. Compound helical configuration of polypeptide chains: Structure of proteins of the α‐keratin type
31. Helix signals in proteins
32. Amino acid preferences for specific locations at the ends of α helices
33. Principles and patterns of protein conformation
34. Numerical integration of a Cartesian system with constraints: Molecular dynamics of n‐alkanes
35. Hydrogen bonding in globular proteins
36. Tropomyosin: A model protein for studying coiled‐coil and α‐helix stabilization
37. Geometry of the N—H ··· O=C hydrogen bond. 2. Three‐center (“bifurcated”) and four‐center (“trifur‐cated”) bonds
38. Do interhelical side chainbackbone hydrogen bonds participate in formation of leucine zipper coiled coils?
39. Inverse protein folding: Designing polymer sequences
40. Synthetic model proteins: Positional effects of interchain hydrophobic interactions on stability of two‐stranded α‐helical coiled coils
41. Disulfide bond contribution to protein stability: Positional effects of substitution in the hydrophobic core of the two‐stranded α‐helical coiled‐coil
42. Relationship between amide proton chemical shifts and hydrogen bonding in amphipathic α‐helical peptides
43. Packing and hydrophobicity effects on protein folding and stability: Effects of β‐branched amino acids, valine and isoleucine, on the formation and stability of twostranded a‐helical coiled coils/leucine zippers