Deriving how far structural information is transmitted through parallel homodimeric coiled-coils: A correlation analysis of helical staggers

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 4, 2013, Pages 635-643

  Brown, Jerry H ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

Asymmetry; Chromosomal rearrangements; End effects; Hydrogen bond deformations; Leukemia; Long range communication; Muscle regulation; Myosin; Tropomyosin

Indexed keywords

ACTIN; F ACTIN; HOMODIMER; TROPOMYOSIN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CHROMOSOME REARRANGEMENT; CONFORMATION; CORRELATION COEFFICIENT; DRUG DESIGN; DRUG TARGETING; HYDROGEN BOND; MUSCLE CONTRACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; TROPOMYOSIN;

EID: 84874809288     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24218     Document Type: Article

References (49)

1. Parry DA. Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins. Biosci Rep 1982; 2: 1017-1024.
2. Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS. Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci U S A 1995; 92: 8259-8263.
3. Gruber M, Soding J, Lupas AN. Comparative analysis of coiled-coil prediction methods. J Struct Biol 2006; 155: 140-145.
4. Crick FHC. The packing of alpha-helices: simple coiled coils. Acta Crystallogr 1953; 6: 689-697.
5. Cohen C, Parry DAD. Alpha-helical coiled coils and bundles: how to design an alpha-helical protein. Prot Struct Funct Genet 1990; 7: 1-15.
6. Musafia B, Buchner V, Arad D. Complex salt bridges in proteins: statistical analysis of structure and function. J Mol Biol 1995; 254: 761-770.
7. Burkhard P, Ivaninskii S, Lustig A. Improving coiled-coil stability by optimizing ionic interactions. J Mol Biol 2002; 318: 901-910.
8. Meier M, Lustig A, Aebi U, Burkhard P. Removing an interhelical salt bridge abolishes coiled-coil formation in a de novo designed peptide. J Struct Biol 2002; 137: 65-72.
9. O'shea EK, Klemm JD, Kim PS, Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991; 254: 539-544.
10. Lupas A, Van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science 1991; 252: 1162-1164.
11. Woolfson DN. The design of coiled-coil structures and assemblies. Adv Prot Chem 2005; 70: 79-112.
12. Lupas AN, Gruber M. The structure of alpha-helical coiled coils. Adv Prot Chem 2005; 70: 37-78.
13. Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions. Curr Opin Struct Biol 2008; 18: 477-483.
14. Brown JH. How sequence directs bending in tropomyosin and other two-stranded alpha-helical coiled coils. Prot Sci 2010; 19: 1366-1375.
15. Brown JH, Kim K-H, Jun G, Greenfield NJ, Dominguez R, Volkmann N, Hitchcock-DeGregori SE, Cohen C. Deciphering the design of the tropomyosin molecule. Proc Natl Acad Sci U S A 2001; 98: 8496-8501.
16. Blankenfeldt W, Thoma NH, Wray JS, Gautel M, Schlichting I. Crystal structures of human cardiac beta-myosin II S2-Delta provide insight into the functional role of the S2 subfragment. Proc Natl Acad Sci U S A 2006; 103: 17713-17717.
17. Gernert KM, Surles MC, Labean TH, Richardson JS, Richardson DC. The Alacoil: a very tight, antiparallel coiled-coil of helices. Prot Sci 1995; 4: 2252-2260.
18. Walther D, Eisenhaber F, Argos P. Principles of helix-helix packing in proteins: the helical lattice superposition model. J Mol Biol 1996; 255: 536-553.
19. Pfaff M, Liu S, Erle DJ, Ginsberg MH. Integrin beta cytoplasmic domains differentially bind to cytoskeletal proteins. J Biol Chem 1998; 273: 6104-6109.
20. Ulmer TS, Yaspan B, Ginsberg MH, Campbell ID. NMR analysis of structure and dynamics of the cytosolic tails of integrin alpha IIb beta 3 in aqueous solution. Biochemistry 2001; 40: 7498-7508.
21. Laughton CA, Luisi BF, Pratap JV, Calladine CR. A potential molecular switch in an alpha-helical coiled coil. Proteins 2008; 70: 25-30.
22. Brown JH. Breaking symmetry in protein dimers: designs and functions. Prot Sci 2006; 15: 1-13.
23. Goodsell DS, Olson AJ. Structural symmetry and protein function. Annu Rev Biophys Biomol Struct 2000; 29: 105-153.
24. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536-540.
25. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucl Acids Res 2000; 28: 235-242.
26. Winkler RL, Hays WL. Statistics: probability, inference, and decision. New York: Holt, Rinehart, and Winston; 1975.
27. Bewick V, Cheek L, Ball J. Statistics review 7: correlation and regression. Critical care 2003; 7: 451-459.
28. Arora N, Jayaram B. Strength of hydrogen bonds in alpha helices. J Comput Chem 1997; 18: 1245-1252.
29. Conway JF, Parry DAD. Structural features in the heptad substructure and longer range repeats of two-stranded alpha-fibrous proteins. Int J Biol Macromol 1990; 12: 328-334.
30. Singh A, Hitchcock-Degregori SE. A peek into tropomyosin binding and unfolding on the actin filament. PloS one 2009; 4: e6336.
31. Parry DA. Analysis of the primary sequence of alpha-tropomyosin from rabbit skeletal muscle. J Mol Biol 1975; 98: 519-535.
32. McLachlan AD, Stewart M. The 14-fold periodicity in alpha-tropomyosin and the interaction with actin. J Mol Biol 1976; 103: 271-298.
33. Phillips GN, Fillers JP, Cohen C. Tropomyosin crystal structure and muscle regulation. J Mol Biol 1986; 192: 111-131.
34. McKillop DFA, Geeves MA. Regulation of the interaction between actin and myosin subfragment 1: evidence for three states of the thin filament. Biophys J 1993; 65: 693-701.
35. Vibert P, Craig R, Lehman W. Steric-model for activation of muscle thin filaments. J Mol Biol 1997; 266: 8-14.
36. Lehman W, Galinska-Rakoczy A, Hatch V, Tobacman LS, Craig R. Structural basis for the activation of muscle contraction by troponin and tropomyosin. J Mol Biol 2009; 388: 673-681.
37. Tobacman LS. Cooperative binding of tropomyosin to actin. Adv Exp Med Biol 2008; 644: 85-94.
38. Smith DA, Maytum R, Geeves MA. Cooperative regulation of myosin-actin interactions by a continuous flexible chain I: actin-tropomyosin systems. Biophys J 2003; 84: 3155-3167.
39. Ly S, Lehrer SS. Long-range effects of familial hypertrophic cardiomyopathy mutations E180G and D175N on the properties of tropomyosin. Biochemistry 2012; 51: 6413-6420.
40. So CW, Cleary ML. Dimerization: a versatile switch for oncogenesis. Blood Rev 2004; 104: 919-922.
41. Guasch G, Mack GJ, Popovici C, Dastugue N, Birnbaum D, Rattner JB, Pebusque MJ. FGFR1 is fused to the centrosome-associated protein CEP110 in the 8p12 stem cell myeloproliferative disorder with t(8;9)(p12;q33). Blood 2000; 95: 1788-1796.
42. Liu PP, Hajra A, Wijmenga C, Collins FS. Molecular pathogenesis of the chromosome 16 inversion in the M4Eo subtype of acute myeloid leukemia. Blood 1995; 85: 2289-2302.
43. Lowey S, Trybus KM. Common structural motifs for the regulation of divergent class II myosins. J Biol Chem 2010; 285: 16403-16407.
44. Carter AP, Vale RD. Communication between the AAA+ ring and microtubule-binding domain of dynein. Biochem Cell Biol 2010; 88: 15-21.
45. Lupas A. Coiled coils: new structures and new functions. Trends Biochem Sci 1996; 21: 375-382.
46. Burkhard P, Stetefeld J, Strelkov SV. Coiled coils: a highly versatile protein folding motif. Trends Cell Biol 2001; 11: 82-88.
47. Yu YB. Coiled-coils: stability, specificity, and drug delivery potential. Adv Drug Deliv Rev 2002; 54: 1113-1129.
48. Mason JM, Arndt KM. Coiled coil domains: stability, specificity, and biological implications. Chembiochem: Eur J Chem Biol 2004; 5: 170-176.
49. Woolfson DN. Building fibrous biomaterials from alpha-helical and collagen-like coiled-coil peptides. Biopolymers 2010; 94: 118-127.