MultiCoil: a Program for Predicting Two- and Three-stranded Coiled Coils

Overview

Journal Protein Sci

Specialty Biochemistry

Date 1997 Jun 1

PMID 9194178

Citations 288

Authors

E Wolf

P S Kim

B Berger

Affiliations

Soon will be listed here.

Abstract

A new multidimensional scoring approach for identifying and distinguishing trimeric and dimeric coiled coils is implemented in the MultiCoil program. The program extends the two-stranded coiled-coil prediction program PairCoil to the identification of three-stranded coiled coils. The computations are based upon data gathered from a three-stranded coiled-coil database comprising 6,319 amino acid residues, as well as from the previously constructed two-stranded coiled-coil database. In addition to identifying coiled coils not predicted by the two-stranded database programs, MultiCoil accurately classifies the oligomerization states of known dimeric and trimeric coiled coils. Analysis of the MultiCoil scores provides insight into structural features of coiled coils, and yields estimates that 0.9% of all protein residues form three-stranded coiled coils and that 1.5% form two-stranded coiled coils. The MultiCoil program is available at http:/(/)theory.lcs.mit.edu/multicoil.

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References

Strong D, Moore M, Cottrell B, Bohonus V, Pontes M, Evans B . Lamprey fibrinogen gamma chain: cloning, cDNA sequencing, and general characterization. Biochemistry. 1985; 24(1):92-101. DOI: 10.1021/bi00322a014. View

. A protein sequence/structure database. Protein Engineering Club Database Group. Nature. 1988; 335(6192):745-6. DOI: 10.1038/335745a0. View

Montell D, Goodman C . Drosophila laminin: sequence of B2 subunit and expression of all three subunits during embryogenesis. J Cell Biol. 1989; 109(5):2441-53. PMC: 2115843. DOI: 10.1083/jcb.109.5.2441. View

Sorger P, NELSON H . Trimerization of a yeast transcriptional activator via a coiled-coil motif. Cell. 1989; 59(5):807-13. DOI: 10.1016/0092-8674(89)90604-1. View

Wang Y, Patterson J, Gray J, Yu C, Cottrell B, Shimizu A . Complete sequence of the lamprey fibrinogen alpha chain. Biochemistry. 1989; 28(25):9801-6. DOI: 10.1021/bi00451a039. View

Bleasby A, Wootton J . Construction of validated, non-redundant composite protein sequence databases. Protein Eng. 1990; 3(3):153-9. DOI: 10.1093/protein/3.3.153. View

Pastori R, Moskaitis J, SMITH Jr L, Schoenberg D . Estrogen regulation of Xenopus laevis gamma-fibrinogen gene expression. Biochemistry. 1990; 29(10):2599-605. DOI: 10.1021/bi00462a024. View

Weissbach L, Grieninger G . Bipartite mRNA for chicken alpha-fibrinogen potentially encodes an amino acid sequence homologous to beta- and gamma-fibrinogens. Proc Natl Acad Sci U S A. 1990; 87(13):5198-202. PMC: 54289. DOI: 10.1073/pnas.87.13.5198. View

Lupas A, Van Dyke M, Stock J . Predicting coiled coils from protein sequences. Science. 1991; 252(5009):1162-4. DOI: 10.1126/science.252.5009.1162. View

10.

Conway J, Parry D . Three-stranded alpha-fibrous proteins: the heptad repeat and its implications for structure. Int J Biol Macromol. 1991; 13(1):14-6. DOI: 10.1016/0141-8130(91)90004-e. View

11.

Wilson C, Wardell M, Weisgraber K, Mahley R, Agard D . Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. Science. 1991; 252(5014):1817-22. DOI: 10.1126/science.2063194. View

12.

OShea E, Klemm J, Kim P, Alber T . X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 1991; 254(5031):539-44. DOI: 10.1126/science.1948029. View

13.

Pan Y, Doolittle R . cDNA sequence of a second fibrinogen alpha chain in lamprey: an archetypal version alignable with full-length beta and gamma chains. Proc Natl Acad Sci U S A. 1992; 89(6):2066-70. PMC: 48597. DOI: 10.1073/pnas.89.6.2066. View

14.

Kallunki P, Sainio K, Eddy R, Byers M, Kallunki T, Sariola H . A truncated laminin chain homologous to the B2 chain: structure, spatial expression, and chromosomal assignment. J Cell Biol. 1992; 119(3):679-93. PMC: 2289671. DOI: 10.1083/jcb.119.3.679. View

15.

Nomizu M, Utani A, Shiraishi N, Yamada Y, Roller P . Synthesis and conformation of the trimeric coiled-coil segment of laminin. Int J Pept Protein Res. 1992; 40(1):72-9. DOI: 10.1111/j.1399-3011.1992.tb00107.x. View

16.

Peteranderl R, NELSON H . Trimerization of the heat shock transcription factor by a triple-stranded alpha-helical coiled-coil. Biochemistry. 1992; 31(48):12272-6. DOI: 10.1021/bi00163a042. View

17.

Rabindran S, Haroun R, Clos J, Wisniewski J, Wu C . Regulation of heat shock factor trimer formation: role of a conserved leucine zipper. Science. 1993; 259(5092):230-4. DOI: 10.1126/science.8421783. View

18.

Porter B, Justice M, Copeland N, Jenkins N, Hunter D, Merlie J . S-laminin: mapping to mouse chromosome 9 and expression in the linked mutants tippy and ducky. Genomics. 1993; 16(1):278-81. DOI: 10.1006/geno.1993.1178. View

19.

Beck K, Dixon T, Engel J, Parry D . Ionic interactions in the coiled-coil domain of laminin determine the specificity of chain assembly. J Mol Biol. 1993; 231(2):311-23. DOI: 10.1006/jmbi.1993.1284. View

20.

Fujinaga M, Berthet-Colominas C, Yaremchuk A, Tukalo M, Cusack S . Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution. J Mol Biol. 1993; 234(1):222-33. DOI: 10.1006/jmbi.1993.1576. View