Identifying repeated structural elements in folded proteins

R. T. Miller, R. J. Douthart, A. K. Dunker

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

A previously described method for partitioning amino acid dihedral angle space generates a set of cluster centers which may be used to represent residue backbones in three dimensional protein structures. 99 non-homologous polypeptide chains are extracted from Brookhaven Protein Data Bank files and abstracted into sequences of these cluster centers, then this data set is examined for repeated sub-sequences. Repeated sequences of amino acid conformational clusters indicate duplicated motifs or sub-structures in folded proteins, independent of amino acid sequence identity. This representation is significantly more detailed than standard secondary structure descriptors (helix, strand, turn, etc.) and facilitates the identification of common structural elements without regard to sequence length. The current work examines the degree to which three example proteins share sub-structures with the remainder of the data set (ribonuclease A, erythrocruorin, and actinoxanthin), the specification of α-helices and β-strands under this system, and the sensitivity of the method to visual differences between structures.

Original languageEnglish (US)
Title of host publicationProceedings of the Hawaii International Conference on System Sciences
EditorsJay F. Nunamaker, Ralph H.Jr. Sprague
PublisherPubl by IEEE
Pages235-244
Number of pages10
ISBN (Print)0818650907
StatePublished - Jan 1 1995
Externally publishedYes
EventProceedings of the 27th Hawaii International Conference on System Sciences (HICSS-27). Part 4 (of 5) - Wailea, HI, USA
Duration: Jan 4 1994Jan 7 1994

Publication series

NameProceedings of the Hawaii International Conference on System Sciences
Volume5
ISSN (Print)1060-3425

Other

OtherProceedings of the 27th Hawaii International Conference on System Sciences (HICSS-27). Part 4 (of 5)
CityWailea, HI, USA
Period1/4/941/7/94

ASJC Scopus subject areas

  • Computer Science(all)

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  • Cite this

    Miller, R. T., Douthart, R. J., & Dunker, A. K. (1995). Identifying repeated structural elements in folded proteins. In J. F. Nunamaker, & R. H. J. Sprague (Eds.), Proceedings of the Hawaii International Conference on System Sciences (pp. 235-244). (Proceedings of the Hawaii International Conference on System Sciences; Vol. 5). Publ by IEEE.