On the universe of protein folds

Rachel Kolodny, Leonid Pereyaslavets, Abraham O. Samson, Michael Levitt

Research output: Contribution to journalArticlepeer-review

62 Scopus citations

Abstract

In the fifty years since the first atomic structure of a protein was revealed, tens of thousands of additional structures have been solved. Like all objects in biology, proteins structures show common patterns that seem to define family relationships. Classification of proteins structures, which started in the 1970s with about a dozen structures, has continued with increasing enthusiasm, leading to two main fold classifications, SCOP and CATH, as well as many additional databases. Classification is complicated by deciding what constitutes a domain, the fundamental unit of structure. Also difficult is deciding when two given structures are similar. Like all of biology, fold classification is beset by exceptions to all rules. Thus, the perspectives of protein fold space that the fold classifications offer differ from each other. In spite of these ambiguities, fold classifications are useful for prediction of structure and function. Studying the characteristics of fold space can shed light on protein evolution and the physical laws that govern protein behavior.

Original languageEnglish
Pages (from-to)559-582
Number of pages24
JournalAnnual Review of Biophysics
Volume42
Issue number1
DOIs
StatePublished - May 2013

Funding

FundersFunder number
National Institute of General Medical SciencesR01GM063817

    Keywords

    • fold classification
    • fold evolution
    • fold use
    • protein fold

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