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New computational approaches to understanding molecular protein function

J. Fetrow,P. Babbitt

Published 2018 in PLoS Comput. Biol.

ABSTRACT

Function is like beauty—its definition lies in the eye of the beholder or, in this case, the researcher. At the broadest level, we define organismal function—the function that the protein plays in the overall organism. This function can be observed by understanding the impact on the organism of deletion or mutation of the protein. Physiological function is the function the protein plays in pathways, such as metabolic or signaling pathways. Another level of function is the cellular level. Approaches to understanding cellular function attempt to identify a protein’s interaction partners and its location within the cell. Biochemical or molecular function is another level of function, one that identifies the molecular functional details of a functional site, including reaction mechanism, substrate binding, and molecular details of the binding of regulatory molecules. The International Union of Pure and Applied Chemistry (IUPAC) Enzyme Classification (EC) system was an early approach to identifying molecular function. The Gene Ontology (GO) system of classifying function recognizes ways of defining function, using distinct cellular components, molecular function, and biological process hierarchies [1]. The emphasis in the collection of research articles that comprise this Focus Feature is on understanding the different molecular functions that can exist within a protein superfamily and the features that define those differences.

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