Abstract
A computer algorithm for assessment of globularity of protein structures is presented. By enclosing the input protein in a minimum volume ellipsoid (MVEE) and calculating a profile measuring how voxelized space within this shape (cubes on a uniform grid) is occupied by atoms, it is possible to estimate how well the molecule resembles a globule. For any protein to satisfy the proposed globularity criterion, its ellipsoid profile (EP) should first confirm that atoms adequately fill the ellipsoid’s center. This property should then propagate towards the surface of the ellipsoid, although with diminishing importance. It is not required to compute the molecular surface. Globular status (full or partial) is assigned to proteins with values of their ellipsoid profiles, called here the ellipsoid indexes (EI), above certain levels. Due to structural outliers which may considerably distort the measurements, a companion method for their detection and reduction of their influence is also introduced. It is based on kernel density estimation and is shown to work well as an optional input preparation step for MVEE. Finally, the complete workflow is applied to over two thousand representatives of SCOP 2.08 domain superfamilies, surveying the landscape of tertiary structure of proteins from the Protein Data Bank.
Highlights
Steven Brenner and colleagues begin their 1995 paper with following statement [1]:“The structure of a protein can elucidate its function, in both general and specific terms, and its evolutionary history.” In the paragraph, the same authors add: “(...) protein structures can be fundamentally understood in ways that most of their sequences cannot.”both sequence and structure of proteins have their own means of providing insight into biological role and ancestry of these molecules [2]
In this paper we present a simple method for general assessment of shape of tertiary structure of proteins for the purpose of determining how well they resemble a globule and to facilitate their comparison based on this property
To reiterate the Introduction, we are aiming here for the best approximation of a smallest ellipsoid that encloses the input protein (MVEE) in a way that is less influenced by surficial details, but without erasing too much information
Summary
Steven Brenner and colleagues begin their 1995 paper with following statement [1]:“The structure of a protein can elucidate its function, in both general and specific terms, and its evolutionary history.” In the paragraph, the same authors add: “(...) protein structures can be fundamentally understood in ways that most of their sequences cannot.”both sequence and structure of proteins have their own means of providing insight into biological role and ancestry of these molecules [2]. “The structure of a protein can elucidate its function, in both general and specific terms, and its evolutionary history.”. The same authors add: “(...) protein structures can be fundamentally understood in ways that most of their sequences cannot.”. Both sequence and structure of proteins have their own means of providing insight into biological role and ancestry of these molecules [2]. This in turn allows them to be classified, stored in databases and explored in the light of current state of knowledge.
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