Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins

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Citation: Russ B. Altman and Mark Gerstein. (1995) Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins. In KSL-95-25, March,1995.

Publication techreport ( Edit )
type Technical Report
bibtype techreport
Bibtex basics
author Russ B. Altman and Mark Gerstein
title Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins
number KSL-95-25
institution Knowledge Systems, AI Laboratory
address Stanford, CA, USA
year 1995
month March
Bibtex more
note Medical Computer Science
Access Paper
abstract A variety of methods are currently available for creating multiple alignments,and these can be used to define and characterize families of related proteins,such as the globins and the immunoglobulins. We have developed a method for using a multiple alignment to identify an average structural "core," a subset of atoms with low structural variation. We show how the means and variances of core-atom positions summarize the commonalities and differences within a family, making them particularly useful in compiling libraries of protein folds. We show further how it is possible to describe the rotation and translation relating two core structures, as in two domains of a multi-domain protein, in a consistent fashion in terms of a "mean" transformation and a deviation about this mean. Once determined, our average core structures (with their implicit measure of structural variation) allow us to define a measure of structural similarity more informative than the usual RMS deviation in atomic position, i.e. a "better RMS." Our average structures also permit straightforward comparisons between variation in structure and sequence at each position in a family. We have applied our core finding methodology in detail to the immunoglobulin family. We find that the structural variability we observe just within the VL and VH domains anticipates the variability that others have observed throughout the whole immunoglobulin superfamily; that a core definition based on sequence conservation, somewhat surprisingly, does not agree with one based on structural similarity; and that the cores of the VLand VH domains vary about 5° in relative orientation across the known structures.

KSL Technical Report ID: KSL-95-25
Facts about Average Core Structures and Variability Measures for Protein Families: Application to the ImmunoglobulinsRDF feed
Abstract A variety of methods are currently availab … A variety of methods are currently available for creating multiple alignments,and these can be used to define and characterize families of related proteins,such as the globins and the immunoglobulins. We have developed a method for using a multiple alignment to identify an average structural "core," a subset of atoms with low structural variation. We show how the means and variances of core-atom positions summarize the commonalities and differences within a family, making them particularly useful in compiling libraries of protein folds. We show further how it is possible to describe the rotation and translation relating two core structures, as in two domains of a multi-domain protein, in a consistent fashion in terms of a "mean" transformation and a deviation about this mean. Once determined, our average core structures (with their implicit measure of structural variation) allow us to define a measure of structural similarity more informative than the usual RMS deviation in atomic position, i.e. a "better RMS." Our average structures also permit straightforward comparisons between variation in structure and sequence at each position in a family. We have applied our core finding methodology in detail to the immunoglobulin family. We find that the structural variability we observe just within the VL and VH domains anticipates the variability that others have observed throughout the whole immunoglobulin superfamily; that a core definition based on sequence conservation, somewhat surprisingly, does not agree with one based on structural similarity; and that the cores of the VLand VH domains vary about 5° in relative orientation across the known structures. e orientation across the known structures.
Address Stanford, CA, USA  +
Author Russ B. Altman and Mark Gerstein  +
Bibtype techreport  +
Has author Russ B. Altman and Mark Gerstein  +
Has identifier KSL-95-25  +
Has publishing details March,1995  +
Has title Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins  +
Has where published KSL-95-25  +
Has year 1995  +
Institution Knowledge Systems, AI Laboratory  +
Ksl tr id KSL-95-25  +
Month March  +
Note Medical Computer Science
Number KSL-95-25  +
Process note NO  +
Title Average Core Structures and Variability Measures for Protein Families: Application to the Immunoglobulins  +
Year 1995  +
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