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          Institute: MPI für Informatik     Collection: Computational Biology and Applied Algorithmics     Display Documents



ID: 356583.0, MPI für Informatik / Computational Biology and Applied Algorithmics
Structural Descriptors of gp120 V3 Loop for the Prediction of {HIV-1} Coreceptor Usage
Authors:Sander, Oliver; Sing, Tobias; Sommer, Ingolf; Low, Andrew J.; Cheung, Peter K.; Harrigan, P. Richard; Lengauer, Thomas; Domingues, Francisco S.
Language:English
Date of Publication (YYYY-MM-DD):2007
Title of Journal:PLoS Computational Biology
Volume:3
Issue / Number:3
Start Page:e58.555
End Page:564
Copyright:Copyright: © 2007 Sander et al. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Review Status:Peer-review
Audience:Experts Only
Intended Educational Use:No
Abstract / Description:HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine
receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is
critical for monitoring disease progression as well as for supporting therapy
with the novel drug class of coreceptor antagonists. Predictive methods for
inferring coreceptor usage based on the third hypervariable (V3) loop region of
the viral gene coding for the envelope protein gp120 can provide these
monitoring facilities while avoiding expensive phenotypic tests. All simple
heuristics (like the 11/25 rule) as well as statistical learning methods
proposed to date predict coreceptor usage based on sequence features of the V3
loop exclusively. Here, we show, based on a recently resolved structure of
gp120 with an untruncated V3 loop, that using structural information on the V3
loop in combination with sequence features of V3 variants improves prediction
of coreceptor usage. In particular, we propose a distance-based descriptor of
the spatial arrangement of physicochemical properties that increases
discriminative performance. For a fixed specificity of 0.95, a sensitivity of
0.77 was achieved, improving further to 0.80 when combined with a
sequence-based representation using amino acid indicators. This compares
favorably with the sensitivities of 0.62 for the traditional 11/25 rule and
0.73 for a prediction based on sequence information as input to a support
vector machine (SVM) and constitutes a statistically significant improvement. A
detailed analysis and interpretation of structural features important for
classification shows the relevance of several specific hydrogen-bond donor
sites and aliphatic side chains to coreceptor specificity towards CCR5 or
CXCR4. Furthermore, an analysis of side chain orientation of the specificity
determining residues suggests a major role of one side of the V3 loop in the
selection of the coreceptor. The proposed method constitutes the first approach
to an improved prediction of coreceptor usage based on an original integration
of structural bioinformatics methods with statistical learning.
Last Change of the Resource (YYYY-MM-DD):2008-03-11
External Publication Status:published
Document Type:Article
Communicated by:Thomas Lengauer
Affiliations:MPI für Informatik/Computational Biology and Applied Algorithmics
Identifiers:LOCALID:C12573CC004A8E26-9809883503D11D5DC12572A500529A60-...
DOI:10.1371/journal.pcbi.0030058
ISSN:1553-734X
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