High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics

  • Hunjoong Lee
  • Zhaohui Li
  • Antonina Silkov
  • Markus Fischer
  • Donald Petrey
  • Barry Honig
  • Diana Murray
Article

Abstract

SkyLine, a high-throughput homology modeling pipeline tool, detects and models true sequence homologs to a given protein structure. Structures and models are stored in SkyBase with links to computational function annotation, as calculated by MarkUs. The SkyLine/SkyBase/MarkUs technology represents a novel structure-based approach that is more objective and versatile than other protein classification resources. This structure-centric strategy provides a multi-dimensional organization and coverage of protein space at the levels of family, function, and genome. The concept of “modelability”, the ability to model sequences on related structures, provides a reliable criterion for membership in a protein family (“leverage”) and underlies the unique success of this approach. The overall procedure is illustrated by its application to START domains, which comprise a Biomedical Theme for the Northeast Structural Genomics Consortium as part of the Protein Structure Initiative. START domains are typically involved in the non-vesicular transport of lipids. While 19 experimentally determined structures are available, the family, whose evolutionary hierarchy is not well determined, is highly sequence diverse, and the ligand-binding potential of many family members is unknown. The SkyLine/SkyBase/MarkUs approach provides significant insights and predicts: (1) many more family members (~4,000) than any other resource; (2) the function for a large number of unannotated proteins; (3) instances of START domains in genomes from which they were thought to be absent; and (4) the existence of two types of novel proteins, those containing dual START domain and those containing N-terminal START domains.

Keywords

Homology modeling Structural genomics Bioinformatics Protein function annotation START domain Arabidopsis thaliana 

Abbreviations

BA

Birch antigen

BAC

Bacterial

CSD

Classical START domain

MLN64

Metastatic lymph node 64 protein

NCBI

National Center for Biotechnology Information

NESG

Northeast Structural Genomics Consortium

START

StAR-related lipid transfer

PCTP

Phosphatidylcholine transfer protein

PDB

Protein data bank

pG

A score derived from the log-transformed length-normalized integration over the residue by residue ProsaII structure evaluation profile

PSI

Protein structure initiative

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Hunjoong Lee
    • 1
  • Zhaohui Li
    • 1
  • Antonina Silkov
    • 1
  • Markus Fischer
    • 2
  • Donald Petrey
    • 2
  • Barry Honig
    • 2
  • Diana Murray
    • 1
  1. 1.Department of Pharmacology, College of Physicians and Surgeons of Columbia UniversityCenter for Computational Biology and BioinformaticsNew YorkUSA
  2. 2.Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and BioinformaticsColumbia UniversityNew YorkUSA

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