Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

Kajava, A. V. and Kobe, B. (2002) Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information. Protein Science, 11 5: 1082-1090. doi:10.1110/ps.4010102


Author Kajava, A. V.
Kobe, B.
Title Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information
Journal name Protein Science   Check publisher's open access policy
ISSN 0961-8368
Publication date 2002
Sub-type Article (original research)
DOI 10.1110/ps.4010102
Open Access Status
Volume 11
Issue 5
Start page 1082
End page 1090
Total pages 9
Place of publication Plainview
Publisher Cold Spring Harbor Laboratory Press
Collection year 2002
Language eng
Subject C1
270105 Cellular Interactions (incl. Adhesion, Matrix, Cell Wall)
780105 Biological sciences
Abstract The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.
Keyword Biochemistry & Molecular Biology
Crystal Structure
Leucine-rich Repeat
Molecular Modeling
Solenoid-like Proteins
Structural Bioinformatics
Crystal-structure
Molecular Characterization
Chorionic-gonadotropin
Signal-transduction
Binding Protein
Domain
Motif
Sequence
Receptor
Expression
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Tue, 14 Aug 2007, 17:22:32 EST