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J. Mol. Model. 1997, 3, 117-123
Molecular Modeling of Immunoglobulin Superfamily Proteins:
Predicting the Three-Dimensional Structure of the Extracellular
Domain of CTLA-4 (CD152)
Jürgen Bajorath 1,2* and Peter S. Linsley 1
1 Bristol-Myers Squibb Pharmaceutical Research Institute, 3005 First Avenue, Seattle, WA 98121, USA; Tel: (206) 727-3612; Fax: (206) 727-3602
bajorath@protos.bms.com
2 Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
Abstract
The interactions between CD28/CTLA-4 (CD152) on T cells and their ligands CD80/CD86 on antigen presenting cells provide costimulatory signals critical for T cell activation. CD28/CTLA-4 and CD80/CD86 are members of the immunoglobulin superfamily (IgSF). CD28 and CTLA-4 both contain a single extracellular immunoglobulin (Ig) domain which binds CD80/CD86. Here we report modeling studies on the three-dimensional (3D) structure of the CTLA-4 ligand binding domain. Since CTLA-4 displays only very weak sequence homology to proteins with known 3D structure, conventional modeling techniques were difficult to apply. Structure-oriented sequence comparison, consensus residue analysis, conformational searching, and inverse folding analysis were used to aid in the generation of a comparative CTLA-4 model. Regions of high and low prediction confidence were identified, and the sequence-structure compatibility of the model was determined. Characteristics of the modeled structure, which resembles an Ig V-domain, were analyzed, and the model was used to map N-linked glycosylation sites and residues critical for CTLA-4 function. The modeling approach described here can be applied to predict 3D structures of other IgSF proteins.
Figure 1. Solid ribbon representation of the CTLA-4 model. The left image focuses on the beta-sheet surface formed by the A'GFCC'C'' strands (yellow). The center image shows a side view of the model. The B-C (CDR1) and F-G (CDR3) loops are colored green and red, respectively. The right image focuses on the ABED beta-sheet surface (magenta) of the domain.
Figure 2. ProsaII (Sippl, 1993) energy profile of the CTLA-4 model, calculated using a 50 residue window for energy averaging at each position. Pairwise residue interaction energy is given in E/kT (E, interaction energy in kcal/mol (1 kcal = 4.18 kJ); k, Boltzmann constant; T, absolute temperature in K). The profile trace indicates that the sequence-structure compatibility of the model is sound.
Figure 3. Mapping of CTLA-4 residues. The protein backbone of the model is shown in grey. In this orientation, the A'GFCC'C'' face is on top and the CDR-analogous loops are on the right. The canonical Ig disulfide bond and an additional disulfide bond are shown in magenta and gold, respectively. Potential N-linked glycosylation sites in CTLA-4 (green) and residues which, when mutated, affect CTLA-4 function are also shown.
Keywords: Immunoglobulin superfamily, Protein structure prediction, Sequence-structure analysis, Comparative modeling, Model assessment
* Author to whom correspondence should be addressed.
J.Mol.Model. (electronic publication) - ISSN 0948-5023
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