Information Technology Reference
In-Depth Information
1.5.2 IMGT
®
Structure Analysis Tools
Several on-line IMGT
®
structure analysis tools are available for the analysis of 2D
and 3D structures, and particularly for the comparison of V, C, and G domains. The
IMGT/StructuralQuery tool (Kaas et al. 2004) analyses the interactions of the resi-
dues of the antigen receptors (IG and TR), MHC, RPI, antigens and ligands. The
contacts are described per domain (intra- and inter-domain contacts) and annotated in
term of IMGT labels (chains, domains), positions (IMGT unique numbering) with
backbone or side-chain implication. IMGT/StructuralQuery allows users to retrieve
the IMGT/3Dstructure-DB entries, based on specific structural characteristics: φ (phi)
and ψ (psi) angles, accessible surface area (ASA), amino acid type, distance in
angstroms between amino acids, CDR-IMGT lengths. IMGT/StructuralQuery is
currently available for the V-DOMAINs. IMGT/DomainGapAlign aligns users'
amino acid sequences against the closest reference sequences from the IMGT
domain sequence directory. IMGT/DomainGapAlign also provides the IMGT gaps
and thus allows users to graphically represent their domain sequences with the
IMGT/Collier-de-Perles tool. IMGT/DomainSuperimpose allows superimposing two
3D structures of domains from IMGT/3Dstructure-DB.
1.5.3 IMGT
®
Structural Web Resources
The IMGT
®
structural Web resources are compiled in the IMGT Repertoire “2D and
3D structures” section which includes 2D representations or IMGT Colliers de Perles
(Lefranc et al. 2003; Lefranc et al. 2005b; Lefranc et al. 2005c; Ruiz and Lefranc
2002; Kaas and Lefranc 2007), 3D representations, FR-IMGT and CDR-IMGT
lengths, and amino acid physico-chemical characteristic profiles (Pommié, Sabatier,
Lefranc, and Lefranc 2004).
In order to appropriately analyse the amino acid resemblances and differences
between IG, TR, MHC, and RPI chains, 11 IMGT classes were defined for the
“chemical characteristics” amino acid properties and used to set up IMGT Colliers
de Perles reference profiles (Pommié et al. 2004). The IMGT Colliers de Perles ref-
erence profiles allow one to easily compare amino acid properties at each position
whatever the domain, the chain, the receptor, or the species. The IG and TR variable
and constant domains represent a privileged situation for the analysis of amino acid
properties in relation to 3D structures, by the conservation of their 3D structure de-
spite divergent amino acid sequences, and by the considerable amount of genomic
(IMGT Repertoire), structural (IMGT/3Dstructure-DB), and functional data avail-
able. These data are not only useful to study mutations and allele polymorphisms, but
are also needed to establish correlations between amino acids in the protein se-
quences and 3D structures and to determine amino acids potentially involved in the
immunogenicity.
