Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules.
We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the C alpha (I) - C alpha (J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units--strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures leads to the identification of two geometrical core sets of C alpha atom positions for the VL and VH domains. Applications of the core sets are described.
Department of Mathematics, Rutgers University, New Brunswick, NJ 08903, USA.
I
I
Gelfand
A
A
Kister
C
C
Kulikowski
O
O
Stoyanov
D000465:Algorithms; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry*; D007147:Immunoglobulin Light Chains / Q000737:chemistry*; D007135:Immunoglobulin Variable Region / Q000737:chemistry*; D008956:Models, Chemical; D011487:Protein Conformation
D007143:Immunoglobulin Heavy Chains; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region