Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.
BACKGROUND
Quantitative information on the types of inter-atomic interactions at the MHC-peptide interface will provide insights to backbone/sidechain atom preference during binding. Qualitative descriptions of such interactions in each complex have been documented by protein crystallographers. However, no comprehensive report is available to account for the common types of inter-atomic interactions in a set of MHC-peptide complexes characterized by variation in MHC allele and peptide sequence. The available x-ray crystallography data for these complexes in the Protein Databank (PDB) provides an opportunity to identify the prevalent types of such interactions at the binding interface.


RESULTS
We calculated the percentage distributions of four types of interactions at varying inter-atomic distances. The mean percentage distribution for these interactions and their standard deviation about the mean distribution is presented. The prevalence of SS and SB interactions at the MHC-peptide interface is shown in this study. SB is clearly dominant at an inter-atomic distance of 3A.


CONCLUSIONS
The prevalently dominant SB interactions at the interface suggest the importance of peptide backbone conformation during MHC-peptide binding. Currently, available algorithms are developed for protein sidechain prediction upon fixed backbone template. This study shows the preference of backbone atoms in MHC-peptide binding and hence emphasizes the need for accurate peptide backbone prediction in quantitative MHC-peptide binding calculations.
Adrian
Png Eak Hock
PE
National University of Singapore, Department of Microbiology, Medical Drive, Singapore. micpnga@nus.edu.sg
Rajaseger
Ganapathy
G
Mathura
Venkatarajan Subramanian
VS
Sakharkar
Meena Kishore
MK
Kangueane
Pandjassarame
P
D001665:Binding Sites; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006649:Histocompatibility Antigens / Q000737:chemistry* / Q000378:metabolism*; D046911:Macromolecular Substances; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation
D006649:Histocompatibility Antigens; D046911:Macromolecular Substances; D010455:Peptides