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Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.

Adrian PE, Rajaseger G, Mathura VS, Sakharkar MK, Kangueane P - BMC Struct. Biol. (2002)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National University of Singapore, Department of Microbiology, Medical Drive, Singapore. micpnga@nus.edu.sg

ABSTRACT

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.

Conclusion: 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.

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Standard deviation about the mean percentage distribution of the four interaction types in class I MHC-peptide complexes. Inter-atomic distances are expressed in Å units.
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Figure 5: Standard deviation about the mean percentage distribution of the four interaction types in class I MHC-peptide complexes. Inter-atomic distances are expressed in Å units.

Mentions: We calculated the percentage prominence for each of the four types of interactions (BB, SS, BS and SB) at the interface of these complexes (Figures 1 and 2). The backbone or sidechain atom preference at the interface induced by MHC-peptide sequence variation is estimated by calculating the mean percentage for each type in the dataset (Figures 3 and 4). The preferences for the interaction types are found to be similar between complexes but not identical (Figures 1 and 2). Therefore, we calculated the standard deviation about the mean percentage preference for each of the interaction types in both the data sets (Figures 5 and 6).


Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.

Adrian PE, Rajaseger G, Mathura VS, Sakharkar MK, Kangueane P - BMC Struct. Biol. (2002)

Standard deviation about the mean percentage distribution of the four interaction types in class I MHC-peptide complexes. Inter-atomic distances are expressed in Å units.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC113755&req=5

Figure 5: Standard deviation about the mean percentage distribution of the four interaction types in class I MHC-peptide complexes. Inter-atomic distances are expressed in Å units.
Mentions: We calculated the percentage prominence for each of the four types of interactions (BB, SS, BS and SB) at the interface of these complexes (Figures 1 and 2). The backbone or sidechain atom preference at the interface induced by MHC-peptide sequence variation is estimated by calculating the mean percentage for each type in the dataset (Figures 3 and 4). The preferences for the interaction types are found to be similar between complexes but not identical (Figures 1 and 2). Therefore, we calculated the standard deviation about the mean percentage preference for each of the interaction types in both the data sets (Figures 5 and 6).

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National University of Singapore, Department of Microbiology, Medical Drive, Singapore. micpnga@nus.edu.sg

ABSTRACT

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.

Conclusion: 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.

Show MeSH