PMID- 18450000
OWN - NLM
STAT- MEDLINE
DCOM- 20080605
LR  - 20081121
IS  - 1064-3745 (Print)
IS  - 1064-3745 (Linking)
VI  - 409
DP  - 2007
TI  - Grouping of class I HLA alleles using electrostatic distribution maps of the 
      peptide binding grooves.
PG  - 175-81
LID - 10.1007/978-1-60327-118-9_12 [doi]
AB  - Human leukocyte antigen (HLA) molecules involved in immune function by binding to 
      short peptides (8-20 residues) have different sequences in different individuals 
      belonging to distinct ethnic population. Hence, the peptide-binding function of 
      HLA alleles is specific. Class I HLA alleles (alternative forms of a gene) are 
      associated with CD8+ T cells, and their allele-specific sequence information is 
      available at the IMGT/HLA database. The available sequences are one-dimensional 
      (ID), and the peptide-binding functional inference often requires 3-dimensional 
      (3D) structural models of respective alleles. Hence, 3D structures were 
      constructed for 1,000 class I HLA alleles (310 A, 570 B, and 120 C) using 
      MODELLER (a comparative protein modeling program for modeling protein 
      structures). The electrostatic distribution maps were generated for each modeled 
      structure using Deep View (Swiss PDB Viewer Version 3.7). The 1,000 models were 
      then grouped into different categories by visual inspection of their 
      electrostatic distribution maps in the peptide binding grooves. The distribution 
      of the models based on electrostatic distribution was 30% negative (300), 1% 
      positive (12), 8% neutral (84), and 60% (604) mixed (random mixture of negative, 
      positive, and neutral). This grouping provides insight toward the inference for 
      functional overlap among HLA alleles.
FAU - Kangueane, Pandjassarame
AU  - Kangueane P
AD  - School of Mechanical and Aerospace Engineering, Nanyang Technological University, 
      Singapore.
FAU - Sakharkar, Meena Kishore
AU  - Sakharkar MK
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Binding Sites
MH  - Computational Biology
MH  - Computer Simulation
MH  - Genes, MHC Class I
MH  - HLA Antigens/*chemistry/*classification/genetics
MH  - Immunogenetics
MH  - Models, Molecular
MH  - Protein Binding
MH  - Protein Conformation
MH  - Static Electricity
EDAT- 2008/05/03 09:00
MHDA- 2008/06/06 09:00
CRDT- 2008/05/03 09:00
PHST- 2008/05/03 09:00 [pubmed]
PHST- 2008/06/06 09:00 [medline]
PHST- 2008/05/03 09:00 [entrez]
AID - 10.1007/978-1-60327-118-9_12 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2007;409:175-81. doi: 10.1007/978-1-60327-118-9_12.