PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors

2013 ◽  
Vol 387 (1-2) ◽  
pp. 293-302 ◽  
Author(s):  
Thammakorn Saethang ◽  
Osamu Hirose ◽  
Ingorn Kimkong ◽  
Vu Anh Tran ◽  
Xuan Tho Dang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Mhc Class I ◽  
Molecular Similarity ◽  
Class I ◽  
Binding Peptides

A set of new amino acid descriptors applied in prediction of MHC class I binding peptides

2009 ◽  
Vol 44 (3) ◽  
pp. 1144-1154 ◽  
Author(s):  
Guizhao Liang ◽  
Li Yang ◽  
Zecong Chen ◽  
Hu Mei ◽  
Mao Shu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Mhc Class I ◽  
Class I ◽  
Amino Acid Descriptors ◽  
Binding Peptides

scholarly journals Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3' UTR

2014 ◽  
Vol 111 (15) ◽  
pp. 5670-5675 ◽  
Author(s):  
E. Goodenough ◽  
T. M. Robinson ◽  
M. B. Zook ◽  
K. M. Flanigan ◽  
J. F. Atkins ◽  
...  
Keyword(s):  
Mhc Class I ◽  
Stop Codon ◽  
Class I ◽  
Binding Peptides

scholarly journals Amino Acid Polymorphisms in Hepatitis C Virus Core Affect Infectious Virus Production and Major Histocompatibility Complex Class I Molecule Expression

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Megumi Tasaka-Fujita ◽  
Nao Sugiyama ◽  
Wonseok Kang ◽  
Takahiro Masaki ◽  
Asako Murayama ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Mhc Class I ◽  
Infectious Virus ◽  
Core Protein ◽  
Virus Production ◽  
Class I ◽  
Histocompatibility Complex

Abstract Amino acid (aa) polymorphisms in the hepatitis C virus (HCV) genotype 1b core protein have been reported to be a potent predictor for poor response to interferon (IFN)-based therapy and a risk factor for hepatocarcinogenesis. We investigated the effects of these polymorphisms with genotype 1b/2a chimeric viruses that contained polymorphisms of Arg/Gln at aa 70 and Leu/Met at aa 91. We found that infectious virus production was reduced in cells transfected with chimeric virus RNA that had Gln at aa 70 (aa70Q) compared with RNA with Arg at aa 70 (aa70R). Using flow cytometry analysis, we confirmed that HCV core protein accumulated in aa70Q clone transfected cells and it caused a reduction in cell-surface expression of major histocompatibility complex (MHC) class I molecules induced by IFN treatment through enhanced protein kinase R phosphorylation. We could not detect any effects due to the polymorphism at aa 91. In conclusion, the polymorphism at aa 70 was associated with efficiency of infectious virus production and this deteriorated virus production in strains with aa70Q resulted in the intracellular accumulation of HCV proteins and attenuation of MHC class I molecule expression. These observations may explain the strain-associated resistance to IFN-based therapy and hepatocarcinogenesis of HCV.

scholarly journals Prediction of MHC class I binding peptides using profile motifs

2002 ◽  
Vol 63 (9) ◽  
pp. 701-709 ◽  
Author(s):  
Pedro A Reche ◽  
John-Paul Glutting ◽  
Ellis L Reinherz
Keyword(s):  
Mhc Class I ◽  
Class I ◽  
Binding Peptides
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