Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules

2005 ◽  
pp. 446-453 ◽  
Author(s):  
Jochen Supper ◽  
Pierre Dönnes ◽  
Oliver Kohlbacher
Keyword(s):  
Amino Acid ◽  
Peptide Binding ◽  
Decision Rules ◽  
Amino Acid Property ◽  
Acid Property

scholarly journals TMpro web server and web service: transmembrane helix prediction through amino acid property analysis

2007 ◽  
Vol 23 (20) ◽  
pp. 2795-2796 ◽  
Author(s):  
M. Ganapathiraju ◽  
C. J. Jursa ◽  
H. A. Karimi ◽  
J. Klein-Seetharaman
Keyword(s):  
Amino Acid ◽  
Web Service ◽  
Transmembrane Helix ◽  
Web Server ◽  
Amino Acid Property ◽  
Acid Property ◽  
Property Analysis ◽  
Transmembrane Helix Prediction

HIV-1 protease cleavage site prediction based on amino acid property

2009 ◽  
Vol 30 (1) ◽  
pp. 33-39 ◽  
Author(s):  
Bing Niu ◽  
Lin Lu ◽  
Liang Liu ◽  
Tian Hong Gu ◽  
Kai-Yan Feng ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cleavage Site ◽  
Amino Acid Property ◽  
Acid Property ◽  
Site Prediction ◽  
Protease Cleavage Site ◽  
Protease Cleavage ◽  
Cleavage Site Prediction ◽  
Hiv 1

scholarly journals Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information

2008 ◽  
Vol 4 (9) ◽  
pp. e1000181 ◽  
Author(s):  
Kai Wang ◽  
Jeremy A. Horst ◽  
Gong Cheng ◽  
David C. Nickle ◽  
Ram Samudrala
Keyword(s):  
Amino Acid ◽  
Amino Acid Property ◽  
Structure Evolution ◽  
Acid Property ◽  
Sequence Structure

scholarly journals A C-peptide complex with albumin and Zn2+ increases measurable GLUT1 levels in membranes of human red blood cells

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
M. Geiger ◽  
T. Janes ◽  
H. Keshavarz ◽  
S. Summers ◽  
C. Pinger ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Amino Acid ◽  
Blood Cells ◽  
Glucose Transporter ◽  
Peptide Binding ◽  
C Peptide ◽  
Amino Acid Peptide ◽  
Human Red Blood Cells

Abstract People with type 1 diabetes (T1D) require exogenous administration of insulin, which stimulates the translocation of the GLUT4 glucose transporter to cell membranes. However, most bloodstream cells contain GLUT1 and are not directly affected by insulin. Here, we report that C-peptide, the 31-amino acid peptide secreted in equal amounts with insulin in vivo, is part of a 3-component complex that affects red blood cell (RBC) membranes. Multiple techniques were used to demonstrate saturable and specific C-peptide binding to RBCs when delivered as part of a complex with albumin. Importantly, when the complex also included Zn2+, a significant increase in cell membrane GLUT1 was measured, thus providing a cellular effect similar to insulin, but on a transporter on which insulin has no effect.

scholarly journals HLA-DQB1 codon 57 is critical for peptide binding and recognition.

1996 ◽  
Vol 183 (3) ◽  
pp. 1253-1258 ◽  
Author(s):  
W W Kwok ◽  
M E Domeier ◽  
M L Johnson ◽  
G T Nepom ◽  
D M Koelle
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
Cell Clone ◽  
Peptide Binding ◽  
Class Ii ◽  
Binding Studies ◽  
Peptide Complex ◽  
Mhc Molecules ◽  
Hla Dq ◽  
T Cell Clone

The association of specific HLA-DQ alleles with autoimmunity is correlated with discrete polymorphisms in the HLA-DQ sequence that are localized within sites suitable for peptide recognition. The polymorphism at residue 57 of the DQB1 polypeptide is of particular interest since it may play a major structural role in the formation of a salt bridge structure at one end of the peptide-binding cleft of the DQ molecules. This polymorphism at residue 57 is a recurrent feature of HLA-DQ evolution, occurring in multiple distinct allelic families, which implies a functional selection for maintaining variation at this position in the class II molecule. We directly tested the amino acid polymorphism at this site as a determinant for peptide binding and for antigen-specific T cell stimulation. We found that a single Ala-->Asp amino acid 57 substitution in an HLA-DQ3.2 molecule regulated binding of an HSV-2 VP-16-derived peptide. A complementary single-residue substitution in the peptide abolished its binding to DQ3.2 and converted it to a peptide that can bind to DQ3.1 and DQ3.3 Asp-57-positive MHC molecules. These binding studies were paralleled by specific T cell recognition of the class II-peptide complex, in which the substituted peptide abolished T cell reactivity, which was directed to the DQ3.2-peptide complex, whereas the same T cell clone recognized the substituted peptide presented by DQ3.3, a class II restriction element differing from DQ3.2 only at residue 57. This structural and functional complementarity for residue 57 and a specific peptide residue identifies this interaction as a key controlling determinant of restricted recognition in HLA-DQ-specific immune response.

scholarly journals Genetic risk factors for sclerotic graft-versus-host disease

Blood ◽  
2016 ◽  
Vol 128 (11) ◽  
pp. 1516-1524 ◽  
Author(s):  
Yoshihiro Inamoto ◽  
Paul J. Martin ◽  
Mary E. D. Flowers ◽  
Stephanie J. Lee ◽  
Paul A. Carpenter ◽  
...  
Keyword(s):  
Risk Factors ◽  
Amino Acid ◽  
Graft Versus Host Disease ◽  
Genetic Risk ◽  
Peptide Binding ◽  
Binding Pocket ◽  
Genetic Risk Factors ◽  
Amino Acid Substitutions ◽  
Graft Versus Host ◽  
Key Points

Key Points SNPs in BANK1, CD247, and HLA-DPA1 were associated with risk of sclerotic GVHD. HLA-DPA1∼B1 haplotypes and amino acid substitutions in the HLA-DP P1 peptide-binding pocket were associated with risk of sclerotic GVHD.

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