scholarly journals Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2

2015 ◽  
Vol 290 (43) ◽  
pp. 26021-26032 ◽  
Author(s):  
Anastasia Mpakali ◽  
Petros Giastas ◽  
Nikolas Mathioudakis ◽  
Irene M. Mavridis ◽  
Emmanuel Saridakis ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Antigenic Peptide ◽  
Structural Basis ◽  
Peptide Recognition

scholarly journals Structural Basis For Antigenic Peptide Precursor Processing by the Endoplasmic Reticulum Aminopeptidase ERAP1

2011 ◽  
Vol 25 (S1) ◽  
Author(s):  
Tina T Nguyen ◽  
Shih‐Chung Chang ◽  
Irini Evnouchidou ◽  
Ian York ◽  
Christos Zikos ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Antigenic Peptide ◽  
Structural Basis ◽  
Precursor Processing ◽  
Peptide Precursor

scholarly journals Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1

2011 ◽  
Vol 18 (5) ◽  
pp. 604-613 ◽  
Author(s):  
Tina T Nguyen ◽  
Shih-Chung Chang ◽  
Irini Evnouchidou ◽  
Ian A York ◽  
Christos Zikos ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Antigenic Peptide ◽  
Structural Basis ◽  
Precursor Processing ◽  
Peptide Precursor

scholarly journals Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum

Science ◽  
2018 ◽  
Vol 360 (6385) ◽  
pp. 215-219 ◽  
Author(s):  
Katharina Braunger ◽  
Stefan Pfeffer ◽  
Shiteshu Shrimal ◽  
Reid Gilmore ◽  
Otto Berninghausen ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Transport ◽  
Structural Basis ◽  
Coupling Protein

scholarly journals Structural basis of internal peptide recognition by PDZ domains using molecular dynamics simulations

2019 ◽  
Author(s):  
Neetu Sain ◽  
Debasisa Mohanty
Keyword(s):  
Pdz Domain ◽  
Md Simulations ◽  
Open Loop ◽  
Structural Basis ◽  
Pdz Domains ◽  
Peptide Recognition ◽  
Interaction Partners ◽  
Internal Peptide ◽  
Dynamics Simulations ◽  
Loop Conformation

AbstractPDZ domains are important peptide recognition modules which usually recognize short C-terminal stretches of their interaction partners, but certain PDZ domains can also recognize internal peptides in the interacting proteins. Due to the scarcity of data on internal peptide recognition and lack of understanding of the mechanistic details of internal peptide recognition, identification of PDZ domains capable of recognizing internal peptides has been a difficult task. Since Par-6 PDZ domain can recognize both C-terminal and internal peptides, we have carried out multiple explicit solvent MD simulations of 1 μs duration on free and peptide bound Par-6 PDZ to decipher mechanistic details of internal peptide recognition. These simulations have been analyzed to identify residues which play a crucial role in internal peptide recognition by PDZ domains. Based on the conservation profile of the identified residues, we have predicted 47 human PDZ domains to be capable of recognizing internal peptides in human. We have also investigated how binding of CDC42 to the CRIB domain adjacent to the Par6 PDZ allosterically modulate the peptide recognition by Par6 PDZ. Our MD simulations on CRIB-Par6_PDZ di-domain in isolation as well as in complex with CDC42, indicate that in absence of CDC42 the adjacent CRIB domain induces open loop conformation of PDZ facilitating internal peptide recognition. On the other hand, upon binding of CDC42 to the CRIB domain, Par6 PDZ adopts closed loop conformation required for recognition of C-terminus peptides. These results provide atomistic details of how binding of interaction partners onto adjacent domains can allosterically regulate substrate binding to PDZ domains. In summary, MD simulations provide novel insights into the modulation of substrate recognition preference of PDZ by specific peptides, adjacent domains and binding of interaction partners at allosteric sites.

scholarly journals Structural basis of signal peptide recognition by the signal recognition particle

2012 ◽  
Vol 68 (a1) ◽  
pp. s38-s38
Author(s):  
E. Sauer-Eriksson ◽  
S. Huang ◽  
G. Meriläinen ◽  
K. Brännström ◽  
T. Hainzl
Keyword(s):  
Signal Peptide ◽  
Signal Recognition Particle ◽  
Structural Basis ◽  
Signal Recognition ◽  
Peptide Recognition

scholarly journals ERAAP Synergizes with MHC Class I Molecules to Make the Final Cut in the Antigenic Peptide Precursors in the Endoplasmic Reticulum

Immunity ◽  
2006 ◽  
Vol 25 (5) ◽  
pp. 795-806 ◽  
Author(s):  
Takayuki Kanaseki ◽  
Nicolas Blanchard ◽  
Gianna Elena Hammer ◽  
Federico Gonzalez ◽  
Nilabh Shastri
Keyword(s):  
Endoplasmic Reticulum ◽  
Mhc Class I ◽  
Class I ◽  
Antigenic Peptide ◽  
Peptide Precursors ◽  
Mhc Class I Molecules
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