Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein–protein Interactions

2019 ◽  
Vol 21 (35) ◽  
pp. 18958-18969 ◽  
Author(s):  
Ercheng Wang ◽  
Gaoqi Weng ◽  
Huiyong Sun ◽  
Hongyan Du ◽  
Feng Zhu ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Interactions ◽  
Conformational Transitions ◽  
Protein Recognition ◽  
Enhanced Sampling ◽  
Protein Protein Interactions ◽  
Dielectric Model

Enhanced sampling has been extensively used to capture the conformational transitions in protein folding, but it attracts much less attention in the studies of protein–protein recognition.

Neuronal SNARE complex: A protein folding system with intricate protein-protein interactions, and its common neuropathological hallmark, SNAP25

2019 ◽  
Vol 122 ◽  
pp. 196-207 ◽  
Author(s):  
Srijeeb Karmakar ◽  
Laipubam Gayatri Sharma ◽  
Abhishek Roy ◽  
Anjali Patel ◽  
Lalit Mohan Pandey
Keyword(s):  
Protein Folding ◽  
Protein Interactions ◽  
Snare Complex ◽  
Protein Protein Interactions

Divide-and-Link Peptide Docking: A Fragment-Based Peptide Docking Protocol

2021 ◽  
Author(s):  
Lu Sun ◽  
Tingting Fu ◽  
Dan Zhao ◽  
Hongjun Fan ◽  
Shijun Zhong
Keyword(s):  
Protein Folding ◽  
Drug Design ◽  
Protein Interactions ◽  
Structural Data ◽  
Peptide Drug ◽  
Protein Protein Interactions ◽  
Peptide Docking ◽  
Docking Protocol ◽  
Peptide Interaction

Protein-peptide interaction is crucial for various important cellular regulations, and also a basis for understanding protein-protein interactions, protein folding and peptide drug design. Due to the limited structural data obtained...

scholarly journals Methylation of PhoP by CheR Regulates Salmonella Virulence

mBio ◽  
2021 ◽  
Author(s):  
Yang Su ◽  
Jianhui Li ◽  
Wenting Zhang ◽  
Jinjing Ni ◽  
Rui Huang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Response Regulator ◽  
Protein Recognition ◽  
Amino Acid Residues ◽  
Biological Functions ◽  
Protein Protein Interactions ◽  
Two Component System ◽  
Two Component ◽  
Salmonella Virulence

Posttranslational modifications (PTMs) play an important role in regulating enzyme activities, protein-protein interactions, or DNA-protein recognition and, consequently, modulate many biological functions. We demonstrated that PhoP, the response regulator of PhoP/PhoQ two-component system, could be methylated on several evolutionally conserved amino acid residues.

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