Statistically Derived Amino Acid Pair Potentials: Applications to Protein Folding and Protein-Protein Interactions

1991 ◽  
Author(s):  
S. Doniach
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Protein Interactions ◽  
Amino Acid Pair ◽  
Protein Protein Interactions ◽  
Pair Potentials

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

Engineering an acetyllysine reader with photocrosslinking amino acid for interactome profiling

2021 ◽  
Author(s):  
Babu Sudhamalla ◽  
Anirban Roy ◽  
Soumen Barman ◽  
Jyotirmayee Padhan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Interactions ◽  
Unnatural Amino Acids ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Powerful Approach

The site-specific installation of light-activable crosslinker unnatural amino acids offers a powerful approach to trap transient protein-protein interactions both in vitro and in vivo. Herein, we engineer a bromodomain to...

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.

scholarly journals Engineering bromodomains with a photoactive amino acid by engaging ‘Privileged’ tRNA synthetases

2020 ◽  
Vol 56 (25) ◽  
pp. 3641-3644
Author(s):  
Shana Wagner ◽  
Babu Sudhamalla ◽  
Philip Mannes ◽  
Sushma Sappa ◽  
Sam Kavoosi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chemical Synthesis ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Trna Synthetases

An improved chemical synthesis, site-specific incorporation and enhanced photo-crosslinking ability of tmdF have been demonstrated in the context of protein–protein interactions.

scholarly journals Single Amino Acid Replacements in RocA Disrupt Protein-Protein Interactions To Alter the Molecular Pathogenesis of Group A Streptococcus

2020 ◽  
Vol 88 (11) ◽  
Author(s):  
Paul E. Bernard ◽  
Amey Duarte ◽  
Mikhail Bogdanov ◽  
James M. Musser ◽  
Randall J. Olsen
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Molecular Pathogenesis ◽  
Single Amino Acid ◽  
Accessory Protein ◽  
Protein Protein Interactions ◽  
Tissue Destruction ◽  
Intact Cells ◽  
Group A

ABSTRACT Group A Streptococcus (GAS) is a human-specific pathogen and major cause of disease worldwide. The molecular pathogenesis of GAS, like many pathogens, is dependent on the coordinated expression of genes encoding different virulence factors. The control of virulence regulator/sensor (CovRS) two-component system is a major virulence regulator of GAS that has been extensively studied. More recent investigations have also involved regulator of Cov (RocA), a regulatory accessory protein to CovRS. RocA interacts, in some manner, with CovRS; however, the precise molecular mechanism is unknown. Here, we demonstrate that RocA is a membrane protein containing seven transmembrane helices with an extracytoplasmically located N terminus and cytoplasmically located C terminus. For the first time, we demonstrate that RocA directly interacts with itself (RocA) and CovS, but not CovR, in intact cells. Single amino acid replacements along the entire length of RocA disrupt RocA-RocA and RocA-CovS interactions to significantly alter the GAS virulence phenotype as defined by secreted virulence factor activity in vitro and tissue destruction and mortality in vivo. In summary, we show that single amino acid replacements in a regulatory accessory protein can affect protein-protein interactions to significantly alter the virulence of a major human pathogen.

Regulative interactions of the osmosensing C-terminal domain in the trimeric glycine betaine transporter BetP from Corynebacterium glutamicum

2009 ◽  
Vol 390 (8) ◽  
Author(s):  
Reinhard Krämer ◽  
Christine Ziegler
Keyword(s):  
Amino Acid ◽  
Corynebacterium Glutamicum ◽  
Protein Interactions ◽  
Regulation Mechanism ◽  
Protein Protein Interactions ◽  
Molecular Switching ◽  
X Ray ◽  
X Ray Crystallography ◽  
Terminal Domain ◽  
Domain Reorientation

Abstract Activation of the osmoregulated trimeric betaine transporter BetP from Corynebacterium glutamicum was shown to depend mainly on the correct folding and integrity of its 55 amino acid long, partly α-helical C-terminal domain. Reorientation of the three C-terminal domains in the BetP trimer indicates different lipid-protein and protein-protein interactions of the C-terminal domain during osmoregulation. A regulation mechanism is suggested where this domain switches the transporter from the inactive to the active state. Interpretation of recently obtained electron and X-ray crystallography data of BetP led to a structure-function based model of C-terminal molecular switching involved in osmoregulation.

scholarly journals A bifunctional amino acid to study protein–protein interactions

RSC Advances ◽  
2020 ◽  
Vol 10 (69) ◽  
pp. 42076-42083
Author(s):  
Tangpo Yang ◽  
Xin Li ◽  
Xiang David Li
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Protein Protein Interactions

dzANA is a novel bifunctional (photo-reactive and bioorthogonal) amino acid to study protein–protein interactions.

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