Influence of Halide Binding on the Hydrogen Bonding Network in the Active Site of Salinibacter Sensory Rhodopsin I

Biochemistry ◽  
2012 ◽  
Vol 51 (44) ◽  
pp. 8802-8813 ◽  
Author(s):  
Louisa Reissig ◽  
Tatsuya Iwata ◽  
Takashi Kikukawa ◽  
Makoto Demura ◽  
Naoki Kamo ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Active Site ◽  
Sensory Rhodopsin ◽  
Hydrogen Bonding Network ◽  
Sensory Rhodopsin I

scholarly journals Kinetic Study of CO2 Hydration by Small-Molecule Catalysts with A Second Coordination Sphere that Mimic the Effect of the Thr-199 Residue of Carbonic Anhydrase

Biomimetics ◽  
2019 ◽  
Vol 4 (4) ◽  
pp. 66
Author(s):  
Park ◽  
Lee
Keyword(s):  
Hydrogen Bonding ◽  
Carbonic Anhydrase ◽  
Coordination Sphere ◽  
Active Site ◽  
Hydration Reaction ◽  
Ph Titration ◽  
Hydration Rate ◽  
Pka Value ◽  
Secondary Coordination Sphere ◽  
Hydrogen Bonding Network

Zinc complexes were synthesized as catalysts that mimic the ability of carbonic anhydrase (CA) for the CO2 hydration reaction (H2O + CO2 → H+ + HCO3-). For these complexes, a tris(2-pyridylmethyl)amine (TPA) ligand mimicking only the active site, and a 6-((bis(pyridin-2-ylmethyl)amino)methyl)pyridin-2-ol (TPA-OH) ligand mimicking the hydrogen-bonding network of the secondary coordination sphere of CA were used. Potentiometric pH titration was used to determine the deprotonation ability of the Zn complexes, and their pKa values were found to be 8.0 and 6.8, respectively. Stopped-flow spectrophotometry was used to confirm the CO2 hydration rate. The rate constants were measured to be 648.4 and 730.6 M-1s-1, respectively. The low pKa value was attributed to the hydrogen-bonding network of the secondary coordination sphere of the catalyst that mimics the behavior of CA, and this was found to increase the CO2 hydration rate of the catalyst.

scholarly journals Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+Ions and the Hydrogen-Bonding Network in the Active Site

Biochemistry ◽  
2016 ◽  
Vol 55 (27) ◽  
pp. 3834-3846 ◽  
Author(s):  
Melek N. Ucisik ◽  
Philip C. Bevilacqua ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Active Site ◽  
Hydrogen Bonding Network

Signal relay from sensory rhodopsin I to the cognate transducer HtrI: Assessing the critical change in hydrogen-bonding between Tyr-210 and Asn-53

2010 ◽  
Vol 150 (1-3) ◽  
pp. 23-28 ◽  
Author(s):  
Ionela Radu ◽  
Ivan L. Budyak ◽  
Torben Hoomann ◽  
Young Jun Kim ◽  
Martin Engelhard ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Sensory Rhodopsin ◽  
Signal Relay ◽  
Sensory Rhodopsin I ◽  
Critical Change

scholarly journals Streptomyces albus G serine β-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes

1992 ◽  
Vol 282 (1) ◽  
pp. 189-195 ◽  
Author(s):  
J Lamotte-Brasseur ◽  
F Jacob-Dubuisson ◽  
G Dive ◽  
J M Frère ◽  
J M Ghuysen
Keyword(s):  
Hydrogen Bonding ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Site Directed Mutagenesis ◽  
Network Configuration ◽  
Beta Lactam ◽  
Beta Lactamases ◽  
Class A ◽  
Streptomyces Albus ◽  
Hydrogen Bonding Network

In previous studies, several amino acids of the active site of class A beta-lactamases have been modified by site-directed mutagenesis. On the basis of the catalytic mechanism proposed for the Streptomyces albus G beta-lactamase [Lamotte-Brasseur, Dive, Dideberg, Charlier, Frère & Ghuysen (1991) Biochem. J. 279, 213-221], the influence that these mutations exert on the hydrogen-bonding network of the active site has been analysed by molecular mechanics. The results satisfactorily explain the effects of the mutations on the kinetic parameters of the enzyme's activity towards a set of substrates. The present study also shows that, upon binding a properly structured beta-lactam compound, the impaired cavity of a mutant enzyme can readopt a functional hydrogen-bonding-network configuration.

Hydrogen-bonding network in heme active site regulates the hydrolysis activity of myoglobin

2015 ◽  
Vol 111 ◽  
pp. 9-15 ◽  
Author(s):  
Jin Zeng ◽  
Yuan Zhao ◽  
Wei Li ◽  
Xiangshi Tan ◽  
Ge-Bo Wen ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Active Site ◽  
Hydrogen Bonding Network ◽  
Hydrolysis Activity

Cysteine-Mediated Dynamic Hydrogen-Bonding Network in the Active Site of Pin1

Biochemistry ◽  
2014 ◽  
Vol 53 (23) ◽  
pp. 3839-3850 ◽  
Author(s):  
Arghya Barman ◽  
Donald Hamelberg
Keyword(s):  
Hydrogen Bonding ◽  
Active Site ◽  
Hydrogen Bonding Network

scholarly journals Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases

2020 ◽  
Vol 21 (20) ◽  
pp. 7515
Author(s):  
Chih-Hsuan Lai ◽  
Co-Chih Chang ◽  
Huai-Chia Chuang ◽  
Tse-Hua Tan ◽  
Ping-Chiang Lyu
Keyword(s):  
Hydrogen Bonding ◽  
Phosphatase Activity ◽  
Conformational Changes ◽  
Active Site ◽  
Protein Tyrosine Phosphatases ◽  
Site Formation ◽  
Tyrosine Phosphatases ◽  
Conserved Residues ◽  
Protein Tyrosine ◽  
Hydrogen Bonding Network

Cysteine-based protein tyrosine phosphatases (Cys-based PTPs) perform dephosphorylation to regulate signaling pathways in cellular responses. The hydrogen bonding network in their active site plays an important conformational role and supports the phosphatase activity. Nearly half of dual-specificity phosphatases (DUSPs) use three conserved residues, including aspartate in the D-loop, serine in the P-loop, and asparagine in the N-loop, to form the hydrogen bonding network, the D-, P-, N-triloop interaction (DPN–triloop interaction). In this study, DUSP22 is used to investigate the importance of the DPN–triloop interaction in active site formation. Alanine mutations and somatic mutations of the conserved residues, D57, S93, and N128 substantially decrease catalytic efficiency (kcat/KM) by more than 102-fold. Structural studies by NMR and crystallography reveal that each residue can perturb the three loops and induce conformational changes, indicating that the hydrogen bonding network aligns the residues in the correct positions for substrate interaction and catalysis. Studying the DPN–triloop interaction reveals the mechanism maintaining phosphatase activity in N-loop-containing PTPs and provides a foundation for further investigation of active site formation in different members of this protein class.

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