Molecular hydration of propofol dimers in supersonic expansions: formation of active centre-like structures

2014 ◽  
Vol 16 (42) ◽  
pp. 23301-23307 ◽  
Author(s):  
Iker León ◽  
Judith Millán ◽  
Emilio J. Cocinero ◽  
Alberto Lesarri ◽  
José A. Fernández
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Active Centre ◽  
Hydrogen Bond Networks ◽  
Supersonic Expansions

Solvation of propofol dimers is characterized by the formation of hydrogen bond networks attached to an active site-like centre.

scholarly journals A “Deep Dive” into the SARS-Cov-2 Polymerase Assembly: Identifying Novel Allosteric Sites and Analyzing the Hydrogen Bond Networks and Correlated Dynamics

2020 ◽  
Author(s):  
Khaled Barakat ◽  
Marawan Ahmed ◽  
Yasser Tabana ◽  
Minwoo Ha
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Binding Modes ◽  
Deep Dive ◽  
Recent Success ◽  
Virus Life Cycle ◽  
Hydrogen Bond Networks ◽  
Allosteric Sites ◽  
Polymerase Structure ◽  
Correlated Motion

AbstractReplication of the SARS-CoV-2 genome is a fundamental step in the virus life cycle and inhibiting the SARS-CoV2 replicase machinery has been proven recently as a promising approach in combating the virus. Despite this recent success, there are still several aspects related to the structure, function and dynamics of the CoV-2 polymerase that still need to be addressed. This includes understanding the dynamicity of the various polymerase subdomains, analyzing the hydrogen bond networks at the active site and at the template entry in the presence of water, studying the binding modes of the nucleotides at the active site, highlighting positions for acceptable nucleotides’ substitutions that can be tolerated at different positions within the nascent RNA strand, identifying possible allosteric sites within the polymerase structure and studying their correlated dynamics relative to the catalytic site. Here, we combined various cutting-edge modelling tools with the recently resolved SARS-CoV-2 cryo-EM polymerase structures to fill this gap in knowledge. Our findings provide a detailed analysis of the hydrogen bond networks at various parts of the polymerase structure and suggest possible nucleotides’ substitutions that can be tolerated by the polymerase complex. We also report here three “druggable” allosteric sites within the nsp12 RdRp that can be targeted by small molecule inhibitors. Our correlated motion analysis shows that the dynamics within one of the newly identified sites are linked to the active site, indicating that targeting this site can significantly impact the catalytic activity of the SARS-CoV-2 polymerase.

scholarly journals Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein

2018 ◽  
Vol 140 (31) ◽  
pp. 9827-9843 ◽  
Author(s):  
Margaux M. Pinney ◽  
Aditya Natarajan ◽  
Filip Yabukarski ◽  
David M. Sanchez ◽  
Fang Liu ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Photoactive Yellow Protein ◽  
Ketosteroid Isomerase ◽  
Structural Coupling ◽  
Hydrogen Bond Networks

High proton conductivity in a nickel(ii) complex and its hybrid membrane

2019 ◽  
Vol 48 (6) ◽  
pp. 2190-2196 ◽  
Author(s):  
Shuai-Liang Yang ◽  
Yue-Ying Yuan ◽  
Fei Ren ◽  
Chen-Xi Zhang ◽  
Qing-Lun Wang
Keyword(s):  
Hydrogen Bond ◽  
Proton Conductivity ◽  
Hybrid Membrane ◽  
Water Molecules ◽  
Hybrid Membranes ◽  
High Proton Conductivity ◽  
High Proton ◽  
Hydrogen Bond Networks

A novel 2D nickel(ii) complex (1) has been successfully synthesized using a 2,2′-bipyridyl, polycarboxylsulfonate ligand H4SBTC and Ni2+ ions. Owing to the presence of abundant water molecules, hydrogen bond networks and other protons, 1 and its hybrid membranes demonstrate high proton conductivity.

scholarly journals A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase

JACS Au ◽  
2021 ◽  
Author(s):  
Mary Ortmayer ◽  
Florence J. Hardy ◽  
Matthew G. Quesne ◽  
Karl Fisher ◽  
Colin Levy ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Heme Peroxidase

Hydrogen-bond networks between the C-terminus and Arg from the first α-helix stabilize photoprotein molecules

2014 ◽  
Vol 13 (3) ◽  
pp. 541 ◽  
Author(s):  
Elena V. Eremeeva ◽  
Ludmila P. Burakova ◽  
Vasilisa V. Krasitskaya ◽  
Alexander N. Kudryavtsev ◽  
Osamu Shimomura ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
C Terminus ◽  
Hydrogen Bond Networks ◽  
Α Helix
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