Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site

2010 ◽  
Vol 50 (6) ◽  
pp. 1101-1112 ◽  
Author(s):  
Jans H. Alzate-Morales ◽  
Ariela Vergara-Jaque ◽  
Julio Caballero
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Computational Study ◽  
Pyrazole Derivatives ◽  
Hydrogen Bond Network ◽  
Raf Kinase ◽  
Bond Network ◽  
Novel Interactions

scholarly journals Rhomboids make do with a weak hydrogen bond

2019 ◽  
Vol 151 (3) ◽  
pp. 274-274 ◽  
Author(s):  
Caitlin Sedwick
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Hydrogen Bond Network ◽  
Weak Hydrogen Bond ◽  
Bond Network

JGP paper explores the strength of the hydrogen bond network at the active site of GlpG.

scholarly journals Organic photovoltaics without p–n junctions: a computational study of ferroelectric columnar molecular clusters

2015 ◽  
Vol 17 (32) ◽  
pp. 20580-20587 ◽  
Author(s):  
Andrzej L. Sobolewski
Keyword(s):  
Hydrogen Bond ◽  
Organic Photovoltaics ◽  
Computational Study ◽  
Intermolecular Hydrogen Bond ◽  
Molecular Clusters ◽  
Charge Carriers ◽  
Hydrogen Bond Network ◽  
Photovoltaic Effects ◽  
Bond Network

A ferroelectrically arranged intermolecular hydrogen bond network provides a force for splitting exciton into charge carriers and the generation of photovoltaic effects.

scholarly journals Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

2014 ◽  
Vol 111 (52) ◽  
pp. 18454-18459 ◽  
Author(s):  
Lu Wang ◽  
Stephen D. Fried ◽  
Steven G. Boxer ◽  
Thomas E. Markland
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Hydrogen Bond Network ◽  
Enzyme Active Site ◽  
Bond Network ◽  
Quantum Delocalization

scholarly journals Altered Orientation of Active Site Residues in Variants of Human Ferrochelatase. Evidence for a Hydrogen Bond Network Involved in Catalysis†

Biochemistry ◽  
2007 ◽  
Vol 46 (27) ◽  
pp. 7973-7979 ◽  
Author(s):  
Harry A. Dailey ◽  
Chia-Kuei Wu ◽  
Peter Horanyi ◽  
Amy E. Medlock ◽  
Wided Najahi-Missaoui ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Hydrogen Bond Network ◽  
Active Site Residues ◽  
Bond Network

Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin

2016 ◽  
Vol 12 (10) ◽  
pp. 3139-3145 ◽  
Author(s):  
Fei Liao ◽  
Hong Yuan ◽  
Ke-Jie Du ◽  
Yong You ◽  
Shu-Qin Gao ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Heme Proteins ◽  
Structure And Function ◽  
Fine Tuning ◽  
Hydrogen Bond Network ◽  
Protein Properties ◽  
Bond Network ◽  
And Function

A single Tyr introduced in the secondary sphere of the heme active site in myoglobin at position 107 or 138 forms a distinct Tyr-associated H-bond network, regulating both the protein properties and functions.

scholarly journals Interrupting the Hydrogen Bond Network at the Active Site of Human Manganese Superoxide Dismutase

1999 ◽  
Vol 274 (39) ◽  
pp. 27711-27716 ◽  
Author(s):  
Cecilia A. Ramilo ◽  
Vincent Leveque ◽  
Yue Guan ◽  
James R. Lepock ◽  
John A. Tainer ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Superoxide Dismutase ◽  
Active Site ◽  
Manganese Superoxide Dismutase ◽  
Hydrogen Bond Network ◽  
Manganese Superoxide ◽  
Bond Network

A hydrogen-bond network at the active site of subtilisin BPN'

1970 ◽  
Vol 257 (813) ◽  
pp. 119-124 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Serine Proteases ◽  
Catalytic Mechanism ◽  
Three Dimensional ◽  
Hydrogen Bond Network ◽  
The Common ◽  
Bond Network ◽  
The One ◽  
Active Site Region

Further examination of the active site region in our X-ray crystallographic model of subtilisin BPN' reveals a hydrogen-bond network that bears a remarkable resemblance to the one found in a- chymotrypsin. It involves the side chains of the reactive Ser-221, His-64, Asp-32 and Ser-33. Otherwise the two enzymes have entirely different three-dimensional structures. This observation suggests that the common hydrogen bond network plays some essential role in the catalytic mechanism of serine proteases generally.

scholarly journals A functionally conserved basic residue in glutathione transferases interacts with the glycine moiety of glutathione and is pivotal for enzyme catalysis

2007 ◽  
Vol 406 (2) ◽  
pp. 247-256 ◽  
Author(s):  
Ardcharaporn Vararattanavech ◽  
Albert J. Ketterman
Keyword(s):  
Hydrogen Bond ◽  
Active Site ◽  
Enzyme Catalysis ◽  
Glutathione Transferase ◽  
Specific Activity ◽  
Critical Role ◽  
Minor Role ◽  
Hydrogen Bond Network ◽  
Basic Residue ◽  
Bond Network

The present study characterized conserved residues in a GST (glutathione transferase) in the active-site region that interacts with glutathione. This region of the active site is near the glycine moiety of glutathione and consists of a hydrogen bond network. In the GSTD (Delta class GST) studied, adGSTD4-4, the network consisted of His38, Met39, Asn47, Gln49, His50 and Cys51. In addition to contributing to glutathione binding, this region also had major effects on enzyme catalysis, as shown by changes in kinetic parameters and substrate-specific activity. The results also suggest that the electron distribution of this network plays a role in stabilization of the ionized thiol of glutathione as well as impacting on the catalytic rate-limiting step. This area constitutes a second glutathione active-site network involved in glutathione ionization distinct from a network previously observed interacting with the glutamyl end of glutathione. This second network also appears to be functionally conserved in GSTs. In the present study, His50 is the key basic residue stabilized by this network, as shown by up to a 300-fold decrease in kcat and 5200-fold decrease in kcat/Km for glutathione. Although these network residues have a minor role in structural integrity, the replaced residues induced changes in active-site topography as well as generating positive co-operativity towards glutathione. Moreover, this network at the glycine moiety of GSH (glutathione) also contributed to the ‘base-assisted deprotonation model’ for GSH ionization. Taken together, the results indicate a critical role for the functionally conserved basic residue His50 and this hydrogen bond network in the active site.

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