Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids

1975 ◽  
Vol 79 (22) ◽  
pp. 2361-2381 ◽  
Author(s):  
F. A. Momany ◽  
R. F. McGuire ◽  
A. W. Burgess ◽  
Harold A. Scheraga
Keyword(s):  
Amino Acids ◽  
Hydrogen Bond ◽  
Geometric Parameters ◽  
Atomic Charges ◽  
Nonbonded Interactions ◽  
Energy Parameters ◽  
Hydrogen Bond Interactions ◽  
Naturally Occurring ◽  
Partial Atomic Charges ◽  
Torsional Potentials

Partial atomic charges of amino acids in proteins

2004 ◽  
Vol 56 (1) ◽  
pp. 102-109 ◽  
Author(s):  
Annick Thomas ◽  
Alain Milon ◽  
Robert Brasseur
Keyword(s):  
Amino Acids ◽  
Atomic Charges ◽  
Partial Atomic Charges

scholarly journals Molecular Basis for the Reduced Catalytic Activity of the Naturally Occurring T560M Mutant of Human 12/15-Lipoxygenase That Has Been Implicated in Coronary Artery Disease

2011 ◽  
Vol 286 (27) ◽  
pp. 23920-23927 ◽  
Author(s):  
Kathrin Schurmann ◽  
Monika Anton ◽  
Igor Ivanov ◽  
Constanze Richter ◽  
Hartmut Kuhn ◽  
...  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bond ◽  
Catalytic Activity ◽  
Active Site ◽  
Side Chain ◽  
Lag Phase ◽  
Hydrogen Bond Network ◽  
Binding Partner ◽  
Naturally Occurring ◽  
Bond Network

Lipoxygenases have been implicated in cardiovascular disease. A rare single-nucleotide polymorphism causing T560M exchange has recently been described, and this mutation leads to a near null variant of the enzyme encoded for by the ALOX15 gene. When we inspected the three-dimensional structure of the rabbit ortholog, we localized Thr-560 outside the active site and identified a hydrogen bridge between its side chain and Gln-294. This interaction is part of a complex hydrogen bond network that appears to be conserved in other mammalian lipoxygenases. Gln-294 and Asn-287 are key amino acids in this network, and we hypothesized that disturbance of this hydrogen bond system causes the low activity of the T560M mutant. To test this hypothesis, we first mutated Thr-560 to amino acids not capable of forming side chain hydrogen bridges (T560M and T560A) and obtained enzyme variants with strongly reduced catalytic activity. In contrast, enzymatic activity was retained after T560S exchange. Enzyme variants with strongly reduced activity were also obtained when we mutated Gln-294 (binding partner of Thr-560) and Asn-287 (binding partner of Gln-294 and Met-418) to Leu. Basic kinetic characterization of the T560M mutant indicated that the enzyme lacks a kinetic lag phase but is rapidly inactivated. These data suggest that the low catalytic efficiency of the naturally occurring T560M mutant is caused by alterations of a hydrogen bond network interconnecting this residue with active site constituents. Disturbance of this bonding network increases the susceptibility of the enzyme for suicidal inactivation.

scholarly journals Molecular docking studies of 1, 3, 4 oxadiazoles Derivatives as anti-convulsive agents

2020 ◽  
Vol 8 (1) ◽  
pp. 151-179
Author(s):  
Sachin Jangra ◽  
Sachin Kumar ◽  
Manjusha Choudhary
Keyword(s):  
Amino Acids ◽  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Site ◽  
Gabaa Receptor ◽  
Small Molecule ◽  
Future Research ◽  
Computational Technique ◽  
Standard Drug ◽  
Hydrogen Bond Interactions

Molecular docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. The present study attempted the high throughput in-silico screening of 65 compounds docked with the GABAA receptor (PDB ID: 4COF) using Molegro virtual docker (6.0). Out of these 65 compounds, 17 compounds showed very good mol dock score in ranging between -66.344 & -102.653. Ethosuximide and Carbamazepine drugs was used as a standard drug which showed mol dock score -50.6357 & -58.5047 respectively. Most of test compounds demonstrated excellent number of hydrogen bond interactions viz compounds 33, 38, 39, 45, 47, 53, 54, 59, 61, 62, 63, 64 & 65 which showed 7 to 11 number of hydrogen bond interactions as compared to standard drug interactions values 6 & 5 respectively and also showed the interaction with same amino acids Glu52, Ser51and Val53 and some other amino acids Asn54, Thr58 and Thr133 also showed very acceptable bond length less than 3.91Å. The obtained results indicated that all studied ligands have similar position and orientation inside the putative binding site of GABAA receptor (PDB ID: 4COF) which reveals a large space bounded by a membrane-binding domain which serves as an entry channel for substrate to the active site. In addition, the affinity of any small molecule can be considered as a unique tool in the field of drug design and offer prospective in future research to develop a potent anticonvulsant agent.

scholarly journals Bis[2-(2-hydroxymethyl)pyridine-κ2N,O](pivalato-κO)copper(II)

2012 ◽  
Vol 68 (8) ◽  
pp. m1055-m1055 ◽  
Author(s):  
M. Mobin Shaikh ◽  
Veenu Mishra ◽  
Priti Ram ◽  
Anil Birla
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Octahedral Geometry ◽  
Title Complex ◽  
Distorted Octahedral Geometry ◽  
Pyridine Ligands ◽  
Hydrogen Bond Interactions ◽  
Distorted Octahedral

The structure of the centrosymmetric title complex, [Cu(C5H9O2)2(C6H7NO)2], has the CuIIatom on a centre of inversion. The CuIIatom is six-coordinate with a distorted octahedral geometry, defined by the N and O atoms of the chelating 2-(2-hydroxymethyl)pyridine ligands and two carboxylate O atoms from two monodentate pivalate ions. The crystal packing is stabilized by intermolecular C—H...O and intramolecular O—H...O hydrogen-bond interactions.

Rietveld refinement of the cocrystal 2,4-dihydroxybenzoic acid–N′-(propan-2-ylidene)nicotinohydrazide (1/1)

2012 ◽  
Vol 68 (9) ◽  
pp. o335-o337 ◽  
Author(s):  
Saul H. Lapidus ◽  
Andreas Lemmerer ◽  
Joel Bernstein ◽  
Peter W. Stephens
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Powder Diffraction ◽  
Supramolecular Assembly ◽  
Covalent Bond ◽  
Analytical Tool ◽  
Powder Diffraction Data ◽  
Dihydroxybenzoic Acid ◽  
Bond Forming ◽  
Hydrogen Bond Interactions

A further example of using a covalent-bond-forming reaction to alter supramolecular assembly by modification of hydrogen-bonding possibilities is presented. This concept was introduced by Lemmerer, Bernstein & Kahlenberg [CrystEngComm(2011),13, 55–59]. The title structure, C9H11N3O·C7H6O4, which consists of a reacted niazid molecule,viz.N′-(propan-2-ylidene)nicotinohydrazide, and 2,4-dihydroxybenzoic acid, was solved from powder diffraction data using simulated annealing. The results further demonstrate the relevance and utility of powder diffraction as an analytical tool in the study of cocrystals and their hydrogen-bond interactions.

scholarly journals Regulation of rat magnocellular neurosecretory system by D-aspartate: evidence for biological role(s) of a naturally occurring free D-amino acid in mammals

2000 ◽  
Vol 167 (2) ◽  
pp. 247-252 ◽  
Author(s):  
H Wang ◽  
H Wolosker ◽  
J Pevsner ◽  
SH Snyder ◽  
DJ Selkoe
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Physiological Function ◽  
Neurosecretory System ◽  
Milk Ejection ◽  
Magnocellular Neurons ◽  
Rat Hypothalamus ◽  
Naturally Occurring

Little evidence is available for the physiological function of D-amino acids in species other than bacteria. Here we demonstrate that naturally occurring freed -aspartate (D-Asp) is present in all magnocellular neurons of rat hypothalamus. The levels of this naturally occurring D-amino acid were elevated during lactation and returned to normal thereafter in the magnocellular neurosecretory system, which produces oxytocin, a hormone responsible for milk ejection during lactation. Intraperitoneal injections of D-Asp reproducibly increased oxytocin gene expression and decreased the concentration of circulating oxytocin in vivo. Similar changes were observed in the vasopressin system. These results provide evidence for the role(s) of naturally occurring free D-Asp in mammalian physiology. The findings argue against the conventional concept that only L-stereoisomers of amino acids are functional in higher species.

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