A comparison of the binding affinity of the common amino acids with different metal cations

2008 ◽  
pp. 6441 ◽  
Author(s):  
Jesús Jover ◽  
Ramón Bosque ◽  
Joaquim Sales
Keyword(s):  
Amino Acids ◽  
Binding Affinity ◽  
Metal Cations ◽  
The Common

In silico study of binding affinity of nitrogenous bicyclic heterocycles: fragment-to-fragment approach

2020 ◽  
Vol 15 (2) ◽  
pp. 49-59
Author(s):  
Yevheniia Velihina ◽  
Nataliya Obernikhina ◽  
Stepan Pilyo ◽  
Maryna Kachaeva ◽  
Oleksiy Kachkovsky ◽  
...  
Keyword(s):  
Amino Acids ◽  
Binding Affinity ◽  
In Silico ◽  
Density Functional ◽  
Energy Levels ◽  
Aromatic Amino Acids ◽  
Electron System ◽  
High Energy ◽  
Proton Donor ◽  
Stabilization Energy

The binding affinity of model aromatic amino acids and heterocycles and their derivatives condensed with pyridine were investigated in silico and are presented in the framework of fragment-to-fragment approach. The presented model describes interaction between pharmacophores and biomolecules. Scrupulous data analysis shows that expansion of the π-electron system by heterocycles annelation causes the shifting up of high energy levels, while the appearance of new the dicoordinated nitrogen atom is accompanied by decreasing of the donor-acceptor properties. Density Functional Theory (DFT) wB97XD/6-31(d,p)/calculations of π-complexes of the heterocycles 1-3 with model fragments of aromatic amino acids, which were formed by π-stack interaction, show an increase in the stabilization energy of π-complexes during the moving from phenylalanine to tryptophan. DFT calculation of pharmacophore complexes with model proton-donor amino acid by the hydrogen bonding mechanism (H-B complex) shows that stabilization energy (DE) increases from monoheterocycles to their condensed derivatives. The expansion of the π-electron system by introducing phenyl radicals to the oxazole cycle as reported earlier [18] leads to a decrease in the stabilization energy of the [Pharm-BioM] complexes in comparison with the annelated oxazole by the pyridine cycle.

scholarly journals A reevaluation of computed proton affinities for the common α-amino acids

2009 ◽  
Vol 20 (11) ◽  
pp. 2116-2123 ◽  
Author(s):  
Scott Gronert ◽  
David C. Simpson ◽  
Keyanna M. Conner
Keyword(s):  
Amino Acids ◽  
Proton Affinities ◽  
The Common

A comparative study of the adsorption of amino acids on to calcium minerals found in renal calculi

2001 ◽  
Vol 101 (2) ◽  
pp. 159-168 ◽  
Author(s):  
David E. FLEMING ◽  
Wilhelm VAN BRONSWIJK ◽  
Rosemary Lyons RYALL
Keyword(s):  
Amino Acids ◽  
Calcium Oxalate ◽  
Binding Affinity ◽  
Stone Formation ◽  
Human Kidney ◽  
Renal Calculi ◽  
Calcium Oxalate Monohydrate ◽  
Carboxyglutamic Acid ◽  
Calcium Minerals ◽  
Ph Range

To assess the binding of individual amino acids to the principal calcium minerals found in human kidney stones, the adsorption of 20 amino acids on to calcium oxalate monohydrate, CaHPO4.2H2O, Ca3(PO4)2 and Ca5(PO4)3OH crystals was determined over the physiological urinary pH range (pH 5–8) in aqueous solutions. All amino acids adsorbed most strongly at pH 5, and this decreased in all cases as the pH was increased. The amino acids which adsorbed most strongly were aspartic acid, glutamic acid and γ-carboxyglutamic acid, with the last displaying the strongest affinity. All amino acids bound more avidly to calcium oxalate monohydrate than to any of the phosphate minerals. Adsorption on to CaHPO4.2H2O was generally higher than for Ca3(PO4)2 and Ca5(PO4)3OH, for which all amino acids, with the exception of γ-carboxyglutamic acid, had only a weak affinity. The binding affinity of these acids is thought to be due to their zwitterions being able to adopt conformations in which two carboxyl groups, and possibly the amino group, can interact with the mineral surface without further rotation. The strong binding affinity of di-and tri-carboxylic acids for calcium stone minerals indicates that proteins rich in these amino acids are more likely to play a functional role in stone pathogenesis than those possessing only a few such residues. These findings, as well as the preferential adsorption of the amino acids for calcium oxalate monohydrate rather than calcium phosphate minerals, have ramifications for research aimed at discovering the true role of proteins in stone formation and for potential application in the design of synthetic peptides for use in stone therapy.

Investigation of Optimum Conformations and Structure Analysis of RL and LR Nests using Ramachandran Plot

2015 ◽  
pp. 209-224
Author(s):  
Sumukh Deshpande ◽  
Saikat Kumar Basu ◽  
Pooja Purohit
Keyword(s):  
Amino Acids ◽  
Ring Structure ◽  
Ramachandran Plot ◽  
Binding Motifs ◽  
Automated Algorithm ◽  
Automation And Control ◽  
The Common ◽  
And Control ◽  
Common Anion ◽  
Unique Application

We have surveyed polypeptides with the optimal conformations of nests which are the common anion-binding motifs comprising 8% of the amino acids which are characterized by a structural depression or a hole. Using automated bioinformatics algorithm, novel ring structure of the nest has been found. Using automated algorithm, models of polypeptides were made in-silico (computationally) and oxygen atoms are inserted along the extension of the NH groups. These sophisticated algorithms allow insertion of atoms along the NH group at the correct distance which causes extension of the group thus forming hydrogen bond. Optimal conformations of these structures are found from these customized models. This study chapter provides a demonstration of an important discovery of optimum conformations of RL and LR nests by the use of sophisticated bioinformatics automation pipeline and a unique application of automation and control in bioinformatics.

Structural basis of the binding affinity of chemoreceptors Mlp24p and Mlp37p for various amino acids

2020 ◽  
Vol 523 (1) ◽  
pp. 233-238 ◽  
Author(s):  
Yohei Takahashi ◽  
So-ichiro Nishiyama ◽  
Ikuro Kawagishi ◽  
Katsumi Imada
Keyword(s):  
Amino Acids ◽  
Binding Affinity ◽  
Structural Basis

scholarly journals A Practical Approach to the Investigation of Amino Acid Disorders

1988 ◽  
Vol 25 (2) ◽  
pp. 129-141 ◽  
Author(s):  
M A Edwards ◽  
S Grant ◽  
A Green
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Analysis ◽  
Practical Approach ◽  
The Common ◽  
Common Problems

We have, in this paper, highlighted some of the common problems in amino acid analysis in our experience and listed the possible causes for increases in specific amino acids in urine—together with guidance on appropriate follow-up investigations.

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