Site specific interaction of aromatic amino acids with ZnO nanotubes: A density functional approach

2016 ◽  
Vol 1086 ◽  
pp. 36-44 ◽  
Author(s):  
Pari Sadat Maddahi ◽  
Nasser Shahtahmassebi ◽  
Mahmood Rezaee Roknabadi ◽  
Fatemeh Moosavi
Keyword(s):  
Amino Acids ◽  
Density Functional ◽  
Specific Interaction ◽  
Aromatic Amino Acids ◽  
Functional Approach ◽  
Site Specific ◽  
Zno Nanotubes

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.

Role of Guanidinium-Carboxylate Interaction in Enzyme Inhibition with Implication for Drug Design

2019 ◽  
Author(s):  
Aswathy Muttathukattil ◽  
Sriraksha Srinivasan ◽  
Antarip Halder ◽  
Govardhan Reddy
Keyword(s):  
Amino Acids ◽  
Active Sites ◽  
Density Functional ◽  
Specific Interaction ◽  
Density Functional Theory Calculations ◽  
Enzyme Active Site ◽  
Acidic Amino Acids ◽  
Low Concentrations ◽  
Activity Measurements ◽  
Acidic Residues

Guanidinium cation (Gdm<sup>+</sup>) interacts strongly with amino acids of different polarities modulating protein structure and function. Using density functional theory calculations and molecular dynamics simulations we studied the interaction of Gdm<sup>+</sup> with carboxylate ions mimicking its interaction with acidic amino acids and explored its effect in enzymatic folding and activity. We show that in low concentrations, Gdm<sup>+</sup> stabilizes carboxylate ion dimers by acting as a bridge between them thereby reducing the electrostatic repulsion. We further show that this carboxylate-Gdm<sup>+</sup>-carboxylate interaction can have an effect on the structure-activity relationship in enzymes with active sites containing two acidic residues. Using five enzymes (hen egg white lysozyme, T4 lysozyme, HIV-1 protease, pepsin and creatine kinase), which have two acidic amino acids in their active sites, we show that in low concentrations (< 0.5 M), Gdm<sup>+</sup> strongly binds to the enzyme active site, thereby potentially inhibiting its activity without unfolding it. This can lead to misleading conclusions in experiments, which infer the extent of enzyme unfolding from activity measurements. However, the carboxylate-Gdm<sup>+</sup>-carboxylate specific interaction can be exploited in drug discovery as drugs based on guanidinium derivatives are already being used to treat various maladies related to muscle weakness, cancer, diabetes etc. Guanidinium derivatives can be designed as potential drug molecules to inhibit activity or functioning of enzymes, which have binding pockets with two acidic residues in close vicinity.<br>

Theoretical study of the adsorption of aromatic amino acids on a single-wall boron nitride nanotube with empirical dispersion correction

2017 ◽  
Vol 95 (6) ◽  
pp. 710-716 ◽  
Author(s):  
Guohong Fan ◽  
Sheng Zhu ◽  
Ke Ni ◽  
Hong Xu
Keyword(s):  
Amino Acids ◽  
Boron Nitride ◽  
Density Functional ◽  
Energy Charge ◽  
Tight Binding ◽  
Excited State Absorption ◽  
Aromatic Amino Acids ◽  
Boron Nitride Nanotubes ◽  
Dispersion Correction ◽  
Tight Binding Method

In the present study, the adsorption and properties of three popularly studied aromatic amino acids, namely phenylalanine, tyrosine, and tryptophan, on the surface of the single-wall boron nitride nanotubes (BNNTs) have been explored with an empirical dispersion corrected density functional tight-binding method. A serials of armchair BNNTs (n = 4–12) and zigzag BNNTs (n = 8–18) with the aromatic amino acid adsorbed on the surface are investigated. With the dispersion correction explicitly considered in the density functional tight-binding method, the adsorption properties between amino acids and BNNTs are described by including long-range van der Waals interactions. It is found that the π–π and H–π stacking interactions are the main forces stabilizing the system. Based on the evidence of adsorption energy, charge density plots, and density of states analysis, the study concludes that the BNNT adsorbs the amino acids with no bonded interactions between the two parts. The interactions of amino with the BNNT were further studied by analyzing molecular orbitals and excited state absorption spectrum of the stable complexes.

scholarly journals Arginine-Amino Acid Interactions and Implications to Protein Solubility and Aggregation

2015 ◽  
Vol 12 (2) ◽  
pp. 1 ◽  
Author(s):  
A. R. Shaikh ◽  
D. Shah
Keyword(s):  
Amino Acids ◽  
Protein Interactions ◽  
Density Functional ◽  
Protein Solubility ◽  
Aromatic Amino Acids ◽  
Hydrogen Bond Interactions ◽  
Stable Clusters ◽  
Pharmaceutical Industries ◽  
The Stability

Arginine, useful in protein refolding, solubilization of proteins, and suppression of protein aggregation and non-specific adsorption during formulation and purification, is a ubiquitous additive in the biotechnology and pharmaceutical industries. In order to provide a framework for analyzing the molecular level mechanisms behind arginine/protein interactions in the above context, density functional theory was used to systematically examine how arginine interacts with naturally occurring amino acids. The results show that the most favorable interaction of arginine is with acidic amino acids and arises from charge interactions and hydrogen-bond interactions. Arginine is also shown to form stacking and T-shaped structures with aromatic amino acids, the types of cation–p and N–H…p interactions, respectively, known to be important contributors to protein stability. The analysis also shows that arginine-arginine interactions lead to stable clusters, with the stability of the clusters arising from the stacking of the guanidinium part of arginine. The results show that the unique ability of arginine to form clusters with itself makes it an effective aggregation suppressant and support the interpretations of the current study using experimental and molecular dynamics results available in the literature. The results also contribute to understanding the role of arginine in increasing protein solubility, imparting thermal stability of important enzymes, and designing better additives.  

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