In silico Complexes of Amino Acids and Diamondoids

ChemPhysChem ◽  
2019 ◽  
Vol 20 (17) ◽  
pp. 2166-2170
Author(s):  
Pouya Partovi‐Azar ◽  
Chandra Shekar Sarap ◽  
Maria Fyta
Keyword(s):  
Amino Acids ◽  
In Silico

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 An In Silico study of TiO2 nanoparticles interaction with twenty standard amino acids in aqueous solution

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Shengtang Liu ◽  
Xuan-Yu Meng ◽  
Jose Manuel Perez-Aguilar ◽  
Ruhong Zhou
Keyword(s):  
Aqueous Solution ◽  
Amino Acids ◽  
Tio2 Nanoparticles ◽  
In Silico ◽  
In Silico Study

scholarly journals Interrogation of the Perturbed Gut Microbiota in Gouty Arthritis Patients Through in silico Metabolic Modeling

2020 ◽  
Author(s):  
Michael A. Henson
Keyword(s):  
Amino Acids ◽  
Uric Acid ◽  
Amino Acid ◽  
Gut Microbiota ◽  
In Silico ◽  
Gouty Arthritis ◽  
Metabolic Modeling ◽  
Patient Specific ◽  
Surprising Result ◽  
Sulfur Containing

Recent studies have shown perturbed gut microbiota associated with gouty arthritis, a metabolic disease in which an imbalance between uric acid production and excretion leads to the deposition of uric acid crystals in joints. To mechanistically investigate altered microbiota metabolism in gout disease, 16S rRNA gene amplicon sequence data from stool samples of gout patients and healthy controls were computationally analyzed through bacterial community metabolic modeling. Patient-specific models were used to cluster samples according to their metabolic capabilities and to generate statistically significant partitioning of the samples into a Bacteroides-dominated, high gout cluster and a Faecalibacterium-elevated, low gout cluster. The high gout cluster samples were predicted to allow elevated synthesis of the amino acids D-alanine and L-alanine and byproducts of branched-chain amino acid catabolism, while the low gout cluster samples allowed higher production of butyrate, the sulfur-containing amino acids L-cysteine and L-methionine and the L-cysteine catabolic product H2S. The models predicted an important role for metabolite crossfeeding, including the exchange of acetate, D-lactate and succinate from Bacteroides to Faecalibacterium to allow higher butyrate production differences than would be expected based on taxa abundances in the two clusters. The surprising result that the high gout cluster could underproduce H2S despite having a higher abundance of H2S-synthesizing bacteria was rationalized by reduced L-cysteine production from Faecalibacterium in this cluster. Model predictions were not substantially altered by constraining uptake rates with different in silico diets, suggesting that sulfur-containing amino acid metabolism generally and H2S more specifically could be novel gout disease markers.

scholarly journals In silico study to examine the role of amino acids in Jasmonate induced plant defense process

2018 ◽  
Vol 5 (10) ◽  
pp. 289-301
Author(s):  
Ruma Ganguly ◽  
Sailesh K. Mehta
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Jasmonic Acid ◽  
Plant Defense ◽  
In Silico ◽  
Induced Plant Defense ◽  
In Silico Study

The role of amino acid is important to Jasmonate induce plant defense process. Jasmonic acid and amino acid Isoleucine conjugate (JA-Ile) has been found to be necessary to achieve such process effectively. We have examined the origin of such process computationally and showed that Isoleucine is more active compared to other Jasmonic acid conjugates. The epimerization process revealed that Isoleucine conjugated Jasmonic acid is energetically a favoured process compared to JA-Leu and JA-Val. Water has functioned as a catalyst in the whole epimerization process. This study would unravel the importance of Isoleucine in the Jasmonic acid induced plant defense process.

scholarly journals Analisis In-Silico Struktur Tiga Dimensi Reseptor Trk A dan Trk B Protein Neurotrophin 3 Pada Gallus gallus (Chicken)

2020 ◽  
Vol 12 (2) ◽  
pp. 78-84
Author(s):  
Muhammad F. Rahman ◽  
Amiruddin Kasim ◽  
Muchlis L. Djirimu ◽  
I. Made Budiarsa
Keyword(s):  
Amino Acids ◽  
In Silico ◽  
Three Dimensional ◽  
Gallus Gallus ◽  
Dimensional Structure ◽  
Neurotrophin 3 ◽  
Trk A ◽  
And Function ◽  
Trk B ◽  
Ucsf Chimera

NT3 protein is expressed by Neurotrophin 3 (NTF-3) which plays a role in the process of differentiation, survival of peripheral and neuropathological of neurons. The information of structure and function of NT-3 proteins is still very limited, especially in Gallus gallus. This study aims to predict the three-dimensional structure of the Trk A and Trk B proteins in Gallus gallus. The target protein obtained from the UniProt server with access codes Q91009 (Trk A) and Q91987 (Trk B) using the 6kzc 1.A (PDB ID) template was analyzed in silico through a homology approach and describing the structural assessment using Chimera UCSF software. The analysis showed that the Trk A protein had a QMEAN value of -0.08, composed of 778 amino acids, mass 87334.30 Daltons, and Seq Identity 79.93%. Trk B had a QMEAN value of 0.16, consisting of 818 amino acids, mass 91732.05 Daltons, and Seq Identity 84.30%. Key words: NT3; homology; UCSF chimera; G. gallus

In silico Characterization of a Candidate Protein from Aphid Gelling Saliva with Potential for Aphid Control in Plants

2020 ◽  
Vol 27 (2) ◽  
pp. 158-167 ◽  
Author(s):  
Rao Sohail Ahmad Khan ◽  
Zainab Ali ◽  
Adnan Khan Niazi ◽  
James C. Carolan ◽  
Thomas L. Wilkinson
Keyword(s):  
Amino Acids ◽  
In Silico ◽  
Acyrthosiphon Pisum ◽  
Specific Gene ◽  
Specific Information ◽  
Hard Material ◽  
Drosophila Genome ◽  
Potential Candidate ◽  
Aphid Control ◽  
Candidate Protein

Background: Sheath or gelling saliva, secreted during feeding by aphids, is a hard material that supports the piercing mouthparts and remains in the plant after feeding. Solidification or gelling of the saliva might be due to the composition of amino acids in the constituent proteins, many of which probably interact with plant defenses. Objective : The complete complement of proteins in the gelling saliva are still unknown, although one sheath protein (SHP) has previously been identified as a potential candidate protein to control aphid feeding, but its structure and its physiochemical role remains obscure. The current study provides structural information and biochemical properties of the aphid sheath protein. Methods: The Sheath protein encoding gene was amplified from cDNA of the pea aphid (Acyrthosiphon pisum) through PCR using specific gene primers. Sequence was in silico characterized by using EXPASY, Berkeley Drosophila Genome Project (BDGP) Neural Network Promoter Prediction, BioEdit, Mega7, ProtParam, Phyre server, 3D LigandSite SMART, MEME and GSDS programs, available online. Results: BLASTp analysis revealed that the sequenced gene was identical (100%) to the sequence from Acyrthosiphon pisum, with 87% identity to Metpolophium dirhodum and 84% identity to Sitobion avenae. Phylogenetically monocot feeders such as M. dirhodum and S. avenae are in a sister taxa to dicot feeders. In silico analysis of the sequence revealed that sheath protein has a molecular weight of 144 kDa and 50% of the protein is composed of only six amino acids, i.e., threonine, serine, aspartic acid, glutamic acid, isoleucine and tyrosine. The computed IP value revealed that sheath protein is acidic in nature. Ligand binding sites for sheath protein were predicted on residues 1123 and 1125 (isoleucine and glutamine, respectively). Metallic heterogens are also present in sheath protein that are iron, zinc and magnesium, respectively. Conclusion : It is conceivable that variation in the salivary gene sequences may reveal important biological information of relevance to the insect-plant interaction. Further exploration of insect salivary proteins, their composition and structure will provide powerful information, especially when these proteins are interacting with plant proteins, and specific information about the sheath protein, which is interacting with plants at a molecular/cellular level, will be important to progress strategies aimed specifically against sucking pests such as aphids.

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