In silico comparative analysis of HIV protease inhibitors effect on 2019-nCoV coronavirus 3CLpro
Published on: 3rd July, 2020
OCLC Number/Unique Identifier: 8627241132
The novel coronavirus 2019-nCoV has become a bane to mankind and spread worldwide and infected many people. Thus, there is an urgent need of a cure for the severe pneumonia disease caused by this virus. In this study, In silico comparative analysis has been done for HIV protease inhibitors on coronavirus 3CLpro protein which has shown the major interactions and common amino acid residues involved in interactions. The amino acid interaction analysis has revealed two amino acids ARG4, LYS5 to be the major amino acids targets among selected ligands. The binding energy analysis has also revealed Cobicistat as one of these best suited ligand for 3CLpro.
Poly-dopamine-Beta-Cyclodextrin Modified Glassy Carbon Electrode as a Sensor for the Voltammetric Detection of L-Tryptophan at Physiological pH
Published on: 9th January, 2017
OCLC Number/Unique Identifier: 7286355385
The main purpose of this report was to develop application of poly-dopamine-beta-cyclodextrin modified glassy carbon electrode (PDA-β-CD-GCE) towards electrooxidation and determination of L-Tryptophan (L-Trp) and also the evaluation its kinetic parameters. In continuation of our efforts to use PDA-β-CD-GCE for amino acids detection, our objective in the present work was to expand application of this sensor for the determination of L-Trp which is very sensitive.
Role of HECT ubiquitin protein ligases in Arabidopsis thaliana
Published on: 20th March, 2018
OCLC Number/Unique Identifier: 7794148150
Ubiquitination is a kind of posttranslational modification of proteins in eukaryotes, and it plays an important role in the growth and development of organisms. The ubiquitination of proteins is a cascade enzymatic reaction involving three enzymes. The homologous to E6-AP carboxy terminus ubiquitin-protein ligases (HECT E3s) family is an important ubiquitin-protein ligases family. The family all have a HECT domain of approximately 350 amino acids in the C-terminus. However, studies on plant HECT E3s, such as structural features, prediction of HECT domain function, and their regulatory mechanisms, are very limited. In this paper, Arabidopsis thaliana HECT family genes were analyzed, including gene structure and functional domains and its limited known functions in protein degradation, gene transcription regulation, epigenetically regulation or other functions, finally speculate their roles in plant morphologies, aging or responsive to environmental stress.
Cloning and Characterization of a Pseudo-Response Regulator 7 (PRR7) Gene from Medicago Sativa Involved In Regulating the Circadian Clock
Published on: 16th July, 2019
OCLC Number/Unique Identifier: 8185507893
The circadian clock is an endogenous molecular oscillator with a period of about 24 hours, which regulates the physiology and developmental processes of almost all higher plants. Pseudo-response regulators (PRRs) are an important part of the central clock oscillator, together with other clock genes, constituting interlinked transcriptional feedback loops, which partly influence plant growth and development. In this study, a circadian clock-related gene MsPRR7 was cloned from Medicago sativa (alfalfa) by homologous cloning. The full length MsPRR7 gene was 2648 bp in length, with an open reading frame of 2385 bp encoding a protein of 795amino acids. Phylogenetic analysis showed that the MsPRR7 was closely related to PRR7 from the PRR family of Arabidopsis thaliana. Subcellular localization analysis found that MsPRR7 was located in the nucleus. Quantitative reverse-transcription polymerase chain reactions (qRT-PCR) demonstrated that expression of MsPRR7 gene transcripts in leaves was affected by circadian rhythms, and that its expression level increased with an extension of illumination time, reaching a peak around 8–10 hours. These results will provide the experimental basis for further study of the regulation of PRR family genes in alfalfa.
Discovering the right treatments for diabetes (2), blood’s pressure, and relating diseases
Published on: 15th August, 2018
OCLC Number/Unique Identifier: 8220392115
For last decades diabetes type 2, blood’s pressure (especially hypertension) and relating diseases are most serious problems for much people over the world. These diseases are not like other different diseases then for studying them very accuracy, this research choose sample from different societies a small city called “Al-Mejar Al-Kabeer” in south of Iraq. People of this city do same activities than other Iraqi cities and during the last twenty years the only change happened in this city is; they changed them drinking water from tap water to commercial water called it R.O. Population of this city is about 70000 persons and about 20000 from them have diabetes that means more than 28% from all people of this city have this disease, this ratio or may be more for hypertension.
Results of this research show that the main reason for diabetes type 2, blood’s pressure and relating diseases is civilization. It shows according good evidences that the right treatment for diabetes, hypertension and relating diseases is about 5g/day potassium ions (K+) with less amounts from sodium ions such as 2:1. In fact, insulin forming from known amino acids so each body need sufficient amounts from these acids therefore the right treatment for diabetes type 2 is not only potassium it must there sufficient amounts from proteins each day or each three days.
References of this research indicated; Diabetes and hypertension are well understood but this research find that these diseases need a chemist touch to be fully understood.
Food applications of Aloe species: A review
Published on: 4th May, 2022
OCLC Number/Unique Identifier: 9507334452
Plants have a high concentration of biologically active molecules. Aloe plants tend to store water and important chemical constituents in their swollen and succulent leaves due to their ability to survive in hot and dry conditions, which makes them a unique source of phytochemicals. The Aloe leaf contains more than 200 nutritional substances, including vitamins, minerals, amino acids, and active enzymes. These constituents are analyzed as phytochemical screening (qualitative analysis) or proximate and mineral content analyses (quantitative analysis). Aloe is used as a food product and beverage ingredient. Functional and nutraceutical foods, edible coatings/films, Aloe species as cooked vegetables, and raw eating of Aloe species are how the Aloe plant is considered in food applications. The researchers reported edible Aloes for several species. However, it is not mean that all species of Aloe are edible. It is not only the leaves of Aloe that have nutritional values also other parts of the plant do. The study evaluated the nutritional value of Aloe flowers and their possible use as edible flowers. Aloe species are increasingly being incorporated into different health drinks, foods, and beverages due to the beneficial biological activities of the phytochemicals.
Evaluation of Biostimulants Based on Recovered Protein Hydrolysates from Animal By-products as Plant Growth Enhancers
Published on: 3rd July, 2023
Free amino acids-based biostimulants are gaining momentum in Europe for sustainable agriculture. They stimulate plant growth, improve crop productivity, and reduce reliance on harmful fertilizers. Enzymatic hydrolysis is used to develop biostimulants from animal by-products, such as greaves and protein-rich wastewater from processed animal proteins. The effectiveness of enzymatic hydrolysis depends on selecting the appropriate conditioning stage for the by-products, yielding protein in the range of 86% to 97%. These protein hydrolysates, with optimal amino acid compositions, are evaluated as biostimulants. Promising results show growth improvements of 17% to 31% in Chinese cabbage and lettuce seeds. The optimal dilution concentration ranges from 0.05% to 0.3%, depending on the protein hydrolysate used. The findings highlight the potential of these biostimulants to enhance plant growth and productivity while reducing environmental impact by replacing chemical fertilizers. They offer sustainable alternatives for promoting environmentally friendly practices in agriculture.
Sites and Zones of Maximum Reactivity of the most Stable Structure of the Receptor-binding Domain of Wild-type SARS-CoV-2 Spike Protein: A Quantum Density Functional Theory Study
Published on: 12th April, 2024
Today, it is well known that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has four types of proteins within its structure, between them the spike protein (S). The infection mechanism is carried out by the entry of the virus into the human host cell through the S protein, which strongly interacts with the human cell receptor angiotensin-converting enzyme 2 (ACE2). In this work, we propose an atomic model of the Receptor Binding Domain (RBD) of the S spike protein of the wild-type SARS-CoV-2 virus. The molecular structure of the model was composed of 50 amino acids that were chemically bonded, starting with Leucine and ending with one amino acid Tyrosine. The novelty of our work lies in the importance of knowing the sites and zones of maximum reactivity of the RBD from the fundamental levels of quantum mechanics considering the atomic structure of matter. For this, the local and global reactivity indices of the RBD were calculated, such as frontier orbitals, Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO), Fukui indices, chemical potential, chemical hardness, electrophilicity index; with this, it will be possible to know what type of molecules are more likely to interact with the RBD structure, and in this way, new knowledge will be generated at the quantum, atomic and molecular level to inhibit the virulent effects of wild-type SARS-CoV-2. Finally, in order to identify the functional groups within the most stable structure and thereby verify the future reactions that can be carried out between the RBD structure and biomolecules, the Infrared (IR) absorption spectrum was calculated. For this work, we used Material Studio v6.0 which uses the density functional theory (DFT) implemented in its DMol3 computational code. The IR spectrum was obtained using the Spartan ‘94 computer code. One novelty would be that we found nine amino acids more that could make the RBD and ACE2 binding further the already known. Thus, the Mulliken charge distribution indicates that the highest concentrations of positive and negative charge are found in the zones 477S, 478T, 484E, and 501N amino acids letting ionic or Van der Waals possible interactions with other structures.
A Critical Review on Some Recent Developments in Comparison of Biological Sequences
Published on: 25th April, 2024
The present review highlights some of the very important contributions to non-alignment ways of comparing biological sequences, which may be genome sequences of nucleotides, protein sequences of amino acids, or sequences of protein secondary structures. The discussion centers around specific methods applicable to the comparison of three types of sequences. The methods of comparison of genome sequences are based on three pairs of biological groups of nucleotides; the same for protein sequences are based on either physio-chemical property values of amino acids or on classified groups of amino acids of different cardinalities obtained from the physio-chemical properties; the same for sequences of secondary structures of proteins are based on their sequential expressions of structure elements of cardinality three and four. Comparison is made in the time domain and also in the frequency domain. Different taxa of known phylogeny are considered for comparison. It tries to find out the specific method of comparison, which can show the exact phylogeny of the taxa. If a new sequence appears in the database, it becomes essential to know its phylogeny. For this purpose, a phylogenetic tree is drawn on the sequences of the known taxa together with this new sequence using the best possible method. If the species having this new sequence belongs to the old taxa, there is nothing to worry about. Otherwise, the species with the new sequence has to be studied separately. This is the general reason for the construction of a phylogenetic tree in any form of biological sequence comparison.
Coronaviruses have reached at Pre-elimination Stage with Nine Amino Acid Spike Deletions and Forty-nine Nucleotide 3’-UTR Deletions
Published on: 17th September, 2024
Background: Human 30kb coronaviruses entered through the ACE-2 receptors causing fibrosis of the lungs and causing six million deaths worldwide. Here, we have investigated the mutations, deletions and insertions of the recent JN.1 omicron coronaviruses to demonstrate that coronaviruses have reached the pre-elimination stage. Methods: We multi-aligned the genomes of recent JN.1 variants using NCBI Virus Portal and CLUSTAL-Omega. The spike proteins are multi-aligned using MultAlin software and CLUSTAL-Omega.Results: The 17MPLF spike insertion was confirmed to compensate 24LPP, 31S, 69HV, 145Y, 211N and 483V deletions. The 49nt deletions in the 3’-UTR were found in 4997 JN.1 sequences although 26nt deletion was initiated previously in JN.1 as well as BA.5, BF.7, BQ.1 and XBB.1.5 omicron viruses. We first compare 3-D structures of spike proteins with or without 17MPLF four amino acids insertion and nine amino acids deletions using SWISS MODELLING. The JN.1 viruses caused a more stable trimeric spike involving Thr342, Lys436, Lys440, His441, Ser442, Gly443, Tyr445, Lys479, Ser489, Tyr490, Arg493, Pro494, Thr495, and Gln501 amino acids to interact with ACE-2 receptors. The FLiRT spike mutations were found in most KP.2 variants and other changes occurred at the NH2 terminus.Conclusion: We claimed that pre-death changes were initiated in JN.1 COVID-19 lineages and computer simulation showed that the Howard spike with 17MPLF spike insertion appeared more stable than the Oppentrons-spike without 17MPLF insertion. Surely, conflicts of COVID-19 spike sequences must be resolved.
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