scholarly journals Computing wide range of protein/peptide features from their sequence and structure

2019 ◽  
Author(s):  
Akshara Pande ◽  
Sumeet Patiyal ◽  
Anjali Lathwal ◽  
Chakit Arora ◽  
Dilraj Kaur ◽  
...  
Keyword(s):  
Amino Acid ◽  
Information Structure ◽  
Complete Information ◽  
Low Complexity ◽  
Residue Level ◽  
Amino Acid Sequences ◽  
Evolutionary Information ◽  
Post Translational Modification ◽  
Link Type ◽  
Wide Range

AbstractMotivationIn last three decades, a wide range of protein descriptors/features have been discovered to annotate a protein with high precision. A wide range of features have been integrated in numerous software packages (e.g., PROFEAT, PyBioMed, iFeature, protr, Rcpi, propy) to predict function of a protein. These features are not suitable to predict function of a protein at residue level such as prediction of ligand binding residues, DNA interacting residues, post translational modification etc.ResultsIn order to facilitate scientific community, we have developed a software package that computes more than 50,000 features, important for predicting function of a protein and its residues. It has five major modules for computing; composition-based features, binary profiles, evolutionary information, structure-based features and patterns. The composition-based module allows user to compute; i) simple compositions like amino acid, dipeptide, tripeptide; ii) Properties based compositions; iii) Repeats and distribution of amino acids; iv) Shannon entropy to measure the low complexity regions; iv) Miscellaneous compositions like pseudo amino acid, autocorrelation, conjoint triad, quasi-sequence order. Binary profile of amino acid sequences provides complete information including order of residues or type of residues; specifically, suitable to predict function of a protein at residue level. Pfeature allows one to compute evolutionary information-based features in form of PSSM profile generated using PSIBLAST. Structure based module allows computing structure-based features, specifically suitable to annotate chemically modified peptides/proteins. Pfeature also allows generating overlapping patterns and feature from whole protein or its parts (e.g., N-terminal, C-terminal). In summary, Pfeature comprises of almost all features used till now, for predicting function of a protein/peptide including its residues.AvailabilityIt is available in form of a web server, named as Pfeature (https://webs.iiitd.edu.in/raghava/pfeature/), as well as python library and standalone package (https://github.com/raghavagps/Pfeature) suitable for Windows, Ubuntu, Fedora, MacOS and Centos based operating system.

Application of the Innovative and Non-Invasive Technique, Molecular Music Therapy (MMT), Bio-Frequency Therapy, for the Treatment of a Wide Range of Disorders and Pathologies, with Consequent Verification of Molecular Parameters by Using Bi-Digital O-Ring Test (BDORT)

2020 ◽  
Vol 44 (3) ◽  
pp. 177-189
Author(s):  
Momir Dunjic ◽  
Stefano Turini ◽  
Dejan Krstic ◽  
Katarina Dunjic ◽  
Marija Dunjic ◽  
...  
Keyword(s):  
Amino Acid ◽  
Music Therapy ◽  
Amino Acid Sequences ◽  
Sirtuin 1 ◽  
Ring Test ◽  
Invasive Technique ◽  
Specific Gene ◽  
Radiofrequency Therapy ◽  
Wide Range ◽  
Clinical Pictures

Radiofrequency therapy is an unconventional method, already applied for some time, with numerous results in numerous clinical pictures. Our group has developed a software, later called SONGENPROT-SOLARIS, capable of directly converting nucleotide sequences (DNA and/or RNA) and amino acid sequences (polypeptides and proteins) into musical sequences, based on mathematic matrices, designed by the French physicist and musician Joel Sternheimer, which allows to associate a musical note with a nucleotide or an amino acid. Innovation in our software is that, in the algorithm that defines it, a variant is directly implemented that allows the reproduction of sounds, phase-shifted by 30 Hz, between one ear and another reproducing the phenomenon of Binaural Tones, capable of induce a specific brain activity and also the release of particles called solitons. Thanks to this software we have developed a technique called MMT (Molecular Music Therapy) and currently, we are in the phase of applying the technique on a cohort of 91 patients, with a high spectrum of clinical pictures, examining the same, using the technique Bi-Digital-ORing-Test (BDORT), before and after treatment with MMT. Aim of project is to stimulate the expression of a specific gene (the same genetic sequence that the patient listens to, translated into music), only through the use of sound sequences. We have concentrated our attention on three main molecules: Sirtuin-1, Telomers and TP-53. The results obtained with BDORT, after treatment with MMT, showed a significant increase in the values of the three molecules, on all the examined patients, demonstrating the operative efficacy of the technique and the its applicability to numerous diseases. In order to confirm the data obtained by BDORT, we propose, with the help of an accredited laboratory, to perform epigenetic tests on the three parameters listed above, paving the way to understanding how frequencies can influence gene expression.

scholarly journals In vitro and In Silico Approach For Characterization of Antimicrobial Peptide From Probiotics Against Staphylococcus Aureus and Escherichia Coli

2021 ◽  
Author(s):  
Amrutha Bindu ◽  
Lakshmi Devi
Keyword(s):  
Amino Acid ◽  
Antimicrobial Peptide ◽  
Lactobacillus Plantarum ◽  
Exchange Chromatography ◽  
Amino Acid Sequences ◽  
Proteinase K ◽  
Kinetic Assay ◽  
Wide Range

Abstract The focus of present study was to characterize antimicrobial peptide produced by probiotic cultures, Enterococcus durans DB-1aa (MCC4243), Lactobacillus plantarum Cu2-PM7 (MCC4246) and Lactobacillus fermentum Cu3-PM8 (MCC4233) against Staphylococus aureus and E. coli. The growth kinetic assay revealed 24 h of incubation to be optimum for bacteriocin production. The partially purified compound after ion-exchange chromatography was found to be thermoresistant and stable under wide range of pH. The compound was sensitive to proteinase-K, but resistant to trypsin, a-amylase and lipase. The apparent molecular weight of bacteriocin from MCC4243 and MCC4246 was found to be 3.5 KDa. Translated partial amino acid sequence of plnA gene in MCC4246 displayed 48 amino acid sequences showing 100% similarity with plantaricin A of Lactobacillus plantarum (WP_0036419). The sequence revealed 7 β sheets, 6 α sheets, 6 predicted coils and 9 predicted turns. The functions on cytoplasm show 10.82 isoelectric point and 48.6% hydrophobicity. The molecular approach of using Geneious Prime software and protein prediction data base for characterization of bacteriocin is novel and predicts “KSSAYSLQMGATAIKQVKKLFKKWGW” as peptide responsible for antimicrobial activity. The study provides information about broad spectrum bacteriocin in native probiotic culture and paves a way towards its application in functional foods as biopreservative agents.

Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis

2021 ◽  
Author(s):  
Siyan Zhao ◽  
Chen Zhang ◽  
Matthew J. Rogers ◽  
Xuejie Zhao ◽  
Jianzhong He
Keyword(s):  
Amino Acid ◽  
Microbial Communities ◽  
Genetic Marker ◽  
Genetic Markers ◽  
Unknown Function ◽  
Computational Approach ◽  
Amino Acid Sequences ◽  
Reductive Dehalogenation ◽  
Wide Range

As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences ( in silico ) and 10 different Dehalococcoides isolates ( in vitro ). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides , an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.

scholarly journals Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 8 ◽  
Author(s):  
Michael S. Wang ◽  
Kenric J. Hoegler ◽  
Michael H. Hecht
Keyword(s):  
Amino Acid ◽  
Transition Metals ◽  
Metal Binding ◽  
Combinatorial Library ◽  
De Novo ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Ancestral Sequences ◽  
Wide Range ◽  
Catalytic Functions

Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles. Although these sequences were neither designed nor evolved to bind metals, the majority of them have innate tendencies to bind the transition metals copper, cobalt, and zinc with high nanomolar to low-micromolar affinity.

scholarly journals Role of Glutamine Synthetase in Nitrogen Metabolite Repression in Aspergillus nidulans

2001 ◽  
Vol 183 (20) ◽  
pp. 5826-5833 ◽  
Author(s):  
Soula Margelis ◽  
Cletus D'Souza ◽  
Anna J. Small ◽  
Michael J. Hynes ◽  
Thomas H. Adams ◽  
...  
Keyword(s):  
Amino Acid ◽  
Glutamine Synthetase ◽  
Heterologous Expression ◽  
Aspergillus Nidulans ◽  
Essential Amino Acid ◽  
Gene Encoding ◽  
Nitrogen Metabolite Repression ◽  
Link Type ◽  
Wide Range

ABSTRACT Glutamine synthetase (GS), EC 6.3.1.2 , is a central enzyme in the assimilation of nitrogen and the biosynthesis of glutamine. We have isolated the Aspergillus nidulans glnA gene encoding GS and have shown that glnA encodes a highly expressed but not highly regulated mRNA. Inactivation of glnA results in an absolute glutamine requirement, indicating that GS is responsible for the synthesis of this essential amino acid. Even when supplemented with high levels of glutamine, strains lacking a functionalglnA gene have an inhibited morphology, and a wide range of compounds have been shown to interfere with repair of the glutamine auxotrophy. Heterologous expression of the prokaryotic Anabaena glnA gene from the A. nidulans alcA promoter allowed full complementation of the A. nidulans glnAΔ mutation. However, the A. nidulans fluG gene, which encodes a protein with similarity to prokaryotic GS, did not replace A. nidulans glnA function when similarly expressed. Our studies with theglnAΔ mutant confirm that glutamine, and not GS, is the key effector of nitrogen metabolite repression. Additionally, ammonium and its immediate product glutamate may also act directly to signal nitrogen sufficiency.

scholarly journals New 19-Residue Peptaibols from Trichoderma Clade Viride

2018 ◽  
Vol 6 (3) ◽  
pp. 85 ◽  
Author(s):  
Tamás Marik ◽  
Chetna Tyagi ◽  
Gordana Racić ◽  
Dávid Rakk ◽  
András Szekeres ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structural Investigation ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Helix Formation ◽  
Left Handed ◽  
Wall Structures ◽  
High Preference ◽  
Wide Range ◽  
Unusual Amino Acid

Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues of peptaibols, i.e., α-aminoisobutyric acid (Aib), isovaline (Iva), and the C-terminal 1,2-amino alcohol make them unique among peptides. In this study, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS. The examined strains appeared to produce 19-residue peptaibols, most of which are unknown from literature, but their amino acid sequences are similar to those of trikoningins, tricholongins, trichostrigocins, trichorzianins, and trichorzins. A new group of peptaibols detected in T. koningiopsis are described here under the name “Koningiopsin”. Trikoningin KA V, the closest peptaibol compound to the peptaibols produced by these two strains, was selected for structural investigation by short MD simulation, which revealed that many residues show high preference for left handed helix formation. The bioactivity of the peptaibol mixtures produced by T. koningiopsis and T. gamsii was tested on agar plates against bacteria, yeasts, and filamentous fungi. The results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures.

scholarly journals Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases

2004 ◽  
Vol 381 (1) ◽  
pp. 295-306 ◽  
Author(s):  
Senarath B. P. ATHAUDA ◽  
Koji MATSUMOTO ◽  
Sanath RAJAPAKSHE ◽  
Masayuki KURIBAYASHI ◽  
Masaki KOJIMA ◽  
...  
Keyword(s):  
Amino Acid ◽  
Computer Modelling ◽  
Structural Characteristics ◽  
Amino Acid Sequences ◽  
Cysteine Residues ◽  
Aspartic Proteinases ◽  
Protein Databases ◽  
Wide Range ◽  
First Time

Carnivorous plants are known to secrete acid proteinases to digest prey, mainly insects, for nitrogen uptake. In the present study, we have purified, for the first time, to homogeneity two acid proteinases (nepenthesins I and II) from the pitcher fluid of Nepenthes distillatoria (a pitcher-plant known locally as badura) and investigated their enzymic and structural characteristics. Both enzymes were optimally active at pH approx. 2.6 towards acid-denatured haemoglobin; the specificity of nepenthesin I towards oxidized insulin B chain appears to be similar, but slightly wider than those of other APs (aspartic proteinases). Among the enzymic properties, however, the most notable is their unusual stability: both enzymes were remarkably stable at or below 50 °C, especially nepenthesin I was extremely stable over a wide range of pH from 3 to 10 for over 30 days. This suggests an evolutionary adaptation of the enzymes to their specific habitat. We have also cloned the cDNAs and deduced the complete amino acid sequences of the precursors of nepenthesins I and II (437 and 438 residues respectively) from the pitcher tissue of N. gracilis. Although the corresponding mature enzymes (each 359 residues) are homologous with ordinary pepsin-type APs, both enzymes had a high content of cysteine residues (12 residues/molecule), which are assumed to form six unique disulphide bonds as suggested by computer modelling and are supposed to contribute towards the remarkable stability of nepenthesins. Moreover, the amino acid sequence identity of nepenthesins with ordinary APs, including plant vacuolar APs, is remarkably low (approx. 20%), and phylogenetic comparison shows that nepenthesins are distantly related to them to form a novel subfamily of APs with a high content of cysteine residues and a characteristic insertion, named ‘the nepenthesin-type AP-specific insertion’, that includes a large number of novel, orthologous plant APs emerging in the gene/protein databases.

scholarly journals Dye Decoloring Peroxidase Structure, Catalytic Properties and Applications: Current Advancement and Futurity

Catalysts ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 955
Author(s):  
Lingxia Xu ◽  
Jianzhong Sun ◽  
Majjid A. Qaria ◽  
Lu Gao ◽  
Daochen Zhu
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
High Efficiency ◽  
Chemical Properties ◽  
Catalytic Efficiency ◽  
Industrial Applications ◽  
Research Strategy ◽  
Amino Acid Sequences ◽  
Alkali Resistance ◽  
Wide Range

Dye decoloring peroxidases (DyPs) were named after their high efficiency to decolorize and degrade a wide range of dyes. DyPs are a type of heme peroxidase and are quite different from known heme peroxidases in terms of amino acid sequences, protein structure, catalytic residues, and physical and chemical properties. DyPs oxidize polycyclic dyes and phenolic compounds. Thus they find high application potentials in dealing with environmental problems. The structure and catalytic characteristics of DyPs of different families from the amino acid sequence, protein structure, and enzymatic properties, and analyzes the high-efficiency degradation ability of some DyPs in dye and lignin degradation, which vary greatly among DyPs classes. In addition, application prospects of DyPs in biomedicine and other fields are also discussed briefly. At the same time, the research strategy based on genetic engineering and synthetic biology in improving the stability and catalytic activity of DyPs are summarized along with the important industrial applications of DyPs and associated challenges. Moreover, according to the current research findings, bringing DyPs to the industrial level may require improving the catalytic efficiency of DyP, increasing production, and enhancing alkali resistance and toxicity.

scholarly journals Relatedness of type IV pilin PilA amongst geographically diverse Moraxella bovoculi isolated from cattle with infectious bovine keratoconjunctivitis

2021 ◽  
Author(s):  
John A. Angelos ◽  
Kristin A. Clothier ◽  
Regina L. Agulto ◽  
Boguslav Mandzyuk ◽  
Morten Tryland
Keyword(s):  
Amino Acid ◽  
Type Species ◽  
Amino Acid Sequences ◽  
Similar Degree ◽  
Content Type ◽  
Infectious Bovine Keratoconjunctivitis ◽  
Link Type ◽  
Type Iv ◽  
Type Iv Pilin ◽  
Moraxella Bovoculi

Introduction. Moraxella bovoculi is frequently isolated from the eyes of cattle with infectious bovine keratoconjunctivitis (IBK; pinkeye). As with M. bovis, which has been causally linked to IBK, M. bovoculi expresses an RTX (repeats in the structural toxin) cytotoxin that is related to M. bovis cytotoxin. Pilin, another pathogenic factor in M. bovis , is required for corneal attachment. Seven antigenically distinct pilin serogroups have been described in M. bovis . Hypothesis/Gap Statement. Multiple different serogroups exist amongst type IV pilin encoded by M. bovis , however, it is not known whether M. bovoculi exhibits a similar degree of diversity in type IV pilin that it encodes. Aim. This study was done to characterize a structural pilin (PilA) encoded by M. bovoculi isolated from cases of IBK to determine if diversity exists amongst PilA sequences. Methodology. Ninety-four isolates of M. bovoculi collected between 2002 and 2017 from 23 counties throughout California and from five counties in four other Western states were evaluated. Results. DNA sequencing and determination of deduced amino acid sequences revealed ten (designated groups A through J) unique PilA sequences that were ~96.1–99.3 % identical. Pilin groups A and C matched previously reported putative PilA sequences from M. bovoculi isolated from IBK-affected cattle in the USA (Virginia, Nebraska, and Kansas) and Asia (Kazakhstan). The ten pilin sequences identified were only ~74–76 % identical to deduced amino acid sequences of putative pilin proteins identified from the previously reported whole-genome sequences of M. bovoculi derived from deep nasopharyngeal swabs of IBK-asymptomatic cattle. Conclusions. Compared to the diversity reported between structural pilin proteins amongst different serogroups of M. bovis , M. bovoculi PilA from geographically diverse isolates derived from IBK-affected cattle are more conserved.

Evolutionary Computing to Examine Variation in Proteins with Evolution

2016 ◽  
pp. 187-202
Author(s):  
Sujay Ray
Keyword(s):  
Genetic Algorithms ◽  
Global Optimization ◽  
Amino Acid ◽  
Residue Level ◽  
Amino Acid Sequences ◽  
Single Amino Acid ◽  
Protein Alignment ◽  
Computational Approaches ◽  
Structure Of Proteins ◽  
State Of Art

Amino-acid sequences play a pivotal role for the structure of proteins. Alterations in a single amino-acid may vary the protein functioning. Alignment of sequences recognizes evolutionary and structurally related residues in a group of amino-acid sequences. It also aids to perceive the regions that are conserved throughout and are also functionally important. Although protein alignment issue has been studied in the past decades, but computational approaches serves as more accurate to investigate the entire process in a comparably lesser time. Evolutionary algorithms, more specifically, genetic algorithms are very beneficial. It leads to the global optimization of the protein after observance of “the fittest” among the rest. On global optimization, the protein tends to be more stable, thereby, helping the process of interactions among other stable proteins and provides a residue level study. Thus, this state-of-art can be implemented for alignment of macro-molecules, which serves as an essential criterion for further molecular level analyses.

Sign in / Sign up

Export Citation Format

Share Document