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)

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.

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

10.21203/rs.3.rs-366314/v2 ◽

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.02181-21 ◽

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.

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Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals

Life ◽

10.3390/life9010008 ◽

2019 ◽

Vol 9 (1) ◽

pp. 8 ◽

Cited By ~ 4

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.

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New 19-Residue Peptaibols from Trichoderma Clade Viride

Microorganisms ◽

10.3390/microorganisms6030085 ◽

2018 ◽

Vol 6 (3) ◽

pp. 85 ◽

Cited By ~ 10

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.

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

Biochemical Journal ◽

10.1042/bj20031575 ◽

2004 ◽

Vol 381 (1) ◽

pp. 295-306 ◽

Cited By ~ 80

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.

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

10.1101/599126 ◽

2019 ◽

Cited By ~ 5

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.

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

Catalysts ◽

10.3390/catal11080955 ◽

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.

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Soritesidine, a Novel Proteinous Toxin from the Okinawan Marine Sponge Spongosorites sp.

Marine Drugs ◽

10.3390/md17040216 ◽

2019 ◽

Vol 17 (4) ◽

pp. 216

Author(s):

Ryuichi Sakai ◽

Kota Tanano ◽

Takumi Ono ◽

Masaya Kitano ◽

Yusuke Iida ◽

...

Keyword(s):

Amino Acid ◽

Marine Sponge ◽

Brine Shrimp ◽

Mammalian Cells ◽

Metal Ion ◽

Artemia Salina ◽

Amino Acid Sequences ◽

Dependent Manner ◽

L1210 Cells ◽

Wide Range

A novel protein, soritesidine (SOR) with potent toxicity was isolated from the marine sponge Spongosorites sp. SOR exhibited wide range of toxicities over various organisms and cells including brine shrimp (Artemia salina) larvae, sea hare (Aplysia kurodai) eggs, mice, and cultured mammalian cells. Toxicities of SOR were extraordinary potent. It killed mice at 5 ng/mouse after intracerebroventricular (i.c.v.) injection, and brine shrimp and at 0.34 µg/mL. Cytotoxicity for cultured mammalian cancer cell lines against HeLa and L1210 cells were determined to be 0.062 and 12.11 ng/mL, respectively. The SOR-containing fraction cleaved plasmid DNA in a metal ion dependent manner showing genotoxicity of SOR. Purified SOR exhibited molecular weight of 108.7 kDa in MALDI-TOF MS data and isoelectric point of approximately 4.5. N-terminal amino acid sequence up to the 25th residue was determined by Edman degradation. Internal amino acid sequences for fifteen peptides isolated from the enzyme digest of SOR were also determined. None of those amino acid sequences showed similarity to existing proteins, suggesting that SOR is a new proteinous toxin.

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Purification, Characterization, and Application of a Novel Dye-Linked l-Proline Dehydrogenase from a Hyperthermophilic Archaeon, Thermococcus profundus

Applied and Environmental Microbiology ◽

10.1128/aem.67.4.1470-1475.2001 ◽

2001 ◽

Vol 67 (4) ◽

pp. 1470-1475 ◽

Cited By ~ 29

Author(s):

Haruhiko Sakuraba ◽

Yoshinori Takamatsu ◽

Takenori Satomura ◽

Ryushi Kawakami ◽

Toshihisa Ohshima

Keyword(s):

Amino Acid ◽

Crude Extract ◽

Specific Activity ◽

Amino Acid Sequences ◽

Proline Dehydrogenase ◽

Prosthetic Group ◽

Α Subunit ◽

Hyperthermophilic Archaeon ◽

Wide Range ◽

Michaelis Constants

ABSTRACT The distribution of dye-linked l-amino acid dehydrogenases was investigated in several hyperthermophiles, and the activity of dye-linked l-proline dehydrogenase (dye-l-proDH, l-proline:acceptor oxidoreductase) was found in the crude extract of someThermococcales strains. The enzyme was purified to homogeneity from a hyperthermophilic archaeon, Thermococcus profundus DSM 9503, which exhibited the highest specific activity in the crude extract. The molecular mass of the enzyme was about 160 kDa, and the enzyme consisted of heterotetrameric subunits (α2 β2) with two different molecular masses of about 50 and 40 kDa. The N-terminal amino acid sequences of the α-subunit (50-kDa subunit) and the β-subunit (40-kDa subunit) were MRLTEHPILDFSERRGRKVTIHF and XRSEAKTVIIGGGIIGLSIAYNLAK, respectively. Dye-l-proDH was extraordinarily stable among the dye-linked dehydrogenases under various conditions: the enzyme retained its full activity upon incubation at 70°C for 10 min, and ca. 40% of the activity still remained after heating at 80°C for 120 min. The enzyme did not lose the activity upon incubation over a wide range of pHs from 4.0 to 10.0 at 50°C for 10 min. The enzyme exclusively catalyzed l-proline dehydrogenation using 2,6-dichloroindophenol (Cl2Ind) as an electron acceptor. The Michaelis constants for l-proline and Cl2Ind were determined to be 2.05 and 0.073 mM, respectively. The reaction product was identified as Δ1-pyrroline-5-carboxylate by thin-layer chromatography. The prosthetic group of the enzyme was identified as flavin adenine dinucleotide by high-pressure liquid chromatography. In addition, the simple and specific determination of l-proline at concentrations from 0.10 to 2.5 mM using the stable dye-l-proDH was achieved.

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Development of a screening system for inteins active in protein splicing based on intein insertion into the LacZα-peptide

Biological Chemistry ◽

10.1515/hsz-2016-0229 ◽

2017 ◽

Vol 398 (1) ◽

pp. 57-67 ◽

Cited By ~ 8

Author(s):

Maximilian Neugebauer ◽

Jana K. Böcker ◽

Julian C.J. Matern ◽

Shmuel Pietrokovski ◽

Henning D. Mootz

Keyword(s):

Amino Acid ◽

Biochemical Characterization ◽

Amino Acid Sequences ◽

Side Reactions ◽

Protein Chemistry ◽

Protein Splicing ◽

Catalytic Center ◽

Host System ◽

Identify Amino Acid ◽

Wide Range

Abstract Protein splicing by inteins has found diverse applications in biotechnology, protein chemistry and chemical biology. Inteins display a wide range of efficiencies and rates unpredictable from their amino acid sequences. Here, we identified positions T22S and S35 in the LacZα peptide as intein insertion sites that strictly require protein splicing, in contrast to cleavage side-reactions, to allow for complementation of β-galactosidase activity. Both the cis-variant of the M86 mutant of the Ssp DnaB intein and a split form undergoing protein trans-splicing gave rise to formation of blue colonies in the β-galactosidase read-out. Furthermore, we report the two novel, naturally split VidaL T4Lh-1 and VidaL UvsX-2 inteins whose N-terminal fragments consist of only 15 and 16 amino acids, respectively. Initial biochemical characterization with the LacZα host system of these inteins further underlines its utility. Finally, we used the LacZα host system to rapidly identify amino acid substitutions from a small randomized library at the structurally conserved intein position 2 next to the catalytic center, that are tolerated for protein splicing activity of the M86 intein. These findings demonstrate the potential of the system for initial testing and directed evolution of inteins.

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