Computational approach for selection of epitope-based dengue vaccine targets

High antigenic variability in the envelope (E) protein of different virus strains has been a major obstacle in designing effective vaccines for Dengue virus (DENV). To maintain their biological function, some parts of viral proteins remain stable during evolution thus one possible approach to solve this problem is to recognize specific regions within different protein sequences of E that have the tendency to stay constant through evolution. These regions may possess some special attributes to become a vaccine candidate against dengue virus. In this study, a computational approach was utilized to identify and analyze highly conserved amino acid sequences of the DENV E protein. Sequences of 9 amino acids or more were specifically focused due to their immune-relevant as T-cell determinants. Different bioinformatics tools were responsible for revealing conserved regions in the DENV E protein and constructing the phylogenetic tree from the sequence database. The tools also predicted immunogenicity of the identified vaccine targets. Ultimately, two peptide regions of at least 9 amino acids were chosen due to their high conserved attribute in more than 95% of all collected DENV sequences. Moreover, both of them was found to be immune-relevant by their correspondence to known or putative HLA-restricted T cell determinants. The conserved attribute of these sequences through the entire analysis of this study supports their potential as candidates for further in vitro experiments for rational design a universal vaccine which has longer and broader impact.

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Analisis Pohon Filogenik dari Protein Non-Struktural 1 (NS1) Virus Dengue di Kawasan Asia Tenggara

JURNAL Al-AZHAR INDONESIA SERI SAINS DAN TEKNOLOGI ◽

10.36722/sst.v1i2.28 ◽

2011 ◽

Vol 1 (2) ◽

pp. 69

Author(s):

Vanny Narita ◽

Asma Omar ◽

Agus Masduki

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Dengue Virus ◽

Protein Sequences ◽

Amino Acid Sequences ◽

South East Asia ◽

Phylogenetic Relation ◽

Phylogenetic Tree Analysis ◽

Tree Analysis ◽

Different Strains

Protein non-struktural 1 adalah protein Virus Dengue yang terkonservasi, tetapi protein non-struktural 1 dari Virus Dengue yang berbeda strain memiliki epitop berbeda yang dapat dikenali oleh sel-B. Epitop-epitop ini mungkin disusun oleh asam amino yang sama dalam urutan yang berbeda. Kemungkinan ini perlu dipertimbangkan dalam rangka memprediksi epitop sekuensial Virus Dengue. Tujuan penelitian kami adalah menganalisis hubungan kekerabatan dan susunan asam amino pada epitop spesifik yang telah dikonfirmasi dari sampel representatif gen protein NS1 dari Virus Dengue di kawasan Asia Tenggara. Hubungan kekerabatan protein non-struktural 1 dianalisis dengan perangkat lunak Lasergene®. Sekuen gen ditranslasi terlebih dahulu ke urutan asam amino, dan analisis pohon filogenetik kemudian dilakukan. Hasilnya menunjukkan bahwa hubungan kekerabatan protein non-struktural 1 berkisar antara 72-98%. Selanjutnya, epitop serospesifik dibandingkan berdasarkan hasil pengolahan data dnegan Lasergene. Perbandingan epitop serospesifik menunjukkan bahwa asam amino yang dominan dalam epitop adalah histidin, tirosin, glutamine dan serin<h6 style="text-align: center;"> Abstract</h6>Non-structural 1 protein is a conserved protein of dengue virus, but non-structural 1 proteins of dengue virus from different strains have different epitopes which can be recognized by B-cell. These epitopes may be constructed of similar amino acids in a different arrangement. This possibility must be considered in order to predict the sequencial epitope of dengue virus. The objective of our study was to analyze the phylogenetic relation and the arrangment of confirmed specific epitopes of dengue strains from representatives of South East Asia’s NS1 dengue gene samples. The phylogenetic relation of non-structural 1 protein sequences from South East Asia was analyzed with Lasergene® software. The gene sequences were translated to amino acid sequences, and phylogenetic tree analysis was performed. The results showed that the relatedness values among full sequences of non-structural 1 protein were 72-98%. Furthermore, the serospesific epitopes were compared according to the Lasergene results. The serospesific epitope comparation showed that the dominant amino acids in these epitopes were histidine, tyrosine, glutamine and serine.

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Determinants of adenine-mutagenesis in diversity-generating retroelements

Nucleic Acids Research ◽

10.1093/nar/gkaa1240 ◽

2020 ◽

Author(s):

Sumit Handa ◽

Andres Reyna ◽

Timothy Wiryaman ◽

Partho Ghosh

Keyword(s):

Amino Acids ◽

Dark Matter ◽

Reverse Transcription ◽

Genetic Information ◽

Human Microbiome ◽

Protein Sequences ◽

Catalytic Efficiency ◽

Natural World ◽

In Vitro System

Abstract Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.

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Interactions of mouse glycophorin A with the dRTA-related mutant G719D of the mouse Cl–/HCO3– exchanger Ae1This paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process.

Biochemistry and Cell Biology ◽

10.1139/o10-147 ◽

2011 ◽

Vol 89 (2) ◽

pp. 224-235 ◽

Cited By ~ 2

Author(s):

Andrew K. Stewart ◽

Fouad T. Chebib ◽

Syed W. Akbar ◽

Maria J. Salas ◽

Rajan A. Sonik ◽

...

Keyword(s):

Amino Acids ◽

Transmembrane Domain ◽

Peer Review Process ◽

Surface Expression ◽

Amino Acid Sequences ◽

Glycophorin A ◽

Specific Expression ◽

Health And Disease ◽

Renal Tubular

The AE1 mutation G701D, associated with recessive distal renal tubular acidosis (dRTA), produces only minimal erythroid phenotype, reflecting erythroid-specific expression of stimulatory AE1 subunit glycophorin A (GPA). GPA transgene expression could theoretically treat recessive dRTA in patients and in mice expressing cognate Ae1 mutation G719D. However, human (h) GPA and mouse (m) Gpa amino acid sequences are widely divergent, and mGpa function in vitro has not been investigated. We therefore studied in Xenopus oocytes the effects of coexpressed mGpa and hGPA on anion transport by erythroid (e) and kidney (k) isoforms of wild-type mAe1 (meAe1, mkAe1) and of mAe1 mutant G719D. Coexpression of hGPA or mGpa enhanced the function of meAe1 and mkAe1 and rescued the nonfunctional meAe1 and mkAe1 G719D mutants through increased surface expression. Progressive N-terminal truncation studies revealed a role for meAe1 amino acids 22–28 in GPA-responsiveness of meAe1 G719D. MouseN-cyto/humanTMD and humanN-cyto/mouseTMD kAE1 chimeras were active and GPA-responsive. In contrast, whereas chimera mkAe1N-cyto/hkAE1 G701DTMD was GPA-responsive, chimera hkAE1N-cyto/mkAe1 G719DTMD was GPA-insensitive. Moreover, whereas the isolated transmembrane domain (TMD) of hAE1 G701D was GPA-responsive, that of mAe1 G719D was GPA-insensitive. Thus, mGpa increases surface expression and activity of meAe1 and mkAe1. However, the G719D mutation renders certain mAe1 mutant constructs GPA-unresponsive and highlights a role for erythroid-specific meAe1 amino acids 22–28 in GPA-responsiveness.

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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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BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

International Journal of Molecular Sciences ◽

10.3390/ijms20235978 ◽

2019 ◽

Vol 20 (23) ◽

pp. 5978 ◽

Cited By ~ 49

Author(s):

Minkiewicz ◽

Iwaniak ◽

Darewicz

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Chronic Diseases ◽

Bioactive Peptides ◽

Protein Sequences ◽

Batch Processing ◽

Amino Acid Sequences ◽

Quantitative Parameters ◽

New Information

The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

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Identification of amino acid sequences determining interaction between the cucumber mosaic virus-encoded 2a polymerase and 3a movement proteins

Journal of General Virology ◽

10.1099/vir.0.83207-0 ◽

2007 ◽

Vol 88 (12) ◽

pp. 3445-3451 ◽

Cited By ~ 11

Author(s):

Min Sook Hwang ◽

Kyung Nam Kim ◽

Jeong Hyun Lee ◽

Young In Park

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Critical Role ◽

Amino Acid Sequences ◽

Multiple Sequence ◽

Movement Proteins ◽

Gdd Motif

The cucumber mosaic virus (CMV)-encoded 3a movement protein (MP) is indispensable for CMV movement in plants. We have previously shown that MP interacts directly with the CMV-encoded 2a polymerase protein in vitro. Here, we further dissected this interaction and determined the amino acid sequences that are responsible for the MP and 2a polymerase protein interaction. Both the N-terminal 21 amino acids and the central GDD motif of the 2a polymerase protein were important for interacting with the MP. Although each of the regions alone was sufficient for the interaction with MP, quantitative yeast two-hybrid analyses showed that they acted synergistically to enhance the binding affinity. The MP N-terminal 20 amino acids were sufficient for interacting with the 2a polymerase protein, and the serine residue at position 14 played a critical role in the interaction. Multiple sequence alignment showed that the 2a protein interacting regions and the serine at position 14 in the MP are highly conserved among subgroup I and II CMV isolates.

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N-terminal binding domain of Gα subunits: involvement of amino acids 11–14 of Gα0 in membrane attachment

Biochemical Journal ◽

10.1042/bj3230239 ◽

1997 ◽

Vol 323 (1) ◽

pp. 239-244 ◽

Cited By ~ 5

Author(s):

Liliana BUSCONI ◽

Paula M. BOUTIN ◽

Bradley M. DENKER

Keyword(s):

Signal Transduction ◽

Amino Acids ◽

G Proteins ◽

Membrane Binding ◽

Amino Acid Sequences ◽

Membrane Receptors ◽

In Vitro Translation ◽

Membrane Attachment ◽

Membrane Components

Heterotrimeric guanine nucleotide binding proteins (G-proteins) transmit signals from membrane receptors to a variety of intracellular effectors. G-proteins reversibly associate with components of the signal transduction system, yet remain membrane attached throughout the cycle of activation. The Gα subunits remain attached to the plasma membrane through a combination of factors that are only partially defined. We now demonstrate that amino acids within the N-terminal domain of Gα subunits are involved in membrane binding. We used in vitro translation, a technique widely utilized to characterize functional aspects of G-proteins, and interactions with donor-acceptor membranes to demonstrate that amino acids 11-14 of Gαo contribute to membrane binding. The membrane binding of Gαo lacking amino acids 11-14 (D[11-14]) was significantly reduced at all membrane concentrations in comparison with wild-type Gαo. Several other N-terminal mutants of Gαo were characterized as controls, and these results indicate that differences in myristoylation, palmitoylation and βγ interactions do not account for the reduced membrane binding of D[11-14]. Furthermore, when membrane attachment of Gαo and mutants was characterized in transiently transfected 35S-labelled and [3H]myristate-labelled COS cells, amino acids 11-14 contributed to membrane binding. These studies reveal that membrane binding of Gα subunits occurs by a combination of factors that include lipids and amino acid sequences. These regions may provide novel sites for interaction with membrane components and allow additional modulation of signal transduction.

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In Vitro Reconstitution Reveals Key Intermediate States of Trimer Formation by the Dengue Virus Membrane Fusion Protein

Journal of Virology ◽

10.1128/jvi.00170-10 ◽

2010 ◽

Vol 84 (11) ◽

pp. 5730-5740 ◽

Cited By ~ 35

Author(s):

Maofu Liao ◽

Claudia Sánchez-San Martín ◽

Aihua Zheng ◽

Margaret Kielian

Keyword(s):

Dengue Virus ◽

Membrane Fusion ◽

Transmembrane Protein ◽

Fusion Reaction ◽

Low Ph ◽

Viral Envelope ◽

Interaction Sites ◽

E Protein ◽

Hairpin Formation

ABSTRACT The flavivirus dengue virus (DV) infects cells through a low-pH-triggered membrane fusion reaction mediated by the viral envelope protein E. E is an elongated transmembrane protein with three domains and is organized as a homodimer on the mature virus particle. During fusion, the E protein homodimer dissociates, inserts the hydrophobic fusion loop into target membranes, and refolds into a trimeric hairpin in which domain III (DIII) packs against the central trimer. It is clear that E refolding drives membrane fusion, but the steps in hairpin formation and their pH requirements are unclear. Here, we have used truncated forms of the DV E protein to reconstitute trimerization in vitro. Protein constructs containing domains I and II (DI/II) were monomeric and interacted with membranes to form core trimers. DI/II-membrane interaction and trimerization occurred efficiently at both neutral and low pH. The DI/II core trimer was relatively unstable and could be stabilized by binding exogenous DIII or by the formation of mixed trimers containing DI/II plus E protein with all three domains. The mixed trimer had unoccupied DIII interaction sites that could specifically bind exogenous DIII at either low or neutral pH. Truncated DV E proteins thus reconstitute hairpin formation and define properties of key domain interactions during DV fusion.

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Characterization of a New Bacteriocin, Carocin D, from Pectobacterium carotovorum subsp. carotovorum Pcc21

Applied and Environmental Microbiology ◽

10.1128/aem.03103-09 ◽

2010 ◽

Vol 76 (22) ◽

pp. 7541-7549 ◽

Cited By ~ 28

Author(s):

Eunjung Roh ◽

Tae-Ho Park ◽

Myung-il Kim ◽

Seungdon Lee ◽

Sangryeol Ryu ◽

...

Keyword(s):

Amino Acids ◽

Antibacterial Activity ◽

Biological Control Agent ◽

Soft Rot ◽

Control Agent ◽

Indicator Strain ◽

Amino Acid Sequences ◽

Pectobacterium Carotovorum ◽

N Terminus

ABSTRACT Two different bacteriocins, carotovoricin and carocin S1, had been found in Pectobacterium carotovorum subsp. carotovorum, which causes soft-rot disease in diverse plants. Previously, we reported that the particular strain Pcc21, producing only one high-molecular-weight bacteriocin, carried a new antibacterial activity against the indicator strain Pcc3. Here, we report that this new antibacterial activity is due to a new bacteriocin produced by strain Pcc21 and named carocin D. Carocin D is encoded by the caroDK gene located in the genomic DNA together with the caroDI gene, which seems to encode an immunity protein. N-terminal amino acid sequences of purified carocin D were determined by Edman degradation. In comparison with the primary translation product of caroDK, it was found that 8 amino acids are missing at the N terminus. This finding proved that carocin D is synthesized as a precursor peptide and that 8 amino acids are removed from its N terminus during maturation. Carocin D has two putative translocation domains; the N-terminal and C-terminal domains are homologous to those of Escherichia coli colicin E3 and Pseudomonas aeruginosa S-type pyocin, respectively. When caroDK and caroDI genes were transformed into carocin D-sensitive bacteria such as Pcc3, the bacteria became resistant to this bacteriocin. Carocin D has one putative DNase domain at the extreme C terminus and showed DNase activity in vitro. This bacteriocin had slight tolerance to heat but not to proteases. The caroDK gene was present in only 5 of 54 strains of P. carotovorum subsp. carotovorum. These results indicate that carocin D is a third bacteriocin found in P. carotovorum subsp. carotovorum, and this bacteriocin can be readily expressed in carocin D-sensitive nonpathogenic bacteria, which may have high potential as a biological control agent in the field.

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Triazine Inhibits Toxoplasma gondii Tachyzoites In Vitro and In Vivo

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.8.3463-3467.2005 ◽

2005 ◽

Vol 49 (8) ◽

pp. 3463-3467 ◽

Cited By ~ 21

Author(s):

Ernest J. Mui ◽

David Jacobus ◽

Wilbur K. Milhous ◽

Guy Schiehser ◽

Honghue Hsu ◽

...

Keyword(s):

Amino Acids ◽

Toxoplasma Gondii ◽

Homo Sapiens ◽

Intraperitoneal Administration ◽

Development Program ◽

Amino Acid Sequences ◽

Peroral Administration ◽

Mammalian Host

ABSTRACT The triazine WR99210 [4,6-diamino-1,2-dihydro-2,2-dimethyl-1-(2,4,5-trichlorophenoxypropyloxy)-1,3,5 triazine] inhibits Toxoplasma gondii in vitro at nanomolar levels (P < 0.05). The 50% inhibitory concentration (IC50) was approximately 50 nM. It is a potent inhibitor in vitro and is also effective in vivo. Administration of WR99210 parenterally (i.e., intraperitoneally) reduced the mean number of RH strain tachyzoites present in peritoneal fluid substantially 4 days after intraperitoneal infection of mice. There was a mean of approximately 35 million parasites in control mice as contrasted with approximately 2 million parasites in mice treated with 1.25 mg WR99210/kg of body weight in a representative experiment (P < 0.05). In addition the prodrug PS-15 N′-[3-(2,4, 5-trichlorophenoxy)propyloxy]-N9-(1-methylethyl) imidocarbonimidicdiamide is converted to 4,6-diamino-1,2-dihydro-2,2-dimethyl-1-(2,4,5-trichlorophenoxypropyloxy)-1,3,5 triazine in vivo when the prodrug is administered orally. PS-15 administered by gavage also reduced intraperitoneal RH strain T. gondii tachyzoite numbers. WR99210 has high efficacy and relatively low toxicity because of its substantial effect on T. gondii dihydrofolate reductase (DHFR) but not the mammalian host DHFR. Amino acid sequences of T. gondii, Plasmodium falciparum, and Homo sapiens DHFRs were compared. It is of interest that of the DHFR amino acids considered to be interacting with WR99210 in P. falciparum within interatomic distances within 3 to 5 Å, four of eight were shared with T. gondii DHFR. H. sapiens also shared four amino acids thought to be interacting with WR99210. Efficacy of intraperitoneal administration of WR99210 and peroral administration of PS-15 demonstrate the potential usefulness of this class of compounds in treatment of toxoplasmosis administered either parenterally or perorally. The recent development program for this class of antimicrobials as antimalarials makes our proof of principle of improved efficacy of triazines (compared with the gold standard treatment, pyrimethamine) against T. gondii especially promising.

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