scholarly journals Disoxaril Mutants of Coxsackievirus B1: Phenotypic Characteristics and Analysis of the Target VP1 Gene

2011 ◽  
Vol 66 (11-12) ◽  
pp. 627-636 ◽  
Author(s):  
Ivanka Nikolova ◽  
Angel S. Galabov ◽  
Rumena Petkova ◽  
Stoyan Chakarov ◽  
Boris Atanasov
Keyword(s):  
Amino Acid ◽  
Point Mutations ◽  
Resistant Mutant ◽  
Binding Pocket ◽  
Amino Acid Sequences ◽  
Coxsackie Virus ◽  
Reference Structure ◽  
Phenotypic Characteristics ◽  
Rna Sequences ◽  
Particle Assembly

Disoxaril inhibits enterovirus replication by binding to the hydrophobic pocket within the VP1 coat protein, thus stabilizing the virion and blocking its uncoating. Disoxaril-resistant (RES) mutants of the Coxsackie virus B1 (CVB1/RES) were derived from the wild disoxaril- sensitive (SOF) strain (CVB1/SOF) using a selection approach. A disoxaril-dependent (DEP) mutant (CVB1/DEP) was obtained following nine consecutive passages of the disoxaril- resistant mutant in the presence of disoxaril. Phenotypic characteristics of the disoxaril mutants were investigated. A timing-of-addition study of the CVB1/DEP replication demonstrated that in the absence of disoxaril the virus particle assembly stopped. VP1 RNA sequences of disoxaril mutants were compared with the existing Gen Bank CVB1 reference structure. The amino acid sequence of a large VP1 196 - 258 peptide (disoxaril-binding region) of CVB1/RES was significantly different from that of the CVB1/SOF. Crucially important changes in CVB1/RES were two point mutations, M213H and F237L, both in the ligand-binding pocket. The sequence analysis of the CVB1/DEP showed some reversion to CVB1/SOF. The amino acid sequences of the three VP1 proteins are presented

Structure and function of voltage-dependent sodium channels: comparison of brain II and cardiac isoforms

1996 ◽  
Vol 76 (3) ◽  
pp. 887-926 ◽  
Author(s):  
H. A. Fozzard ◽  
D. A. Hanck
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Point Mutations ◽  
Amino Acid Sequences ◽  
Na Channel ◽  
Na Channels ◽  
Voltage Dependent ◽  
And Function ◽  
Relationship Of ◽  
The Relationship

Cardiac and nerve Na channels have broadly similar functional properties and amino acid sequences, but they demonstrate specific differences in gating, permeation, ionic block, modulation, and pharmacology. Resolution of three-dimensional structures of Na channels is unlikely in the near future, but a number of amino acid sequences from a variety of species and isoforms are known so that channel differences can be exploited to gain insight into the relationship of structure to function. The combination of molecular biology to create chimeras and channels with point mutations and high-resolution electrophysiological techniques to study function encourage the idea that predictions of structure from function are possible. With the goal of understanding the special properties of the cardiac Na channel, this review examines the structural (sequence) similarities between the cardiac and nerve channels and considers what is known about the relationship of structure to function for voltage-dependent Na channels in general and for the cardiac Na channels in particular.

scholarly journals Cloning and Expression Analysis of a Farnesyl Diphosphate Synthase (FPPS) Gene from Chamaemelum nobile

2017 ◽  
Vol 45 (2) ◽  
pp. 358-364 ◽  
Author(s):  
Xiao-Meng LIU ◽  
Ting-Ting TAO ◽  
Xiang-Xiang MENG ◽  
Wei-Wei ZHANG ◽  
Jie CHANG ◽  
...  
Keyword(s):  
Amino Acid ◽  
Condensation Reaction ◽  
Binding Pocket ◽  
Amino Acid Sequences ◽  
Farnesyl Diphosphate ◽  
Cloning And Expression ◽  
Farnesyl Diphosphate Synthase ◽  
Reading Frame ◽  
Chamaemelum Nobile ◽  
Multiple Alignment Analysis

Farnesyl diphosphate synthase (FPPS), an isopentenyl transferase, catalyzes the condensation reaction of five carbon isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) to form fifteen carbon farnesyl pyrophosphate (FPP), which is the key precursor for sesquiterpene biosynthesis. In this study, a FPPS gene (CnFPPS) was cloned from Chamaemelum nobile. The full-length cDNA of CnFPPS is 1239 bp and contains an open reading frame (ORF) of 1029 bp encoding 342 amino acids. The theoretical molecular weight and pI of the CnFPPS protein are 39.38 kDa and 5.59, respectively. Multiple alignment analysis showed the protein sequence of CnFPPS had a high homology with FPPS proteins from other plants. The deduced amino acid of CnFPPS contained five conservative domains such as substrate binding pocket, substrate-Mg2+ binding site, catalytic site, aspartate-rich region 1 and 2, suggesting CnFPPS is one member of FPPS family in C. nobile. Phylogenetic analysis based on the amino acid sequences of FPPSs showed that CnFPPS was closely related to the FPPS of Matricaria chamomilla. The result of qRT-PCR revealed that CnFPPS gene was constitutively expressed in different tissues of C. nobile, with the highest expression in the root. These findings improve the understanding of the synthesis and regulation of the terpenoid compounds at the molecular level and lay a foundation for studying the regulatory functions of CnFPPS in terpenoid biosynthetic pathway in C. nobile.

scholarly journals Saccharomyces cerevisiae contains a complex multigene family related to the major heat shock-inducible gene of Drosophila.

1982 ◽  
Vol 2 (11) ◽  
pp. 1388-1398 ◽  
Author(s):  
T D Ingolia ◽  
M R Slater ◽  
E A Craig
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Heat Shock ◽  
Dna Sequences ◽  
Multigene Family ◽  
Amino Acid Sequences ◽  
Hsp 70 ◽  
Rna Sequences ◽  
Yeast Genes ◽  
Differential Control

Saccharomyces cerevisiae contains a family of genes related to the major heat shock-induced gene of Drosophila (hsp 70). Two members of the multigene family (YG100 and YG101) were isolated. The primary DNA sequences of more than one-half of the protein-encoding regions of YG100 and YG101 were determined and compared with the Drosophila hsp 70 gene sequence; the predicted amino acid sequences were 72 and 64% homologous to the sequence of the Drosophila hsp 70 protein, respectively. The predicted amino acid sequences of the yeast genes were 65% homologous. Our results demonstrate a striking sequence conservation of hsp 70-related sequences in evolution. Hybridization of the S. cerevisiae genes to total S. cerevisiae DNA indicated that the multigene family consists of approximately 10 members. Hybridization of labeled RNAs from heat-shocked and control cells suggested that, like transcription of the Drosophila hsp 70 gene, transcription of YG100 or a closely related gene is enhanced after heat shock. However, the amount of RNA sequences homologous to YG101 was reduced after heat shock. A multigene family related to the hsp 70 gene exists in Drosophila; transcription of some members is induced by heat shock, whereas transcription of others is not. Our results suggest that S. cerevisiae, like Drosophila, contains a multigene family of hsp 70-related sequences under complex transcriptional regulation and that the differential control, as well as the nucleotide sequence, has been highly conserved in evolution.

scholarly journals RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tomasz Woźniak ◽  
Małgorzata Sajek ◽  
Jadwiga Jaruzelska ◽  
Marcin Piotr Sajek
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Rna Structure ◽  
Structural Information ◽  
Amino Acid Sequences ◽  
Substitution Matrix ◽  
Rna Sequences ◽  
Rna Molecules ◽  
Bioinformatic Tools ◽  
Amino Acid Substitution Matrix

Abstract Background The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA molecules into RNA families. However, the existing multiple RNA alignment tools, which use structural information, are slow in aligning long molecules and/or a large number of molecules. Therefore, a more rapid tool for multiple RNA alignment may improve the classification of known RNAs and help to reveal the functions of newly discovered RNAs. Results Here, we introduce an extremely fast Python-based tool called RNAlign2D. It converts RNA sequences to pseudo-amino acid sequences, which incorporate structural information, and uses a customizable scoring matrix to align these RNA molecules via the multiple protein sequence alignment tool MUSCLE. Conclusions RNAlign2D produces accurate RNA alignments in a very short time. The pseudo-amino acid substitution matrix approach utilized in RNAlign2D is applicable for virtually all protein aligners.

scholarly journals Genetic Diversity in the Protective Antigen Gene ofBacillus anthracis

1999 ◽  
Vol 181 (8) ◽  
pp. 2358-2362 ◽  
Author(s):  
Lance B. Price ◽  
Martin Hugh-Jones ◽  
Paul J. Jackson ◽  
Paul Keim
Keyword(s):  
Amino Acid ◽  
Protective Antigen ◽  
Lethal Factor ◽  
Point Mutations ◽  
Cladistic Analysis ◽  
Amino Acid Sequences ◽  
Sample Survey ◽  
Plasmid Evolution ◽  
Antigen Gene ◽  
Antigenic Region

ABSTRACT Bacillus anthracis is a gram-positive spore-forming bacterium that causes the disease anthrax. The anthrax toxin contains three components, including the protective antigen (PA), which binds to eucaryotic cell surface receptors and mediates the transport of toxins into the cell. In this study, the entire 2,294-nucleotide protective antigen gene (pag) was sequenced from 26 of the most diverse B. anthracis strains to identify potential variation in the toxin and to further our understanding of B. anthracis evolution. Five point mutations, three synonymous and two missense, were identified. These differences correspond to six different haploid types, which translate into three different amino acid sequences. The two amino acid changes were shown to be located in an area near a highly antigenic region critical to lethal factor binding. Nested primers were used to amplify and sequence this same region of pag from necropsy samples taken from victims of the 1979 Sverdlovsk incident. This investigation uncovered five different alleles among the strains present in the tissues, including two not seen in the 26-sample survey. One of these two alleles included a novel missense mutation, again located just adjacent to the highly antigenic region. Phylogenetic (cladistic) analysis of thepag corresponded with previous strain grouping based on chromosomal variation, suggesting that plasmid evolution in B. anthracis has occurred with little or no horizontal transfer between the different strains.

New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory

2012 ◽  
Vol 442 (1) ◽  
pp. 27-37 ◽  
Author(s):  
Aleksander W. Roszak ◽  
Vladimíra Moulisová ◽  
Adhie D. P. Reksodipuro ◽  
Alastair T. Gardiner ◽  
Ritsuko Fujii ◽  
...  
Keyword(s):  
Amino Acid ◽  
Point Mutations ◽  
Binding Pocket ◽  
High Rate ◽  
Purple Bacterium ◽  
Reaction Centre ◽  
Continuous Growth ◽  
Bacterial Cultures ◽  
Blastochloris Viridis ◽  
Pure Bacterial Cultures

Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.

Saccharomyces cerevisiae contains a complex multigene family related to the major heat shock-inducible gene of Drosophila

1982 ◽  
Vol 2 (11) ◽  
pp. 1388-1398
Author(s):  
T D Ingolia ◽  
M R Slater ◽  
E A Craig
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Heat Shock ◽  
Dna Sequences ◽  
Multigene Family ◽  
Amino Acid Sequences ◽  
Hsp 70 ◽  
Rna Sequences ◽  
Yeast Genes ◽  
Differential Control

Saccharomyces cerevisiae contains a family of genes related to the major heat shock-induced gene of Drosophila (hsp 70). Two members of the multigene family (YG100 and YG101) were isolated. The primary DNA sequences of more than one-half of the protein-encoding regions of YG100 and YG101 were determined and compared with the Drosophila hsp 70 gene sequence; the predicted amino acid sequences were 72 and 64% homologous to the sequence of the Drosophila hsp 70 protein, respectively. The predicted amino acid sequences of the yeast genes were 65% homologous. Our results demonstrate a striking sequence conservation of hsp 70-related sequences in evolution. Hybridization of the S. cerevisiae genes to total S. cerevisiae DNA indicated that the multigene family consists of approximately 10 members. Hybridization of labeled RNAs from heat-shocked and control cells suggested that, like transcription of the Drosophila hsp 70 gene, transcription of YG100 or a closely related gene is enhanced after heat shock. However, the amount of RNA sequences homologous to YG101 was reduced after heat shock. A multigene family related to the hsp 70 gene exists in Drosophila; transcription of some members is induced by heat shock, whereas transcription of others is not. Our results suggest that S. cerevisiae, like Drosophila, contains a multigene family of hsp 70-related sequences under complex transcriptional regulation and that the differential control, as well as the nucleotide sequence, has been highly conserved in evolution.

scholarly journals Different pattern of haemagglutinin immunoreactivity of equine influenza virus strains isolated in Poland

2015 ◽  
Vol 59 (4) ◽  
pp. 463-466
Author(s):  
Małgorzata Kwaśnik ◽  
Ilona Marcelina Góra ◽  
Wojciech Rożek
Keyword(s):  
Monoclonal Antibody ◽  
Influenza Virus ◽  
Amino Acid ◽  
Point Mutations ◽  
Amino Acid Sequences ◽  
Equine Influenza Virus ◽  
Equine Influenza ◽  
Antigenic Sites ◽  
Virus Strains

Abstract The immunoreactivity of haemagglutinin (HA) polypeptides of equine influenza virus was compared among the strains isolated in Poland, using H3 monoclonal antibody. A stronger signal in immunoblot reaction was observed for A/equi/Pulawy/2008 HA polypeptides compared to A/equi/Pulawy/2006, despite the fact that both strains are phylogenetically closely related and belong to Florida clade 2 of American lineage. The strongest signal, observed in the case of A/equi/Pulawy/2008, seemed to be connected with the presence of G135, I213, E379, and/or V530 instead of R135, M213, G379, and I530 present in A/equi/Pulawy/2006 HA sequence. This implies that point mutations within amino acid sequences of HA polypeptides of equine influenza virus may change their immunoreactivity even when they are not located within five basic antigenic sites.

scholarly journals Mutation and Phylogenetic Analysis of Spike Glycoprotein of Indonesian Isolates of Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2)

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Shabarni Gaffar ◽  
◽  
Syifa Al Fauziah Rahmani ◽  
Ari Hardianto
Keyword(s):  
Amino Acid ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Surface Protein ◽  
Amino Acid Sequences ◽  
Effective Vaccine ◽  
Neighbor Joining ◽  
Multiple Sequence ◽  
Spike Gene ◽  
Relationship Of

Coronavirus disease-2019 (COVID-19) is an infectious acute respiratory disease caused by SARS-CoV-2. The protein that plays a role in the entry of SARS-CoV-2 into human cells is the surface protein, or the Spike, which is thought to be the effective vaccine target to prevent SARS-CoV-2 infection. Until December 2020, Indonesia has reported 106 SARS-CoV-2 genome sequences identified from COVID-19 positive patients. The purpose of this study was to analyze the phylogenetic relationship of the Spike protein of the Indonesian isolates of SARS-CoV-2 Indonesian, as well as the virus mutations and their effects on changes in the amino acid. The 106 Indonesian SARS-CoV-2 genomes were downloaded from GISAID and the Spike nucleotide and amino acid sequences were analyzed by multiple sequence alignment (MSA) and mutation analysis using the ClustalW method. Phylogenetic trees were created using the Neighbor-Joining method in MEGA-X software. The results showed that 30 of the 106 Indonesian isolate SARS-CoV-2 Spike were 100% identical to the Wuhan-Hu-1, while the remaining 76 had experienced mutations at 1-4 sites. There were 43-point mutations in the Spike gene, 27 of which led to amino acid changes and four had not been reported in other countries. The global mutation D614G was found in 60 Indonesian isolates , of which West Java was the province with the most reports. The phylogenetic of Spike showed that the Indonesian samples have been divided into several branches that are far from Wuhan-Hu-1. This study indicates the possibility of differences in the protein structure of Indonesian isolate SARS-CoV-2 Spike that need to be further studied to manufacture a vaccine against the Indonesian strain of SARS-CoV-2.

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