scholarly journals Interaction of human cytokeratins with isatin analogues

2010 ◽  
Vol 56 (1) ◽  
pp. 138-145 ◽  
Author(s):  
O.A. Buneeva ◽  
O.V. Gnedenko ◽  
V.I. Fedchenko ◽  
A.S. Ivanov ◽  
A.E. Medvedev
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Specific Binding ◽  
Optical Biosensor ◽  
Amino Acid Sequences ◽  
Chip Surface ◽  
High Affinity ◽  
Terminal Domain ◽  
Carboxymethyl Dextran

Using an optical biosensor Biacore 3000 the interaction of human recombinant cytokeratins (CK) with isatin analogues (5-aminocaproyl-isatin and 5-aminoisatin) immobilized on the CM-5 chip has been investigated. CK-14 effectively interacted with 5-aminocaproyl-isatin immobilized on the carboxymethyl dextran chip surface, but not with a "shorter" analogue (5-aminoisatin). In contrast to CK14 CK8 effectively interacted only with 5-aminoisatin. In both cases cytokeratin binding with the immobilized isatin analogues was characterized by rather high affinity (Kd of 0.7 μM for the pair CK14/immobilized 5-aminocaproylisatin and 1.7 μM for the pair CK8/immobilized 5-aminoisatin). CK20 did not interact with both immobilized isatin analogues. Taking into consideration non-specific binding of mouse CK14 and rat CK8 with 5-aminocaproyl-Sepharose we have performed comparative analysis of amino acid sequences of human, mouse, and rat CK8 and CK14. The data obtained suggest that in the case of human, mouse, and rat CK14 the N-terminal domain is the most variable amoung these species, whereas the major differences between amino acid sequences of human, mouse, and rat CK8 have been found both in N-terminal and C-terminal regions.

Y-box proteins combine versatile cold shock domains and arginine-rich motifs (ARMs) for pleiotropic functions in RNA biology

2018 ◽  
Vol 475 (17) ◽  
pp. 2769-2784 ◽  
Author(s):  
Kenneth C. Kleene
Keyword(s):  
Amino Acid ◽  
Cold Shock ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Amino Acid Sequences ◽  
Site Specific ◽  
Terminal Domain ◽  
Rna Backbone ◽  
Specific Regulation

Y-box proteins are single-strand DNA- and RNA-binding proteins distinguished by a conserved cold shock domain (CSD) and a variable C-terminal domain organized into alternating short modules rich in basic or acidic amino acids. A huge literature depicts Y-box proteins as highly abundant, staggeringly versatile proteins that interact with all mRNAs and function in most forms of mRNA-specific regulation. The mechanisms by which Y-box proteins recognize mRNAs are unclear, because their CSDs bind a jumble of diverse elements, and the basic modules in the C-terminal domain are considered to bind nonspecifically to phosphates in the RNA backbone. A survey of vertebrate Y-box proteins clarifies the confusing names for Y-box proteins, their domains, and RNA-binding motifs, and identifies several novel conserved sequences: first, the CSD is flanked by linkers that extend its binding surface or regulate co-operative binding of the CSD and N-terminal and C-terminal domains to proteins and RNA. Second, the basic modules in the C-terminal domain are bona fide arginine-rich motifs (ARMs), because arginine is the predominant amino acid and comprises 99% of basic residues. Third, conserved differences in AA (amino acid) sequences between isoforms probably affect RNA-binding specificity. C-terminal ARMs connect with many studies, demonstrating that ARMs avidly bind sites containing specific RNA structures. ARMs crystallize insights into the under-appreciated contributions of the C-terminal domain to site-specific binding by Y-box proteins and difficulties in identifying site-specific binding by the C-terminal domain. Validated structural biology techniques are available to elucidate the mechanisms by which YBXprot (Y-box element-binding protein) CSDs and ARMs identify targets.

scholarly journals Comparative Analysis of the Putative Amino Acid Sequences of Chlamydial Heat Shock Protein 60 and Escherichia coli GroEL.

2000 ◽  
Vol 62 (9) ◽  
pp. 941-945 ◽  
Author(s):  
Yoshitsugu OCHIAI ◽  
Hideto FUKUSHI ◽  
Cai YAN ◽  
Tsuyoshi YAMAGUCHI ◽  
Katsuya HIRAI
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Amino Acid ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Amino Acid Sequences ◽  
Heat Shock Protein 60

scholarly journals Diversity of radA Genes from Cultured and UnculturedArchaea: Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker

1999 ◽  
Vol 181 (3) ◽  
pp. 907-915 ◽  
Author(s):  
Steven J. Sandler ◽  
Philip Hugenholtz ◽  
Christa Schleper ◽  
Edward F. DeLong ◽  
Norman R. Pace ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Tissue Sample ◽  
Reca Protein ◽  
Amino Acid Sequences ◽  
Sponge Tissue ◽  
Amino Acid Deletion ◽  
Archaeal Species ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species ofCrenarcheota. The two most deeply branching archaealradA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.

scholarly journals Identification of the Amino Acid Sequences Responsible for High Affinity Activation of cGMP Kinase Iα

1997 ◽  
Vol 272 (16) ◽  
pp. 10522-10528 ◽  
Author(s):  
Peter Ruth ◽  
Alexander Pfeifer ◽  
Simone Kamm ◽  
Peter Klatt ◽  
Wolfgang R. G. Dostmann ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
High Affinity

Amino acid sequences from the N-terminal domain of Bacillus thuringiensis , subspecies alesti , δ-endotoxin

FEBS Letters ◽  
1986 ◽  
Vol 198 (2) ◽  
pp. 283-286 ◽  
Author(s):  
G.G. Chestukhina ◽  
S.A. Tyurin ◽  
A.L. Osterman ◽  
O.P. Khodova ◽  
V.M. Stepanov
Keyword(s):  
Amino Acid ◽  
Bacillus Thuringiensis ◽  
Amino Acid Sequences ◽  
Terminal Domain

scholarly journals Subtypes of NanS-p Sialate O-Acetylesterase Encoded by Stx2a Bacteriophages

Proceedings ◽  
2021 ◽  
Vol 66 (1) ◽  
pp. 15
Author(s):  
Stefanía B. Pascal ◽  
Juan R. Lorenzo Lopez ◽  
Paula M. A. Lucchesi ◽  
Alejandra Krüger
Keyword(s):  
Amino Acid ◽  
Foodborne Pathogens ◽  
Dna Sequences ◽  
Query Sequence ◽  
Amino Acid Sequences ◽  
Bacterial Genomes ◽  
Gene Encoding ◽  
Terminal Domain ◽  
Structural Differences ◽  
Blast Program

Shiga toxin (Stx)-producing Escherichia coli strains are foodborne pathogens that can cause severe human diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Stxs are encoded by bacteriophages (Stx phages) which show remarkable variations in genome composition and harbour several genes of unknown function. Recently, a gene encoding a sialate O-acetylesterase (NanS-p) was identified in some relevant Stx2a phages and it was suggested that it could provide advantages for bacterial growth in the gut. The aim of this study was to analyse the presence and sequence of nanS-p genes in available Stx2a phage genomes. A total of 59 DNA sequences of Stx2a phages were extracted from the NCBI GenBank database with the BLAST program using the stx2a sequence from phage 933W as a query sequence, either as complete phage genomes (45) or from bacterial genomes by subsequent analysis with the PHASTER web server (14). Comparative analysis revealed that nanS-p was located downstream of stx2a in all genomes. Twenty different amino acid sequences of NanS-p were identified. Specifically, catalytic esterase domains showed only 11 possible sequences, with differences mainly observed in nine amino acid positions. Sequences corresponding to the N-terminal domain (DUF1737) showed three possible sequences, two of them closely related, while the C-terminal domain was highly variable, with four groups with structural differences. Since sialate O-acetylesterase activity has been determined from particular Stx2a phages, new studies are necessary to evaluate if the NanS-p subtypes identified in the present study also differ in their biological activity.

scholarly journals Unique and Universal Proteins in Human Genome

2020 ◽  
Vol 16 (11) ◽  
pp. 45
Author(s):  
Essam Al-Daoud ◽  
Ghadeer Albesani
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Human Genome ◽  
Reference Genome ◽  
Amino Acid Sequences ◽  
The Other ◽  
Entire Genome ◽  
Whole Genomes ◽  
The Common ◽  
Similar Amino Acid

<span>One of the major troubles with a comparative analysis between human and other species is that only similar amino acid sequences are selected for analysis. To find the connection among the species and find out the unique, the common and the universal proteins, the entire genome of 40 species are compared with the human genome which is utilized as reference genome. More than 11 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 330 unique proteins in human genome and have insignificant hits in all tested genomes, the number of universal proteins in human genome and conserved in all tested species is 82, and there are 180 proteins common in vertebrates genomes, but have insignificant hits in the other tested species. In contrary to the previous studies which use selected set of the genes and do not consider the whole genomes, this study proves that the similarity between human and chimpanzee is only 94.8.</span>

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