scholarly journals Streptococcus mutans Strains Harboring Collagen-binding Adhesin

2004 ◽  
Vol 83 (7) ◽  
pp. 534-539 ◽  
Author(s):  
Y. Sato ◽  
K. Okamoto ◽  
A. Kagami ◽  
Y. Yamamoto ◽  
T. Igarashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Recombinant Protein ◽  
Amino Acid Sequence ◽  
Streptococcus Mutans ◽  
Parental Strain ◽  
Random Mutagenesis ◽  
Gene Fragment ◽  
High Similarity ◽  
Collagen Binding ◽  
Negative Mutant

A previously unidentified 120-kDa protein was detected in Streptococcus mutans strain Z1 and was involved in the cold-agglutination of the strain. We have identified the gene, designated cnm, as being involved in the agglutination of strain Z1 following random mutagenesis. The amino acid sequence of the deduced Cnm protein exhibited high similarity to those of collagen-binding adhesins from staphylococci and other organisms. To confirm whether the protein is involved in collagen-binding, we cloned a cnm gene fragment, overexpressed it in E.coli, and prepared crude extracts. The extracts containing recombinant protein exhibited binding to immobilized collagen and laminin but not to fibronectin. Compared with the parental strain Z1, the cold-agglutination-negative mutant 05A02 exhibited reduced binding to collagen and laminin but retained that to fibronectin. This gene was detected in some strains of S. mutans. Therefore, the cnm gene encoded a new strain-specific member of the collagen-binding adhesin family.

scholarly journals Data mining of coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jung Eun Huh ◽  
Seunghee Han ◽  
Taeseon Yoon
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Decision Tree ◽  
Machine Learning Algorithms ◽  
High Similarity ◽  
Incubation Periods ◽  
Initial Question ◽  
The Difference ◽  
Blast Program

Abstract Objective In this study we compare the amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence can lead to different incubation periods and outbreak periods. Our initial question was to compare SARS-CoV-2 to different viruses in the coronavirus family using BLAST program of NCBI and machine learning algorithms. Results The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence. The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can be focused on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

scholarly journals The primary structure of the VLA-2/collagen receptor alpha 2 subunit (platelet GPIa): homology to other integrins and the presence of a possible collagen-binding domain.

1989 ◽  
Vol 109 (1) ◽  
pp. 397-407 ◽  
Author(s):  
Y Takada ◽  
M E Hemler
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Matrix Protein ◽  
Transmembrane Domain ◽  
Cdna Clones ◽  
Terminal Sequence ◽  
Collagen Binding ◽  
Collagen Receptor ◽  
Integrin Family

VLA-2 (also called gpIa/IIa on platelets) is a collagen receptor with a unique alpha subunit and a beta subunit common to other adhesion receptors in the VLA/integrin family. Multiple cDNA clones for the human VLA-2 alpha 2 subunit have been selected from a lambda gtll library by specific antibody screening. The 5,374-bp nucleotide sequence encoded for 1,181 amino acids, including a signal peptide of 29 amino acids followed by a long extracellular domain (1,103 amino acids), a transmembrane domain, and a short cytoplasmic segment (22 amino acids). Direct sequencing of purified alpha 2 protein confirmed the identity of the 15 NH2-terminal amino acids. Overall, the alpha 2 amino acid sequence was 18-25% similar to the sequences known for other integrin alpha subunits. In particular, the alpha 2 sequence matched other integrin alpha chains in (a) the positions of 17 of its 20 cysteine residues; (b) the presence of three metal-binding domains of the general structure DXDXDGXXD; and (c) the transmembrane domain sequence. In addition, the alpha 2 sequence has a 191-amino acid insert (called the I-domain), previously found only in leukocyte integrins of the beta 2 integrin family. The alpha 2 I-domain was 23-41% similar to domains in cartilage matrix protein and von Willebrand factor, which are perhaps associated with collagen binding. The NH2-terminal sequence reported here for alpha 2 does not match the previously reported alpha 2 NH2-terminal sequence (Takada, Y., J. L. Strominger, and M. E. Hemler. 1987. Proc. Natl. Acad. Sci. USA. 84:3239-3243). Resolution of this discrepancy suggests that there may be another VLA heterodimer that resembles VLA-2 in size but has a different amino acid sequence.

The ADP-ribosylating thermozyme from Sulfolobus solfataricus is a DING protein

2009 ◽  
Vol 390 (1) ◽  
Author(s):  
Antimo Di Maro ◽  
Anna De Maio ◽  
Sabrina Castellano ◽  
Augusto Parente ◽  
Benedetta Farina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sulfolobus Solfataricus ◽  
Terminal Region ◽  
High Similarity ◽  
Partial Amino Acid Sequence ◽  
Tryptic Peptides ◽  
Ding Protein ◽  
N Terminus

Abstract The partial amino acid sequence of the sulfolobal thermoprotein biochemically characterized as poly(ADP-ribose)polymerase-like enzyme overlaps those of DING proteins. This group of proteins, widely occurring in animals, plants and eubacteria, shows a characteristic and highly conserved N-terminus, DINGGGATL. The sequence of the N-terminal region and of the analyzed tryptic peptides of the sulfolobal thermozyme shows a high similarity with most of the DING proteins from databases. This is the first example of a DING protein from a sulfolobal source.

scholarly journals Cloning and expression of Toxoplasma gondii GRA-4 recombinant protein as a toxoplasmosis diagnostic kit candidate

2020 ◽  
Vol 13 (10) ◽  
pp. 2085-2091
Author(s):  
Muhammad Hanafiah ◽  
Teuku Zahrial Helmi ◽  
Amalia Sutriana ◽  
Dwi Priyowidodo ◽  
Fihiruddin Fihiruddin
Keyword(s):  
Amino Acid ◽  
Toxoplasma Gondii ◽  
Recombinant Protein ◽  
Amino Acid Sequence ◽  
Dna Isolation ◽  
Recombinant Protein Expression ◽  
Cloning And Expression ◽  
Local Isolate ◽  
Competent Cells ◽  
Polymerase Chain

Aim: The objective of this study was to produce recombinant protein GRA-4 (rGRA-4) of a local Toxoplasma gondii isolate as a candidate for a toxoplasmosis diagnosis kit in Escherichia coli BL21 (DE3) competent cells using pET SUMO plasmid. Materials and Methods: Samples used were stock T. gondii tachyzoites DNA from the Parasitology Laboratory, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta. Amplified GRA-4 polymerase chain reaction product of T. gondii tachyzoite DNA was cloned in the pET-SUMO TAR cloning vector. The GRA-4 gene from T. gondii local isolate was sequenced, followed by plasmid transformation, recombinant plasmid DNA isolation, and recombinant protein expression in DE3 competent cells. Results: The amplification product of GRA-4 T. gondii gene was 1036 bp, with 48 kDa molecular weight after expression in DE3 competent cells. An alignment of the amino acid sequence of GRA-4 from the local isolate which was cloned with GRA-4 was obtained from NCBI database and showed 99.61% homology to the predicted GRA-4 from the T. gondii Izatnagar isolate. Amino acid sequence of the predicted GRA-4 protein from local isolate was different at positions 19 and 304. Conclusion: This research cloned rGRA-4 in pET SUMO plasmid.

scholarly journals Characterization of the Gene Encoding a 26-Kilodalton Protein (OMP26) from Nontypeable Haemophilus influenzae and Immune Responses to the Recombinant Protein

1999 ◽  
Vol 67 (4) ◽  
pp. 1935-1942 ◽  
Author(s):  
Wafa El-Adhami ◽  
Jennelle M. Kyd ◽  
David A. Bastin ◽  
Allan W. Cripps
Keyword(s):  
Amino Acid ◽  
Recombinant Protein ◽  
Amino Acid Sequence ◽  
Haemophilus Influenzae ◽  
Cell Envelope ◽  
Leader Peptide ◽  
Polymorphism Analysis ◽  
Nontypeable Haemophilus Influenzae ◽  
Gene Encoding ◽  
Mucosal Antibody

ABSTRACT A 26-kDa protein (OMP26) isolated and purified from nontypeableHaemophilus influenzae (NTHI) strain 289 has been shown to enhance clearance of infection following pulmonary challenge with NTHI in rats. DNA sequence analysis revealed that it was 99% identical to a gene encoding a cell envelope protein of the H. influenzaeRd strain (TIGR accession no. HI0916). The deduced amino acid sequence revealed a hydrophilic polypeptide rich in basic amino acids. Restriction fragment length polymorphism analysis suggested that the OMP26 gene was relatively conserved among isolates of NTHI. Analysis of the deduced amino acid sequence of the OMP26 gene from 20 different isolates showed that similarity with NTHI-289 ranged from 96.5% (1 isolate) to 99.5% (14 isolates). Two recombinant forms of OMP26, a full length 28-kDa protein (equivalent to preprotein) and a 26-kDa protein lacking a 23-amino-acid leader peptide (equivalent to processed protein), were assessed in immunization studies for the ability to induce an immune response that would be as effective as the native protein in enhancing the clearance of NTHI following pulmonary challenge in rats. Immunization with the recombinant protein that included the leader peptide was more effective in enhancing pulmonary clearance, and it induced a better cell-mediated response and higher titers of systemic and mucosal antibody. This study has characterized a 26-kDa protein from NTHI that shows significant potential as a vaccine candidate.

scholarly journals The Collagen-binding A-domains of Integrins α1β1and α2β1Recognize the Same Specific Amino Acid Sequence, GFOGER, in Native (Triple-helical) Collagens

2000 ◽  
Vol 275 (1) ◽  
pp. 35-40 ◽  
Author(s):  
C. Graham Knight ◽  
Laurence F. Morton ◽  
Anthony R. Peachey ◽  
Danny S. Tuckwell ◽  
Richard W. Farndale ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Collagen Binding ◽  
Specific Amino Acid ◽  
A Domains

scholarly journals Data Mining of Coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

2021 ◽  
Author(s):  
Jung Eun Huh ◽  
Seunghee Han ◽  
Taeseon Yoon
Keyword(s):  
Data Mining ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Decision Tree ◽  
High Similarity ◽  
Incubation Periods ◽  
Initial Question ◽  
Non Linear ◽  
The Difference

Abstract Objectives: All three SARS-CoV-2, SARS-CoV and MERS-CoV belong to the Coronaviridae family. In this study we compare amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence lead to different incubation periods and outbreak periods.Results: The initial question we had was to compare SARS-CoV-2 to different viruses in the coronavirus family to understand its characteristics. The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment has proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence.The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can focus on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

scholarly journals A Novel Gene Required for Rhamnose-Glucose Polysaccharide Synthesis in Streptococcus mutans

1999 ◽  
Vol 181 (20) ◽  
pp. 6556-6559 ◽  
Author(s):  
Yoshihisa Yamashita ◽  
Yukie Shibata ◽  
Yoshio Nakano ◽  
Hiromasa Tsuda ◽  
Nobuo Kido ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Streptococcus Mutans ◽  
Common Antigen ◽  
E Coli ◽  
Novel Gene ◽  
Enterobacterial Common Antigen ◽  
Polysaccharide Synthesis ◽  
O Antigens

ABSTRACT Gene rgpG is required for biosynthesis of rhamnose-glucose polysaccharide (RGP) in Streptococcus mutans. Its deduced amino acid sequence had similarity to WecA, which initiates syntheses of enterobacterial common antigen and some O antigens in Escherichia coli. Gene rgpGcomplemented a wecA mutation of E. coli, suggesting that rgpG may function similarly in RGP synthesis.

scholarly journals Dissecting the Interaction Deficiency of a Cartilaginous Fish Digestive Lipase with Pancreatic Colipase: Biochemical and Structural Insights

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Neila Achouri ◽  
Màrius Tomàs-Gamisans ◽  
Soumaya Triki ◽  
Francisco Valero ◽  
Nabil Miled ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Bile Salts ◽  
Structural Model ◽  
Catalytic Triad ◽  
Cartilaginous Fish ◽  
Residue Level ◽  
High Similarity ◽  
Structural Insights

A full-length cDNA encoding digestive lipase (SmDL) was cloned from the pancreas of the smooth-hound (Mustelus mustelus). The obtained cDNA was 1350 bp long encoding 451 amino acids. The deduced amino acid sequence has high similarity with known pancreatic lipases. Catalytic triad and disulphide bond positions are also conserved. According to the established phylogeny, the SmDL was grouped with those of tuna and Sparidae lipases into one fish digestive lipase cluster. The recently purified enzyme shows no dependence for bile salts and colipase. For this, the residue-level interactions between lipase-colipase are yet to be clearly understood. The structural model of the SmDL was built, and several dissimilarities were noticed when analyzing the SmDL amino acids corresponding to those involved in HPL binding to colipase. Interestingly, the C-terminal domain of SmDL which holds the colipase shows a significant role for colipase interaction. This is apt to prevent the interaction between fish lipase and the pancreatic colipase which and can provide more explanation on the fact that the classical colipase is unable to activate the SmDL.

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