Faculty Opinions recommendation of A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition.

2005 ◽  
Author(s):  
Robert Michell
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Polar Lipid ◽  
Lipid Composition ◽  
Lipid Synthesis ◽  
Sequence Information ◽  
Amino Acid Sequence Information

scholarly journals Molecular Identification of Family 38 α-Mannosidase of Bacillus sp. Strain GL1, Responsible for Complete Depolymerization of Xanthan

2002 ◽  
Vol 68 (6) ◽  
pp. 2731-2736 ◽  
Author(s):  
Hirokazu Nankai ◽  
Wataru Hashimoto ◽  
Kousaku Murata
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Cell Extract ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolase Family ◽  
Sequence Information ◽  
Reading Frame ◽  
A Cell ◽  
Terminal Amino ◽  
Amino Acid Sequence Information

ABSTRACT When cells of Bacillus sp. strain GL1 were grown in a medium containing xanthan as a carbon source, α-mannosidase exhibiting activity toward p-nitrophenyl-α-d-mannopyranoside (pNP-α-d-Man) was produced intracellularly. The 350-kDa α-mannosidase purified from a cell extract of the bacterium was a trimer comprising three identical subunits, each with a molecular mass of 110 kDa. The enzyme hydrolyzed pNP-α-d-Man (Km = 0.49 mM) and d-mannosyl-(α-1,3)-d-glucose most efficiently at pH 7.5 to 9.0, indicating that the enzyme catalyzes the last step of the xanthan depolymerization pathway of Bacillus sp. strain GL1. The gene for α-mannosidase cloned most by using N-terminal amino acid sequence information contained an open reading frame (3,144 bp) capable of coding for a polypeptide with a molecular weight of 119,239. The deduced amino acid sequence showed homology with the amino acid sequences of α-mannosidases belonging to glycoside hydrolase family 38.

scholarly journals CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 938
Author(s):  
Kriti Chopra ◽  
Bhawna Burdak ◽  
Kaushal Sharma ◽  
Ajit Kembhavi ◽  
Shekhar C. Mande ◽  
...  
Keyword(s):  
Amino Acid ◽  
Random Forest ◽  
Amino Acid Sequence ◽  
Protein Complexes ◽  
Sequence Information ◽  
Contact Potential ◽  
Prokaryotic Protein ◽  
The Individual ◽  
Amino Acid Sequence Information ◽  
Interface Residues

Decrypting the interface residues of the protein complexes provides insight into the functions of the proteins and, hence, the overall cellular machinery. Computational methods have been devised in the past to predict the interface residues using amino acid sequence information, but all these methods have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence is different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here, we report a new hybrid pipeline for predicting the protein-protein interaction interfaces in a pairwise manner from the amino acid sequence information of the interacting proteins. It is based on the framework of Co-evolution, machine learning (Random Forest), and Network Analysis named CoRNeA trained specifically on eukaryotic protein complexes. We use Co-evolution, physicochemical properties, and contact potential as major group of features to train the Random Forest classifier. We also incorporate the intra-contact information of the individual proteins to eliminate false positives from the predictions keeping in mind that the amino acid sequence of a protein also holds information for its own folding and not only the interface propensities. Our prediction on example datasets shows that CoRNeA not only enhances the prediction of true interface residues but also reduces false positive rates significantly.

scholarly journals MATLAB software for extracting protein name and sequence information from FASTA formatted proteome file

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Sequence Information ◽  
Amino Acid Residues ◽  
Protein Database ◽  
Matlab Software ◽  
Amino Acid Sequence Information ◽  
New Protein

FASTA file format is a common file type for distributing proteome information, especially those obtained from Uniprot. While MATLAB could automatically read fasta files using the built-in function, fastaread, important information such as protein name and organism name remain enmeshed in a character array. Hence, difficulty exists in automatic extraction of protein names from fasta proteome file to help in building a database with fields comprising protein name and its amino acid sequence. The objective of this work was in developing a MATLAB software that could automatically extract protein name and amino acid sequence information from fasta proteome file and assign them to a new database that comprises fields such as protein name, amino acid sequence, number of amino acid residues, molecular weight of protein and nucleotide sequence of protein. Information on number of amino acid residues came from the use of the length built-in function in MATLAB analyzing the length of the amino acid sequence of a protein. The final two fields were provided by MATLAB built-in functions molweight and aa2nt, respectively. Molecular weight of proteins is useful for a variety of applications while nucleotide sequence is essential for gene synthesis applications in molecular cloning. Finally, the MATLAB software is also equipped with an error check function to help detect letters in the amino acid sequence that are not part of the family of 20 natural amino acids. Sequences with such letters would constitute as error inputs to molweight and aa2nt, and would not be processed. Collectively, given that important information such as protein name is enmeshed in a character array in fasta proteome file, this work sets out to develop a MATLAB software that could automatically extract protein name and amino acid sequence information, and assigns them to a new protein database. Using built-in functions, number of amino acid residues, molecular weight and nucleotide sequence of each protein were calculated; thereby, yielding a new protein database with improved functionalities that could support a variety of biology workflows ranging from sequence alignment to molecular cloning.

scholarly journals Sequence of cDNA for rat cystathionine γ-lyase and comparison of deduced amino acid sequence with related Escherichia coli enzymes

1990 ◽  
Vol 269 (2) ◽  
pp. 335-340 ◽  
Author(s):  
P F Erickson ◽  
I H Maxwell ◽  
L J Su ◽  
M Baumann ◽  
L M Glode
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Blot Hybridization ◽  
Cdna Clones ◽  
Sequence Information ◽  
Northern Blot Hybridization ◽  
Monospecific Antiserum ◽  
Positive Hybridization ◽  
Amino Acid Sequence Information

A cDNA clone for cystathionine gamma-lyase was isolated from a rat cDNA library in lambda gt11 by screening with a monospecific antiserum. The identity of this clone, containing 600 bp proximal to the 3′-end of the gene, was confirmed by positive hybridization selection. Northern-blot hybridization showed the expected higher abundance of the corresponding mRNA in liver than in brain. Two further cDNA clones from a plasmid pcD library were isolated by colony hybridization with the first clone and were found to contain inserts of 1600 and 1850 bp. One of these was confirmed as encoding cystathionine gamma-lyase by hybridization with two independent pools of oligodeoxynucleotides corresponding to partial amino acid sequence information for cystathionine gamma-lyase. The other clone (estimated to represent all but 8% of the 5′-end of the mRNA) was sequenced and its deduced amino acid sequence showed similarity to those of the Escherichia coli enzymes cystathionine beta-lyase and cystathionine gamma-synthase throughout its length, especially to that of the latter.

scholarly journals Amino acid sequence determination by g.l.c.-mass spectrometry of permethylated peptides. Optimization of the formation of chemical derivatives at the 2-10 nmol level

1983 ◽  
Vol 215 (2) ◽  
pp. 261-272 ◽  
Author(s):  
K Rose ◽  
M G Simona ◽  
R E Offord
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sodium Dodecyl ◽  
Sequence Information ◽  
Sequence Determination ◽  
Chemical Derivatives ◽  
Peptide Derivatives ◽  
A New Technique ◽  
Amino Acid Sequence Information

A new technique is described that permits the permethylation of acylated peptides at the 2-10 nmol level. The presence of up to 400 micrograms of sodium dodecyl sulphate per sample does not affect the reaction yields. The technique, which is a miniaturization of the widely used methyl iodide/dimethylsulphinyl carbanion procedure, employs a layer of hexane to exclude moisture and oxygen from the reaction mixture. Analysis of the peptide derivatives by combined g.l.c.-mass spectrometry permits amino acid sequence information to be obtained. In addition to studies of digests of a model substrate (glucagon), the new permethylation technique has been used to identify a peptide of interest from a digest of a cytochrome and to define the N-termini of two proteins at the 5 nmol level.

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