scholarly journals Theoretical ribosomal protein mass fingerprint database

2018 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ribosomal Protein ◽  
Molecular Mass ◽  
Ribosomal Proteins ◽  
Sequence Information ◽  
Protein Mass ◽  
And Function ◽  
Fingerprint Database ◽  
Amino Acid Sequence Information

Ribosomes are highly conserved macromolecular machines whose critical function is protein synthesis. However, existence of unique molecular mass of the same type of ribosomal protein for individual species in the same domain of life raises the interesting question concerning the interaction between natural selection forces and the conservation of structure and function of ribosomal proteins. Thus, given differentiated molecular mass and sequence of ribosomal proteins across species, the structures of ribosomes are correspondingly differentiated even though the general structure and function of the macromolecular machine is conserved across species in the same domain of life. The collection of molecular mass of all ribosomal proteins in the large and small ribosome subunits can be understood as the ribosomal protein mass fingerprint of the species useful for gaining fundamental knowledge of ribosomal proteins, as well as serving as tools for species identification through comparison of ribosomal protein mass spectra. This preprint introduces the Theoretical Ribosomal Protein Mass Fingerprint database that comprises the theoretical molecular mass of all ribosomal proteins of a species calculated based on available amino acid sequence information of the ribosomal proteins. Using amino acid sequence information from the Ribosomal Protein Gene Database, the Theoretical Ribosomal Protein Mass Fingerprint database ( https://ngwenfa.wordpress.com/database/ ) spans species from cyanobacteria, fungus, bacteria, archaea, nematodes, diatoms, micro-algae, and various model organisms. The database should be useful as a resource for gaining fundamental understanding of the mass distribution of ribosomal proteins of a species, or serving as a limited reference database for identifying species based on comparing experimental ribosomal protein mass fingerprint of unknown species against theoretically calculated ones of known species. Future expansion of the database will aim to catalogue the theoretical ribosomal protein mass fingerprint of more microbial species using amino acid sequence information from UniProt.

scholarly journals Theoretical ribosomal protein mass fingerprint database

2018 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ribosomal Protein ◽  
Molecular Mass ◽  
Ribosomal Proteins ◽  
Sequence Information ◽  
Protein Mass ◽  
And Function ◽  
Fingerprint Database ◽  
Amino Acid Sequence Information

Ribosomes are highly conserved macromolecular machines whose critical function is protein synthesis. However, existence of unique molecular mass of the same type of ribosomal protein for individual species in the same domain of life raises the interesting question concerning the interaction between natural selection forces and the conservation of structure and function of ribosomal proteins. Thus, given differentiated molecular mass and sequence of ribosomal proteins across species, the structures of ribosomes are correspondingly differentiated even though the general structure and function of the macromolecular machine is conserved across species in the same domain of life. The collection of molecular mass of all ribosomal proteins in the large and small ribosome subunits can be understood as the ribosomal protein mass fingerprint of the species useful for gaining fundamental knowledge of ribosomal proteins, as well as serving as tools for species identification through comparison of ribosomal protein mass spectra. This preprint introduces the Theoretical Ribosomal Protein Mass Fingerprint database that comprises the theoretical molecular mass of all ribosomal proteins of a species calculated based on available amino acid sequence information of the ribosomal proteins. Using amino acid sequence information from the Ribosomal Protein Gene Database, the Theoretical Ribosomal Protein Mass Fingerprint database ( https://ngwenfa.wordpress.com/database/ ) spans species from cyanobacteria, fungus, bacteria, archaea, nematodes, diatoms, micro-algae, and various model organisms. The database should be useful as a resource for gaining fundamental understanding of the mass distribution of ribosomal proteins of a species, or serving as a limited reference database for identifying species based on comparing experimental ribosomal protein mass fingerprint of unknown species against theoretically calculated ones of known species. Future expansion of the database will aim to catalogue the theoretical ribosomal protein mass fingerprint of more microbial species using amino acid sequence information from UniProt.

scholarly journals Ribosomal protein database profiling lends clarity to ribosomal protein evolution and mass distribution

2021 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Information ◽  
Protein Database ◽  
Microbial Identification ◽  
Microbial Species ◽  
Amino Acid Sequence Information

Existence of theoretical ribosomal protein mass fingerprint as well as utility of ribosomal protein as biomarkers in mass spectrometry microbial identification suggests phylogenetic significance for this class of proteins. To serve the above two functions, facile means of identifying and extracting important attributes of ribosomal proteins from proteome data file of microbial species must be found. Additionally, there is a need to calculate important properties of ribosomal proteins such as molecular weight and nucleotide sequence based on amino acid sequence information from FASTA proteome file. This work sought to support the above endeavour through developing a MATLAB software that extracts the amino acid sequence information of all ribosomal proteins from the FASTA proteome datafile of a microbial species downloaded from UniProt. Built-in functions in MATLAB are subsequently employed to calculate important properties of extracted ribosomal proteins such as number of amino acid residue, molecular weight and nucleotide sequence. All information above are output, as a database, to an Excel file for ease of storage and retrieval. Data available from the analysis of an Escherichia coli K-12 proteome revealed that the bacterium possess a total of 59 ribosomal proteins distributed between the large and small ribosome subunits. The ribosomal protein ranges in sequence length from 38 (50S ribosomal protein L36) to 557 (30S ribosomal protein S1). In terms of molecular weight distribution, the profiled ribosomal proteins range in weight from 4364.305 Da (50S ribosomal protein L36) to 61157.66 Da (30S ribosomal protein S1). More important, analysis of the distribution of the molecular weight of different ribosomal proteins in E. coli reveals a smooth curve that suggests strong co-evolution of ribosomal protein sequence and mass given the tight constraints that a functional ribosome presents. Finally, cluster analysis reveals a preponderance of small ribosomal proteins compared to larger ones, which remains to be a mystery to evolutionary biologists. Overall, the information encapsulated in the ribosomal protein database should find use in gaining a better appreciation for the molecular weight distribution of ribosomal proteins in a species, as well as delivering information for using ribosomal protein biomarkers in identifying particular microbial species in mass spectrometry microbial identification.

scholarly journals Existence of theoretical ribosomal protein mass fingerprints in bacteria, archaea and eukaryotes

2018 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Mass Spectrometry ◽  
Ribosomal Protein ◽  
Molecular Mass ◽  
Ribosomal Proteins ◽  
General Structure ◽  
Structure And Function ◽  
Microbial Identification ◽  
Protein Mass ◽  
Domains Of Life ◽  
And Function

Ribosomes are highly conserved given the importance of protein synthesis to cell survival. Although small differences in structure and functions exists in ribosomes from different species of bacteria, archaea and eukaryotes, the general structure and function remains conserved across species in the same domain of life. Thus, are ribosomal proteins that constitute ribosomes highly conserved between species in the same domain or do they possess sufficient sequence variation that help identify individual species? Having differentiated sequence would mean that ribosomal proteins from different species might account for differences in structure and function of the ribosomes in different species. Using ribosomal protein amino acid sequence information from Ribosomal Protein Gene Database for calculating molecular mass of ribosomal proteins, this study sought to determine if the molecular mass of a set of ribosomal proteins from a species could constitute a unique ribosomal protein mass fingerprint. In addition, the question of whether unique ribosomal protein mass fingerprint exists between different species in the three domains of life was also examined. Results revealed that distinct molecular mass of individual ribosomal protein could aggregate into a unique ribosomal protein mass fingerprint for individual bacterial, archaeal and eukaryotic species. Such ribosomal protein mass fingerprints could potentially find use in microbial identification through gel-free matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling of solubilized ribosomal proteins. Obtained ribosomal protein mass spectrum could be compared with those catalogued in a reference database of known microorganisms where pattern recognition algorithms could determine a match. Additionally, existence of theoretical ribosomal protein mass fingerprint across species in the three domains of life also pointed to the presence of small differences in structure and function of both the large and small ribosome subunit. Such differences could reveal possible differentiated ribosomal structure and function in different species even though the general structure and function of the ribosome is conserved across species. Collectively, distinct molecular mass of individual ribosomal proteins in species pointed to a unique ribosomal protein mass fingerprint that could find use in microbial identification through gel-free mass spectrometry analysis of solubilized ribosomal proteins. Differences in mass of ribosomal proteins across species also highlighted existence of ribosomes of differentiated structure and function between different species even though the general structure and function of the ribosome remains highly conserved.

scholarly journals Existence of theoretical ribosomal protein mass fingerprints in bacteria, archaea and eukaryotes

2018 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Mass Spectrometry ◽  
Ribosomal Protein ◽  
Molecular Mass ◽  
Ribosomal Proteins ◽  
General Structure ◽  
Structure And Function ◽  
Microbial Identification ◽  
Protein Mass ◽  
Domains Of Life ◽  
And Function

Ribosomes are highly conserved given the importance of protein synthesis to cell survival. Although small differences in structure and functions exists in ribosomes from different species of bacteria, archaea and eukaryotes, the general structure and function remains conserved across species in the same domain of life. Thus, are ribosomal proteins that constitute ribosomes highly conserved between species in the same domain or do they possess sufficient sequence variation that help identify individual species? Having differentiated sequence would mean that ribosomal proteins from different species might account for differences in structure and function of the ribosomes in different species. Using ribosomal protein amino acid sequence information from Ribosomal Protein Gene Database for calculating molecular mass of ribosomal proteins, this study sought to determine if the molecular mass of a set of ribosomal proteins from a species could constitute a unique ribosomal protein mass fingerprint. In addition, the question of whether unique ribosomal protein mass fingerprint exists between different species in the three domains of life was also examined. Results revealed that distinct molecular mass of individual ribosomal protein could aggregate into a unique ribosomal protein mass fingerprint for individual bacterial, archaeal and eukaryotic species. Such ribosomal protein mass fingerprints could potentially find use in microbial identification through gel-free matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling of solubilized ribosomal proteins. Obtained ribosomal protein mass spectrum could be compared with those catalogued in a reference database of known microorganisms where pattern recognition algorithms could determine a match. Additionally, existence of theoretical ribosomal protein mass fingerprint across species in the three domains of life also pointed to the presence of small differences in structure and function of both the large and small ribosome subunit. Such differences could reveal possible differentiated ribosomal structure and function in different species even though the general structure and function of the ribosome is conserved across species. Collectively, distinct molecular mass of individual ribosomal proteins in species pointed to a unique ribosomal protein mass fingerprint that could find use in microbial identification through gel-free mass spectrometry analysis of solubilized ribosomal proteins. Differences in mass of ribosomal proteins across species also highlighted existence of ribosomes of differentiated structure and function between different species even though the general structure and function of the ribosome remains highly conserved.

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.

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