scholarly journals Enzymes, Moonlighting Enzymes, Pseudoenzymes: Members of a Protein Superfamily Can Have Similar Amino Acid Sequences but Different Functions

2021 ◽  
Vol 35 (S1) ◽  
Author(s):  
Constance Jeffery
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Protein Superfamily ◽  
Similar Amino Acid

Polypeptide chains with similar amino acid sequences but a distinctly different conformation

FEBS Letters ◽  
1983 ◽  
Vol 164 (1) ◽  
pp. 25-27 ◽  
Author(s):  
Bauke W. Dijkstra ◽  
Wicher J. Weijer ◽  
Rik K. Wierenga
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Polypeptide Chains ◽  
Similar Amino Acid

scholarly journals Succinyl-CoA:(R)-Benzylsuccinate CoA-Transferase: an Enzyme of the Anaerobic Toluene Catabolic Pathway in Denitrifying Bacteria

2001 ◽  
Vol 183 (14) ◽  
pp. 4288-4295 ◽  
Author(s):  
Christina Leutwein ◽  
Johann Heider
Keyword(s):  
Amino Acid ◽  
Electrospray Mass Spectrometry ◽  
Amino Acid Sequences ◽  
Catabolic Pathway ◽  
Methyl Group ◽  
New Family ◽  
Thauera Aromatica ◽  
Coa Transferase ◽  
Similar Amino Acid

ABSTRACT Anaerobic microbial toluene catabolism is initiated by addition of fumarate to the methyl group of toluene, yielding (R)-benzylsuccinate as first intermediate, which is further metabolized via β-oxidation to benzoyl-coenzyme A (CoA) and succinyl-CoA. A specific succinyl-CoA:(R)-benzylsuccinate CoA-transferase activating (R)-benzylsuccinate to the CoA-thioester was purified and characterized from Thauera aromatica. The enzyme is fully reversible and forms exclusively the 2-(R)-benzylsuccinyl-CoA isomer. Only some close chemical analogs of the substrates are accepted by the enzyme: succinate was partially replaced by maleate or methylsuccinate, and (R)-benzylsuccinate was replaced by methylsuccinate, benzylmalonate, or phenylsuccinate. In contrast to all other known CoA-transferases, the enzyme consists of two subunits of similar amino acid sequences and similar sizes (44 and 45 kDa) in an α2β2 conformation. Identity of the subunits with the products of the previously identified toluene-inducedbbsEF genes was confirmed by determination of the exact masses via electrospray-mass spectrometry. The deduced amino acid sequences resemble those of only two other characterized CoA-transferases, oxalyl-CoA:formate CoA-transferase and (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase, which represent a new family of CoA-transferases. As suggested by kinetic analysis, the reaction mechanism of enzymes of this family apparently involves formation of a ternary complex between the enzyme and the two substrates.

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>

PROTEIN SUPERFAMILY CLASSIFICATION USING ADAPTIVE EVOLUTIONARY RADIAL BASIS FUNCTION NETWORK

2012 ◽  
Vol 11 (04) ◽  
pp. 1250026 ◽  
Author(s):  
SWATI VIPSITA ◽  
SANTANU KU. RATH
Keyword(s):  
Genetic Algorithm ◽  
Amino Acid ◽  
Radial Basis Function ◽  
Basis Function ◽  
Radial Basis Function Network ◽  
Amino Acid Sequences ◽  
Protein Superfamily ◽  
Multiobjective Genetic Algorithm ◽  
Radial Basis ◽  
Function Network

In this paper, the concept of adaptive multiobjective genetic algorithm (AMOGA) is applied for the structure optimization of radial basis function network (RBFN). The problem of finding the number of hidden centers remains a critical issue in the design of RBFN. The number of basis function controls the complexity and generalization ability of the network. The most parsimonious network obtained from the pareto front is applied in one of the challenging research area of proteomics and computational biology: Protein superfamily classification. The problem deals with predicting the family membership of a newly discovered amino acid sequence. The modification to the earlier approach of multiobjective genetic algorithm (MOGA) is done based on the two key controlling parameters such as probability of crossover and probability of mutation. These values are adaptively varied based on the performance of the algorithm i.e., based on the percentage of total population present in the best nondomination level. Principal component analysis (PCA) is used for dimension reduction and significant features are extracted from long feature vector of amino acid sequences. Numerical simulation results illustrates the efficiency of our approach in terms of faster convergence, optimal architecture and high level of classification accuracy.

scholarly journals LC-HRMS Screening and Identification of Novel Peptide Markers of Ricin Based on Multiple Protease Digestion Strategies

2019 ◽  
Author(s):  
Long-Hui Liang ◽  
Chang-Cai Liu ◽  
Bo Chen ◽  
Long Yan ◽  
Hui-Lan Yu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Proteinase K ◽  
Amino Acid Residues ◽  
Accurate Analysis ◽  
Ribosome Inactivating Proteins ◽  
Protease Digestion ◽  
Screening And Identification ◽  
Digestion Methods ◽  
Similar Amino Acid

Both ricin and R. communis agglutinin (RCA120), belonging to the type II ribosome-inactivating proteins (RIPs-Ⅱ), are derived from the seeds of castor bean plant. They share very similar amino acid sequences, but ricin is much more toxic than RCA120. It is urgently necessary to distinguish ricin and RCA120 in response to public safety. Currently, mass spectrometric assays are well established for unambiguous identification of ricin by accurate analysis of differentiated amino acid residues after trypsin digestion. However, diagnostic peptides are relatively limited for unambiguous identification of trace ricin, especially in complex matrices. Here, we demonstrate a digestion strategy of multiple proteinases to produce novel peptide markers for unambiguous identification of ricin. LC-HRMS was used to verified the resulting peptides, among which only the peptides with uniqueness and good MS response were selected as peptide markers. Seven novel peptide markers were obtained from tandem digestion of trypsin and endoproteinase Glu-C in PBS buffer. From the chymotrypsin digestion under reduction and non-reduction conditions, eight and seven novel peptides were selected respectively. Using pepsin under pH 1~2 and proteinase K digestion, 6 and 5 peptides were selected as novel peptide markers. In conclusion, the obtained novel peptides from the established digestion methods can be recommended for the unambiguous identification of ricin during the investigation of illegal use of the toxin.

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