A new concept for molecular engineering of artificial enzymes: a multiscale simulation

Soft Matter ◽  
2016 ◽  
Vol 12 (3) ◽  
pp. 689-704 ◽  
Author(s):  
Pavel V. Komarov ◽  
Pavel G. Khalatur ◽  
Alexei R. Khokhlov
Keyword(s):  
Amino Acid ◽  
Multiscale Simulation ◽  
Molecular Engineering ◽  
Artificial Enzymes ◽  
Amino Acid Residues ◽  
Protein Amino Acid ◽  
Functional Analog ◽  
First Time

We have designed, for the first time, a functional analog of chymotrypsin from synthetic monomers imitating protein amino acid residues.

scholarly journals iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou’s 5-steps Rule and Pseudo Components

2019 ◽  
Vol 20 (4) ◽  
pp. 306-320 ◽  
Author(s):  
Omar Barukab ◽  
Yaser Daanial Khan ◽  
Sher Afzal Khan ◽  
Kuo-Chen Chou
Keyword(s):  
Amino Acid ◽  
Computational Model ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Statistical Moments ◽  
Amino Acid Residues ◽  
Tyrosine Sulfation ◽  
Protein Amino Acid ◽  
Jackknife Test ◽  
Self Consistency

Background: The amino acid residues, in protein, undergo post-translation modification (PTM) during protein synthesis, a process of chemical and physical change in an amino acid that in turn alters behavioral properties of proteins. Tyrosine sulfation is a ubiquitous posttranslational modification which is known to be associated with regulation of various biological functions and pathological processes. Thus its identification is necessary to understand its mechanism. Experimental determination through site-directed mutagenesis and high throughput mass spectrometry is a costly and time taking process, thus, the reliable computational model is required for identification of sulfotyrosine sites. Methodology: In this paper, we present a computational model for the prediction of the sulfotyrosine sites named iSulfoTyr-PseAAC in which feature vectors are constructed using statistical moments of protein amino acid sequences and various position/composition relative features. These features are incorporated into PseAAC. The model is validated by jackknife, cross-validation, self-consistency and independent testing. Results: Accuracy determined through validation was 93.93% for jackknife test, 95.16% for crossvalidation, 94.3% for self-consistency and 94.3% for independent testing. Conclusion: The proposed model has better performance as compared to the existing predictors, however, the accuracy can be improved further, in future, due to increasing number of sulfotyrosine sites in proteins.

scholarly journals N-myristoyltransferase: Tracing Steps Backwards to Find a Way Forward

2020 ◽  
Author(s):  
Dean Reddick ◽  
Daniel I Udenwobele ◽  
David Datzkiw ◽  
Revanti Mukherjee ◽  
Shailly Varma Shrivastav ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nuclear Localization ◽  
Potential Role ◽  
Nuclear Localization Sequence ◽  
Amino Acid Residues ◽  
Trace Back ◽  
Carbon Fatty Acid ◽  
Localization Sequence ◽  
History Of ◽  
First Time

AbstractN-myristoylation refers to the attachment of a 14-carbon fatty acid onto the N-terminal glycine residue of a target protein. The myristoylation reaction, catalyzed by N-myristoyltrasnferase (NMT), is essential for regulating cellular activities such as signal transduction, proliferation, migration, differentiation, and transformation. Although a considerable amount of research is performed on the overexpression of NMT in pathogenic conditions, a fundamental knowledge gap exists on the evolution of NMT and the functional impact of myristoylation for normal cellular development and functions. We performed evolutionary analyses of the NMT gene and found that most non-vertebrates harbor a single nmt gene and all vertebrates examined harbor two genes; nmt1 and nmt2. For the first time, we report that teleosts harbor two copies of nmt1, named nmt1a and nmt1b. We traced the evolutionary history of the chromosomal fragments hosting NMT1 and NMT2 in humans and found that NMT1 and NMT2 trace back to a single vertebrate ancestral chromosome. We also report the presence of putative nuclear localization sequence (NLS) and amino acid residues flanking NLS. The presence of phosphorylatable amino acid residues flanking the NLS suggests that nuclear localization of NMT is regulated by phosphorylation. The nuclear localization of NMT suggest its potential role in gene transcription.

scholarly journals Identification of the gene for disaggregatase fromMethanosarcina mazei

Archaea ◽  
2008 ◽  
Vol 2 (3) ◽  
pp. 185-191 ◽  
Author(s):  
Naoki Osumi ◽  
Yoshihiro Kakehashi ◽  
Shiho Matsumoto ◽  
Kazunari Nagaoka ◽  
Junichi Sakai ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Cells ◽  
Pcr Analysis ◽  
Amino Acid Residues ◽  
Wall Function ◽  
Rt Pcr ◽  
Methanosarcina Mazei ◽  
C Terminus ◽  
First Time

The gene sequences encoding disaggregatase (Dag), the enzyme responsible for dispersion of cell aggregates ofMethanosarcina mazeito single cells, were determined for three strains ofM. mazei(S-6T, LYC and TMA). Thedaggenes of the three strains were 3234 bp in length and had almost the same sequences with 97% amino acid sequence identities. Dag was predicted to comprise 1077 amino acid residues and to have a molecular mass of 120 kDa containing three repeats of the DNRLRE domain in the C terminus, which is specific to the genusMethanosarcinaand may be responsible for structural organization and cell wall function. Recombinant Dag was overexpressed inEscherichia coliand preparations of the expressed protein exhibited enzymatic activity. The RT-PCR analysis showed thatdagwas transcribed to mRNA inM. mazeiLYC and indicated that the gene was expressed in vivo. This is the first time the gene involved in the morphological change ofMethanosarcinaspp. from aggregate to single cells has been identified.

scholarly journals Prunus geminivirus A: A Novel Grablovirus Infecting Prunus spp.

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1246-1253 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Olufemi J. Alabi ◽  
Nathaniel M. Westrick ◽  
Deborah Golino
Keyword(s):  
Amino Acid ◽  
Complete Genome ◽  
Quantitative Polymerase Chain Reaction ◽  
Protein Amino Acid ◽  
Virus Diagnosis ◽  
Polymerase Chain ◽  
First Time ◽  
Prunus Spp ◽  
Plum Tree

Increased use of metagenomics for routine virus diagnosis has led to the characterization of several genus level geminiviruses from tree fruit long thought to exclusively host RNA viruses. In this study, the identification and molecular characterization of a novel geminivirus is reported for the first time in Prunus spp. The virus, provisionally named Prunus geminivirus A (PrGVA), was identified by Illumina sequencing from an asymptomatic plum tree. PrGVA was subsequently confirmed by rolling cycle amplification, cloning, and Sanger sequencing of its complete genome (3,174 to 3,176 nucleotides) from an additional 18 (9 apricot and 9 plum) field isolates. Apart from the nonanucleotide motif TAATATT↓AC present in its virion strand origin of replication, other conserved motifs of PrGVA support its geminiviral origin. PrGVA shared highest complete genome (73 to 74%), coat protein amino acid (83 to 85%) and rep-associated amino acid (74%) identities with Grapevine red blotch virus (GRBV). PrGVA was graft but not mechanically transmissible. Quantitative polymerase chain reaction screening of Prunus spp. in the National Clonal Germplasm Repository collection using newly designed primers and probes revealed 69.4% (apricot), 55.8% (plum), and 8.3% (cherry) incidences of PrGVA. PrGVA is proposed as a novel member of the genus Grablovirus based on its close genome and phylogenetic relationship with GRBV.

scholarly journals Non-Protein Amino Acids: A Review of the Biosynthesis and Taxonomic Significance

2008 ◽  
Vol 3 (1) ◽  
pp. 1934578X0800300 ◽  
Author(s):  
E. Arthur Bell ◽  
Alison A. Watson ◽  
Robert J. Nash
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Biosynthetic Pathway ◽  
Amino Acid Residues ◽  
Taxonomic Significance ◽  
Post Translational Modification ◽  
Protein Amino Acid ◽  
Ancestral Form ◽  
Higher Taxa ◽  
Protein Amino Acids

The non-protein amino acids, with which we are concerned here, are not incorporated into the proteins of the organisms that synthesize them nor are their residues formed by the post-translational modification of protein amino acid residues. Non-protein amino acids are of value in the study of relationships between species and higher taxa of organisms because most of them are of restricted distribution. If a particular non-protein amino acid is only known to occur in a limited group of species which are related in other respects then it is probable that these species have all arisen from a common ancestral form in which the biosynthetic pathway to that particular non-protein amino acid already existed.

Human cytoplasmic ProX edits mischarged tRNAPro with amino acid but not tRNA specificity

2013 ◽  
Vol 450 (1) ◽  
pp. 243-252 ◽  
Author(s):  
Liang-Liang Ruan ◽  
Xiao-Long Zhou ◽  
Min Tan ◽  
En-Duo Wang
Keyword(s):  
Amino Acid ◽  
Protein Biosynthesis ◽  
Trna Synthetase ◽  
Main Body ◽  
Amino Acid Residues ◽  
Homologous Proteins ◽  
Gene Encoding ◽  
Trna Synthetases ◽  
Editing Domain ◽  
First Time

aaRSs (aminoacyl-tRNA synthetases) are responsible for ensuring the fidelity of the genetic code translation by accurately linking a particular amino acid to its cognate tRNA isoacceptor. To ensure accuracy of protein biosynthesis, some aaRSs have evolved an editing process to remove mischarged tRNA. The hydrolysis of the mischarged tRNA usually occurs in an editing domain, which is inserted into or appended to the main body of the aaRS. In addition, autonomous, editing domain-homologous proteins can also trans-edit mischarged tRNA in concert or in compensating for the editing function of its corresponding aaRS. The freestanding ProX is a homologue of the editing domain of bacterial ProRS (prolyl-tRNA synthetase). In the present study, we cloned for the first time a gene encoding HsProX (human cytoplasmic ProX) and purified the expressed recombinant protein. The catalytic specificity of HsProX for non-cognate amino acids and identity elements on tRNAPro for editing were also investigated. We found that HsProX could deacylate mischarged Ala-tRNAPro, but not Cys-HstRNAUGGPro, and specifically targeted the alanine moiety of Ala-tRNAPro. The importance of the CCA76 end of the tRNA for deacylation activity and key amino acid residues in HsProX for its editing function were also identified.

scholarly journals Neurotoxins from the venoms of the sea snakes Hydrophis ornatus and Hydrophis lapemoides

1983 ◽  
Vol 213 (1) ◽  
pp. 31-38 ◽  
Author(s):  
N Tamiya ◽  
N Maeda ◽  
H G Cogger
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Paper Electrophoresis ◽  
Amino Acid Sequences ◽  
British Library ◽  
Amino Acid Residues ◽  
Protein Amino Acid ◽  
Tryptic Peptides ◽  
Sea Snakes ◽  
And Migration

The main neurotoxic components, toxins Hydrophis ornatus a and Hydrophis lapemoides a, were isolated from the venoms of the sea snakes Hydrophis ornatus and Hydrophis lapemoides respectively. The amino acid sequence of toxin Hydrophis ornatus a was deduced to be identical with that of toxin Astrotia stokesii a [Maeda & Tamiya (1978) Biochem. J. 175, 507-517] on the basis of identity of the tryptic peptide ‘map’ and the amino acid composition of each peptide. The amino acid sequence of toxin Hydrophis lapemoides a was determined mainly on the basis of identity of the amino acid compositions, mobilities on paper electrophoresis and migration positions on paper chromatography of the tryptic peptides with those of other sea-snake toxins whose sequences are known. Both toxins Hydrophis ornatus a and Hydrophis lapemoides a consisted of 60 amino acid residues and there were six amino acid replacements between them. The taxonomy of sea snakes in the Hydrophis ornatus complex has long been confused, and the above snakes were originally assigned to taxa that proved to be inconsistent with the relationships indicated by the neurotoxin amino acid sequences obtained. A subsequent re-examination of the specimens revealed an error in the original identifications and demonstrated the value of the protein amino acid sequences in systematic and phylogenetic studies. The isolation procedure and results of amino acid analysis of the tryptic peptides have been deposited as Supplementary Publication SUP 50121 (8 pages) with the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained as indicated in Biochem. J. (1983) 209, 5.

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