scholarly journals LC provides peptide sequence information

2007 ◽  
Vol 79 (1) ◽  
pp. 23-23
Author(s):  
Elizabeth Zubritsky
Keyword(s):  
Peptide Sequence ◽  
Sequence Information

scholarly journals CirBiTree: Citrullination Site Inference Based on a Fuzzy Neural Network and Flexible Neural Tree

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Chuandong Song ◽  
Haifeng Wang
Keyword(s):  
Neural Network ◽  
Fuzzy Neural Network ◽  
Classification Model ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Post Translational Modification ◽  
Fuzzy Neural ◽  
Human Complex ◽  
Better Than

Emerging evidence demonstrates that post-translational modification plays an important role in several human complex diseases. Nevertheless, considering the inherent high cost and time consumption of classical and typical in vitro experiments, an increasing attention has been paid to the development of efficient and available computational tools to identify the potential modification sites in the level of protein. In this work, we propose a machine learning-based model called CirBiTree for identification the potential citrullination sites. More specifically, we initially utilize the biprofile Bayesian to extract peptide sequence information. Then, a flexible neural tree and fuzzy neural network are employed as the classification model. Finally, the most available length of identified peptides has been selected in this model. To evaluate the performance of the proposed methods, some state-of-the-art methods have been employed for comparison. The experimental results demonstrate that the proposed method is better than other methods. CirBiTree can achieve 83.07% in sn%, 80.50% in sp, 0.8201 in F1, and 0.6359 in MCC, respectively.

Purification, Characterization, and Heterologous Expression in Fusarium venenatum of a Novel Serine Carboxypeptidase from Aspergillus oryzae

1999 ◽  
Vol 65 (8) ◽  
pp. 3298-3303 ◽  
Author(s):  
Alexander M. Blinkovsky ◽  
Tony Byun ◽  
Kimberly M. Brown ◽  
Elizabeth J. Golightly
Keyword(s):  
Molecular Weight ◽  
Aspergillus Oryzae ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Serine Carboxypeptidase ◽  
Recombinant Enzymes ◽  
Molecular Weights ◽  
Fusarium Venenatum

ABSTRACT A novel serine carboxypeptidase (EC 3.4.16.1 ) was found in anAspergillus oryzae fermentation broth and was purified to homogeneity. This enzyme has a molecular weight of ca. 67,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its specific activity is 21 U/mg for carbobenzoxy (Z)-Ala-Glu at pH 4.5 and 25°C. It has a ratio of bimolecular constants for Z-Ala-Lys and Z-Ala-Phe of 3.75. Optimal enzyme activity occurs at pH 4 to 4.5 and 58 to 60°C for Z-Ala-Ile. The N terminus of this carboxypeptidase is blocked. Internal fragments, obtained by cyanogen bromide digestion, were sequenced. PCR primers were then made based on the peptide sequence information, and the full-length gene sequence was obtained. An expression vector that contained the recombinant carboxypeptidase gene was used to transform aFusarium venenatum host strain. The transformed strain ofF. venenatum expressed an active recombinant carboxypeptidase. In F. venenatum, the recombinant carboxypeptidase produced two bands which had molecular weights greater than the molecular weight of the native carboxypeptidase from A. oryzae. Although the molecular weights of the native and recombinant enzymes differ, these enzymes have very similar kinetic parameters.

scholarly journals A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

2017 ◽  
Vol 284 (1855) ◽  
pp. 20170544 ◽  
Author(s):  
Michael Buckley ◽  
Stacey Warwood ◽  
Bart van Dongen ◽  
Andrew C. Kitchener ◽  
Phillip L. Manning
Keyword(s):  
Peptide Sequence ◽  
Bacterial Biofilms ◽  
Sequence Information ◽  
Cross Contamination ◽  
Laboratory Practice ◽  
True Nature ◽  
Struthio Camelus ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Single Peptide

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus . The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.

scholarly journals Cloning, expression, and chromosomal localization of the 140-kilodalton subunit of replication factor C from mice and humans.

1994 ◽  
Vol 14 (3) ◽  
pp. 1626-1634 ◽  
Author(s):  
B Luckow ◽  
F Bunz ◽  
B Stillman ◽  
P Lichter ◽  
G Schütz
Keyword(s):  
Amino Acids ◽  
Molecular Mass ◽  
Binding Site ◽  
Peptide Sequence ◽  
Atp Binding ◽  
Sequence Information ◽  
Replication Factor C ◽  
Atp Binding Site ◽  
Replication Factor ◽  
Factor C

We have isolated a full-length mouse cDNA encoding a lysine-rich protein of 1,131 amino acids with a calculated molecular mass of 126 kDa. The protein binds in a sequence-unspecific manner to DNA, is localized exclusively in the nucleus, and contains a putative ATP binding site and a stretch of 80 amino acids with homology to the carboxy terminus of prokaryotic DNA ligases. On the basis of the following facts, we conclude that the isolated cDNA encodes the 140-kDa subunit of mouse replication factor C (mRFC140). (i) The sequence around the ATP binding site shows significant homology to three small subunits of human replication factor C. (ii) Polyclonal antibodies raised against the protein encoded by this cDNA cross-react with the 140-kDa subunit of purified human replication factor C (hRFC140) and recognize in mouse cell extracts an authentic protein with an apparent molecular mass of 130 kDa. (iii) Sequence comparison with a human cDNA isolated by using tryptic peptide sequence information from purified hRFC140 revealed 83% identity of the encoded proteins. The mRFC140 gene is ubiquitously expressed, and two mRNAs approximately 5.0 and 4.5 kb long have been detected. The gene was mapped by in situ hybridization to mouse chromosome 5, and its human homolog was mapped to chromosome 4 (p13-p14).

scholarly journals The eosinophil-specific cell surface antigen, EOS47, is a chicken homologue of the oncofetal antigen melanotransferrin

Blood ◽  
1996 ◽  
Vol 87 (4) ◽  
pp. 1343-1352 ◽  
Author(s):  
KM McNagny ◽  
F Rossi ◽  
G Smith ◽  
T Graf
Keyword(s):  
Bone Marrow ◽  
Cell Surface ◽  
Peripheral Blood ◽  
Tertiary Structure ◽  
Surface Glycoprotein ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Specific Cell ◽  
Specific Marker ◽  
Cell Surface Glycoprotein

The EOS47 antigen is a 100-kD cell surface glycoprotein selectively expressed by avian retrovirus-transformed eosinophils and their precursors. We have purified the EOS47 protein to homogeneity and used peptide sequence information to clone EOS47-encoding cDNAs. The open reading frames from these cDNAs predict a 738 amino acid protein with homology to human melanotransferrin, a membrane-found, transferrin-like protein that is expressed at high levels by a subset of melanomas, tumor cell lines, fetal intestine, and liver, but not by most normal adult tissues. The predicted protein sequence of EOS47 displays a 61% sequence identity with melanotransferrin and conservation of all 28 cysteine residues, indicating a similar tertiary structure. The finding that EOS47 lacks several of the iron-coordinating amino acids present in all transferrins suggests that it may be impaired in its ability to bind iron. In nonhematopoietic tissues, EOS47 is expressed at high levels by epithelial brush borders of small intestine and kidney and at lower levels by cells lining the sinusoids of the liver. Within hematopoietic tissues, EOS47 is restricted to a subpopulation of cells (1% to 5%) in bone marrow and early spleen and fluorescence-activated cell sorting of EOS47+ cells leads to a dramatic ( > 30-fold) enrichment of peroxidase+ eosinophils. In contrast, peripheral blood eosinophils are EOS47-, suggesting that the antigen is expressed by newly formed eosinophils and that expression ceases shortly before these cells emigrate from the bone marrow into the peripheral blood. Our results show that melanotransferrin is a stage-specific marker of eosinophils and should be useful for their isolation and further characterization.

scholarly journals PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface

2021 ◽  
Author(s):  
Alisa Khramushin ◽  
Tomer Tsaban ◽  
Julia Varga ◽  
Orly Avraham ◽  
Ora Schueler-Furman
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Protein Structures ◽  
Binding Pocket ◽  
Protein Docking ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Peptide Docking ◽  
Docking Approach ◽  
Conformer Ensemble

AbstractPeptide docking can be perceived as a subproblem of protein-protein docking. However, due to the short length and flexible nature of peptides, many do not adopt one defined conformation prior to binding. Therefore, to tackle a peptide docking problem, not only the relative orientation between the two partners, but also the bound conformation of the peptide needs to be modeled. Traditional peptide-centered approaches use information about the peptide sequence to generate a representative conformer ensemble, which can then be rigid body docked to the receptor. Alternatively, one may look at this problem from the viewpoint of the receptor, namely that the protein surface defines the peptide bound conformation.We present PatchMAN (Patch-Motif AligNments), a novel peptide docking approach which uses structural motifs to map the receptor surface with backbone scaffolds extracted from protein structures. On a non-redundant set of protein-peptide complexes, starting from free receptor structures, PatchMAN successfully models and identifies near-native peptide-protein complexes in 62% / 81% within 2.5Å / 5Å RMSD, with corresponding sampling in 81% / 100% of the cases, outperforming other approaches. PatchMAN leverages the observation that structural units of peptides with their binding pocket can be found not only within interfaces, but also within monomers. We show that the conformation of the bound peptide is sampled based on the structural context of the receptor only, without taking into account any sequence information. Beyond peptide docking, this approach opens exciting new avenues to study principles of peptide-protein association, and to the design of new peptide binders.

scholarly journals Support Vector Machine Classifier for Accurate Identification of piRNA

2018 ◽  
Vol 8 (11) ◽  
pp. 2204 ◽  
Author(s):  
Taoying Li ◽  
Mingyue Gao ◽  
Runyu Song ◽  
Qian Yin ◽  
Yan Chen
Keyword(s):  
Support Vector Machine ◽  
Cell Function ◽  
Nucleotide Composition ◽  
Peptide Sequence ◽  
Single Type ◽  
Support Vector ◽  
Transcriptional Gene Silencing ◽  
Sequence Information ◽  
Accurate Identification ◽  
The Stability

Piwi-interacting RNA (piRNA) is a newly identified class of small non-coding RNAs. It can combine with PIWI proteins to regulate the transcriptional gene silencing process, heterochromatin modifications, and to maintain germline and stem cell function in animals. To better understand the function of piRNA, it is imperative to improve the accuracy of identifying piRNAs. In this study, the sequence information included the single nucleotide composition, and 16 dinucleotides compositions, six physicochemical properties in RNA, the position specificities of nucleotides both in N-terminal and C-terminal, and the proportions of the similar peptide sequence of both N-terminal and C-terminal in positive and negative samples, which were used to construct the feature vector. Then, the F-Score was applied to choose an optimal single type of features. By combining these selected features, we achieved the best results on the jackknife and the 5-fold cross-validation running 10 times based on the support vector machine algorithm. Moreover, we further evaluated the stability and robustness of our new method.

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