scholarly journals Peptide partitions and protein identification: a computational analysis

2016 ◽  
Author(s):  
G. Sampath
Keyword(s):  
Protein Identification ◽  
Computational Analysis ◽  
Protein Sequences ◽  
Peptide Sequence ◽  
Sequence Database ◽  
Information Theoretic ◽  
Identification Rate ◽  
Standard Set ◽  
Exclusive Sets

AbstractPeptide sequences from a proteome can be partitioned into N mutually exclusive sets and used to identify their parent proteins in a sequence database. This is illustrated with the human proteome (http://www.uniprot.org; id UP000005640), which is partitioned into eight subsets KZ*R, KZ*D, KZ*E, KZ*, Z*R, Z*D, Z*E, and Z*, where Z ∈ {A, N, C, Q, G, H, I, L, M, F, P, S, T, W, Y, V} and Z* ≡ 0 or more occurrences of Z. If the full peptide sequence is known then over 98% of the proteins in the proteome can be identified from such sequences. The rate exceeds 78% if the positions of four internal residue types are known. When the standard set of 20 amino acids is replaced with an alphabet of size four based on residue volume the identification rate exceeds 96%. In an information-theoretic sense this last result suggests that protein sequences effectively carry nearly the same amount of information as the exon sequences in the genome that code for them using an alphabet of size four. An appendix discusses possible in vitro methods to create peptide partitions and potential ways to sequence partitioned peptides.

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

2020 ◽  
Vol 20 (10) ◽  
pp. 831-840
Author(s):  
Weibin Li
Keyword(s):  
Pathogenic Bacteria ◽  
Genetic Diagnosis ◽  
Bloodstream Infections ◽  
High Specificity ◽  
Peptide Sequence ◽  
High Morbidity ◽  
Specificity And Sensitivity ◽  
Prospective Application ◽  
Small Molecule Therapeutics

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

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.

scholarly journals A Biochemical and Pharmacological Characterization of Phospholipase A2 and Metalloproteinase Fractions from Eastern Russell’s Viper (Daboia siamensis) Venom: Two Major Components Associated with Acute Kidney Injury

Toxins ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 521
Author(s):  
Janeyuth Chaisakul ◽  
Orawan Khow ◽  
Kulachet Wiwatwarayos ◽  
Muhamad Rusdi Ahmad Rusmili ◽  
Watcharamon Prasert ◽  
...  
Keyword(s):  
Acute Kidney Injury ◽  
Phospholipase A2 ◽  
Protein Identification ◽  
Clinical Manifestations ◽  
Kidney Injury ◽  
Factor X ◽  
Pharmacological Characterization ◽  
Russell’S Viper

Acute kidney injury (AKI) following Eastern Russell’s viper (Daboia siamensis) envenoming is a significant symptom in systemically envenomed victims. A number of venom components have been identified as causing the nephrotoxicity which leads to AKI. However, the precise mechanism of nephrotoxicity caused by these toxins is still unclear. In the present study, we purified two proteins from D. siamensis venom, namely RvPLA2 and RvMP. Protein identification using LCMS/MS confirmed the identity of RvPLA2 to be snake venom phospholipase A2 (SVPLA2) from Thai D. siamensis venom, whereas RvMP exhibited the presence of a factor X activator with two subunits. In vitro and in vivo pharmacological studies demonstrated myotoxicity and histopathological changes of kidney, heart, and spleen. RvPLA2 (3–10 µg/mL) caused inhibition of direct twitches of the chick biventer cervicis muscle preparation. After administration of RvPLA2 or RvMP (300 µg/kg, i.p.) for 24 h, diffuse glomerular congestion and tubular injury with minor loss of brush border were detected in envenomed mice. RvPLA2 and RvMP (300 µg/kg; i.p.) also induced congestion and tissue inflammation of heart muscle as well as diffuse congestion of mouse spleen. This study showed the significant roles of PLA2 and SVMP in snake bite envenoming caused by Thai D. siamensis and their similarities with observed clinical manifestations in envenomed victims. This study also indicated that there is a need to reevaluate the current treatment strategies for Thai D. siamensis envenoming, given the potential for irreversible nephrotoxicity.

scholarly journals Determinants of adenine-mutagenesis in diversity-generating retroelements

2020 ◽  
Author(s):  
Sumit Handa ◽  
Andres Reyna ◽  
Timothy Wiryaman ◽  
Partho Ghosh
Keyword(s):  
Amino Acids ◽  
Dark Matter ◽  
Reverse Transcription ◽  
Genetic Information ◽  
Human Microbiome ◽  
Protein Sequences ◽  
Catalytic Efficiency ◽  
Natural World ◽  
In Vitro System

Abstract Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.

scholarly journals A Novel Tetrapeptide Derivative Exhibits In Vitro Inhibition of Neutrophil-Derived Reactive Oxygen Species and Lysosomal Enzymes Release

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Sumitra Miriyala ◽  
Manikandan Panchatcharam ◽  
Meera Ramanujam ◽  
Rengarajulu Puvanakrishnan
Keyword(s):  
Reactive Oxygen Species ◽  
Superoxide Anion ◽  
Lysosomal Enzymes ◽  
Reactive Oxygen ◽  
Peptide Sequence ◽  
Ros Generation ◽  
Oxygen Species ◽  
Complement Factors

Neutrophil infiltration plays a major role in the pathogenesis of myocardial injury. Oxidative injury is suggested to be a central mechanism of the cellular damage after acute myocardial infarction. This study is pertained to the prognostic role of a tetrapeptide derivative PEP1261 (BOC-Lys(BOC)-Arg-Asp-Ser(tBu)-OtBU), a peptide sequence (39–42) of lactoferrin, studied in the modulation of neutrophil functions in vitro by measuring the reactive oxygen species (ROS) generation, lysosomal enzymes release, and enhanced expression of C proteins. The groundwork experimentation was concerned with the isolation of neutrophils from the normal and acute myocardial infarct rats to find out the efficacy of PEP1261 in the presence of a powerful neutrophil stimulant, phorbol 12-myristate 13 acetate (PMA). Stimulation of neutrophils with PMA resulted in an oxidative burst of superoxide anion and enhanced release of lysosomal enzymes and expression of complement proteins. The present study further demonstrated that the free radicals increase the complement factors in the neutrophils confirming the role of ROS. PEP1261 treatment significantly reduced the levels of superoxide anion and inhibited the release of lysosomal enzymes in the stimulated control and infarct rat neutrophils. This study demonstrated that PEP1261 significantly inhibited the effect on the ROS generation as well as the mRNA synthesis and expression of the complement factors in neutrophils isolated from infarct heart.

Development of Multilayered Chlorogenate-Peptide Based Biocomposite Scaffolds for Potential Applications in Ligament Tissue Engineering - An In Vitro Study

2017 ◽  
Vol 34 ◽  
pp. 37-56 ◽  
Author(s):  
Harrison T. Pajovich ◽  
Alexandra M. Brown ◽  
Andrew M. Smith ◽  
Sara K. Hurley ◽  
Jessica R. Dorilio ◽  
...  
Keyword(s):  
Tissue Regeneration ◽  
Type I Collagen ◽  
Phase Changes ◽  
Peptide Sequence ◽  
Proteoglycan Synthesis ◽  
Type I ◽  
Average Roughness ◽  
Potential Applications ◽  
Self Assembled

In this work, for the first time, chlorogenic acid, a natural phytochemical, was conjugated to a lactoferrin derived antimicrobial peptide sequence RRWQWRMKKLG to develop a self-assembled template. To mimic the components of extracellular matrix, we then incorporated Type I Collagen, followed by a sequence of aggrecan peptide (ATEGQVRVNSIYQDKVSL) onto the self-assembled templates for potential applications in ligament tissue regeneration. Mechanical properties and surface roughness were studied and the scaffolds displayed a Young’s Modulus of 169 MP and an average roughness of 72 nm respectively. Thermal phase changes were studied by DSC analysis. Results showed short endothermic peaks due to water loss and an exothermic peak due to crystallization of the scaffold caused by rearrangement of the components. Biodegradability studies indicated a percent weight loss of 27.5 % over a period of 37 days. Furthermore, the scaffolds were found to adhere to fibroblasts, the main cellular component of ligament tissue. The scaffolds promoted cell proliferation and displayed actin stress fibers indicative of cell motility and attachment. Collagen and proteoglycan synthesis were also promoted, demonstrating increased expression and deposition of collagen and proteoglycans. Additionally, the scaffolds exhibited antimicrobial activity against Staphylococcus epidermis bacteria, which is beneficial for minimizing biofilm formation if potentially used as implants. Thus, we have developed a novel biocomposite that may open new avenues to enhance ligament tissue regeneration.

scholarly journals Reconstituted nuclei depleted of a vertebrate GLFG nuclear pore protein, p97, import but are defective in nuclear growth and replication.

1995 ◽  
Vol 128 (5) ◽  
pp. 721-736 ◽  
Author(s):  
M A Powers ◽  
C Macaulay ◽  
F R Masiarz ◽  
D J Forbes
Keyword(s):  
Protein Import ◽  
Polyclonal Antiserum ◽  
Peptide Sequence ◽  
Nuclear Pore ◽  
Chromosomal Dna ◽  
Nuclear Pore Protein ◽  
Egg Extracts ◽  
Xenopus Egg ◽  
Punctate Pattern

Xenopus egg extracts provide a powerful system for in vitro reconstitution of nuclei and analysis of nuclear transport. Such cell-free extracts contain three major N-acetylglucosaminylated proteins: p200, p97, and p60. Both p200 and p60 have been found to be components of the nuclear pore. Here, the role of p97 has been investigated. Xenopus p97 was isolated and antisera were raised and affinity purified. Immunolocalization experiments indicate that p97 is present in a punctate pattern on the nuclear envelope and also in the nuclear interior. Peptide sequence analysis reveals that p97 contains a GLFG motif which defines a family of yeast nuclear pore proteins, as well as a peptide that is identical at 11/15 amino acids to a specific member of the GLFG family, NUP116. An additional peptide is highly homologous to a second sequence found in NUP116 and other members of the yeast GLFG family. A monoclonal antibody to the GLFG domain cross-reacts with a major Xenopus protein of 97 kD and polyclonal antiserum to p97 recognizes the yeast GLFG nucleoporin family. The p97 antiserum was used to immunodeplete Xenopus egg cytosol and p97-deficient nuclei were reconstituted. The p97-depleted nuclei remained largely competent for nuclear protein import. However, in contrast to control nuclei, nuclei deficient in p97 fail to grow in size over time and do not replicate their chromosomal DNA. ssDNA replication in such extracts remains unaffected. Addition of the N-acetylglucosaminylated nuclear proteins of Xenopus or rat reverses these replication and growth defects. The possible role(s) of p97 in these nuclear functions is discussed.

Protein Identification from 2-D Gels Using In Vitro Transcription Translation Products

2003 ◽  
pp. 17-28
Author(s):  
Nathalie Norais ◽  
Renzo Nogarotto ◽  
Emilia Tiziana Iacobini ◽  
Ignazio Garaguso ◽  
Renata Grifantini ◽  
...  
Keyword(s):  
Protein Identification ◽  
In Vitro Transcription

Coronatin-2 from the entomopathogenic fungus Conidiobolus coronatus kills Galleria mellonella larvae and incapacitates hemocytes

2016 ◽  
Vol 107 (1) ◽  
pp. 66-76 ◽  
Author(s):  
M.I. Boguś ◽  
W. Wieloch ◽  
M. Ligęza-Żuber
Keyword(s):  
Entomopathogenic Fungus ◽  
Galleria Mellonella ◽  
Elongation Factor ◽  
Peptide Sequence ◽  
Mass Spectrometry Analysis ◽  
Sequence Coverage ◽  
Spectrometry Analysis ◽  
Conidiobolus Coronatus ◽  
Liquid Chromatography Tandem Mass

AbstractCoronatin-2, a 14.5 kDa protein, was isolated from culture filtrates of the entomopathogenic fungus Conidiobolus coronatus (Costantin) Batko (Entomophthoramycota: Entomophthorales). After LC–MS/MS (liquid chromatography tandem mass spectrometry) analysis of the tryptic peptide digest of coronatin-2 and a mass spectra database search no orthologs of this protein could be found in fungi. The highest homology was observed to the partial translation elongation factor 1a from Sphaerosporium equinum (protein sequence coverage, 21%), with only one peptide sequence, suggesting that coronatin-2 is a novel fungal protein that has not yet been described. In contrast to coronatin-1, an insecticidal 36 kDa protein, which shows both elastolytic and chitinolytic activity, coronatin-2 showed no enzymatic activity. Addition of coronatin-2 into cultures of hemocytes taken from larvae of Galleria mellonella Linnaeus (Lepidoptera: Pyralidae), resulted in progressive disintegration of nets formed by granulocytes and plasmatocytes due to rapid degranulation of granulocytes, extensive vacuolization of plasmatocytes accompanied by cytoplasm expulsion, and cell disintegration. Spherulocytes remained intact, while oenocytes rapidly disintegrated. Coronatin-2 produced 80% mortality when injected into G. mellonella at 5 µg larva−1. Further study is warranted to determine the relevance of the acute toxicity of coronatin-2 and its effects on hemocytes in vitro to virulence of C. coronatus against its hosts.

Hematopoietic cells express two forms of lyn kinase differing by 21 amino acids in the amino terminus

1991 ◽  
Vol 11 (5) ◽  
pp. 2391-2398
Author(s):  
T L Yi ◽  
J B Bolen ◽  
J N Ihle
Keyword(s):  
Genomic Structure ◽  
Donor Site ◽  
Hematopoietic Cells ◽  
Peptide Sequence ◽  
In Vitro Translation ◽  
Splice Donor Site ◽  
Mouse Bone Marrow ◽  
Kinase Gene ◽  
Amino Terminal

cDNAs for the murine lyn protein tyrosine kinase gene were cloned from mouse bone marrow-derived monocytic cells. Comparison of the human and murine genes demonstrated a 94% homology in peptide sequence. Comparable to the human gene, murine lyn was found to be expressed in myeloid and B-lymphoid lineage cells. During the cloning, two types of cDNAs were obtained that differed by the presence (lynA) or absence (lynB) of 63 bp within the amino-terminal coding region of the gene. The genomic structure of the murine lyn gene demonstrates that the two types of lyn transcripts are derived from alternative splicing utilizing an internal splice donor site. Transcripts for both forms were found to be expressed in myeloid cells. lyn-specific antisera detected comparable levels of proteins of 56 and 53 kDa in hematopoietic cells. these 56- and 53-kDa proteins comigrated with proteins produced by in vitro translation or in vivo expression of the lynA and lynB cDNAs, respectively. The two forms had comparable in vitro kinase activities in immunoprecipitates and showed similar peptide patterns, with partial V8 digestion of the in vitro-phosphorylated proteins. The potential significance of the two lyn proteins is discussed.

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