scholarly journals In Silico Tools and Phosphoproteomic Software Exclusives

Processes ◽  
2019 ◽  
Vol 7 (12) ◽  
pp. 869 ◽  
Author(s):  
Piby Paul ◽  
Manikandan Muthu ◽  
Yojitha Chilukuri ◽  
Steve W. Haga ◽  
Sechul Chun ◽  
...  
Keyword(s):  
Clinical Research ◽  
Clinical Studies ◽  
In Silico ◽  
Cellular Localization ◽  
Intrinsic Activity ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Profound Impact ◽  
Bioinformatics Tools ◽  
First Time

Proteomics and phosphoproteomics have been emerging as new dimensions of omics. Phosphorylation has a profound impact on the biological functions and applications of proteins. It influences everything from intrinsic activity and extrinsic executions to cellular localization. This post-translational modification has been subjected to detailed study and has been an object of analytical curiosity with the advent of faster instrumentation. The major strength of phosphoproteomic research lies in the fact that it gives an overall picture of the workforce of the cell. Phosphoproteomics gives deeper insights into understanding the mechanism behind development and progression of a disease. This review for the first time consolidates the list of existing bioinformatics tools developed for phosphoproteomics. The gap between development of bioinformatics tools and their implementation in clinical research is highlighted. The challenge facing progress is ideally believed to be the interdisciplinary arena this field of research is associated with. For meaningful solutions and deliverables, these tools need to be implemented in clinical studies for obtaining answers to pharmacodynamic questions, saving time, costs and energy. This review hopes to invoke some thought in this direction.

scholarly journals Discovery of indole-modified aptamers for highly specific recognition of protein glycoforms

2021 ◽  
Author(s):  
Alex M. Yoshikawa ◽  
Alexandra Rangel ◽  
Trevor Feagin ◽  
Elizabeth M. Chun ◽  
Leighton Wan ◽  
...  
Keyword(s):  
Clinical Research ◽  
Cell Sorting ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Tertiary Structures ◽  
Affinity Reagents ◽  
Profound Impact ◽  
Specific Recognition ◽  
Wide Range ◽  
Protein Glycoforms

AbstractGlycosylation is one of the most abundant forms of post-translational modification, and can have a profound impact on a wide range of biological processes and diseases. Unfortunately, efforts to characterize such modifications in the context of basic and clinical research are severely hampered by the lack of affinity reagents that can differentiate protein glycoforms. This lack of reagents is largely due to the challenges associated with generating affinity reagents that can bind to particular glycan epitopes with robust affinity and specificity. In this work, we use a fluorescence-activated cell sorting (FACS)-based approach to generate and screen aptamers with indole-modified bases in an effort to isolate reagents that can differentiate between protein glycoforms. Using this approach, we were able to select multiple aptamers that exhibit strong selectivity for specific glycoforms of two different proteins, with the capacity to discriminate between molecules with identical tertiary structures that differ only in terms of their glycan modifications.

Exploring PLAC1 Structure and Underlying Mechanisms to Design a Derivative Vaccine Against Breast Cancer Progression; In-Silico Study

2020 ◽  
Vol 17 (5) ◽  
pp. 379-391
Author(s):  
Farzaneh Afzali ◽  
Parisa Ghahremanifard ◽  
Mohammad Mehdi Ranjbar ◽  
Mahdieh Salimi
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
In Silico ◽  
Tertiary Structure ◽  
Specific Antigen ◽  
Docking Simulation ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Underlying Mechanisms

Background: The tolerogenic homeostasis in Breast Cancer (BC) can be surpassed by rationally designed immune-encouraging constructs against tumor-specific antigens through immunoinformatics approach. Objective: Availability of high throughput data providing the underlying concept of diseases and awarded computational simulations, lead to screening the potential medications and strategies in less time and cost. Despite the extensive effects of Placenta Specific 1 (PLAC1) in BC progression, immune tolerance, invasion, cell cycle regulation, and being a tumor-specific antigen the fundamental mechanisms and regulatory factors were not fully explored. It is also worth to design an immune response inducing construct to surpass the hurdles of traditional anti-cancer treatments. Methods and Result: The study was initiated by predicting and modelling the PLAC1 secondary and tertiary structures and then engineering the fusion pattern of PLAC1 derived immunodominant predicted CD8+ and B-cell epitopes to form a multi-epitope immunogenic construct. The construct was analyzed considering the physiochemical characterization, safety, antigenicity, post-translational modification, solubility, and intrinsically disordered regions. After modelling its tertiary structure, proteinprotein docking simulation was carried out to ensure the attachment of construct with Toll-Like Receptor 4 (TLR4) as an immune receptor. To guarantee the highest expression of the designed construct in E. coli k12 as an expressional host, the codon optimization and in-silico cloning were performed. The PLAC1 related miRNAs in BC were excavated and validated through TCGA BC miRNA-sequencing and databases; the common pathways then were introduced as other probable mechanisms of PLAC1 activity. Conclusion: Regarding the obtained in-silico results, the designed anti-PLAC1 multi-epitope construct can probably trigger humoral and cellular immune responses and inflammatory cascades, therefore may have the potential of halting BC progression and invasion engaging predicted pathways.

scholarly journals Investigator Initiated Clinical Trials (IICTs): A Systematic Search in Registries to Compare the Czech Republic and Portugal in Terms of Funding Policies and Scientific Outcomes

2021 ◽  
Author(s):  
C. Madeira ◽  
L. Hořavová ◽  
F. dos Santos ◽  
J. R. Batuca ◽  
K. Nebeska ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Czech Republic ◽  
Clinical Research ◽  
Systematic Search ◽  
European Countries ◽  
The Czech Republic ◽  
Research Outcomes ◽  
Funding Policies ◽  
Funding Agencies ◽  
First Time

Abstract Objectives Clinical trials provide one of the highest levels of evidence to support medical practice. Investigator initiated clinical trials (IICTs) answer relevant questions in clinical practice that may not be addressed by industry. For the first time, two European Countries are compared in terms of IICTs, respective funders and publications, envisaging to inspire others to use similar indicators to assess clinical research outcomes. Methods A retrospective systematic search of registered IICTs from 2004 to 2017, using four clinical trials registries was carried out in two European countries with similar population, GDP, HDI and medical schools but with different governmental models to fund clinical research. Each IICT was screened for sponsors, funders, type of intervention and associated publications, once completed. Results IICTs involving the Czech Republic and Portugal were n = 439 (42% with hospitals as sponsors) and n = 328 (47% with universities as sponsors), respectively. The Czech Republic and Portuguese funding agencies supported respectively 61 and 27 IICTs. Among these, trials with medicinal products represent 52% in Czech Republic and 4% in Portugal. In the first, a higher percentage of IICTs’ publications in high impact factor journals with national investigators as authors was observed, when compared to Portugal (75% vs 15%). Conclusion The better performance in clinical research by Czech Republic might be related to the existence of specific and periodic funding for clinical research, although further data are still needed to confirm this relationship. In upcoming years, the indicators used herein might be useful to tracking clinical research outcomes in these and other European countries.

scholarly journals Extra-gastric expression of the proton pump H+/K+-ATPase in the gills and kidney of the teleost Oreochromis niloticus

2020 ◽  
Vol 223 (16) ◽  
pp. jeb214890
Author(s):  
Ebtesam Ali Barnawi ◽  
Justine E. Doherty ◽  
Patrícia Gomes Ferreira ◽  
Jonathan M. Wilson
Keyword(s):  
Oreochromis Niloticus ◽  
Cellular Localization ◽  
Ex Vivo ◽  
Uptake Inhibition ◽  
Custom Made ◽  
Potassium Regulation ◽  
Immunohistochemical Techniques ◽  
Collecting Tubules ◽  
First Time

ABSTRACTPotassium regulation is essential for the proper functioning of excitable tissues in vertebrates. The H+/K+-ATPase (HKA), which is composed of the HKα1 (gene: atp4a) and HKβ (gene: atp4b) subunits, has an established role in potassium and acid–base regulation in mammals and is well known for its role in gastric acidification. However, the role of HKA in extra-gastric organs such as the gill and kidney is less clear, especially in fishes. In the present study in Nile tilapia, Oreochromis niloticus, uptake of the K+ surrogate flux marker rubidium (Rb+) was demonstrated in vivo; however, this uptake was not inhibited with omeprazole, a potent inhibitor of the gastric HKA. This contrasts with gill and kidney ex vivo preparations, where tissue Rb+ uptake was significantly inhibited by omeprazole and SCH28080, another gastric HKA inhibitor. The cellular localization of this pump in both the gill and kidney was demonstrated using immunohistochemical techniques with custom-made antibodies specific for Atp4a and Atp4b. Antibodies against the two subunits showed the same apical ionocyte distribution pattern in the gill and collecting tubules/ducts in the kidney. Atp4a antibody specificity was confirmed by western blotting. RT-PCT was used to confirm the expression of both subunits in the gill and kidney. Taken together, these results indicate for the first time K+ (Rb+) uptake in O. niloticus and that HKA is implicated, as shown through the ex vivo uptake inhibition by omeprazole and SCH28080, verifying a role for HKA in K+ absorption in the gill's ionocytes and collecting tubule/duct segments of the kidney.

scholarly journals In Vitro,In Vivo, and Clinical Studies of Tedizolid To Assess the Potential for Peripheral or Central Monoamine Oxidase Interactions

2013 ◽  
Vol 57 (7) ◽  
pp. 3060-3066 ◽  
Author(s):  
S. Flanagan ◽  
K. Bartizal ◽  
S. L. Minassian ◽  
E. Fang ◽  
P. Prokocimer
Keyword(s):  
Blood Pressure ◽  
Monoamine Oxidase ◽  
Clinical Research ◽  
Systolic Blood Pressure ◽  
Clinical Studies ◽  
Geometric Mean ◽  
Interaction Study ◽  
Mao B ◽  
Mao A

ABSTRACTTedizolid phosphate is a novel oxazolidinone prodrug whose active moiety, tedizolid, has improved potency against Gram-positive pathogens and pharmacokinetics, allowing once-daily administration. Given linezolid warnings for drug-drug and drug-food interactions mediated by monoamine oxidase (MAO) inhibition, including sporadic serotonergic toxicity, these studies evaluated tedizolid for potential MAO interactions.In vitro, tedizolid and linezolid were reversible inhibitors of human MAO-A and MAO-B; the 50% inhibitory concentration (IC50) for tedizolid was 8.7 μM for MAO-A and 5.7 μM for MAO-B and 46.0 and 2.1 μM, respectively, with linezolid. Tedizolid phosphate was negative in the mouse head twitch model of serotonergic activity. Two randomized placebo-controlled crossover clinical studies assessed the potential of 200 mg/day tedizolid phosphate (at steady state) to enhance pressor responses to coadministered oral tyramine or pseudoephedrine. Sensitivity to tyramine was determined by comparing the concentration of tyramine required to elicit a ≥30-mmHg increase in systolic blood pressure (TYR30) when administered with placebo versus tedizolid phosphate. The geometric mean tyramine sensitivity ratio (placebo TYR30/tedizolid phosphate TYR30) was 1.33; a ratio of ≥2 is considered clinically relevant. In the pseudoephedrine study, mean maximum systolic blood pressure was not significantly different when pseudoephedrine was coadministered with tedizolid phosphate versus placebo. In summary, tedizolid is a weak, reversible inhibitor of MAO-A and MAO-Bin vitro. Provocative testing in humans and animal models failed to uncover significant signals that would suggest potential for hypertensive or serotonergic adverse consequences at the therapeutic dose of tedizolid phosphate. Clinical studies are registered atwww.clinicaltrials.govas NCT01539473 (tyramine interaction study conducted at Covance Clinical Research Center, Evansville, IN) and NCT01577459 (pseudoephedrine interaction study conducted at Vince and Associates Clinical Research, Overland Park, KS).

Finding appropriate signal peptides for secretory production of recombinant glucarpidase: an in silico method

2021 ◽  
Vol 15 ◽  
Author(s):  
Omid Vakili ◽  
Seyyed Hossein Khatami ◽  
Amir Maleksabet ◽  
Ahmad Movahedpour ◽  
Saeed Ebrahimi Fana ◽  
...  
Keyword(s):  
Signal Peptide ◽  
In Silico ◽  
Cellular Localization ◽  
Clinical Aspects ◽  
Bioinformatics Analyses ◽  
E Coli ◽  
Accuracy And Precision ◽  
Extracellular Compartment ◽  
Human Disorders ◽  
High Doses

Aims: Bioinformatics analysis of suitable signal peptide for recombinant glucarpidase. Background: Methotrexate (MTX) is a general chemotherapeutic agent utilized to treat a variety of malignancies., woefully, its high doses can cause nephrotoxicity and subsequent defect in the process of MTX excretion. The recombinant form of glucarpidase, is produced by engineered E. coli and is a confirmed choice to overcoming this problem. Objective: In the present study, in silico analyses were performed to select suitable SPs for the secretion of recombinant glucarpidase in E. coli. Methods: The signal peptide website and UniProt database were employed to collect the SPs and protein sequences. In the next step, SignalP-5.0 helped us to predict the SPs and the position of cleavage sites. Moreover, physicochemical properties and solubility were evaluated using ProtParam and Protein-sol online software, and finally, ProtCompB was used to predict the final sub-cellular localization. Results: Luckily, all SPs could form soluble fusion proteins. At last, it was found that PPB and TIBA could translocate the glucarpidase into the extracellular compartment. Conclusion: This study showed that there are only 2 applicable SPs for the extracellular translocation of glucarpidase. Although the findings were remarkable with high degrees of accuracy and precision based on the utilization of bioinformatics analyses, additional experimental assessments are required to confirm and validate it. Recent patents revealed several inventions related to the clinical aspects of vaccine peptide against human disorders.

scholarly journals Phosphoregulation of the intracellular termini of K+-Cl− cotransporter 2 (KCC2) enables flexible control of its activity

2018 ◽  
Vol 293 (44) ◽  
pp. 16984-16993 ◽  
Author(s):  
Antje Cordshagen ◽  
Wiebke Busch ◽  
Michael Winklhofer ◽  
Hans Gerd Nothwang ◽  
Anna-Maria Hartmann
Keyword(s):  
Intrinsic Activity ◽  
Hek 293 ◽  
Flexible Control ◽  
Mediated Effects ◽  
293 Cells ◽  
Bona Fide ◽  
Graded Activity ◽  
First Time ◽  
Increased Activity

The pivotal role of K+-Cl− cotransporter 2 (KCC2) in inhibitory neurotransmission and severe human diseases fosters interest in understanding posttranslational regulatory mechanisms such as (de)phosphorylation. Here, the regulatory role of the five bona fide phosphosites Ser31, Thr34, Ser932, Thr999, and Thr1008 was investigated by the use of alanine and aspartate mutants. Tl+-based flux analyses in HEK-293 cells demonstrated increased transport activity for S932D (mimicking phosphorylation) and T1008A (mimicking dephosphorylation), albeit to a different extent. Increased activity was due to changes in intrinsic activity, as it was not caused by increased cell-surface abundance. Substitutions of Ser31, Thr34, or Thr999 had no effect. Additionally, we show that the indirect actions of the known KCC2 activators staurosporine and N-ethylmaleimide (NEM) involved multiple phosphosites. S31D, T34A, S932A/D, T999A, or T1008A/D abrogated staurosporine mediated stimulation, and S31A, T34D, or S932D abolished NEM-mediated stimulation. This demonstrates for the first time differential effects of staurosporine and NEM on KCC2. In addition, the staurosporine-mediated effects involved both KCC2 phosphorylation and dephosphorylation with Ser932 and Thr1008 being bona fide target sites. In summary, our data reveal a complex phosphoregulation of KCC2 that provides the transporter with a toolbox for graded activity and integration of different signaling pathways.

scholarly journals Fluorescent glycan fingerprinting of SARS2 spike proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhengliang L. Wu ◽  
James M. Ertelt
Keyword(s):  
Sialic Acid ◽  
Gel Electrophoresis ◽  
Fluorescent Labeling ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Quick Method ◽  
New Techniques ◽  
S Protein ◽  
Sds Page ◽  
Novel Coronavirus

AbstractGlycosylation is the most common post-translational modification and has myriad of biological functions. However, glycan analysis has always been a challenge. Here, we would like to present new techniques for glycan fingerprinting based on enzymatic fluorescent labeling and gel electrophoresis. The method is illustrated on SARS2 spike (S) glycoproteins. SARS2, a novel coronavirus and the causative agent of the COVID-19 pandemic, has had significant social and economic impacts since the end of 2019. To obtain the N-glycan fingerprint of an S protein, glycans released from the protein are first labeled through enzymatic incorporation of fluorophore-conjugated sialic acid or fucose, then separated by SDS-PAGE, and finally visualized with a fluorescent imager. To identify the labeled glycans of a fingerprint, glycan standards and glycan ladders are enzymatically generated and run alongside the samples as references. By comparing the mobility of a labeled glycan to that of a glycan standard, the identity of glycans maybe determined. O-glycans can also be fingerprinted. Due to the lack of an enzyme for broad O-glycan release, O-glycans on the S protein can be labeled with fluorescent sialic acid and digested with trypsin to obtain labeled glycan peptides that are then separated by gel electrophoresis. Glycan fingerprinting could serve as a quick method for globally assessing the glycosylation of a specific glycoprotein.

scholarly journals A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260054
Author(s):  
Safayat Mahmud Khan ◽  
Ar-Rafi Md. Faisal ◽  
Tasnin Akter Nila ◽  
Nabila Nawar Binti ◽  
Md. Ismail Hosen ◽  
...  
Keyword(s):  
Protein Structure ◽  
T Cell ◽  
Protein Stability ◽  
In Silico ◽  
Catalytic Domain ◽  
Cell Lymphoma ◽  
Computational Study ◽  
Solvent Accessibility ◽  
T Cell Lymphoma ◽  
Post Translational Modification

PLCG1 gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs in PLCG1 were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5’ and 3’ untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. This in silico analysis has provided a structured dataset of PLCG1 gene for further in vivo researches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.

Sign in / Sign up

Export Citation Format

Share Document