Subjects -> CHEMISTRY (Total: 928 journals)
    - ANALYTICAL CHEMISTRY (59 journals)
    - CHEMISTRY (661 journals)
    - CRYSTALLOGRAPHY (23 journals)
    - ELECTROCHEMISTRY (28 journals)
    - INORGANIC CHEMISTRY (45 journals)
    - ORGANIC CHEMISTRY (47 journals)
    - PHYSICAL CHEMISTRY (65 journals)

CHEMISTRY (661 journals)            First | 1 2 3 4     

Showing 601 - 735 of 735 Journals sorted alphabetically
Scientific Reports     Open Access   (Followers: 85)
Sensors and Actuators B: Chemical     Hybrid Journal   (Followers: 18)
Sensors and Actuators Reports     Open Access   (Followers: 5)
Separation & Purification Reviews     Hybrid Journal   (Followers: 7)
Separation Science and Technology     Hybrid Journal   (Followers: 12)
Separations     Open Access   (Followers: 5)
Silicon Chemistry     Hybrid Journal   (Followers: 1)
Small Methods     Hybrid Journal   (Followers: 1)
Small Science     Open Access  
Small Structures     Hybrid Journal   (Followers: 1)
Smart Materials Research     Open Access   (Followers: 7)
SmartMat     Open Access  
Soft     Open Access  
Soft Nanoscience Letters     Open Access   (Followers: 1)
Solar RRL     Hybrid Journal  
Solid State Communications     Hybrid Journal   (Followers: 7)
Solid State Nuclear Magnetic Resonance     Hybrid Journal   (Followers: 3)
Solid State Sciences     Hybrid Journal   (Followers: 9)
Solvent Extraction and Ion Exchange     Hybrid Journal   (Followers: 7)
SPE Polymers     Open Access  
Spectral Analysis Review     Open Access  
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy     Hybrid Journal   (Followers: 15)
Spectrochimica Acta Part B: Atomic Spectroscopy     Hybrid Journal   (Followers: 17)
Spectroscopy and Spectral Analysis     Full-text available via subscription   (Followers: 1)
Starch / Staerke     Hybrid Journal   (Followers: 3)
Steel Research International     Hybrid Journal   (Followers: 22)
Structural Chemistry     Hybrid Journal   (Followers: 1)
Substantia     Open Access  
Supramolecular Chemistry     Hybrid Journal   (Followers: 5)
Supramolecular Materials     Full-text available via subscription   (Followers: 2)
Surface and Coatings Technology     Hybrid Journal   (Followers: 32)
Surface Science     Hybrid Journal   (Followers: 21)
Surface Science Reports     Full-text available via subscription   (Followers: 13)
Surfaces     Open Access   (Followers: 2)
Surfaces and Interfaces     Hybrid Journal   (Followers: 1)
Sustainable Chemical Processes     Open Access   (Followers: 3)
Sustainable Chemistry and Pharmacy     Full-text available via subscription   (Followers: 1)
Synfacts     Hybrid Journal   (Followers: 5)
Synlett     Hybrid Journal   (Followers: 47)
Synthesis     Hybrid Journal   (Followers: 56)
Talanta     Hybrid Journal   (Followers: 10)
Talanta Open     Full-text available via subscription   (Followers: 2)
Tecnología Química     Open Access  
Telematics and Informatics Reports     Full-text available via subscription   (Followers: 2)
Tenside Surfactants Detergents     Full-text available via subscription   (Followers: 2)
Tetrahedron     Hybrid Journal   (Followers: 80)
Tetrahedron Chem     Full-text available via subscription   (Followers: 2)
Tetrahedron Letters     Hybrid Journal   (Followers: 88)
The Alkaloids: Chemistry and Biology     Full-text available via subscription   (Followers: 1)
The All Results Journals : Chem     Open Access  
The Canadian Journal of Chemical Engineering     Hybrid Journal   (Followers: 5)
The Enzymes     Full-text available via subscription   (Followers: 2)
The Protein Journal     Hybrid Journal   (Followers: 5)
Theoretical and Experimental Chemistry     Hybrid Journal  
Theoretical Chemistry Accounts     Hybrid Journal   (Followers: 6)
Thermochimica Acta     Hybrid Journal   (Followers: 18)
Tip Revista Especializada en Ciencias Quimico-Biologicas     Open Access  
Topics in Current Chemistry     Hybrid Journal  
Toxicology International     Full-text available via subscription   (Followers: 5)
Toxicology Research     Partially Free   (Followers: 8)
Transition Metal Chemistry     Hybrid Journal   (Followers: 6)
Trends in Chemistry     Hybrid Journal  
Turkish Computational and Theoretical Chemistry     Open Access  
Ultrasonics Sonochemistry     Hybrid Journal   (Followers: 2)
Universal Journal of Chemistry     Open Access   (Followers: 1)
Vietnam Journal of Chemistry     Hybrid Journal  
Western Undergraduate Research Journal : Health and Natural Sciences     Open Access  
Wiley Interdisciplinary Reviews : Computational Molecular Science     Hybrid Journal   (Followers: 4)
World Journal of Chemical Education     Open Access   (Followers: 2)
X-Ray Spectrometry     Hybrid Journal   (Followers: 4)

  First | 1 2 3 4     

Similar Journals
Journal Cover
The Protein Journal
Journal Prestige (SJR): 0.451
Citation Impact (citeScore): 1
Number of Followers: 5  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1572-3887 - ISSN (Online) 1573-4943
Published by Springer-Verlag Homepage  [2469 journals]
  • Expression, Purification, Characterization and Cellular Uptake of MeCP2
           Variants

    • Free pre-print version: Loading...

      Abstract: Abstract The transcriptional regulator Methyl-CpG-binding protein 2 (MeCP2) is an intrinsically disordered protein, mutations in which, are implicated in the onset of Rett Syndrome, a severe and debilitating neurodevelopmental disorder. Delivery of this protein fused to the cell-penetrating peptide TAT could allow for the intracellular replenishment of functional MeCP2 and hence potentially serve as a prospective Rett Syndrome therapy. This work outlines the expression, purification and characterization of various TAT-MeCP2 constructs as well as their full-length and shortened eGFP fusion variants. The latter two constructs were used for intracellular uptake studies with subsequent analysis via western blotting and live-cell imaging. All purified MeCP2 samples exhibited high degree of stability and very little aggregation propensity. Full length and minimal TAT-MeCP2-eGFP were found to efficiently transduce into human dermal and murine fibroblasts and localize to cell nuclei. These findings clearly support the utility of MeCP2-based protein replacement therapy as a potential Rett Syndrome treatment option.
      PubDate: 2022-05-12
       
  • Expression and purification of recombinant human CCL5 and its biological
           characterization

    • Free pre-print version: Loading...

      Abstract: Abstract C-C motif chemokine ligand 5 (CCL5) is crucial in the tumor microenvironment. It has been previously reported to act as a key role in tumor invasion and metastasis. However, the function of exogenous CCL5 in ovarian cancer has not been well-characterized. The present study attempted to express and purify recombinant CCL5 protein and investigate the exogenous CCL5 in ovarian cancer cell proliferation. The human CCL5 was amplified and inserted into the pET-30a vectors for prokaryotic expression in Escherichia coli BL21. Soluble His-CCL5 was successfully expressed with 0.1 mmol/L of isopropyl-β-D-1-tiogalactopiranoside at 25 ℃ and purified by affinity chromatography. Additionally, methyl thiazolyl tetrazolium (MTT) assay demonstrated that CCL5 promotes ovarian cancer cell proliferation; increases the phosphorylation levels of extracellular-signal-regulated kinase and mitogen-activated protein kinase/ERK kinase, and increases the mRNA levels of Jun, NF-κB2, Nras, Relb, and Traf2. Furthermore, treatment with the MEK inhibitor reduced the Jun, NF-κB2, and Traf2 mRNA levels, indicating that exogenous CCL5 increased ovarian cancer cell proliferation, through MEK/ERK pathway activation, and Jun, NF-κB2, and Traf2 expression. The present study provided primary data for further studies to discover more CCL5 functions in ovarian cancer.
      PubDate: 2022-05-07
       
  • A Trade-off Between Thermostability and Binding Affinity of
           Anti-(4-hydroxy-3-nitrophenyl)Acetyl Antibodies During the Course of
           Affinity Maturation

    • Free pre-print version: Loading...

      Abstract: Abstract Somatic hypermutation (SHM) is one of the driving forces that increases antibody (Ab) affinity. We studied the effects of SHM on thermostability and affinity using three single-chain Fv fragments (scFvs) of anti-(4-hydroxy-3-nitrophenyl)acetyl Abs, namely 9TG, 9T7, and E11. 9TG has a germline structure that lacks SHM and is an ancestor of 9T7 with 11 mutations. E11, which has 21 mutations, is a mature Ab and has its own ancestor. The thermostabilities and antigen-Ab interactions were analyzed by circular dichroism (CD), differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC). Far-UV CD spectra showed that all scFvs were folded into a structure referred to as immunoglobulin-fold and were unfolded by heating at different melting temperatures. Comparison of thermodynamic parameters obtained from DSC and ITC revealed that the magnitude of stabilization free energy at 37 °C was in the order, 9TG > 9T7 > E11, while that of the free energy of interaction with antigen was 9TG < 9T7 < E11, suggesting that Abs make a trade-off between stability and affinity during affinity maturation.
      PubDate: 2022-04-30
       
  • Immobilization of Fungal Cellulases Highlighting β-Glucosidase:
           Techniques, Supports, Chemical, and Physical Changes

    • Free pre-print version: Loading...

      Abstract: Abstract β-Glucosidase is widely used in several industrial segments, among which we can highlight the pharmaceutical industry, beverages, biofuels, animal feed production, and the textile industry. The great applicability of this enzyme, associated with the high cost of its production, justifies the need to find ways to make its use economically viable on an industrial scale. Through enzyme immobilization, the biocatalyst can be reused more than once, without great impact on its catalytic activity, and higher operational and storage stabilities can be achieved as compared to the free form. Accordingly, this review brings information about different techniques and supports that have been studied in the immobilization of cellulases with a focus on β-glucosidase, as well as the application of these immobilized systems to supplement commercial mixtures.
      PubDate: 2022-04-19
       
  • Probing the Interactions Responsible for the Structural Stability of
           Trypanothione Reductase Through Computer Simulation and Biophysical
           Characterization

    • Free pre-print version: Loading...

      Abstract: Abstract With the necessity to develop antileishmanial drugs with substrate specificity, trypanothione reductase (TryR) has gained popularity in parasitology. TryR is unique to be present only in trypanosomatids and is functionally similar to glutathione in mammals. It protects against oxidative stress exerted by the host defense mechanism. The TryR enzyme is essential for the survival of Leishmania parasites in the host as it reduces trypanothione and aids in neutralizing hydrogen peroxide produced by the host macrophages during infection. Henceforth, it becomes vital to decipher their functional stability and behaviour in the presence of denaturants. Our study is focused on structural, functional and behavioural stability aspects of TryR with different concentrations of Urea, Guanidinium chloride, alcohol based compounds followed by extensive molecular dynamics simulations in a lipid bilayer system. The results obtained from the study reveal an interesting insight into the possible mechanisms of modulation of the structure, function and stability of the TryR protein.
      PubDate: 2022-04-02
       
  • Design and Analysis of a Mutant form of the Ice-Binding Protein from
           Choristoneura fumiferana

    • Free pre-print version: Loading...

      Abstract: Abstract Ice-binding proteins are expressed in the cells of some cold adapted organisms, helping them to survive at extremely low temperatures. One of the problems in studying such proteins is the difficulty of their isolation and purification. For example, eight cysteine residues in the cfAF (antifreeze protein from the eastern spruce budworm Choristoneura fumiferana) form intermolecular bridges during the overexpression of this protein. This impedes the process of the protein purification dramatically. To overcome this issue, in this work, we designed a mutant form of the ice-binding protein cfAFP, which is much easier to isolate that the wild-type protein. The mutant form named mIBP83 did not lose the ability to bind to ice surface. Besides, observation of the processes of freezing and melting of ice in the presence of mIBP83 showed that this protein affects the process of ice melting, increasing its melting temperature, and does not decrease the water freezing temperature.
      PubDate: 2022-04-02
       
  • Design of an Epitope-Based Peptide Vaccine Against the Major Allergen Amb
           a 11 Using Immunoinformatic Approaches

    • Free pre-print version: Loading...

      Abstract: Abstract Allergic diseases are a socially significant problem of global importance. The number of people suffering from pollen allergies has increased dramatically in recent decades. Pollen allergies affect up to 30% of the world population. Pollen of the common ragweed (Ambrosia artemisiifolia L.) is one of the most aggressive allergens in the world. We have used a series of immunoinformatics approaches to design an effective epitope-based vaccine, which might induce a competent immunity against a major allergen Amb a 11. CD8+ and CD4+ T-cell epitopes and their corresponding MHC restricted alleles were identified by prediction tools provided by immune epitope database (IEDB). Among T-cell epitopes, MHC class I peptide (GLMEPAFTYV) and MHC class II peptide (LVCFSFSLVLILGLV) were identified as most suitable. From all predicted B-cell epitopes, only one epitope (GKLVKFSEQQLVDC) containing sequence from the conserved region was chosen for next processing. Selected epitopes have been validated by molecular docking analysis. These epitopes showed a very strong binding affinity to MHC I molecule and MHC II molecule with binding energy scores − 729.3 and − 725.0 kcal/mole respectively. Performed experimental validation showed that only the MHC class II peptide (LVCFSFSLVLILGLV) can stimulate T cells from ragweed allergic patients and IgE antibodies specific to the ragweed pollen do not recognize this epitope. Therefore, this peptide could be potentially used as a vaccine against the major allergen Amb a 11. The B-cell epitope GKLVKFSEQQLVDC forms a stable complex with the IgE molecule (energy weighted score − 695,0 kcal/mole). Tested sera from patients with ragweed allergy showed that the ragweed specific IgE antibodies can bind to the identified B-cell epitope. Population coverage analysis was performed for CD8+ and CD4+ T-cell epitopes. It was predicted that CD4+ T-cell epitope (LVCFSFSLVLILGLV) covers 90.56% of the population of Europe and 99.36% of the world population. CD8+ T-cell epitope (GLMEPAFTYV) has a population coverage of 77.37% for Europe and 71.35% for all the world.
      PubDate: 2022-04-01
       
  • Equilibrium Between Dimeric and Monomeric Forms of Human Epidermal Growth
           Factor is Shifted Towards Dimers in a Solution

    • Free pre-print version: Loading...

      Abstract: Abstract An interplay between monomeric and dimeric forms of human epidermal growth factor (EGF) affecting its interaction with EGF receptor (EGFR) is poorly understood. While EGF dimeric structure was resolved at pH 8.1, the possibility of EGF dimerization under physiological conditions is still unclear. This study aimed to describe the oligomeric state of EGF in a solution at physiological pH value. With centrifugal ultrafiltration followed by blue native gel electrophoresis, we showed that synthetic human EGF in a solution at a concentration of 0.1 mg/ml exists mainly in the dimeric form at pH 7.4 and temperature of 37 °C, although a small fraction of its monomers was also observed. Based on bioinformatics predictions, we introduced the D46G substitution to examine if EGF C-terminal part is directly involved in the intermolecular interface formation of the observed dimers. We found a reduced ability of the resulting EGF D46G dimers to dissociate at temperatures up to 50 °C. The D46G substitution also increased the intermolecular antiparallel β-structure content within the EGF peptide in a solution according to the CD spectra analysis that was confirmed by HATR-FTIR results. Additionally, the energy transfer between Tyr and Trp residues was detected by fluorescence spectroscopy for the EGF D46G mutant, but not for the native EGF. This allowed us to suggest the elongation and rearrangement of the intermolecular β-structure that leads to the observed stabilization of EGF D46G dimers. The results imply EGF dimerization under physiological pH value and temperature and the involvement of EGF C-terminal part in this process.
      PubDate: 2022-03-29
       
  • Multi-catalytic Sites Inhibition of Bcl2 Induces Expanding of Hydrophobic
           Groove: A New Avenue Towards Waldenström Macroglobulinemia Therapy

    • Free pre-print version: Loading...

      Abstract: Abstract B-cell lymphoma 2 (Bcl2) is a key protein regulator of apoptosis. The hydrophobic groove in Bcl2 is a unique structural feature to this class of enzymes and found to have a profound impact on protein overall structure, function, and dynamics. Dynamics of the hydrophobic groove is an essential determinant of the catalytic activity of Bcl2, an implicated protein in Waldenström macroglobulinemia (WM). The mobility of α3–α4 helices around the catalytic site of the protein remains crucial to its activity. The preferential binding mechanisms of the multi-catalytic sites of the Bcl2 enzyme have been a subject of debate in the literature. In addition to our previous report on the same protein, herein, we further investigate the preferential binding modes and the conformational implications of Venetoclax-JQ1 dual drug binding at both catalytic active sites of Bcl2. Structural analysis revealed asymmetric α3–α4 helices movement with the expansion of the distance between the α3 and α4 helix in Venetoclax-JQ1 dual inhibition by 15.2% and 26.3%, respectively when compared to JQ1 and Venetoclax individual drug inhibition—resulting in remarkable widening of hydrophobic groove. Moreso, a reciprocal enhanced binding effect was observed: Venetoclax increased the binding affinity of JQ1 by 11.5%, while the JQ1 fostered the binding affinity of Venetoclax by 16.3% compared with individual inhibition of each drug. This divergence has also resulted in higher protein stability, and prominent correlated motions were observed with the least fluctuations and multiple van der Waals interactions. Findings offer vital conformational dynamics and structural mechanisms of enzyme-single ligand and enzyme-dual ligand interactions, which could potentially shift the current therapeutic protocol of Waldenström macroglobulinemia.
      PubDate: 2022-03-02
      DOI: 10.1007/s10930-022-10046-9
       
  • A Phagosomally Expressed Gene, rv0428c, of Mycobacterium tuberculosis
           Demonstrates Acetyl Transferase Activity and Plays a Protective Role Under
           Stress Conditions

    • Free pre-print version: Loading...

      Abstract: Abstract Mycobacterium tuberculosis genome is composed of several hypothetical gene products that need to be characterized for understanding the physiology of bacteria. Rv0428c was one of the 11 proteins exclusively identified within the phagosomal compartment of macrophages infected with mycobacteria and marked as hypothetical. The expression of rv0428c gene was upregulated under acidic and nutritive stress conditions in M. tuberculosis H37Ra, which was supported by potential sigma factor binding sites in the region upstream to the rv0428c gene. The bioinformatics analysis predicted it to be a GCN5- acetyl transferase, belonging to the Histone acetyl transferase (HAT) family. The docking analysis predicted formation of hydrogen bonds and hydrophobic interactions between donor acetyl-co-A and histone H3 tail region. rv0428c gene was cloned and expressed in E. coli. The protein was purified to homogeneity and was fairly stable over a wide range of pH 5.0–9.0 and temperature up to 40 °C. The HAT activity of purified Rv0428c was confirmed by in vitro acetylation assay using recombinant H3 histone expressed in bacteria as substrate, which increased in time dependent manner. The results suggested that it is the second confirmed acetyl transferase in M. tuberculosis H37Rv. Furthermore, rv0428c was over expressed in surrogate host M. smegmatis, which led to enhanced growth rate and altered colony morphology. The expression of rv0428c in M. smegmatis promoted the survival of bacteria under acidic and nutritive stress conditions. In conclusion, Rv0428c, a phagosomal acetyl transferase of M. tuberculosis, might be involved in survival under stress conditions.
      PubDate: 2022-02-17
      DOI: 10.1007/s10930-022-10044-x
       
  • The Influence of Codon Usage, Protein Abundance, and Protein Stability on
           Protein Evolution Vary by Evolutionary Distance and the Type of Protein

    • Free pre-print version: Loading...

      Abstract: Abstract In general, the evolutionary rate of proteins is not primarily related to protein and amino acid functions, and factors such as protein abundance, codon usage, and the protein’s TM are more important. To better understand the factors that affect protein evolution, E. coli MG1655 orthologs were compared to those in closely related bacteria and to more distantly related prokaryotes, eukaryotes, and archaea. Also, the evolution of different types of proteins was studied. The analyses indicate that the amino acid conservation of enzymes that do not use macromolecules (e.g. DNA, RNA, and proteins) as substrates and that carry out metabolic processes involving small molecules (i.e. small molecule enzymes) is different than other enzymes. For example, the small molecule enzymes have a lower percent identity than other enzymes when sequences from closely related bacteria are compared. Analyses indicate the lower percent identity is not a result of the amino acid or codon usage of the small molecule enzymes. The small molecule enzymes also don’t have a significantly lower protein abundance indicating that is also not likely an important factor driving differences in amino acid conservation. Analyses indicate different methods to measure the TM of proteins have different relationships between amino acid conservation over different evolutionary distances. In totality, the results demonstrate that the relationship between the factors thought to affect protein evolution (protein abundance, codon usage, and proteins TMs) and protein evolution are complex and depend on the factor, the organisms, and the type of proteins being analyzed.
      PubDate: 2022-02-11
      DOI: 10.1007/s10930-022-10045-w
       
  • Rifampicin Increases Expression of Plant Codon-Optimized Bacillus
           thuringiensis δ-Endotoxin Genes in Escherichia coli

    • Free pre-print version: Loading...

      Abstract: Abstract Transgenic crops expressing Cry δ-endotoxins of Bacillus thuringiensis for insect resistance have been commercialized worldwide with increased crop productivity and spectacular socioeconomic gains. To attain the enhanced level of protein expression, the cry genes have to be extensively modified for RNA stability and translation efficiency in the plant systems. However, such modifications in nucleotide sequences make it difficult to express the cry genes in Escherichia coli because of the presence of E. coli rare codons. Induction of gene expression through the T7 promoter/lac operator system results in high levels of transcription but limits the availability of activated tRNA corresponding to rare codons that leads to translation stalling at ribosomes. In the present study, an Isopropyl ß-D-1-thiogalactopyranoside (IPTG)/rifampicin combination-based approach was adopted to induce transcription of cry genes through T7 promoter/lac operator while simultaneously inhibiting the transcription of host genes through rifampicin. The results show that the IPTG/rifampicin combination leads to high-level expression of four plant codon-optimized cry genes (cry2Aa, cry1F, cry1Ac, and cry1AcF). Northern blot analysis of the cry gene expressing E. coli samples showed that the RNA expression level in the IPTG-induced samples was higher as compared to that in the IPTG/rifampicin-induced samples. Diet overlay insect bioassay of IPTG/rifampicin-induced Cry toxins with Helicoverpa armigera larvae showed bioactivity (measured as LC50) similar to the previous studies. The experiment has proved that recombinant synthetic gene (plant codon-optimized gene) with the combination of Rifampicin which inhibits DNA-dependent bacterial RNA polymerase and reduces the excessive baggage of translational machinery of the bacterial cell triggers the production of synthetic protein. Purification of protein using high pH buffer increases the solubility of the protein. Further, LC50 analysis shows no reduction of protein activity leads to protein stability. Further, purified cry toxin protein can be used for crop protection against pests and a purified form of the synthetic protein can be used for antibody production and perform the immunoassay for the identification of the transgenic plant. The crystallographic structure of synthetic protein could be used for interaction study with another insect to see insecticidal activity.
      PubDate: 2022-02-04
      DOI: 10.1007/s10930-022-10043-y
       
  • 16S rRNA Methyltransferases as Novel Drug Targets Against Tuberculosis

    • Free pre-print version: Loading...

      Abstract: Abstract Tuberculosis (TB) is an airborne infectious disease caused by Mycobacterium tuberculosis (M.tb) whose natural history traces back to 70,000 years. TB remains a major global health burden. Methylation is a type of post-replication, post-transcriptional and post-translational epi-genetic modification involved in transcription, translation, replication, tissue specific expression, embryonic development, genomic imprinting, genome stability and chromatin structure, protein protein interactions and signal transduction indicating its indispensable role in survival of a pathogen like M.tb. The pathogens use this epigenetic mechanism to develop resistance against certain drug molecules and survive the lethality. Drug resistance has become a major challenge to tackle and also a major concern raised by WHO. Methyltransferases are enzymes that catalyze the methylation of various substrates. None of the current TB targets belong to methyltransferases which provides therapeutic opportunities to develop novel drugs through studying methyltransferases as potential novel targets against TB. Targeting 16S rRNA methyltransferases serves two purposes simultaneously: a) translation inhibition and b) simultaneous elimination of the ability to methylate its substrates hence stopping the emergence of drug resistance strains. There are ~ 40 different rRNA methyltransferases and 13 different 16S rRNA specific methyltransferases which are unexplored and provide a huge opportunity for treatment of TB.
      PubDate: 2022-02-03
      DOI: 10.1007/s10930-021-10029-2
       
  • Purification and Characterization of Trehalase From Acyrthosiphon pisum, a
           Target for Pest Control

    • Free pre-print version: Loading...

      Abstract: Abstract Insect trehalases are glycoside hydrolases essential for trehalose metabolism and stress resistance. We here report the extraction and purification of Acyrthosiphon pisum soluble trehalase (ApTreh-1), its biochemical and structural characterization, as well as the determination of its kinetic properties. The protein has been purified by ammonium sulphate precipitation, first followed by an anion-exchange and then by an affinity chromatography. The SDS-PAGE shows a main band at 70 kDa containing two isoforms of ApTreh-1 (X1 and X2), identified by mass spectrometry and slightly contrasting in the C-terminal region. A phylogenetic tree, a multiple sequence alignment, as well as a modelled 3D-structure were constructed and they all reveal the ApTreh-1 similarity to other insect trehalases, i.e. the two signature motifs 179PGGRFRELYYWDTY192 and 479QWDFPNAWPP489, a glycine-rich region 549GGGGEY554, and the catalytic residues Asp336 and Glu538. The optimum enzyme activity occurs at 45 °C and pH 5.0, with Km and Vmax values of ~ 71 mM and ~ 126 µmol/min/mg, respectively. The present structural and functional characterization of soluble A. pisum trehalase enters the development of new strategies to control the aphids pest without significant risk for non-target organisms and human health.
      PubDate: 2022-02-01
      DOI: 10.1007/s10930-021-10032-7
       
  • Comparison of Periplasmic and Cytoplasmic Expression of Bovine
           Enterokinase Light Chain in E. coli

    • Free pre-print version: Loading...

      Abstract: Abstract Enterokinase enzyme is widely used in production of recombinant proteins. This enzyme is isolated from the intestine and recognizes a specific cleavage site (X↓LYS-ASP4). Several studies have been performed to produce recombinant active enterokinase. In this study, the coding sequence of bovine enteropeptidase light chain (bEKL) was isolated from Iranian Sarabi cattle and its expression was investigated in the periplasm and cytoplasm of E. coli by two different expression vectors, pET22 and pET32RH. RNA was extracted from the duodenum part of cattle, cDNA was amplified, the enterokinase light chain coding fragment was cloned and the expression was examined by SDS-PAGE analysis. The higher amounts of soluble enterokinase as a fusion with thioredoxin (Trx) were detected in cytoplasmic expression. The functional enterokinase was purified with a yield of 45 mg per litter by two-steps Ni2+ affinity chromatography. The effective activity of the enzyme implies that it can be produced in large scale for biotechnological applications.
      PubDate: 2022-01-29
      DOI: 10.1007/s10930-021-10033-6
       
  • Estrogen Sulfotransferase is Highly Expressed in Vascular Endothelial
           Cells Overlying Atherosclerotic Plaques

    • Free pre-print version: Loading...

      Abstract: Abstract Cytosolic estrogen sulfotransferase (SULT1E1) mainly catalyzes the sulfoconjugation and deactivation of estrogens that are known to exert potent anti-atherogenic effects. However, it remains unknown about the connection between SULT1E1 and atherosclerosis. Recently, we reported that SULT1E1 is highly expressed in the aorta with plaques of high fat-fed ApoE knockout (KO) mice (mouse model of atherosclerosis), and interacts with oxidized low-density lipoprotein (Ox-LDL) known as a major component of atherosclerotic lesions. In this study, immunohistochemical staining for SULT1E1 in the aorta of high fat-fed ApoE KO mice showed that SULT1E1 is detected in vascular endothelial cells overlying atherosclerotic plaques. Results from Western blotting showed that Ox-LDL induces the protein expression of both SULT1E1 and peroxisome proliferator-activated receptor (PPAR) γ in human umbilical vein endothelial cells (HUVECs), and then that a PPARγ antagonist GW9662, but not a PPARα antagonist GW6471, inhibited the protein expression of SULT1E1 induced by Ox-LDL. Moreover, GW9662 significantly increased the proliferation of HUVECs induced by Ox-LDL. Our results suggest that SULT1E1 and PPARγ, both of which are increased by Ox-LDL, may interact with each other, and then may reduce cooperatively Ox-LDL-induced proliferation of vascular endothelial cells overlying atherosclerotic plaques, leading to against atherosclerosis.
      PubDate: 2022-01-20
      DOI: 10.1007/s10930-022-10042-z
       
  • Metal Ions Bound to Prion Protein Affect its Interaction with Plasminogen
           Activation System

    • Free pre-print version: Loading...

      Abstract: Abstract Prion diseases are a group of neurodegenerative diseases, which can progress rapidly. Previous data have demonstrated that prion protein (PrP) stimulates activation of plasminogen (Plg) by tissue plasminogen activator (tPA). In this study, using spectroscopic method, we aimed to determine whether PrP’s role in activating Plg is influenced by metal binding. We also investigated the region in PrP involved in binding to tPA and Plg, and whether PrP in fibrillar form behaves the same way as PrP unbound to any metal ion i.e., apo-PrP. We investigated the effect of recombinant mouse PrP (residues 23-231) refolded with nickel, manganese, copper, and a variant devoid of any metal ions, on tPA-catalyzed Plg activation. Using mutant PrP (H95A, H110A), we also investigated whether histidine residues outside the octarepeat region in PrP, which is known to bind tPA and Plg, are also involved in their binding. We demonstrated that apo-PrP is most effective at stimulating Plg. PrP refolded with nickle or manganese behave similar to apo-PrP, and PrP refolded with copper is least effective. The mutant form of PrP did not stimulate Plg activation to the same degree as apo-PrP indicating that the histidine residues outside the octarepeat region are also involved in binding to tPA and Plg. Similarly, the fibrillar form of PrP was ineffective at stimulating Plg activation. Our data suggest that upon loss of copper specifically, a structural rearrangement of PrP occurs that exposes binding sites to Plg and tPA, enhancing the stimulation of Plg activation.
      PubDate: 2022-01-17
      DOI: 10.1007/s10930-021-10035-4
       
  • Ligand Based Virtual Screening Using Self-organizing Maps

    • Free pre-print version: Loading...

      Abstract: Abstract Conventional drug discovery methods rely primarily on in-vitro experiments with a target molecule and an extensive set of small molecules to choose the suitable ligand. The exploration space for the selected ligand being huge; this approach is highly time-consuming and requires high capital for facilitation. Virtual screening, a computational technique used to reduce this search space and identify lead molecules, can speed up the drug discovery process. This paper proposes a ligand-based virtual screening method using an artificial neural network called self-organizing map (SOM). The proposed work uses two SOMs to predict the active and inactive molecules separately. This SOM based technique can uniquely label a small molecule as active, inactive, and undefined as well. This can reduce the number of false positives in the screening process and improve recall; compared to support vector machine and random forest based models. Additionally, by exploiting the parallelism present in the learning and classification phases of a SOM, a graphics processing unit (GPU) based model yields much better execution time. The proposed GPU-based SOM tool can successfully evaluate a large number of molecules in training and screening phases. The source code of the implementation and related files are available at https://github.com/jayarajpbalakrishnan/2_SOM_SCREEN
      PubDate: 2022-01-13
      DOI: 10.1007/s10930-021-10030-9
       
  • Complete Model of Vinculin Suggests the Mechanism of Activation by Helical
           Super-Bundle Unfurling

    • Free pre-print version: Loading...

      Abstract: Abstract To shed light onto the activation mechanism of vinculin, we carried out a detailed refinement of chicken vinculin and compared it to the human protein which is greater than 95% identical. Refinement resulted in a complete and significantly improved model. This model includes important elements such as a pro-rich strap region (PRR) and C-terminus. The conformation of the PRR stabilized by its inter- and intra-molecular contacts shows a dynamic, but relatively stable motif that constitutes a docking platform for multiple molecules. The contact of the C-terminus with the PRR suggests that phosphorylation of Tyr1065 might control activation and membrane binding. Improved electron densities showed the presence of large solvent molecules such as phosphates/sulfates and a head-group of PIP2. The improved model allowed for a computational stability analysis to be performed by the program Corex/Best which located numerous hot-spots of increased and decreased stability. Proximity of the identified binding sites for regulatory partners involved in inducing or suppressing the activation of vinculin to the unstable elements sheds new light onto the activation pathway and differential activation. This stability analysis suggests that the activation pathway proceeds by unfurling of the super-bundle built from four bundles of helices without separation of the Vt region (840–1066) from the head. According to our mechanism, when activating proteins bind at the strap region a separation of N and C terminal bundles occurs, followed by unfurling of the super-bundle and flattening of the general shape of the molecule, which exposes the interaction sites for binding of auxiliary proteins.
      PubDate: 2022-01-10
      DOI: 10.1007/s10930-022-10040-1
       
  • Proteomic Characterization and Target Identification Against Streptococcus
           mutans Under Bacitracin Stress Conditions Using LC–MS and Subtractive
           Proteomics

    • Free pre-print version: Loading...

      Abstract: The aim of the present study, is to identify potential targets against the highly pathogenic bacteria Streptococcus mutans that causes dental caries as well as the deadly infection of endocarditis. The powerful and highly sensitive technique of liquid chromatography-mass spectrometry (LC–MS/MS) identified 321 proteins of S. mutans when grown under stressful conditions induced by the antibiotic bacitracin. These 321 proteins were subjected to the insilico method of subtractive proteomics to screen out potential targets by utilizing different analyses like CD-HIT, non-homologous sequence screening, KEGG pathway, essentiality screening, gut-flora non-homology, and codon usage analysis. A database of essential proteins was employed to find sequence homology of non-paralogous proteins to determine proteins which are essential for bacterial survival. Cellular localization analysis of the selected proteins was done to localize them inside the cell along with physico-chemical characterization and druggability analysis. Using computational tools, 22 proteins out of 321, that are functionally distinguishable from their human counterparts and passed the criterion of a potential therapeutic candidate were identified. The selected proteins comprise central energy metabolic proteins, virulence factors, proteins of the sortase family, and essentiality factors. The presented analyses identified proteins of the sortase family, which appear as key therapeutic targets against caries infection. These proteins regulate a number of virulence factors, thus can be simultaneously inhibited to obstruct multiple virulence pathways. Graphical
      PubDate: 2022-01-06
      DOI: 10.1007/s10930-021-10038-1
       
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
 


Your IP address: 3.235.176.80
 
Home (Search)
API
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-