Subjects -> BIOLOGY (Total: 3174 journals)
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BIOLOGY (1491 journals)            First | 1 2 3 4 5 6 7 8 | Last

Showing 1401 - 1600 of 1720 Journals sorted alphabetically
The Condor     Full-text available via subscription   (Followers: 28)
The Enzymes     Full-text available via subscription   (Followers: 2)
The FASEB Journal     Hybrid Journal   (Followers: 23)
The Herpetological Journal     Full-text available via subscription   (Followers: 6)
The International Journal of Advanced Manufacturing Technology     Hybrid Journal   (Followers: 6)
The Journal of Technology Transfer     Hybrid Journal   (Followers: 15)
The Knee     Hybrid Journal   (Followers: 13)
The Lancet Microbe     Open Access   (Followers: 1)
The Lichenologist     Hybrid Journal   (Followers: 4)
The Nucleus     Hybrid Journal  
The Plant Cell     Full-text available via subscription   (Followers: 23)
The Protein Journal     Hybrid Journal   (Followers: 5)
Theoretical Biology and Medical Modelling     Open Access   (Followers: 1)
Theoretical Population Biology     Hybrid Journal   (Followers: 10)
Therya     Open Access  
Tissue and Cell     Hybrid Journal  
Tissue Engineering and Regenerative Medicine     Hybrid Journal   (Followers: 10)
Tissue Engineering Part A     Hybrid Journal   (Followers: 10)
Tissue Engineering Part B: Reviews     Hybrid Journal   (Followers: 8)
Tissue Engineering Part C: Methods     Hybrid Journal   (Followers: 8)
Toxicological Research     Hybrid Journal  
Toxicology in Vitro     Hybrid Journal   (Followers: 11)
Toxicon     Hybrid Journal   (Followers: 5)
Toxicon : X     Open Access  
Traffic     Hybrid Journal   (Followers: 5)
Transactions of the Royal Society of South Australia     Hybrid Journal  
Transcription     Full-text available via subscription   (Followers: 2)
Transgenic Research     Hybrid Journal   (Followers: 1)
Translational Psychiatry     Open Access   (Followers: 14)
Transportation Planning and Technology     Hybrid Journal   (Followers: 8)
Tree Genetics & Genomes     Hybrid Journal   (Followers: 4)
Trees     Hybrid Journal   (Followers: 3)
Trends in Bioinformatics     Open Access   (Followers: 17)
Trends in Biotechnology     Hybrid Journal   (Followers: 141)
Trends in Cell Biology     Full-text available via subscription   (Followers: 37)
Trends in Microbiology     Full-text available via subscription   (Followers: 42)
Trends in Molecular Sciences     Open Access   (Followers: 2)
Trends in Parasitology     Full-text available via subscription   (Followers: 10)
Trends in Plant Science     Full-text available via subscription   (Followers: 20)
Tropical Drylands     Open Access  
Tropical Ecology     Hybrid Journal  
Tropical Freshwater Biology     Full-text available via subscription  
Tunnelling and Underground Space Technology     Hybrid Journal   (Followers: 10)
Turkish Journal of Agricultural and Natural Science / Türk Tarım ve Doğa Bilimleri Dergisi     Open Access  
Ukrainian Journal of Ecology     Open Access  
Ultrasound in Medicine & Biology     Hybrid Journal   (Followers: 10)
UNED Research Journal / Cuadernos de Investigación UNED     Open Access  
Uniciencia     Open Access  
Universal Journal of Biomedical Engineering     Open Access  
UNM Journal of Biological Education     Open Access  
Unnes Journal of Biology Education     Open Access  
Vakuum in Forschung und Praxis     Hybrid Journal   (Followers: 2)
Vascular Cell     Open Access  
Vegetation Classification and Survey     Open Access  
Victorian Naturalist, The     Full-text available via subscription   (Followers: 2)
View     Open Access   (Followers: 3)
Virchows Archiv     Hybrid Journal   (Followers: 3)
Virologica Sinica     Hybrid Journal  
Virology Journal     Open Access   (Followers: 5)
Virulence     Open Access   (Followers: 1)
Virus Evolution     Open Access   (Followers: 3)
Virus Genes     Hybrid Journal   (Followers: 1)
Virus Research     Hybrid Journal   (Followers: 1)
Visnyk of Dnipropetrovsk University. Biology, ecology     Open Access   (Followers: 1)
Visnyk of Dnipropetrovsk University. Biology, medicine     Open Access  
VITIS : Journal of Grapevine Research     Open Access   (Followers: 1)
Walailak Journal of Science and Technology     Open Access  
Water Biology and Security     Full-text available via subscription   (Followers: 5)
Web Ecology     Open Access   (Followers: 3)
Webbia : Journal of Plant Taxonomy and Geography     Hybrid Journal  
West African Journal of Applied Ecology     Open Access  
Western Undergraduate Research Journal : Health and Natural Sciences     Open Access  
Wetlands     Hybrid Journal   (Followers: 25)
Wildlife Biology     Open Access   (Followers: 16)
Wildlife Research     Hybrid Journal   (Followers: 17)
Wiley Interdisciplinary Reviews - System Biology and Medicine     Hybrid Journal   (Followers: 2)
Wiley Interdisciplinary Reviews : Developmental Biology     Hybrid Journal   (Followers: 2)
Wiley Interdisciplinary Reviews : Membrane Transport and Signaling     Hybrid Journal  
Wiley Interdisciplinary Reviews : RNA     Hybrid Journal   (Followers: 3)
World Mycotoxin Journal     Hybrid Journal   (Followers: 3)
Xenobiotica     Hybrid Journal   (Followers: 7)
Yeast     Hybrid Journal   (Followers: 8)
Zebrafish     Hybrid Journal  
Zeitschrift für Evidenz, Fortbildung und Qualität im Gesundheitswesen     Hybrid Journal   (Followers: 6)
Zitteliana     Open Access  
Zygote     Hybrid Journal  

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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]
  • Investigating a putative transcriptional regulatory protein encoded by
           Rv1719 gene of Mycobacterium tuberculosis

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      Abstract: Abstract Mycobacterium tuberculosis, the causative agent of tuberculosis, demonstrates immense plasticity with which it adapts to a highly dynamic and hostile host environment. This is facilitated by a web of signalling pathways constantly modulated by a multitude of proteins that regulate the flow of genetic information inside the pathogen. Transcription factors (TFs) belongs to one such family of proteins that modulate the signalling by regulating the abundance of proteins at the transcript level. In the current study, we have characterized the putative transcriptional regulatory protein encoded by the Rv1719 gene of Mycobacterium tuberculosis. This TF belongs to the IclR family of proteins with orthologs found in both bacterial and archaeal species. We cloned the Rv1719 gene into the pET28a expression vector and performed heterologous expression of the recombinant protein with E coli as the host. Further, optimization of the purification protocol by affinity chromatography and characterization of proteins for their functional viability has been demonstrated using various biochemical and/or biophysical approaches. Scale-up of purification yielded approximately 30 mg of ~ 28 kDa protein per litre of culture. In-silico protein domain analysis of Rv1719 protein predicted the presence of the helix-turn-helix (HTH) domain suggesting its ability to bind DNA sequence and modulate transcription; a hallmark of a transcriptional regulatory protein. Further, by performing electrophoretic mobility shift assay (EMSA) we demonstrated that the protein binds to a specific DNA fragment harboring the probable binding site of one of the predicted promoters.
      PubDate: 2022-06-17
       
  • Biochemical Characterization of Novel Phenylalanine Ammonia-Lyase from
           Spirulina CPCC-695

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      Abstract: Abstract Phenylalanine ammonia lyase (PAL) catalyzes the deamination of phenylalanine to cinnamic acid and ammonia. It plays a crucial role in the formation of secondary metabolites through the phenylpropanoid pathway. Recently there has been growing interest in exploring the biochemical properties of PAL for its clinical and commercial applications. PAL as a key component has been used in metabolic engineering and synthetic biology. Due to its high substrate specificity and catalytic efficacy, PAL has opened a new area of interest in the biomedical field. PAL has been frequently used in the enzyme replacement therapy of phenylketonuria, cancer treatment and microbial production of l-phe the precursor of noncalorific sweetener aspartame (Methyl l-α-aspartyl-l-phenylalaninate), antimicrobial and health supplements. PAL occurs in few plants, fungi, bacteria, and cyanobacteria. The present investigation is a preliminary study in which an attempt has been made for the isolation, partial purification, and biochemical characterization of PAL (crude and partially purified) from Spirulina CPCC-695. Partially purified PAL exhibited higher enzymatic activity and protein content than the crude enzyme. Molecular weight of the crude and partially purified PAL was ~ 66 kDa. The optimum temperature and pH for PAL activity was observed as 30 ℃ and 8.0 respectively. l-Phe was the most preferred substrate (100 mM) whereas gallic acid showed maximum inhibition of PAL activity. Enzyme kinetics suggested good catalytic efficacy of the PAL enzyme and affinity towards substrate. Both the enzyme (crude and partially purified) showed less than 5% haemolysis suggesting the biocompatible nature of PAL.
      PubDate: 2022-06-17
       
  • Immobilization of Ene Reductase in Polyvinyl Alcohol Hydrogel

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      Abstract: Abstract In this study, ene reductase (ER) was entrapped in polyvinyl alcohol hydrogel, adsorbed on montmorillonite and immobilized covalently on glutaraldehyde activated 3-aminopropyl-functionalized silica gel. Although protein recovery yields were at least 85% for adsorption and covalent immobilization, only the encapsulated ER showed activity. The activity of free and entrapped ER preparations was measured by following NADPH-dependent reduction of 2-cyclohexen-1-one. The both protein recovery and activity recovery yields were calculated as 100% when 1 mg protein was used for immobilization. The both free and entrapped ER preparations showed the same optimum pH and temperature as 7.0 and 30 °C, respectively. The entrapped ER showed 34.4-fold more thermal stability than that of the free ER at 30 °C. Michaelis-Menten constant and maximum velocity values were 0.25 mM and 1.2 U/mg protein, respectively for the free ER towards 2-cyclohexen-1-one. The corresponding values were 1.5 mM and 0.9 U/mg protein for the entrapped ER. The results of time-course reduction of 2-cyclohexen-1-one showed that the entrapped ER catalyzed the reaction as effectively as the free ER. The entrapped ER remained 85% of its initial activity after 10 reused cycles.
      PubDate: 2022-06-17
       
  • Biophysical and Computational Approaches to Unravel pH-Dependent
           Conformational Change of PspA Assist PspA-PspF Complex Formation in
           Yersinia enterocolitica

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      Abstract: Abstract In enteropathogen, Yersinia enterocolitica, the genes encoding phage shock proteins are organized in an operon (pspA-E), which is activated at the various types of cellular stress (i.e., extracytoplasmic or envelop stress) whereas, PspA negatively regulates PspF, a transcriptional activator of pspA-E and pspG, and is also involved in other cellular machinery maintenance processes. The exact mechanism of association and dissociation of PspA and PspF during the stress response is not entirely clear. In this concern, we address conformational change of PspA in different pH conditions using various in-silico and biophysical methods. At the near-neutral pH, CD and FTIR measurements reveal a ß-like conformational change of PspA; however, AFM measurement indicates the lower oligomeric form at the above-mentioned pH. Additionally, the results of the MD simulation also support the conformational changes which indicate salt-bridge strength takes an intermediate position compared to other pHs. Furthermore, the bio-layer interferometry study confirms the stable complex formation that takes place between PspA and PspF at the near-neutral pH. It, thus, appears that PspA conformational change in adverse pH conditions abandons PspF from having a stable complex with it, and thus, the latter can act as a trans-activator. Taken together, it seems that PspA alone can transduce adverse signals by changing its conformation.
      PubDate: 2022-06-16
       
  • SAXS Analysis and Characterization of Anticancer Activity of PNP-UDP
           Family Protein from Putranjiva roxburghii

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      Abstract: Abstract A class of plant defense and storage proteins, including Putranjiva roxburghii PNP protein (PRpnp), belongs to PNP-UDP family. The PRpnp and related plant proteins contain a disrupted PNP-UDP domain as revealed in previous studies. In PRpnp, the insert disrupting the domain contains the trypsin inhibitory site. In the present work, we analyzed native PRpnp (nPRpnp) complex formation with trypsin and inosine using SAXS experiments and established its dual functionality. Results indicated a relatively compact nPRpnp:Inosine structure, whereas trypsin complex showed conformational changes/flexibility. nPRpnp also exhibited a strong anti-cancer activity toward breast cancer (MCF-7), prostate cancer (DU-145) and hepatocellular carcinoma (HepG2) cell lines. MCF-7 and DU-145 were more sensitive to nPRpnp treatment as compared to HepG2. However, nPRpnp treatment showed no effect on the viability of HEK293 cells indicating that nPRpnp is specific for targeting the viability of only cancer cells. Further, acridine orange, DAPI and DNA fragmentation studies showed that cytotoxic effect of nPRpnp is mediated through induction of apoptosis as evident from the apoptosis-associated morphological changes and nuclear fragmentation observed after PRpnp treatment of cancer cells. These results suggest that PRpnp has the potential to be used as an anticancer agent. This is first report of anticancer activity as well as SAXS-based analysis for a PNP enzyme with trypsin inhibitory activity.
      PubDate: 2022-06-08
       
  • Role of ionic liquids on stabilization of therapeutic proteins and model
           proteins

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      Abstract: Abstract Ionic liquids (ILs) exhibit potential as excipients to stabilize proteins in solutions. This mini-review is not a detailed reference book on ILs, rather a brief overview of the main achievements published in the literature on their effect on protein aggregation, unfolding, structural and thermal stability, and activity. The main focus of the manuscript is three widely studied groups of ionic liquids: imidazolium-, cholinium- and alkylammonium-based and their effect on the model and therapeutic proteins.
      PubDate: 2022-06-04
       
  • Neglected N-Truncated Amyloid-β Peptide and Its Mixed Cu–Zn
           Complexes

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      Abstract: Amyloid-β (Aβ) peptides are involved in Alzheimer’s disease (AD) development. The interactions of these peptides with copper and zinc ions also seem to be crucial for this pathology. Although Cu(II) and Zn(II) ions binding by Aβ peptides has been scrupulously investigated, surprisingly, this phenomenon has not been so thoroughly elucidated for N-truncated Aβ4−x—probably the most common version of this biomolecule. This negligence also applies to mixed Cu–Zn complexes. From the structural in silico analysis presented in this work, it appears that there are two possible mixed Cu–Zn(Aβ4−x) complexes with different stoichiometries and, consequently, distinct properties. The Cu–Zn(Aβ4−x) complex with 1:1:1 stoichiometry may have a neuroprotective superoxide dismutase-like activity. On the other hand, another mixed 2:1:2 Cu–Zn(Aβ4−x) complex is perhaps a seed for toxic oligomers. Hence, this work proposes a novel research direction for our better understanding of AD development. Graphical
      PubDate: 2022-06-01
       
  • Expression, Purification, Characterization and Cellular Uptake of MeCP2
           Variants

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      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

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      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

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      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

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      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
      DOI: 10.1007/s10930-022-10048-7
       
  • Probing the Interactions Responsible for the Structural Stability of
           Trypanothione Reductase Through Computer Simulation and Biophysical
           Characterization

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      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
      DOI: 10.1007/s10930-022-10052-x
       
  • Design and Analysis of a Mutant form of the Ice-Binding Protein from
           Choristoneura fumiferana

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      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
      DOI: 10.1007/s10930-022-10049-6
       
  • Design of an Epitope-Based Peptide Vaccine Against the Major Allergen Amb
           a 11 Using Immunoinformatic Approaches

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      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
      DOI: 10.1007/s10930-022-10050-z
       
  • Equilibrium Between Dimeric and Monomeric Forms of Human Epidermal Growth
           Factor is Shifted Towards Dimers in a Solution

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      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
      DOI: 10.1007/s10930-022-10051-y
       
  • Multi-catalytic Sites Inhibition of Bcl2 Induces Expanding of Hydrophobic
           Groove: A New Avenue Towards Waldenström Macroglobulinemia Therapy

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      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

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      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

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      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

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      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
       
  • Estrogen Sulfotransferase is Highly Expressed in Vascular Endothelial
           Cells Overlying Atherosclerotic Plaques

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      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
       
 
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