Subjects -> CHEMISTRY (Total: 928 journals)
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CHEMISTRY (661 journals)            First | 1 2 3 4     

Showing 601 - 735 of 735 Journals sorted alphabetically
Russian Journal of Bioorganic Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of Coordination Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of General Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of Inorganic Chemistry     Hybrid Journal  
Sainstek : Jurnal Sains dan Teknologi     Open Access  
Science China Chemistry     Hybrid Journal   (Followers: 2)
Science Talks     Full-text available via subscription   (Followers: 4)
Sciences & Technologie A : sciences exactes     Open Access  
Scientific Journal of Frontier Chemical Development     Open Access   (Followers: 2)
Scientific Reports     Open Access   (Followers: 82)
Sensors and Actuators B: Chemical     Hybrid Journal   (Followers: 17)
Sensors and Actuators Reports     Open Access   (Followers: 7)
Separation & Purification Reviews     Hybrid Journal   (Followers: 3)
Separation Science and Technology     Hybrid Journal   (Followers: 7)
Separations     Open Access   (Followers: 5)
Silicon Chemistry     Hybrid Journal   (Followers: 1)
Small Methods     Hybrid Journal   (Followers: 1)
Small Science     Open Access   (Followers: 13)
Small Structures     Hybrid Journal   (Followers: 4)
Smart Materials Research     Open Access   (Followers: 7)
SmartMat     Open Access   (Followers: 1)
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: 8)
Solvent Extraction and Ion Exchange     Hybrid Journal   (Followers: 7)
SPE Polymers     Open Access   (Followers: 1)
Spectral Analysis Review     Open Access  
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy     Hybrid Journal   (Followers: 14)
Spectrochimica Acta Part B: Atomic Spectroscopy     Hybrid Journal   (Followers: 16)
Spectroscopy and Spectral Analysis     Full-text available via subscription   (Followers: 1)
Starch / Staerke     Hybrid Journal   (Followers: 2)
Steel Research International     Hybrid Journal   (Followers: 23)
Structural Chemistry     Hybrid Journal   (Followers: 1)
Substantia     Open Access  
Supramolecular Chemistry     Hybrid Journal   (Followers: 5)
Supramolecular Materials     Full-text available via subscription   (Followers: 6)
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: 4)
Sustainable Chemistry and Pharmacy     Full-text available via subscription   (Followers: 1)
Synfacts     Hybrid Journal   (Followers: 5)
Synlett     Hybrid Journal   (Followers: 43)
Synthesis     Hybrid Journal   (Followers: 51)
Talanta     Hybrid Journal   (Followers: 9)
Talanta Open     Full-text available via subscription   (Followers: 4)
Tecnología Química     Open Access  
Telematics and Informatics Reports     Full-text available via subscription   (Followers: 3)
Tenside Surfactants Detergents     Full-text available via subscription   (Followers: 1)
Tetrahedron     Hybrid Journal   (Followers: 86)
Tetrahedron Chem     Full-text available via subscription   (Followers: 2)
Tetrahedron Letters     Hybrid Journal   (Followers: 92)
The Alkaloids: Chemistry and Biology     Full-text available via subscription   (Followers: 1)
The All Results Journals : Chem     Open Access   (Followers: 1)
The Canadian Journal of Chemical Engineering     Hybrid Journal   (Followers: 5)
The Enzymes     Full-text available via subscription   (Followers: 1)
The Protein Journal     Hybrid Journal   (Followers: 2)
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: 4)
Toxicology Research     Partially Free   (Followers: 8)
Transition Metal Chemistry     Hybrid Journal   (Followers: 6)
Trends in Chemistry     Hybrid Journal   (Followers: 3)
Turkish Computational and Theoretical Chemistry     Open Access   (Followers: 1)
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: 5)
World Journal of Chemical Education     Open Access   (Followers: 2)
X-Ray Spectrometry     Hybrid Journal   (Followers: 4)

  First | 1 2 3 4     

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The Protein Journal
Journal Prestige (SJR): 0.451
Citation Impact (citeScore): 1
Number of Followers: 2  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1572-3887 - ISSN (Online) 1573-4943
Published by Springer-Verlag Homepage  [2468 journals]
  • Correction: Kennedy Epitope (KE)-dependent Retrograde Transport of
           Efficiently Cleaved HIV-1 Envelopes (Envs) and its Effect on Env Cell
           Surface Expression and Viral Particle Formation

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      PubDate: 2024-02-26
       
  • A Novel Trypsin Kunitz-Type Inhibitor from Cajanus cajan Leaves and Its
           Inhibitory Activity on New Cancer Serine Proteases and Its Effect on Tumor
           Cell Growth

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      Abstract: A novel trypsin inhibitor from Cajanus cajan (TIC) fresh leaves was partially purified by affinity chromatography. SDS-PAGE revealed one band with about 15 kDa with expressive trypsin inhibitor activity by zymography. TIC showed high affinity for trypsin (Ki = 1.617 μM) and was a competitive inhibitor for this serine protease. TIC activity was maintained after 24 h of treatment at 70 °C, after 1 h treatments with different pH values, and β-mercaptoethanol increasing concentrations, and demonstrated expressive structural stability. However, the activity of TIC was affected in the presence of oxidizing agents. In order to study the effect of TIC on secreted serine proteases, as well as on the cell culture growth curve, SK-MEL-28 metastatic human melanoma cell line and CaCo-2 colon adenocarcinoma was grown in supplemented DMEM, and the extracellular fractions were submitted salting out and affinity chromatography to obtain new secreted serine proteases. TIC inhibited almost completely, 96 to 89%, the activity of these serine proteases and reduced the melanoma and colon adenocarcinoma cells growth of 48 and 77% respectively. Besides, it is the first time that a trypsin inhibitor was isolated and characterized from C. cajan leaves and cancer serine proteases were isolated and partial characterized from SK-MEL-28 and CaCo-2 cancer cell lines. Furthermore, TIC shown to be potent inhibitor of tumor protease affecting cell growth, and can be one potential drug candidate to be employed in chemotherapy of melanoma and colon adenocarcinoma. Graphical
      PubDate: 2024-02-12
       
  • The Structural Features of MlaD Illuminate its Unique Ligand-Transporting
           Mechanism and Ancestry

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      Abstract: Abstract The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3–3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. “asymmetric protomer movement (APM)”. Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.
      PubDate: 2024-02-12
       
  • Methylglyoxal Induced Modifications to Stabilize Therapeutic
           Proteins: A Review

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      Abstract: Therapeutic proteins are potent, fast-acting drugs that are highly effective in treating various conditions. Medicinal protein usage has increased in the past 10 years, and it will evolve further as we better understand disease molecular pathways. However, it is associated with high processing costs, limited stability, difficulty in being administered as an oral medication, and the inability of large proteins to penetrate tissue and reach their target locations. Many methods have been developed to overcome the problems with the stability and chaperone activity of therapeutic proteins, viz., the addition of external agents (changing the properties of the surrounding solvent by using stabilizing excipients, e.g., amino acids, sugars, polyols) and internal agents (chemical modifications that influence its structural properties, e.g., mutations, glycosylation). However, these methods must completely clear protein instability and chaperone issues. There is still much work to be done on finetuning chaperone proteins to increase their biological efficacy and stability. Methylglyoxal (MGO), a potent dicarbonyl compound, reacts with proteins and forms covalent cross-links. Much research on MGO scavengers has been conducted since they are known to alter protein structure, which may result in alterations in biological activity and stability. MGO is naturally produced within our body, however, its impact on chaperones and protein stability needs to be better understood and seems to vary based on concentration. This review highlights the efforts of several research groups on the effect of MGO on various proteins. It also addresses the impact of MGO on a client protein, α-crystallin, to understand the potential solutions to the protein’s chaperone and stability problems. Graphical
      PubDate: 2024-02-01
       
  • Efficient Expression in the Prokaryotic Host System, Purification and
           Structural Analyses of the Recombinant Human ACE2 Catalytic Subunit as a
           Hybrid Protein with the B Subunit of Cholera Toxin (CTB-ACE2)

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      Abstract: Angiotensin-converting enzyme 2 (ACE2) has a specific interaction with the coronavirus spike protein, enabling its entry into human cells. This membrane enzyme converts angiotensin II into angiotensin 1–7, which has an essential role in protecting the heart and improving lung function. Many therapeutic properties have been attributed to the human recombinant ACE2 (hrACE2), especially in combating complications related to diabetes mellitus and hypertension, as well as, preventing the coronavirus from entering the target tissues. In the current study, we designed an appropriate gene construct for the hybrid protein containing the ACE2 catalytic subunit and the B subunit of cholera toxin (CTB-ACE2). This structural feature will probably help the recombinant hybrid protein enter the mucosal tissues, including the lung tissue. Optimization of this hybrid protein expression was investigated in BL21 bacterial host cells. Also, the hybrid protein was identified with an appropriate antibody using the ELISA method. A large amount of the hybrid protein (molecular weight of ~ 100 kDa) was expressed as the inclusion body when the induction was performed in the presence of 0.25 mM IPTG and 1% sucrose for 10 h. Finally, the protein structural features were assessed using several biophysical methods. The fluorescence emission intensity and oligomeric size distribution of the CTB-ACE2 suggested a temperature-dependent alteration. The β-sheet and α-helix were also dominant in the hybrid protein structure, and this protein also displays acceptable chemical stability. In overall, according to our results, the efficient expression and successful purification of the CTB-ACE2 protein may pave the path for its therapeutic applications against diseases such as covid-19, diabetes mellitus and hypertension. Graphical
      PubDate: 2024-02-01
       
  • Use of 2D FFT and DTW in Protein Sequence Comparison

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      Abstract: Abstract Protein sequence comparison remains a challenging work for the researchers owing to the computational complexity due to the presence of 20 amino acids compared with only four nucleotides in Genome sequences. Further, protein sequences of different species are of different lengths; it throws additional changes to the researchers to develop methods, specially alignment-free methods, to compare protein sequences. In this work, an efficient technique to compare protein sequences is developed by a graphical representation. First, the classified grouping of 20 amino acids with a cardinality of 4 based on polar class is considered to narrow down the representational range from 20 to 4. Then a unit vector technique based on a two-quadrant Cartesian system is proposed to provide a new two-dimensional graphical representation of the protein sequence. Now, two approaches are proposed to cope with the varying lengths of protein sequences from various species: one uses Dynamic Time Warping (DTW), while the other one uses a two-dimensional Fast Fourier Transform (2D FFT). Next, the effectiveness of these two techniques is analyzed using two evaluation criteria—quantitative measures based on symmetric distance (SD) and computational speed. An analysis is performed on five data sets of 9 ND4, 9 ND5, 9 ND6, 12 Baculovirus, and 24 TF proteins under the two methods. It is found that the FFT-based method produces the same results as DTW but in less computational time. It is found that the result of the proposed method agrees with the known biological reference. Further, the present method produces better clustering than the existing ones.
      PubDate: 2024-02-01
       
  • Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium
           tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein
           with Quercetin

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      Abstract: Abstract Eis (Enhanced intracellular survival) protein is an aminoglycoside acetyltransferase enzyme classified under the family – GNAT (GCN5-related family of N-acetyltransferases) secreted by Mycobacterium tuberculosis (Mtb). The enzymatic activity of Eis results in the acetylation of kanamycin, thereby impairing the drug’s action. In this study, we expressed and purified recombinant Eis (rEis) to determine the enzymatic activity of Eis and its potential inhibitor. Glide-enhanced precision docking was used to perform molecular docking with chosen ligands. Quercetin was found to interact Eis with a maximum binding affinity of -8.379 kcal/mol as compared to other ligands. Quercetin shows a specific interaction between the positively charged amino acid arginine in Eis and the aromatic ring of quercetin through π-cation interaction. Further, the effect of rEis was studied on the antibiotic activity of kanamycin A in the presence and absence of quercetin. It was observed that the activity of rEis aminoglycoside acetyltransferase decreased with increasing quercetin concentration. The results from the disk diffusion assay confirmed that increasing the concentration of quercetin inhibits the rEis protein activity. In conclusion, quercetin may act as a potential Eis inhibitor.
      PubDate: 2024-02-01
       
  • Refolding, Crystallization, and Crystal Structure Analysis of a Scavenger
           Receptor Cysteine-Rich Domain of Human Salivary Agglutinin Expressed in
           Escherichia coli

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      Abstract: Abstract Scavenger receptors are a protein superfamily that typically consists of one or more repeats of the scavenger receptor cysteine-rich structural domain (SRCRD), which is an ancient and highly conserved protein module. The expression and purification of eukaryotic proteins containing multiple disulfide bonds has always been challenging. The expression systems that are commonly used to express SRCRD proteins mainly consist of eukaryotic protein expression systems. Herein, we established a high-level expression strategy of a Type B SRCRD unit from human salivary agglutinin using the Escherichia coli expression system, followed by a refolding and purification process. The untagged recombinant SRCRD was expressed in E. coli using the pET-32a vector, which was followed by a refolding process using the GSH/GSSG redox system. The SRCRD expressed in E. coli SHuffle T7 showed better solubility after refolding than that expressed in E. coli BL21(DE3), suggesting the importance of the disulfide bond content prior to refolding. The quality of the refolded protein was finally assessed using crystallization and crystal structure analysis. As proteins refolded from inclusion bodies exhibit a high crystal quality and reproducibility, this method is considered a reliable strategy for SRCRD protein expression and purification. To further confirm the structural integrity of the refolded SRCRD protein, the purified protein was subjected to crystallization using sitting-drop vapor diffusion method. The obtained crystals of SRCRD diffracted X-rays to a resolution of 1.47 Å. The solved crystal structure appeared to be highly conserved, with four disulfide bonds appropriately formed. The surface charge distribution of homologous SRCRD proteins indicates that the negatively charged region at the surface is associated with their calcium-dependent ligand recognition. These results suggest that a high-quality SRCRD protein expressed by E. coli SHuffle T7 can be successfully folded and purified, providing new options for the expression of members of the scavenger receptor superfamily.
      PubDate: 2024-01-24
       
  • Interaction of Cecropin A (1–7) Analogs with DNA Analyzed by
           Multi-spectroscopic Methods

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      Abstract: Cecropin A (1–7) is a cationic antimicrobial peptide which contain lots of basic amino acids. To understand the effect of basic amino acids on cecropin A (1–7), analogues CA2, CA3 and CA4 which have more arginine or lysine at the N-terminal or C-terminal were designed and synthesized. The interaction of cecropin A (1–7) and its analogs with DNA was studied using ultraviolet–visible spectroscopy, fluorescence spectroscopy and circular dichroism spectroscopy. Multispectral analysis showed that basic amino acids improved the interaction between the analogues and DNA. The interaction between CA4 and DNA is most pronounced. Fluorescence spectrum indicated that Ksv value of CA4 is 1.19 × 105  L mol−1 compared to original peptide cecropin A (1–7) of 3.73 × 104  L mol−1. The results of antimicrobial experiments with cecropin A (1–7) and its analogues showed that basic amino acids enhanced the antimicrobial effect of the analogues. The antimicrobial activity of CA4 against E. coli was eightfold higher than that of cecropin A (1–7). The importance of basic amino acid in peptides is revealed and provides useful information for subsequent studies of antimicrobial peptides. Graphical
      PubDate: 2024-01-24
       
  • Heterologous Production of Antimicrobial Peptides: Notes to Consider

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      Abstract: Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called “superbugs”, the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed. Graphical Sources of peptide production and their applications. Some AMPs directly extracted from natural sources, some of them are chemically synthesized either using liquid or solid phase peptides synthesis, and for large scale production, recombinant expression using heterologous expression systems have been used.
      PubDate: 2024-01-05
       
  • Engineering Human Pancreatic RNase 1 as an Immunotherapeutic Agent for
           Cancer Therapy Through Computational and Experimental Studies

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      Abstract: Abstract Most plant and bacterial toxins are highly immunogenic with non-specific toxic effects. Human ribonucleases are thought to provide a promising basis for reducing the toxic agent’s immunogenic properties, which are candidates for cancer therapy. In the cell, the ribonuclease inhibitor (RI) protein binds to the ribonuclease enzyme and forms a tight complex. This study aimed to engineer and provide a gene construct encoding an improved version of Human Pancreatic RNase 1 (HP-RNase 1) to reduce connection to RI and modulate the immunogenic effects of immunotoxins. To further characterize the interaction complex of HP-RNase 1 and RI, we established various in silico and in vitro approaches. These methods allowed us to specifically monitor interactions within native and engineered HP-RNase 1/RI complexes. In silico research involved molecular dynamics (MD) simulations of native and mutant HP-RNase 1 in their free form and when bound to RI. For HP-RNase 1 engineering, we designed five mutations (K8A/N72A/N89A/R92D/E112/A) based on literature studies, as this combination proved effective for the intended investigation. Then, the cDNA encoding HP-RNase 1 was generated by RT-PCR from blood and cloned into the pSYN2 expression vector. Consequently, wild-type and the engineered HP-RNase 1 were over-expressed in E. coli TG1 and purified using an IMAC column directed against a poly-his tag. The protein products were detected by SDS–PAGE and Western blot analysis. HP-RNase 1 catalytic activity, in the presence of various concentrations of RI, demonstrated that the mutated version of the protein is able to escape the ribonuclease inhibitor and target the RNA substrate 2.5 folds more than that of the wild type. From these data, we tend to suggest the engineered recombinant HP-RNase 1 potentially as a new immunotherapeutic agent for application in human cancer therapy.
      PubDate: 2023-12-25
       
  • Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic
           Diversity Through Kinetic, Structural and Molecular Docking Analysis

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      Abstract: Abstract Divergently evolved Tartrate dehydrogenase (TDH) exhibits multiple catalytic activities at a single active site; the enzyme from P. putida (pTDH) being structurally and biochemically well-characterized. Occurrence of TDH-associated ability to aerobically metabolize L-tartrate in Bacillus isolates and limited resemblance of ycsA-encoded protein sequences with pTDH rendered Bacillus TDH as an intriguing enzyme with possible catalytic diversity as well as evolutionary significance. The present study explores substrate interactions of TDHs from B. subtilis 168 (168bTDH) and B. licheniformis DSM-13 (429bTDH) through kinetic, structural and molecular docking-based analysis. Heterologously expressed bTDHs, purified from insoluble fractions of E. coli BL21(DE3) cells, could significantly catalyze L-tartrate and meso-tartrate as substrates in forward reaction. Unlike pTDH, bTDHs distinctly and more efficiently catalyzed the reverse reaction using dihydroxyfumarate substrate following sigmoidal kinetics; the ability being ~ 4 fold higher in 168bTDH. Their binding energies predicted from molecular docking, further substantiated the relative substrate specificities, while revealing major residues involved in protein-ligand interactions at active site. The kinetic analysis and homology modelling validated using Ramachandran Plot analysis predicted a dimeric nature for bTDH. Collectively, the results highlight unique catalytic potential of phylogenetically recent bTDHs, offering an important protein engineering target to mediate efficient enantioselective enzymatic biotransformations.
      PubDate: 2023-12-21
       
  • Biochemical Characterization of Laccase from Spirulina CPCC-695 and Their
           Role in Estrone Degradation

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      Abstract: Abstract The addition of exogenous endocrine disrupting compounds (EDCs) like estrone, in the food chain through the aquatic system, disrupts steroid biosynthesis and metabolism by altering either the genomic or non-genomic pathway that eventually results in various diseases. Thus, bioremediation of these compounds is urgently required to prevent their addition and persistence in the environment. Enzymatic degradation has proven to be a knight in shining armour as it is safe and generates no toxic products. The multicopper oxidases (E.C. 1.10.3.2 benzenediol: oxygen oxidoreductase), laccase with the potential to degrade both phenolic and non-phenolic substrates has recently gained attention. In this study, the laccase was purified, characterized, and used to study estrone degradation. The culture filtrate (crude laccase) was concentrated and precipitated using cold-acetone and dialyzed against tris buffer (50 mM) giving a four-fold partially purified form, with 45.56% yield and 204.14 U/mg as specific activity and a single peak at 250–300 nm. The partially purified laccase was approximately 80 kDa as estimated by SDS-PAGE preferred ABTS as substrate. Both crude and partially purified laccase showed maximum activity at pH 3.0, 40 °C, and 4 mM ABTS. Kinetic constants (Km, Vmax) of crude and partially purified laccase were found to be 0.83 mM; 494.31 mM/min, and 0.58 mM; 480.54 mM/min respectively. Iron sulphate and sodium azide inhibited laccase maximally. Crude and partially purified laccase degradation efficiency was 87.55 and 91.35% respectively. Spirulina CPCC-695 laccase with efficient estrone degradation ability renders them promising candidates for EDCs bioremediation.
      PubDate: 2023-12-21
       
  • Structural and Biochemical Studies on Klebsiella Pneumoniae Enoyl-ACP
           Reductase (FabI) Suggest Flexible Substrate Binding Site

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      Abstract: Abstract Klebsiella pneumoniae, a bacterial pathogen infamous for antibiotic resistance, is included in the priority list of pathogens by various public health organizations due to its extraordinary ability to develop multidrug resistance. Bacterial fatty acid biosynthesis pathway-II (FAS-II) has been considered a therapeutic drug target for antibacterial drug discovery. Inhibition of FAS-II enzyme, enoyl-acyl carrier protein reductase, FabI, not only inhibits bacterial infections but also reverses antibiotic resistance. Here, we characterized Klebsiella pneumoniae FabI (KpFabI) using complementary experimental approaches including, biochemical, x-ray crystallography, and molecular dynamics simulation studies. Biophysical studies shows that KpFabI organizes as a tetramer molecular assembly in solution as well as in the crystal structure. Enzyme kinetics studies reveal a distinct catalytic property towards crotonyl CoA and reducing cofactor NADH. Michaelis-Menten constant (Km) values of substrates show that KpFabI has higher preference towards NADH as compared to crotonyl CoA. The crystal structure of tetrameric apo KpFabI folds into a classic Rossman fold in which β-strands are sandwiched between α-helices. A highly flexible substrate binding region is located toward the interior of the tetrameric assembly. Thermal stability assay on KpFabI with its substrate shows that the flexibility is primarily stabilized by cofactor NADH. Moreover, the molecular dynamics further supports that KpFabI has highly flexible regions at the substrate binding site. Together, these findings provide evidence for highly dynamic substrate binding sites in KpFabI, therefore, this information will be vital for specific inhibitors discovery targeting Klebsiella pneumoniae.
      PubDate: 2023-12-21
       
  • Significance of Sequence Features in Classification of Protein–Protein
           Interactions Using Machine Learning

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      Abstract: Abstract Protein–protein interactions are crucial for the entry of viruses into the cell. Understanding the mechanism of interactions is essential in studying human-virus association, developing new biologics and drug candidates, as well as viral infections and antiviral responses. Experimental methods to analyze human-virus protein–protein interactions based on protein sequence data are time-consuming and labor-intensive, so machine learning models are being developed to predict interactions and determine large-scale interactomes between species. The present work highlights the importance of sequence features in classifying interacting and non-interacting proteins from the protein sequence data. Higher dimensional amino acid sequence features such as Amino Acid Composition (AAC), Dipeptide Composition (DPC), Grouped Amino Acid Composition (GAAC), Pseudo-Amino Acid Composition (PAAC) etc., are extracted. Following feature extraction, three datasets were created: Dataset 1 contains all of the extracted features. While Datasets 2 and 3 contain the most relevant features obtained through dimensionality reduction. To analyze the importance of high-dimensional features and their participation in protein–protein interactions, a random forest classifier is trained on three datasets. With dimensionality reduction, the model exhibited exceptional accuracy, indicating that dimensionality reduction fails to capture the complexity of interactions and the underlying relationships between human and viral proteins. As a result of retaining high-dimensional features, it is possible to capture all the characteristics of protein–protein interactions that resemble host–pathogen associations, leading to the development of biologically meaningful models. Our proposed approach is a more realistic and comprehensive classification model, leading to deeper insights and better applications in virology and drug development.
      PubDate: 2023-12-19
       
  • An ITPA Enzyme with Improved Substrate Selectivity

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      Abstract: Abstract Recent clinical data have identified infant patients with lethal ITPA deficiencies. ITPA is known to modulate ITP concentrations in cells and has a critical function in neural development which is not understood. Polymorphism of the ITPA gene affects outcomes for both ribavirin and thiopurine based therapies and nearly one third of the human population is thought to harbor ITPA polymorphism. In a previous site-directed mutagenesis alanine screen of the ITPA substrate selectivity pocket, we identified the ITPA mutant, E22A, as a gain-of function mutant with enhanced ITP hydrolysis activity. Here we report a rational enzyme engineering experiment to investigate the biochemical properties of position 22 ITPA mutants and find that the E22D ITPA has two- and four-fold improved substrate selectivity for ITP over the canonical purine triphosphates ATP and GTP, respectively, while maintaining biological activity. The novel E22D ITPA should be considered as a platform for further development of ITPA therapies.
      PubDate: 2023-12-08
      DOI: 10.1007/s10930-023-10162-0
       
  • Role Transformation of HSPA8 to Heme-peroxidase After Binding Hemin to
           Catalyze Heme Polymerization

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      Abstract: Abstract Hemin, a byproduct of hemoglobin degradation, inflicts oxidative insult to cells. Following its accumulation, several proteins are recruited for heme detoxification with heme oxygenase playing the key role. Chaperones play a protective role primarily by preventing protein degradation and unfolding. They also are known to have miscellaneous secondary roles during similar situations. To discover a secondary role of chaperones during heme stress we studied the role of the chaperone HSPA8 in the detoxification of hemin. In-silico studies indicated that HSPA8 has a well-defined biophoric environment to bind hemin. Through optical difference spectroscopy, we found that HSPA8 binds hemin through its N-terminal domain with a Kd value of 5.9 ± 0.04 µM and transforms into a hemoprotein. The hemoprotein was tested for exhibiting peroxidase activity using guaiacol as substrate. The complex formed reacts with H2O2 and exhibits classical peroxidase activity with an ability to oxidize aromatic and halide substrates. HSPA8 is dose-dependently catalyzing heme polymerization through its N-terminal domain. The IR results reveal that the polymer formed exhibits structural similarities to β-hematin suggesting its covalent nature. The polymerization mechanism was tested through optical spectroscopy, spin-trap, and activity inhibition experiments. The results suggest that the polymerization occurs through a peroxidase-H2O2 system involving a one-electron transfer mechanism, and the formation of free radical and radical-radical interaction. It highlights a possible role of the HSPA8-hemin complex in exhibiting cytoprotective function during pathological conditions like malaria, sickle cell disease, etc.
      PubDate: 2023-12-08
      DOI: 10.1007/s10930-023-10167-9
       
  • Improved Antimicrobial Activity of Bovine Lactoferrin Peptide (LFcinB)
           Based on Rational Design

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      Abstract: Abstract Bovine lactoferrin peptide (LFcinB), as an antimicrobial peptide, is expected to be an alternative of antibiotics owing to its broad-spectrum antimicrobial activity and specific mechanism. However, the weak antimicrobial activity, high hemolysis, and poor stability of LFcinB limited its applications in the field of biomedicine, food and agriculture. In order to improve the antimicrobial activity of LFcinB, five mutants were designed rationally, of which mutant LF4 (M10W/P16R/A24L) showed highest antimicrobial activity. The bioinformatics analysis indicated that the improved antimicrobial activity of LF4 was related to its increased cations, higher amphiphilicity and the extension of the β-sheet in the structure. These studies will highlight the important role of bioinformatic tools in designing ideal biopeptides and lay a foundation for further development of antimicrobial peptides.
      PubDate: 2023-12-01
      DOI: 10.1007/s10930-023-10142-4
       
  • Investigating the Effect of Substituting a Single Cysteine Residue on the
           Thermal Stability of an Engineered Sweet Protein, Single-Chain Monellin

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      Abstract: Abstract Single-chain monellin (SCM) is an engineered protein that links the two chains of monellin, a naturally sweet-tasting protein. This protein is an attractive candidate for use as a sugar replacement in food and beverages and has numerous other applications. Therefore, generating SCM mutants with improved stability is an active area of research to broaden the range of its potential applications. In this study, we focused on the Cys41 residue of SCM, which is a single cysteine residue present at a structurally important position. This residue is often substituted with Ser. However, this substitution may destabilize SCM because Cys41 is buried in the hydrophobic core of the protein. Therefore, we designed mutants that substituted Ala, Val, and Leu for this residue, namely C41A, C41V, and C41L. We characterized these three mutants, SCM C41S, and wild type (WT). Differential scanning fluorimetric analysis revealed that substituting Cys41 with Ala or Val increased the thermal stability of SCM, while substitution with Ser or Leu decreased its stability. Determination of the crystal structures of SCM C41A and C41V mutants revealed that the overall structures and main chain structures around the 41st residue of both mutants were almost identical to the WT. On the other hand, the orientations of the amino acid side chains near the 41st residue differed among the SCM variants. Taken together, our results indicate that substituting Cys41 with Ala or Val increases the stability of SCM and provide insight into the structural basis of this improvement.
      PubDate: 2023-09-22
      DOI: 10.1007/s10930-023-10154-0
       
  • Biophysical Characterization of p51 and p66 Monomers of HIV-1 Reverse
           Transcriptase with Their Inhibitors

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      Abstract: Abstract Human immunodeficiency virus (HIV)-1 reverse transcriptase (HIV-1 RT) is responsible for the transcription of viral RNA genomes into DNA genomes and has become an important target for the treatment of acquired immune deficiency syndrome (AIDS). This study used biophysical techniques to characterize the HIV-1 RT structure, monomer forms, and the non-nucleoside reverse transcriptase inhibitors (NNRTIs) bound forms. Inactive p66W401A and p51W401A were selected as models to study the HIV-1 RT monomer structures. Nuclear magnetic resonance (NMR) spectroscopy revealed that the unliganded forms of p66W401A protein and p51W401A protein had similar conformation to each other in solution. The complexes of p66W401A or p51W401A with inhibitors showed similar conformations to p66 in the RT heterodimer bound to the NNRTIs. Furthermore, the results of paramagnetic relaxation enhancement (PRE)-assisted NMR revealed that the unliganded forms of the p66W401A and p51W401A conformations were different from the unliganded heterodimer, characterized by a greater distance between the fingers and thumb subdomains. Small-angle X-ray scattering (SAXS) experiments confirmed that p66W401A and p51W401A can bind with inhibitors, similar to the p66/p51 heterodimer. The findings of this study increase the structural knowledge base of HIV-1 RT monomers, which may be helpful in the future design of potent viral inhibitors.
      PubDate: 2023-09-20
      DOI: 10.1007/s10930-023-10156-y
       
 
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  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
Russian Journal of Bioorganic Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of Coordination Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of General Chemistry     Hybrid Journal   (Followers: 1)
Russian Journal of Inorganic Chemistry     Hybrid Journal  
Sainstek : Jurnal Sains dan Teknologi     Open Access  
Science China Chemistry     Hybrid Journal   (Followers: 2)
Science Talks     Full-text available via subscription   (Followers: 4)
Sciences & Technologie A : sciences exactes     Open Access  
Scientific Journal of Frontier Chemical Development     Open Access   (Followers: 2)
Scientific Reports     Open Access   (Followers: 82)
Sensors and Actuators B: Chemical     Hybrid Journal   (Followers: 17)
Sensors and Actuators Reports     Open Access   (Followers: 7)
Separation & Purification Reviews     Hybrid Journal   (Followers: 3)
Separation Science and Technology     Hybrid Journal   (Followers: 7)
Separations     Open Access   (Followers: 5)
Silicon Chemistry     Hybrid Journal   (Followers: 1)
Small Methods     Hybrid Journal   (Followers: 1)
Small Science     Open Access   (Followers: 13)
Small Structures     Hybrid Journal   (Followers: 4)
Smart Materials Research     Open Access   (Followers: 7)
SmartMat     Open Access   (Followers: 1)
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: 8)
Solvent Extraction and Ion Exchange     Hybrid Journal   (Followers: 7)
SPE Polymers     Open Access   (Followers: 1)
Spectral Analysis Review     Open Access  
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy     Hybrid Journal   (Followers: 14)
Spectrochimica Acta Part B: Atomic Spectroscopy     Hybrid Journal   (Followers: 16)
Spectroscopy and Spectral Analysis     Full-text available via subscription   (Followers: 1)
Starch / Staerke     Hybrid Journal   (Followers: 2)
Steel Research International     Hybrid Journal   (Followers: 23)
Structural Chemistry     Hybrid Journal   (Followers: 1)
Substantia     Open Access  
Supramolecular Chemistry     Hybrid Journal   (Followers: 5)
Supramolecular Materials     Full-text available via subscription   (Followers: 6)
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: 4)
Sustainable Chemistry and Pharmacy     Full-text available via subscription   (Followers: 1)
Synfacts     Hybrid Journal   (Followers: 5)
Synlett     Hybrid Journal   (Followers: 43)
Synthesis     Hybrid Journal   (Followers: 51)
Talanta     Hybrid Journal   (Followers: 9)
Talanta Open     Full-text available via subscription   (Followers: 4)
Tecnología Química     Open Access  
Telematics and Informatics Reports     Full-text available via subscription   (Followers: 3)
Tenside Surfactants Detergents     Full-text available via subscription   (Followers: 1)
Tetrahedron     Hybrid Journal   (Followers: 86)
Tetrahedron Chem     Full-text available via subscription   (Followers: 2)
Tetrahedron Letters     Hybrid Journal   (Followers: 92)
The Alkaloids: Chemistry and Biology     Full-text available via subscription   (Followers: 1)
The All Results Journals : Chem     Open Access   (Followers: 1)
The Canadian Journal of Chemical Engineering     Hybrid Journal   (Followers: 5)
The Enzymes     Full-text available via subscription   (Followers: 1)
The Protein Journal     Hybrid Journal   (Followers: 2)
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: 4)
Toxicology Research     Partially Free   (Followers: 8)
Transition Metal Chemistry     Hybrid Journal   (Followers: 6)
Trends in Chemistry     Hybrid Journal   (Followers: 3)
Turkish Computational and Theoretical Chemistry     Open Access   (Followers: 1)
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: 5)
World Journal of Chemical Education     Open Access   (Followers: 2)
X-Ray Spectrometry     Hybrid Journal   (Followers: 4)

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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
 


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