journal
https://read.qxmd.com/read/38507106/microenzymes-is-there-anybody-out-there
#1
REVIEW
Jose Carlos Santos Salgado, Robson Carlos Alnoch, Maria de Lourdes Teixeira de Moraes Polizeli, Richard John Ward
Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20-60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature...
March 20, 2024: Protein Journal
https://read.qxmd.com/read/38492188/choice-of-metric-divergence-in-genome-sequence-comparison
#2
JOURNAL ARTICLE
Soumen Ghosh, Jayanta Pal, Bansibadan Maji, Carlo Cattani, Dilip Kumar Bhattacharya
The paper introduces a novel probability descriptor for genome sequence comparison, employing a generalized form of Jensen-Shannon divergence. This divergence metric stems from a one-parameter family, comprising fractions up to a maximum value of half. Utilizing this metric as a distance measure, a distance matrix is computed for the new probability descriptor, shaping Phylogenetic trees via the neighbor-joining method. Initial exploration involves setting the parameter at half for various species. Assessing the impact of parameter variation, trees drawn at different parameter values (half, one-fourth, one-eighth)...
March 16, 2024: Protein Journal
https://read.qxmd.com/read/38492187/molecular-structural-and-functional-diversity-of-universal-stress-proteins-usps-in-bacteria-plants-and-their-biotechnological-applications
#3
REVIEW
Bilkees Nabi, Manoj Kumawat, Neeraj Ahlawat, Sushma Ahlawat
Universal stress proteins (USPs) are widely distributed and play crucial roles in cellular responses to biotic and abiotic stresses. These roles include regulating cell growth and development, cell motility, hypoxia responses, and ion sequestration. With the increasing frequency and intensity of extreme weather events due to climate change, pathogens have developed different strategies to withstand environmental stresses, in which USPs play a significant role in their survival and virulence. In this study, we analyzed the importance of USPs in various organisms, such as archaea, plants, and fungi, as a parameter that influences their survival...
March 16, 2024: Protein Journal
https://read.qxmd.com/read/38491250/the-complex-landscape-of-intracellular-signalling-in-protein-modification-under-hyperglycaemic-stress-leading-to-metabolic-disorders
#4
REVIEW
Hamda Khan, Afreen Khanam, Adnan Ahmad Khan, Rizwan Ahmad, Arbab Husain, Safia Habib, Saheem Ahmad, Moinuddin
Hyperglycaemia is a life-threatening risk factor that occurs in both chronic and acute phases and has been linked to causing injury to many organs. Protein modification was triggered by hyperglycaemic stress, which resulted in pathogenic alterations such as impaired cellular function and tissue damage. Dysregulation in cellular function increases the condition associated with metabolic disorders, including cardiovascular diseases, nephropathy, retinopathy, and neuropathy. Hyperglycaemic stress also increases the proliferation of cancer cells...
March 16, 2024: Protein Journal
https://read.qxmd.com/read/38491249/an-update-on-glycerophosphodiester-phosphodiesterases-from-bacteria-to-human
#5
REVIEW
Seyyedeh Mina Hejazian, Saeed Pirmoradi, Sepideh Zununi Vahed, Ripon Kumar Roy, Seyed Mahdi Hosseiniyan Khatibi
The hydrolysis of deacylated glycerophospholipids into sn-glycerol 3-phosphate and alcohol is facilitated by evolutionarily conserved proteins known as glycerophosphodiester phosphodiesterases (GDPDs). These proteins are crucial for the pathogenicity of bacteria and for bioremediation processes aimed at degrading organophosphorus esters that pose a hazard to both humans and the environment. Additionally, GDPDs are enzymes that respond to multiple nutrients and could potentially serve as candidate genes for addressing deficiencies in zinc, iron, potassium, and especially phosphate in important plants like rice...
March 16, 2024: Protein Journal
https://read.qxmd.com/read/38491248/epdrna-a-model-for-identifying-dna-rna-binding-sites-in-disease-related-proteins
#6
JOURNAL ARTICLE
CanZhuang Sun, YongE Feng
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA binding, it is important to identify which residues in the protein sequence bind to DNA and RNA. At present, there are few methods for specifically identifying the binding sites of disease-related protein-DNA and protein-RNA. In this study, so we combined four machine learning algorithms into an ensemble classifier (EPDRNA) to predict DNA and RNA binding sites in disease-related proteins...
March 16, 2024: Protein Journal
https://read.qxmd.com/read/38488956/a-potential-involvement-of-metallothionein-in-the-zinc-tolerance-of-trichoderma-harzianum-experimental-findings
#7
JOURNAL ARTICLE
Negin Ejmalian, Soheila Mirzaei, Asghar Mirzaie-Asl, Mehrdad Chaichi
Metallothioneins are a group of cysteine-rich proteins that play an important role in the homeostasis and detoxification of heavy metals. The objective of this research was to explore the significance of metallothionein in Trichoderma harzianum tolerance to zinc. At the inhibitory concentration of 1000 ppm, the fungus adsorbed 16.7 ± 0.4 mg/g of metal. The HPLC and SDS-PAGE electrophoresis data suggested that the fungus production of metallothionein was twice as high in the presence of zinc as in the control group...
March 15, 2024: Protein Journal
https://read.qxmd.com/read/38485875/immunosuppressive-cyclotides-a-promising-approach-for-treating-autoimmune-diseases
#8
REVIEW
Nguyen Thai Huynh, Thao N T Ho, Yen N D Pham, Le Hang Dang, Son H Pham, Tien T Dang
The immune system maintains constant surveillance to prevent the infiltration of both endogenous and exogenous threats into host organisms. The process is regulated by effector immune cells that combat external pathogens and regulatory immune cells that inhibit excessive internal body inflammation, ultimately establishing a state of homeostasis within the body. Disruption to this process could lead to autoimmunity, which is often associated with the malfunction of both T cells and B cells with T cells playing a more major role...
March 15, 2024: Protein Journal
https://read.qxmd.com/read/38453735/effect-of-organic-solvents-on-the-activity-stability-and-secondary-structure-of-asclepain-ci-using-ftir-and-molecular-dynamics-simulations
#9
JOURNAL ARTICLE
Anabella L Origone, Esteban G Vega Hissi, Constanza S Liggieri, Gerardo E Camí, Andrés Illanes, Sonia E Barberis
The present study aims at understanding the effect of organic solvents on the specific proteolytic activity and operational stability of asclepain cI in aqueous-organic media, using correlations between geometrical and structural parameters of asclepain cI. These correlations were determined by molecular dynamics (MD) simulations and the secondary structure of the enzyme validated by Fourier-transform Infrared (FTIR) spectroscopy. Asclepain cI exhibited significantly higher catalytic potential in 29 of the 42 aqueous-organic media tested, composed by 0...
March 7, 2024: Protein Journal
https://read.qxmd.com/read/38436837/identification-of-protein-protein-interaction-associated-functions-based-on-gene-ontology
#10
JOURNAL ARTICLE
Yu-Hang Zhang, FeiMing Huang, JiaBo Li, WenFeng Shen, Lei Chen, KaiYan Feng, Tao Huang, Yu-Dong Cai
Protein-protein interactions (PPIs) involve the physical or functional contact between two or more proteins. Generally, proteins that can interact with each other always have special relationships. Some previous studies have reported that gene ontology (GO) terms are related to the determination of PPIs, suggesting the special patterns on the GO terms of proteins in PPIs. In this study, we explored the special GO term patterns on human PPIs, trying to uncover the underlying functional mechanism of PPIs. The experimental validated human PPIs were retrieved from STRING database, which were termed as positive samples...
March 4, 2024: Protein Journal
https://read.qxmd.com/read/38431537/computational-deciphering-of-the-role-of-s100a8-and-s100a9-proteins-and-their-changes-in-the-structure-assembly-influences-their-interaction-with-tlr4-rage-and-cd36
#11
JOURNAL ARTICLE
Sivasakthi Paramasivam, Senthamil Selvan Perumal, Sanmuga Priya Ekambaram
S100A8 and S100A9 belong to the calcium-binding, damage associated molecular pattern (DAMP) proteins shown to aggravate the pathogenesis of rheumatoid arthritis (RA) through their interaction with the TLR4, RAGE and CD36 receptors. S100A8 and S100A9 proteins tend to exist in monomeric, homo and heterodimeric forms, which have been implicated in the pathogenesis of RA, via interacting with Pattern Recognition receptors (PRRs). The study aims to assess the influence of changes in the structure and biological assembly of S100A8 and S100A9 proteins as well as their interaction with significant receptors in RA through computational methods and surface plasmon resonance (SPR) analysis...
March 2, 2024: Protein Journal
https://read.qxmd.com/read/38431536/methotrexate-for-drug-repurposing-as-an-anti-aggregatory-agent-to-mercuric-treated-%C3%AE-chymotrypsinogen-a
#12
JOURNAL ARTICLE
Neha Kausar Ansari, Amaan Rais, Aabgeena Naeem
Protein aggregation is related to numerous pathological conditions like Alzheimer's and Parkinson's disease. In our study, we have shown that an already existing FDA-approved drug; methotrexate (MTX) can be reprofiled on preformed α-chymotrypsinogen A (α-Cgn A) aggregates. The zymogen showed formation of aggregates upon interaction with mercuric ions, with increasing concentration of Hg2 Cl2 (0-150 µM). The hike in ThT and ANS fluorescence concomitant with blue shift, bathochromic shift and the hyperchromic effect in the CR absorbance, RLS and turbidity measurements, substantiate the zymogen β-rich aggregate formation...
March 2, 2024: Protein Journal
https://read.qxmd.com/read/38427271/a-comprehensive-review-on-machine-learning-techniques-for-protein-family-prediction
#13
REVIEW
T Idhaya, A Suruliandi, S P Raja
Proteomics is a field dedicated to the analysis of proteins in cells, tissues, and organisms, aiming to gain insights into their structures, functions, and interactions. A crucial aspect within proteomics is protein family prediction, which involves identifying evolutionary relationships between proteins by examining similarities in their sequences or structures. This approach holds great potential for applications such as drug discovery and functional annotation of genomes. However, current methods for protein family prediction have certain limitations, including limited accuracy, high false positive rates, and challenges in handling large datasets...
March 1, 2024: Protein Journal
https://read.qxmd.com/read/38407740/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
#14
Supratik Das, Hilal Ahmad Parray, Adarsh Kumar Chiranjivi, Prince Kumar, Abhishek Goswami, Manish Bansal, Deepak Kumar Rathore, Rajesh Kumar, Sweety Samal
No abstract text is available yet for this article.
February 26, 2024: Protein Journal
https://read.qxmd.com/read/38347327/the-structural-features-of-mlad-illuminate-its-unique-ligand-transporting-mechanism-and-ancestry
#15
JOURNAL ARTICLE
Angshu Dutta, Shankar Prasad Kanaujia
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...
February 12, 2024: Protein Journal
https://read.qxmd.com/read/38347326/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
#16
JOURNAL ARTICLE
Erika Maria Gomes Ferreira Teixeira, Dario Eluam Kalume, Patrícia Fernandes Ferreira, Thayane Aparecida Alves, Ana Paula G A Fontão, André Luís Franco Sampaio, Danilo Ribeiro de Oliveira, José Andrés Morgado-Díaz, Raquel Elisa Silva-López
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...
February 12, 2024: Protein Journal
https://read.qxmd.com/read/38265733/refolding-crystallization-and-crystal-structure-analysis-of-a-scavenger-receptor-cysteine-rich-domain-of-human-salivary-agglutinin-expressed-in-escherichia-coli
#17
JOURNAL ARTICLE
Changyu Zhang, Peng Lu, Sibo Wei, Chaoyue Hu, Mitsuko Miyoshi, Ken Okamoto, Hideaki Itoh, Suguru Okuda, Michio Suzuki, Hiroshi Kawakami, Koji Nagata
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...
January 24, 2024: Protein Journal
https://read.qxmd.com/read/38265732/interaction-of-cecropin-a-1-7-analogs-with-dna-analyzed-by-multi-spectroscopic-methods
#18
JOURNAL ARTICLE
Libo Yuan, Ke Wang, Yuan Fang, Xiujuan Xu, Yingcun Chen, Dongxin Zhao, Kui Lu
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...
January 24, 2024: Protein Journal
https://read.qxmd.com/read/38180586/heterologous-production-of-antimicrobial-peptides-notes-to-consider
#19
REVIEW
Masoumeh Kordi, Parnian Ghaedi Talkhounche, Helia Vahedi, Naser Farrokhi, Maryam Tabarzad
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...
January 5, 2024: Protein Journal
https://read.qxmd.com/read/38127183/biochemical-characterization-of-laccase-from-spirulina-cpcc-695-and-their-role-in-estrone-degradation
#20
JOURNAL ARTICLE
Neha Sami, Bushra Afzal, Durdana Yasin, Tasneem Fatma
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...
February 2024: Protein Journal
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