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Protein Journal

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https://www.readbyqxmd.com/read/30367348/application-of-proteomics-technologies-in-oil-palm-research
#1
REVIEW
Benjamin Yii Chung Lau, Abrizah Othman, Umi Salamah Ramli
Proteomics technologies were first applied in the oil palm research back in 2008. Since proteins are the gene products that are directly correspond to phenotypic traits, proteomic tools hold a strong advantage above other molecular tools to comprehend the biological and molecular mechanisms in the oil palm system. These emerging technologies have been used as non-overlapping tools to link genome-wide transcriptomics and metabolomics-based studies to enhance the oil palm yield and quality through sustainable plant breeding...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30361938/effect-of-60-co-gamma-ionizing-radiation-and-desiccation-stress-on-protein-profile-of-anabaena-7120
#2
Harinder Singh, Shree Kumar Apte
Physiological stress can bring major molecular and cellular change to a living cell which further decide its survival or tolerance to the stress exposure. Cyanobacteria like Anabaena has been shown to tolerate high levels of different stresses like oxidative, desiccation, UV, and gamma radiation. They are able to withstand and recover remarkably without any lethal mutation when exposed to high doses of gamma radiation or prolonged duration of desiccation. In the present work, the modifications in protein profiles of Anabaena 7120 cells after exposure to 6 kGy of 60 Co γ-rays and 6 days of desiccation, and the proteome dynamics during post stress recovery were investigated...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30343346/proteomic-analysis-of-human-dermal-fibroblast-conditioned-medium-dfcm
#3
Manira Maarof, Yogeswaran Lokanathan, Hj Idrus Ruszymah, Aminuddin Saim, Shiplu Roy Chowdhury
Growth factors and extracellular matrix (ECM) proteins are involved in wound healing. Human dermal fibroblasts secrete wound-healing mediators in culture medium known as dermal fibroblast conditioned medium (DFCM). However, the composition and concentration of the secreted proteins differ with culture conditions and environmental factors. We cultured human skin fibroblasts in vitro using serum-free keratinocyte-specific media (EpiLife™ Medium [KM1] and defined keratinocyte serum-free medium [KM2]) and serum-free fibroblast-specific medium (FM) to obtain DFCM-KM1, DFCM-KM2 and DFCM-FM, respectively...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30334121/low-energy-conformations-for-s100-binding-peptide-from-the-negative-regulatory-domain-of-p53
#4
Robert P Carty, Bo Lin, Daniel Fridman, Matthew R Pincus
We have computed the low energy conformations of the negative regulatory domain of p53, residues 374-388 using Empirical Conformational Energies of Peptides Program including solvation and computed the statistical weights of distinct conformational states. We find that there are two high probability conformations, one an α-helix from Lys 374-Lys 381, followed by another helical structure involving Lys 382-Glu 388 (statistical weight of 0.48) and an all-α-helix for the entire sequence (statistical weight of 0...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30328548/kinetic-analyses-of-the-substrate-inhibition-of-paramecium-arginine-kinase
#5
Daichi Yano, Tomohiko Suzuki
Paramecium tetraurelia expresses four types of arginine kinase (AK1-AK4). In a previous study, we showed that AK3 is characterized by typical arginine substrate inhibition, where enzymatic activity markedly decreases near a concentration of 1 mM of arginine substrate. This is in sharp contrast to the three other AK types, which obey the Michaelis-Menten reaction curve. Since cellular arginine concentration in another ciliate Tetrahymena is estimated to be 3-15 mM in vivo, Paramecium AK3 likely functions in conditions that are strongly affected by substrate inhibition...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30267300/comparative-modeling-and-evaluation-of-leukotriene-b4-receptors-for-selective-drug-discovery-towards-the-treatment-of-inflammatory-diseases
#6
Mahmoud A A Ibrahim, Alaa M A Hassan
Leukotriene B4 (LTB4) exerts its biological effects through stimulation of specific G protein-coupled receptors (GPCRs)-namely BLT1 and BLT2. Due to the absence of human BLT1 and BLT2 crystal structures, the current study was set to predict the 3D structures of these two receptors for structure-based anti-inflammatory drug discovery. Homology modeling of the BLT1 receptor was first constructed, based on various X-ray and NMR GPCR templates, followed by molecular dynamics (MD) refinement. Using a single-template approach, nine well-established alignment methods and ten secondary structure prediction methods during the backbone generation were implemented and assessed...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30259302/family-wide-characterization-of-histone-binding-abilities-of-phd-domains-of-al-proteins-in-arabidopsis-thaliana
#7
Xiao Liang, Ming Lei, Fangzhou Li, Xiajie Yang, Mengqi Zhou, Bing Li, Yu Cao, Siying Gong, Ke Liu, Jinlin Liu, Chao Qi, Yanli Liu
Alfin1-like (AL) is a family of proteins homologous to the alfalfa Alfin1 in plant and bears an Alfin domain and a PHD domain at their N- and C-terminus, respectively. There are 7 AL proteins in Arabidopsis, and the PHD domains of most AL proteins are reported to bind to histone H3K4me3. Here we reported gene cloning, protein expression and purification of the PHD domains of all the AL family proteins in Arabidopsis. We then systematically characterized their histone binding abilities by quantitative isothermal titration calorimetry and fluorescence polarization binding assays...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30259240/identification-of-receptor-ligands-in-apo-b100-reveals-potential-functional-domains
#8
Juan Guevara, Jamie Romo, Ernesto Hernandez, Natalia Valentinova Guevara
LDL, VLDL and other members of the low-density lipoparticles (LLPs) enter cells through a large family of receptors. The actual receptor ligand(s) in apolipoprotein B100, one of the main proteins of LLP, remain(s) unknown. The objective of this study was to identify true receptor ligand(s) in apo B100, a molecule of 4563 residues. Apo B100 contains 33 analogues of Cardin-Weintraub arginine/lysine-based receptor ligand motifs and shares key lysine motifs and sequence similarity with the LDL receptor-associated protein, MESD, and heat shock proteins...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30251087/structural-identification-and-systematic-comparison-of-phorbol-ester-dioleoylglycerol-alcohol-and-sevoflurane-binding-sites-in-pkc%C3%AE-c1a-domain
#9
Lijie Shi
Protein kinase C (PKC) is a family of signal transducing enzymes that have been implicated in anesthetic preconditioning signaling cascade. Evidences are emerging that certain exogenous neuromodulators such as n-alkanols and general anesthetics can stimulate PKC activity by binding to regulatory C1A domain of the enzyme. However, the accurate binding sites in C1A domain as well as the molecular mechanism underlying binding-stimulated PKC activation still remain unelucidated. Here, we report a systematic investigation of the intermolecular interaction of human PKCδ C1A domain with its natural activator phorbol ester (PE) and co-activator dioleoylglycerol (DOG) as well as exogenous stimulators butanol, octanol and sevoflurane...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30242660/c-el-phosphatome-a-catalogue-of-actual-and-pseudo-phosphatases-based-on-in-silico-studies-in-caenorhabditis-elegans
#10
Soobiya Fatima, Shikha Shukla, Aamir Nazir
Phosphatases are well known to carry out important functions via counter activity of kinases and they serve as mechanism for dephosphorylating the monophosphate esters from the phosphorylated serine, threonine, tyrosine and histidine residues. The biological relevance of phosphatases could be explored further employing newer technologies and models. Caenorhabditis elegans is a powerful genetic model system that bears significant homology with humans, hence providing with a precious tool towards studying important signalling pathways...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30232697/exploring-the-structural-mechanism-of-covalently-bound-e3-ubiquitin-ligase-catalytic-or-allosteric-inhibition
#11
Imane Bjij, Shama Khan, Robin Betz, Driss Cherqaoui, Mahmoud E S Soliman
Covalent inhibition has recently gained a resurgence of interest in several drug discovery areas. The expansion of this approach is based on evidence elucidating the selectivity and potency of covalent inhibitors when bound to particular amino acids of a biological target. The Nedd4-1, an E3 ubiquitin ligase, is characterized by two covalent binding sites, of which catalytic Cyscat and allosteric Cysallo are enclosed. This enzyme has demonstrated inhibition at both the above-mentioned binding sites; however, a detailed molecular understanding of the structural mechanism of inhibition upon Cyscat and Cysallo binding remains vague...
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30120635/correction-to-variability-of-some-milk-associated-genes-and-proteins-in-several-breeds-of-saudi-arabian-camels
#12
Elrashdy M Redwan, Saleh A Alkarim, Amr A El-Hanafy, Yasser M Saad, Hussein A Almehdar, Vladimir N Uversky
The original version of this article contained mistakes in author names and affiliations. The last names of the authors Salah Korim, Amro Samra, and Hussein A. Amhedar were misspelled. The corrected spelling is Saleh A. Alkarim, Amr A. El-Hanafy, and Hussein A. Almehdar. The correct list of author names and affiliations are published with this erratum.
December 2018: Protein Journal
https://www.readbyqxmd.com/read/30128635/synthesis-and-biological-activity-of-scyllatoxin-based-bh3-domain-mimetics-containing-two-disulfide-linkages
#13
Danushka Arachchige, Justin M Holub
The B cell lymphoma 2 (BCL2) proteins are a family of evolutionarily related proteins that act as positive or negative regulators of the intrinsic apoptosis pathway. Overexpression of anti-apoptotic BCL2 proteins in cells is associated with apoptotic resistance, which can result in cancerous phenotypes and pathogenic cell survival. Consequently, anti-apoptotic BCL2 proteins have attracted considerable interest as therapeutic targets. We recently reported the development of a novel class of synthetic protein based on scyllatoxin (ScTx) designed to mimic the helical BH3 interaction domain of the pro-apoptotic BCL2 protein Bax...
October 2018: Protein Journal
https://www.readbyqxmd.com/read/30123929/characterization-of-a-theme-c-glycoside-hydrolase-family-9-endo-beta-glucanase-from-a-biogas-reactor-metagenome
#14
Carola Schröder, Christin Burkhardt, Philip Busch, Georg Schirrmacher, Jörg Claren, Garabed Antranikian
From a biogas reactor metagenome an ORF (bp_cel9A) encoding a bacterial theme C glycoside hydrolase family 9 (GH9) enzyme was recombinantly produced in E. coli BL21 pQE-80L. BP_Cel9A exhibited ≤ 55% identity to annotated sequences. Subsequently, the enzyme was purified to homogeneity by affinity chromatography. The endo-beta-glucanase BP_Cel9A hydrolyzed the beta-1,3-1,4-linked barley beta-glucan with 24 U/mg at 30 °C and pH 6.0. More than 62% of activity was measured between 10 and 40 °C. Lichenan and xyloglucan were hydrolyzed with 67% and 40% of activity, respectively...
October 2018: Protein Journal
https://www.readbyqxmd.com/read/30123928/multifunctional-proteins-involvement-in-human-diseases-and-targets-of-current-drugs
#15
Luis Franco-Serrano, Mario Huerta, Sergio Hernández, Juan Cedano, JosepAntoni Perez-Pons, Jaume Piñol, Angel Mozo-Villarias, Isaac Amela, Enrique Querol
Multifunctionality or multitasking is the capability of some proteins to execute two or more biochemical functions. The objective of this work is to explore the relationship between multifunctional proteins, human diseases and drug targeting. The analysis of the proportion of multitasking proteins from the MultitaskProtDB-II database shows that 78% of the proteins analyzed are involved in human diseases. This percentage is much higher than the 17.9% found in human proteins in general. A similar analysis using drug target databases shows that 48% of these analyzed human multitasking proteins are targets of current drugs, while only 9...
October 2018: Protein Journal
https://www.readbyqxmd.com/read/30097831/expression-and-functional-characterization-of-pseudomonas-aeruginosa-recombinant-l-asparaginase
#16
Hesham Saeed, Hadeer Soudan, Amany El-Sharkawy, Aida Farag, Amira Embaby, Farid Ataya
Recombinant l .asparaginase, L.ASNase, from Pseudomonas aeruginosa was purified using nickel affinity chromatography. The affinity purified L.ASNase exhibited a protein band with a molecular weight of 72.4 kDa on a native polyacrylamide gel and 36.276 kDa using SDS-PAGE. The activity of the purified L.ASNase was enhanced by Mg2+ and inhibited by Zn2+ at a concentration of 5 mM. The specificity of the recombinant L.ASNase towards different substrates was examined, and it was found that the enzyme showed the highest activity towards l...
October 2018: Protein Journal
https://www.readbyqxmd.com/read/30097830/nonfunctional-missense-mutants-in-two-well-characterized-cytosolic-enzymes-reveal-important-information-about-protein-structure-and-function
#17
Ashley E Cole, Fatmah M Hani, Brian W Allen, Paul C Kline, Elliot Altman
The isolation and characterization of 42 unique nonfunctional missense mutants in the bacterial cytosolic β-galactosidase and catechol 2,3-dioxygenase enzymes allowed us to examine some of the basic general trends regarding protein structure and function. A total of 6 out of the 42, or 14.29% of the missense mutants were in α-helices, 17 out of the 42, or 40.48%, of the missense mutants were in β-sheets and 19 out of the 42, or 45.24% of the missense mutants were in unstructured coil, turn or loop regions...
October 2018: Protein Journal
https://www.readbyqxmd.com/read/30069656/wd40-repeat-proteins-signalling-scaffold-with-diverse-functions
#18
REVIEW
Buddhi Prakash Jain, Shweta Pandey
The WD40 domain is one of the most abundant and interacting domains in the eukaryotic genome. In proteins the WD domain folds into a β-propeller structure, providing a platform for the interaction and assembly of several proteins into a signalosome. WD40 repeats containing proteins, in lower eukaryotes, are mainly involved in growth, cell cycle, development and virulence, while in higher organisms, they play an important role in diverse cellular functions like signal transduction, cell cycle control, intracellular transport, chromatin remodelling, cytoskeletal organization, apoptosis, development, transcriptional regulation, immune responses...
October 2018: Protein Journal
https://www.readbyqxmd.com/read/30019321/evolutionarily-related-dihydrofolate-reductases-perform-coequal-functions-yet-show-divergence-in-their-trajectories
#19
REVIEW
Naira Rashid, Pratima Chaudhuri Chattopadhyay
The enzyme dihydrofolate reductase (DHFR) catalyzes NADPH dependent reduction of dihydrofolate to tetrahydrofolate. It plays a crucial role in the DNA synthesis. The investigation of evolution of DHFR generates immense curiosity. It aids in predicting how the enzyme has adapted to the surroundings of various cell types. In spite of great similarity in the structure of E. coli DHFR and human DHFR, their primary sequences are divergent to a great extent, which is evident in variations in the kinetics mechanism of their catalysis...
August 2018: Protein Journal
https://www.readbyqxmd.com/read/30014259/comparative-profiling-of-three-atheris-snake-venoms-a-squamigera-a-nitschei-and-a-chlorechis
#20
He Wang, Xiaole Chen, Enrico König, Mei Zhou, Lei Wang, Tianbao Chen, Chris Shaw
A proteomic and transcriptomic comparative analysis of the venoms of three Atheris species (A. squamigera, A. nitschei and A. chlorechis) was carried out by size exclusion liquid chromatography, gel electrophoresis, mass spectrometry, and mRNA sequencing. The improved proteomic profiling utilised in this work was combined with transcript studies, advancing our insights into venom composition, protein distribution and inter-species variation among the three bush vipers. Crude venoms of all three samples contained at least 10-20 protein components, ranging in size from ≤ 3 to > 98 kDa...
August 2018: Protein Journal
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