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Protein Journal

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https://read.qxmd.com/read/30759302/two-approaches-to-enhance-the-processivity-and-salt-tolerance-of-staphylococcus-aureus-dna-polymerase
#1
Bing Zhai, Joseph Chow, Qi Cheng
In this article, two engineering-strategies were carried out to enhance the processivity of the DNA polymerase used in recombinase polymerase amplification (RPA). We demonstrate that covalent linkage of a non-specific, double-stranded DNA binding protein, Sso7d, to the large fragment of Staphylococcus aureus Pol I (Sau) caused a moderate enhancement of processivity and a significant improvement in the salt tolerance of Sau. Meanwhile, we provide evidence suggesting that insertion of the thioredoxin-binding domain from bacteriophage T7 DNA polymerase into the analogous position of the large fragment of Sau dramatically enhanced the processivity and mildly increased the salt tolerance of Sau when a host DNA binding protein, thioredoxin, was annexed...
February 13, 2019: Protein Journal
https://read.qxmd.com/read/30747325/2019-letter-from-the-editor-in-chief
#2
EDITORIAL
Lawrence J Berliner
No abstract text is available yet for this article.
February 12, 2019: Protein Journal
https://read.qxmd.com/read/30719619/scalable-non-denaturing-purification-of-phosphoproteins-using-ga-3-imac-n2a-and-m1m2-titin-components-as-study-case
#3
Michael Adams, Jennifer R Fleming, Eva Riehle, Tiankun Zhou, Thomas Zacharchenko, Marija Markovic, Olga Mayans
The purification of phosphorylated proteins in a folded state and in large enough quantity for biochemical or biophysical analysis remains a challenging task. Here, we develop a new implementation of the method of gallium immobilized metal chromatography (Ga3+ -IMAC) as to permit the selective enrichment of phosphoproteins in the milligram scale and under native conditions using automated FPLC instrumentation. We apply this method to the purification of the UN2A and M1M2 components of the muscle protein titin upon being monophosphorylated in vitro by cAMP-dependent protein kinase (PKA)...
February 4, 2019: Protein Journal
https://read.qxmd.com/read/30707333/determination-of-the-activity-of-1-deoxy-d-xylulose-5-phosphate-synthase-by-pre-column-derivatization-hplc-using-1-2-diamino-4-5-methylenedioxybenzene-as-a-derivatizing-reagent
#4
Yan-Fei Liang, Hui Liu, Heng Li, Wen-Yun Gao
α-Ketoacids can be determined by HPLC through pre-column derivatization with 1,2-diamino-4,5-methylenedioxybenzene (DMB) as a derivatizing reagent. Using this method, the specific activity and the steady-state kinetic of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) were measured. Firstly, DXS substrate pyruvate was derivatized with DMB in acidic solution; then the corresponding quinoxalinone was elucidated by LC-ESI-MS and quantified by HPLC-UV. The optimum derivatization conditions were as follows: aqueous medium at pH 1...
February 1, 2019: Protein Journal
https://read.qxmd.com/read/30701485/computational-investigation-on-electrostatic-loop-mutants-instigating-destabilization-and-aggregation-on-human-sod1-protein-causing-amyotrophic-lateral-sclerosis
#5
E Srinivasan, R Rajasekaran
Mutations in the gene encoding Cu/Zn Superoxide Dismutase 1 (SOD1) protein are contemplated to be a protruding reason for Amyotrophic lateral sclerosis (ALS), which leads towards protein aggregation, misfolding and destabilization. Thus, we investigated the systematic action of entire mutations reported on electrostatic loop of SOD1 protein through thermodynamical and discrete molecular dynamics (DMD) studies. Accordingly, we analyzed the outcomes distinctly for screening the mutant structures having both, deleterious and destabilizing effect...
January 30, 2019: Protein Journal
https://read.qxmd.com/read/30697667/the-amphibian-diacylglycerol-o-acyltransferase-2-dgat2-a-paleo-protein-with-conserved-function-but-unique-folding
#6
Juliana M Sciani, Adriana Neves, Ruth C Vassão, Patrick Spencer, Marta M Antoniazzi, Carlos Jared, Daniel C Pimenta
Amphibians are, currently, considered the first vertebrates that had performed the aquatic to terrestrial transition during evolution; therefore, water balance and dehydration control were prerequisites for such environment conquering. Among anurans, Phyllomedusa is a well-studied genus, due to its peptide-rich skin secretion. Here, we have analyzed the skin secretion of Phyllomedusa distincta targeting the proteins present in the skin secretion. The major soluble protein was chromatographically isolated and utilized to immunize rabbits...
January 29, 2019: Protein Journal
https://read.qxmd.com/read/30684070/genetic-analysis-of-protein-translocation
#7
REVIEW
Thomas J Silhavy, Angela M Mitchell
Cells in all domains of life must translocate newly synthesized proteins both across membranes and into membranes. In eukaryotes, proteins are translocated into the lumen of the ER or the ER membrane. In prokaryotes, proteins are translocated into the cytoplasmic membrane or through the membrane into the periplasm for Gram-negative bacteria or the extracellular space for Gram-positive bacteria. Much of what we know about protein translocation was learned through genetic selections and screens utilizing lacZ gene fusions in Escherichia coli...
January 25, 2019: Protein Journal
https://read.qxmd.com/read/30666487/optimized-procedure-for-recovering-hiv-1-protease-c-sa-from-inclusion-bodies
#8
Sibusiso B Maseko, Deidre Govender, Thavendran Govender, Tricia Naicker, Johnson Lin, Glenn E M Maguire, Hendrik G Kruger
HIV-1 is an infectious virus that causes acquired immunodeficiency syndrome (AIDS) and it is one of the major causes of deaths worldwide. The production of HIV-1 protease (PR) on a large scale has been a problem for scientists due to its cytotoxicity, low yield, insolubility, and low activity. HIV-1 C-SA protease has been cloned, expressed, and purified previously, however, with low recovery (0.25 mg/L). Herein we report an optimal expression and solubilisation procedure to recover active HIV-1 C-SA protease enzyme from inclusion bodies...
January 21, 2019: Protein Journal
https://read.qxmd.com/read/30666486/adenylate-kinase-a-ubiquitous-enzyme-correlated-with-medical-conditions
#9
REVIEW
Mihaela Ileana Ionescu
Adenylate kinase is a small, usually monomeric, enzyme found in every living thing due to its crucial role in energetic metabolism. This paper outlines the most relevant data about adenylate kinases isoforms, and the connection between dysregulation or mutation of human adenylate kinase and medical conditions. The following datadases were consulted: National Centre for Biotechnology Information, Protein Data Bank, and Mouse Genomic Informatics. The SmartBLAST tool, EMBOSS Needle Program, and Clustal Omega Program were used to analyze the best protein match, and to perform pairwise sequence alignment and multiple sequence alignment...
January 21, 2019: Protein Journal
https://read.qxmd.com/read/30628007/identification-of-novel-binding-partners-for-transcription-factor-emx2
#10
Jennifer A Groves, Cody Gillman, Cierra N DeLay, Todd T Kroll
The mammalian homolog of Drosophila empty spiracles 2 (Emx2) is a homeobox transcription factor that plays central roles in early development of the inner ear, pelvic and shoulder girdles, cerebral cortex, and urogenital organs. The role for Emx2 is best understood within the context of the development of the neocortical region of the cortex, where Emx2 is expressed in a high posterior-medial to low anterior-lateral gradient that regulates the partitioning of the neocortex into different functional fields that perform discrete computational tasks...
January 9, 2019: Protein Journal
https://read.qxmd.com/read/30604108/grafting-stripping-and-stapling-of-helical-peptides-from-the-dimerization-interface-of-onfh-related-bone-morphogenetic-protein-2
#11
Wenqi Song, Kunzheng Wang, Wei Wang, Pei Yang, Xiaoqian Dang
Transforming growth factor-β/bone morphogenetic protein (TGF-β/BMP) signaling plays a fundamental role in embryonic skeletal development and postnatal bone homeostasis. The signaling pivot protein BMP-2 belongs to the TGF-β superfamily and has been implicated in the pathogenesis of osteonecrosis of femoral head (ONFH). The biologically functional BMP-2 is a homodimer that has two tightly packed cores at its dimerization interface; each core is defined by the intermolecular interaction between a helical arm from one monomer and a hydrophobic pocket from another monomer...
January 2, 2019: Protein Journal
https://read.qxmd.com/read/30604107/trans-sialidase-protein-as-a-potential-serological-marker-for-african-trypanosomiasis
#12
Ana Filipa Teixeira, João Gomes Pereira, Sónia Pestana-Ascensão, Marcelo Sousa Silva
Trypanosoma brucei is the etiological agent of African trypanosomiasis responsible for human and animal infections. T. brucei is transmitted by infected tsetse flies. There is no vaccine for the disease and drugs available for treatment are inefficient and high toxicity. In this context, it is a priority to find antigenic targets suitable for the development of new diagnostic tools, drugs and vaccines. In this work, we report that mice infected with T. b. brucei produce antibodies against trans-sialidase recombinant protein (TS)...
January 2, 2019: Protein Journal
https://read.qxmd.com/read/30564965/changes-due-to-ageing-in-the-glycan-structure-of-alpha-2-macroglobulin-and-its-reactivity-with-ligands
#13
Miloš Šunderić, Martina Križáková, Vesna Malenković, Danica Ćujić, Jaroslav Katrlík, Olgica Nedić
Alpha-2-macroglobulin (α2M) is a molecule generally associated with inflammation, and chronic inflammation is associated with ageing and cancer. The degree of inflammation was recently proposed to be considered as a biomarker of biological ageing. In this study, glycans attached to α2M were analysed in a human population of different ages by lectin-based protein microarray. Higher reactivity of α2M with several lectins was detected in older individuals indicating an increased content of specific monosaccharides: α2,6 sialic acid, mannose and N-acetylglucosamine, and multiantennary complex type N-glycans...
December 18, 2018: Protein Journal
https://read.qxmd.com/read/30511317/genome-wide-analysis-of-wd40-proteins-in-saccharomyces-cerevisiae-and-their-orthologs-in-candida-albicans
#14
Buddhi Prakash Jain
The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc...
December 3, 2018: Protein Journal
https://read.qxmd.com/read/30367348/application-of-proteomics-technologies-in-oil-palm-research
#15
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://read.qxmd.com/read/30361938/effect-of-60-co-gamma-ionizing-radiation-and-desiccation-stress-on-protein-profile-of-anabaena-7120
#16
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://read.qxmd.com/read/30343346/proteomic-analysis-of-human-dermal-fibroblast-conditioned-medium-dfcm
#17
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://read.qxmd.com/read/30334121/low-energy-conformations-for-s100-binding-peptide-from-the-negative-regulatory-domain-of-p53
#18
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://read.qxmd.com/read/30328548/kinetic-analyses-of-the-substrate-inhibition-of-paramecium-arginine-kinase
#19
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://read.qxmd.com/read/30267300/comparative-modeling-and-evaluation-of-leukotriene-b4-receptors-for-selective-drug-discovery-towards-the-treatment-of-inflammatory-diseases
#20
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
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