keyword
https://read.qxmd.com/read/38293990/-bioinformatics-analysis-and-validation-of-the-interaction-between-pml-protein-and-tab1-protein
#21
JOURNAL ARTICLE
J Cheng, Z Li, Y Liu, C Li, X Huang, Y Tian, F Shen
OBJECTIVE: To analyze the interaction between PML protein and TAB1 protein using bioinformatic approaches and experimentally verify the results. METHODS: Using Rosetta software, a 3D model of TAB1 protein was constructed through a comparative modeling approach; the secondary structure of PML protein was retrieved in the PDB database and its crystal structure and 3D structure were resolved. Zdock 3.0.2 software was used to perform protein-protein docking of PML and TAB1, and the best conformation was extracted for molecular structure analysis of the docking model...
January 20, 2024: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://read.qxmd.com/read/38281859/metabolome-analysis-of-metabolic-burden-in-escherichia-coli-caused-by-overexpression-of-green-fluorescent-protein-and-delta-rhodopsin
#22
JOURNAL ARTICLE
Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y Hara, Yoko Hirono-Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda
Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E. coli strains have distinct metabolic capacities. In this study, two proteins were overexpressed in four E. coli strains (MG1655(DE3), W3110(DE3), BL21star(DE3), and Rosetta(DE3)), and their effects on metabolic burden were investigated...
January 27, 2024: Journal of Bioscience and Bioengineering
https://read.qxmd.com/read/38280431/proteomics-modeling-and-fluorescence-assays-delineate-cytochrome-b-5-residues-involved-in-binding-and-stimulation-of-cytochrome-p450-17a1-17-20-lyase
#23
JOURNAL ARTICLE
Yasuhiro Tateishi, Stephany N Webb, Bian Li, Lu Liu, Kristie Lindsey Rose, Micheal Leser, Purvi Patel, F Peter Guengerich
Cytochrome b5 (b5 ) is known to stimulate some catalytic activities of cytochrome P450 (P450, CYP) enzymes, although mechanisms still need to be defined. The reactions most strongly enhanced by b5 are the 17,20-lyase reactions of P450 17A1 involved in steroid biosynthesis. We had previously used a fluorescently labeled human b5 variant (Alexa 488-T70C-b5 ) to characterize human P450 17A1-b5 interactions, but subsequent proteomic analyses indicated that lysines in b5 were also modified with Alexa 488 maleimide in addition to Cys-70, due to disulfide dimerization of the T70C mutant...
January 25, 2024: Journal of Biological Chemistry
https://read.qxmd.com/read/38252125/design-principles-for-inflammasome-inhibition-by-pyrin-only-proteins
#24
JOURNAL ARTICLE
Shuai Wu, Archit Garg, Zachary Mazanek, Gretchen Belotte, Jeffery J Zhou, Christina M Stallings, Jacob Lueck, Aubrey Roland, Michael A Chattergoon, Jungsan Sohn
Inflammasomes are filamentous signaling platforms essential for host defense against various intracellular calamities such as pathogen invasion and genotoxic stresses. However, dysregulated inflammasomes cause an array of human diseases including autoinflammatory disorders and cancer. It was recently identified that endogenous pyrin-only-proteins (POPs) regulate inflammasomes by directly inhibiting their filament assembly. Here, by combining Rosetta in silico, in vitro, and in cellulo methods, we investigate the target specificity and inhibition mechanisms of POPs...
January 22, 2024: ELife
https://read.qxmd.com/read/38235376/next-generation-of-multispecific-antibody-engineering
#25
REVIEW
Daniel Keri, Matt Walker, Isha Singh, Kyle Nishikawa, Fernando Garces
Multispecific antibodies recognize two or more epitopes located on the same or distinct targets. This added capability through protein design allows these man-made molecules to address unmet medical needs that are no longer possible with single targeting such as with monoclonal antibodies or cytokines alone. However, the approach to the development of these multispecific molecules has been met with numerous road bumps, which suggests that a new workflow for multispecific molecules is required. The investigation of the molecular basis that mediates the successful assembly of the building blocks into non-native quaternary structures will lead to the writing of a playbook for multispecifics...
January 2024: Antibody Therapeutics
https://read.qxmd.com/read/38205774/comparison-of-five-escherichia-coli-strains-to-achieve-the-maximum-yield-of-a-recombinant-immunotoxin-consisting-of-an-antibody-against-vegf-conjugated-with-map30-toxin-in-a-benchtop-bioreactor
#26
JOURNAL ARTICLE
Mina Zarei, Mohammad Hossein Morowvat
BACKGROUND: Cancer is among the leading causes of death worldwide, imposing high costs on the health systems of all societies. Extensive biological studies are required to discover appropriate therapies. Escherichia coli has long been regarded as one of the main biotechnological bio-factories to produce recombinant protein-based therapeutics. In the present study, five strains of E. coli were compared to achieve the maximum production of a previously designed recombinant immunotoxin-carrying MAP30 toxin against VEGF-overexpressed cancer cells in a benchtop bioreactor...
2024: Recent Patents on Biotechnology
https://read.qxmd.com/read/38191802/varpa-in-silico-additive-screening-for-protein-based-lighting-devices
#27
JOURNAL ARTICLE
Jesús Agustín Banda-Vázquez, Alexander Mauz, Juan Pablo Fuenzalida Werner, Rubén D Costa
Protein optoelectronics is an emerging field facing implementation and stabilization challenges of proteins in harsh non-natural environments, such as dry polymers, inorganic materials, etc., operating at high temperatures/irradiations. In this context, additives promoting structural and functional protein stabilization are paramount to realize highly performing devices. On one hand, trial-error experimental assays based on previous knowledge of classical additives in aqueous solutions are effort/time-consuming, while their translation to water-less matrices is uncertain...
January 8, 2024: Small Methods
https://read.qxmd.com/read/38187664/invariant-point-message-passing-for-protein-side-chain-packing
#28
Nicholas Z Randolph, Brian Kuhlman
Protein side chain packing (PSCP) is a fundamental problem in the field of protein engineering, as high-confidence and low-energy conformations of amino acid side chains are crucial for understanding (and designing) protein folding, protein-protein interactions, and protein-ligand interactions. Traditional PSCP methods (such as the Rosetta Packer) often rely on a library of discrete side chain conformations, or rotamers, and a forcefield to guide the structure to low-energy conformations. Recently, deep learning (DL) based methods (such as DLPacker, AttnPacker, and DiffPack) have demonstrated state-of-the-art predictions and speed in the PSCP task...
December 21, 2023: bioRxiv
https://read.qxmd.com/read/38184160/expression-purification-characterization-and-crystallization-of-panax-quinquefolius-ginsenoside-glycosyltransferase-pq3-o-ugt2
#29
JOURNAL ARTICLE
Qiushuang Ji, Yirong Liu, Cheng Chen, Huanyu Zhang, Juan Wang, Kunrong Mei
Pq3-O-UGT2, derived from Panax quinquefolius, functions as a ginsenoside glucosyltransferase, utilizing UDP-glucose (UDPG) as the sugar donor to catalyze the glycosylation of Rh2 and F2. An essential step in comprehending its catalytic mechanism involves structural analysis. In preparation for structural analysis, we expressed Pq3-O-UGT2 in the Escherichia coli (E. coli) strain Rosetta (DE3). The recombinant Pq3-O-UGT2 was purified through Ni-NTA affinity purification, a two-step ion exchange chromatography, and subsequently size-exclusion chromatography (SEC)...
January 4, 2024: Protein Expression and Purification
https://read.qxmd.com/read/38172216/functional-characterization-of-a-manganese-superoxide-dismutase-from-avicennia-marina-insights-into-its-role-in-salt-hydrogen-peroxide-and-heavy-metal-tolerance
#30
JOURNAL ARTICLE
Hamid Abedi, Azar Shahpiri
Avicennia marina is a salt-tolerance plant with high antioxidant and antibacterial potential. In the present work, a gene encoding MnSOD from Avicennia marina (AmSOD2) was cloned in the expression vectors pET28a. The resulting constructs were transformed into Escherichia coli strains Rosetta (DE3). Following the induction with Isopropyl β-D-1-thiogalactopyranoside, the protein His-AmSOD2 was expressed but dominantly found in the insoluble fraction of strain R-AmSOD2. Due to detection of mitochondrial transit peptide in the amino acid sequence of AmSOD2, the transit peptide was removed and AmSOD2 without transit peptide (tAmSOD2) was expressed in E...
January 3, 2024: Scientific Reports
https://read.qxmd.com/read/38171930/comprehensive-assessment-of-protein-loop-modeling-programs-on-large-scale-datasets-prediction-accuracy-and-efficiency
#31
JOURNAL ARTICLE
Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Tingjun Hou
Protein loops play a critical role in the dynamics of proteins and are essential for numerous biological functions, and various computational approaches to loop modeling have been proposed over the past decades. However, a comprehensive understanding of the strengths and weaknesses of each method is lacking. In this work, we constructed two high-quality datasets (i.e. the General dataset and the CASP dataset) and systematically evaluated the accuracy and efficiency of 13 commonly used loop modeling approaches from the perspective of loop lengths, protein classes and residue types...
November 22, 2023: Briefings in Bioinformatics
https://read.qxmd.com/read/38166591/molecular-identification-and-functional-characterization-of-a-transcription-factor-gerav1-from-gelsemium-elegans
#32
JOURNAL ARTICLE
Tianzhen Cui, Shoujian Zang, Xinlu Sun, Jing Zhang, Yachun Su, Dongjiao Wang, Guran Wu, Ruiqi Chen, Youxiong Que, Qing Lin, Chuihuai You
BACKGROUND: Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported. RESULTS: In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G...
January 2, 2024: BMC Genomics
https://read.qxmd.com/read/38159570/recognition-of-the-trna-structure-everything-everywhere-but-not-all-at-once
#33
REVIEW
Jinwei Zhang
tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers literally bridge the worlds of RNAs and proteins, and serve as Rosetta stones that decipher and interpret the genetic code. Their ubiquitous presence, functional irreplaceability, and privileged access to cellular compartments and ribosomes render them prime targets for both endogenous regulation and exogenous manipulation. There is essentially no part of the tRNA that is not touched by another interaction partner, either as programmed or imposed by an external adversary...
December 27, 2023: Cell Chemical Biology
https://read.qxmd.com/read/38149850/molecular-docking-and-md-simulations-reveal-protease-inhibitors-block-the-catalytic-residues-in-prp8-intein-of-aspergillus-fumigatus-a-potential-target-for-antimycotics
#34
JOURNAL ARTICLE
Sunita Panda, Madhusmita Rout, Sarbani Mishra, Jyotirmayee Turuk, Sanghamitra Pati, Budheswar Dehury
Resistance to azoles and amphotericin B especially in Aspergillus fumigatus is a growing concern towards the treatment of invasive fungal infection. At this critical juncture, intein splicing would be a productive, and innovative target to establish therapies against resistant strains. Intein splicing is the central event for the activation of host protein, essential for the growth and survival of various microorganisms including A. fumigatus . The splicing process is a four-step protease-like nucleophilic cascade...
December 27, 2023: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/38147991/-preparation-of-colloidal-gold-test-strips-for-the-detection-of-antibodies-to-peste-des-petits-ruminants-based-on-monoclonal-antibodies-to-n-protein
#35
JOURNAL ARTICLE
Shuai Dong, Weiqin Meng, Ling Mo, Jinlong Chen, Jingnan Shi, Zhe Yang, Tong Li, Qianqian Xu, Zhiqiang Shen, Jianchai Liu, Jinliang Wang
A simple, fast, and visual method for detecting antibodies against peste des petits ruminants virus (PPRV) using colloidal gold strips was developed. In this study, the pET-32a-N was transformed into Escherichia coli Rosetta (DE3) for expression. Hybridoma cell lines were generated by fusing SP2/0 myeloma cells with splenocytes from immunized mice with the expressed and purified N protein of PPRV. The PPRV N protein was labeled with colloidal gold particles as the gold-labeled antigen. The N protein served as the gold standard antigen and as the test (T) line-coated antigen, while the monoclonal antibody served as the quality control (C) line-coated antibody to assemble the colloidal gold immunochromatographic test strips for detecting antibodies against the N protein of PPRV...
December 25, 2023: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://read.qxmd.com/read/38143053/expression-purification-and-activity-of-novel-allergen-tyr-p-31-from-tyrophagus-putrescentiae
#36
JOURNAL ARTICLE
Dongmei Zhou, Yaning Ren, Ying Zhou, Xuan Tao, Yuanfen Liao, Cunyin Yuan, Mei-Ping Lu, Yubao Cui
Allergen component products, such as recombinant proteins and epitope peptides of allergic components, are used as an adjunct to allergen-specific immunotherapy. We characterized a novel allergen, Tyr p 31, from Tyrophagus putrescentiae, a common allergenic mite. T. putrescentiae total RNA was amplified to Tyr p 31-encoding cDNA, which was inserted into pET28 (+). pET28a-Tyr p 31 was then transformed into Rosetta 2 (DE3) pLysS cells and expressed under isopropyl β-D-thiogalactoside induction. Next, we visualized Tyr p 31 through sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blotting based on its theoretical molecular weight...
December 22, 2023: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38137566/a-possible-role-for-nerve-growth-factor-and-its-receptors-in-human-sperm-pathology
#37
JOURNAL ARTICLE
Anna Maria Stabile, Alessandra Pistilli, Elena Moretti, Desirée Bartolini, Mariangela Ruggirello, Mario Rende, Cesare Castellini, Simona Mattioli, Rosetta Ponchia, Sergio Antonio Tripodi, Giulia Collodel
Nerve growth factor (NGF) signalling affects spermatogenesis and mature sperm traits. In this paper, we aimed to evaluate the distribution and the role of NGF and its receptors (p75NTR and TrKA) on the reproductive apparatus (testis and epididymis) and sperm of fertile men (F) and men with different pathologies, namely varicocele (V) and urogenital infections (UGIs). We collected semen samples from 21 individuals (31-40 years old) subdivided as follows: V ( n = 7), UGIs ( n = 7), and F ( n = 7). We submitted the semen samples to bacteriological analysis, leucocyte identification, and analysis of sperm parameters (concentration, motility, morphology, and viability)...
December 18, 2023: Biomedicines
https://read.qxmd.com/read/38130460/development-of-a-recombinant-protein-based-elisa-for-detection-of-antibodies-against-bovine-herpesvirus-6-bohv6
#38
JOURNAL ARTICLE
Piotr Kubiś, Jacek Kuźmak
INTRODUCTION: Bovine herpesvirus 6 (BoHV6) belongs to the Herpesviridae family, Gammaherpesvirinae subfamily and Macavirus genus. It is common in cattle, but was also detected in American bison (Bison bison) and water buffalo (Bubalus bubalis ). The aim of the experiment was to develop an ELISA for serological examination of cattle sera for the presence of anti-BoHV6 specific antibodies. MATERIAL AND METHODS: Viral DNA from a BoHV6-positive cow was amplified by qPCR and the resulting fragments of the gB and gH genes encoding glycoproteins B and H (gB and gH) were cloned into the pLATE52 vector to express recombinant gB (rgB) and gH (rgH) in Rosetta (DE3) E...
December 2023: Journal of Veterinary Research
https://read.qxmd.com/read/38127314/elucidating-molecular-mechanisms-of-protoxin-ii-state-specific-binding-to-the-human-nav1-7-channel
#39
JOURNAL ARTICLE
Khoa Ngo, Diego Lopez Mateos, Yanxiao Han, Kyle C Rouen, Surl-Hee Ahn, Heike Wulff, Colleen E Clancy, Vladimir Yarov-Yarovoy, Igor Vorobyov
Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells, and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-II (PTx2) has high selectivity for hNaV1.7 and is a valuable scaffold for designing novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1...
February 5, 2024: Journal of General Physiology
https://read.qxmd.com/read/38110299/computational-prediction-of-coiled-coil-protein-gelation-dynamics-and-structure
#40
JOURNAL ARTICLE
Dustin Britton, Luc F Christians, Chengliang Liu, Jakub Legocki, Yingxin Xiao, Michael Meleties, Lin Yang, Michael Cammer, Sihan Jia, Zihan Zhang, Farbod Mahmoudinobar, Zuzanna Kowalski, P Douglas Renfrew, Richard Bonneau, Darrin J Pochan, Alexander J Pak, Jin Kim Montclare
Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled-coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled-coil hydrogel design. Using Rosetta energy scores and Poisson-Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled-coil proteins while simultaneously exploring five new coiled-coil protein hydrogel sequences...
December 18, 2023: Biomacromolecules
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