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Protein design

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https://www.readbyqxmd.com/read/29778048/pathogens-constancy-harbinger-of-nosocomial-infection-cum-identification-of-resistant-genes-and-drug-designing
#1
Sana Farooq Ahmad, Ibrar Khan, Abdul Wadood, Sadiq Azam, Noor Rehman, Muhammad Waqas, Kashif Bashir, Asaf Ali Khan
Hospitals are the most prominent places for the growth and spread of bacteria which are resistant to the available antibiotics. This antibiotic resistance is due to the over and misuse of antibiotic dosages of a high-density of patient population which are in frequent interaction with inanimate items of the hospitals and the consequent risk of cross infection. Out of 1010 samples of the current study, 510 (50.49%) were culture positive of which 329 (64.5%) were Gram-positive while 181 (35.49%) Gram negative...
April 22, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29777988/insight-into-structural-requirements-for-selective-and-or-dual-cxcr3-and-cxcr4-allosteric-modulators
#2
Anja Kolarič, Urban Švajger, Tihomir Tomašič, Regine Brox, Theresa Frank, Nikola Minovski, Nuska Tschammer, Marko Anderluh
Based on the previously published pyrazolopyridine-based hit compound for which negative allosteric modulation of both CXCR3 and CXCR4 receptors was disclosed, we designed, synthesized and biologically evaluated a set of novel, not only negative, but also positive allosteric modulators with preserved pyrazolopyridine core. Compound 9e is a dual negative modulator, inhibiting G protein activity of both receptors. For CXCR4 receptor para-substituted aromatic group of compounds distinguishes between negative and positive modulation...
May 11, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29777793/homocysteine-induces-vascular-inflammatory-response-via-smad7-hypermethylation-in-human-umbilical-vein-smooth-muscle-cells
#3
Li-Hua Wei, Nai-Xia Chao, Si Gao, Ya-Ting Yu, Lin Shi, Xin-Bo Ma, Na Liao, Ke Lan, Yu Luo, Zheng-Yi Xie, Yuan-Yuan Li
Homocysteine (Hcy) can induce atherosclerosis through the inflammatory response and DNA methylation disorder. Our recent study has reported a novel epigenetic modified gene related to atherosclerosis -SMAD7. To further understand the pathogenesis of atherosclerosis, the current study was designed to investigate an inflammatory role of Hcy in human umbilical vein smooth muscle cells (HUVSMCs) through interfering with SMAD7 methylation. Using MALDI-TOF MS, we found that Hcy increased DNA methylation levels of SMAD7 promoter in a dose and time-dependent manner in HUVSMCs...
May 16, 2018: Microvascular Research
https://www.readbyqxmd.com/read/29777594/il-3-producing-basophils-are-required-to-exacerbate-airway-hyper-responsiveness-in-a-murine-inflammatory-model
#4
Rachel Rignault-Bricard, François Machavoine, Salah Mecheri, Olivier Hermine, Elke Schneider, Michel Dy, Maria Leite-de-Moraes
BACKGROUND: Basophils are commonly associated with allergic responses because of their ability to produce large amounts of pro-Th2 cytokines and histamine. However, the mechanisms through which bone marrow-resident basophils (BMRB) become fully competent cytokine and histamine producers in response to IgE crosslinking are poorly understood. Here, we sought to determine the role of IL-3 in promoting pro-Th2 basophils. METHODS: BMRB and basophils exposed to IL-3 in vitro and in vivo were evaluated for their production of Th2 cytokines and histamine in response to FcεRI crosslinking on both protein and gene expression levels...
May 19, 2018: Allergy
https://www.readbyqxmd.com/read/29777592/early-identification-of-unusually-clustered-mutations-and-a-root-cause-in-therapeutic-antibody-development
#5
Yueming Qian, Zhiqiang Chen, Xin Huang, Xuning Wang, Xuankuo Xu, Stefan Kirov, Richard Ludwig, Nan-Xin Qian, Kandasamy Ravi, Li Tao, Michael C Borys, Zheng Jian Li
This study reports findings of an unusual cluster of mutations spanning 22 base pairs in a monoclonal antibody (mAb) expression vector. It was identified by two orthogonal methods: mass spectrometry on expressed protein and next-generation sequencing (NGS) on the plasmid DNA. While the initial NGS analysis confirmed the designed sequence modification, intact mass analysis detected an additional mass of the antibody molecule expressed in CHO cells. The extra mass was eventually found to be associated with unmatched nucleotides in a distal region by checking full-length sequence alignment plots...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777476/comparison-of-procalcitonin-a-potentially-new-inflammatory-biomarker-of-frailty-to-interleukin-6-and-c-reactive-protein-among-older-chinese-hospitalized-patients
#6
Ying Yang, Qiukui Hao, Joseph H Flaherty, Li Cao, Jianghua Zhou, Li Su, Yanjiao Shen, Birong Dong
AIM: Procalcitonin (PCT) has predictive value for patients with infectious diseases, but has not been studied in frailty. The purpose of this study was to compare PCT to two other inflammatory biomarkers [interleukin-6 (IL-6)] and C-reactive protein (CRP) in their association with frailty among older hospitalized patients. METHODS: Retrospective study of inpatients (June-December, 2016), who had all three biomarkers measured within 24 h of admission. Frailty was defined according to the Chinese version of a validated frailty scale...
May 17, 2018: Aging Clinical and Experimental Research
https://www.readbyqxmd.com/read/29777339/characterization-of-a-cryptic-rolling-circle-replication-plasmid-pmk8-from-enterococcus-durans-1-8
#7
Penyu Zhou, Zhengyuan Zhai, Xiong Yao, Peihua Ma, Yanling Hao
A novel cryptic plasmid from Enterococcus durans 1-8, designated as pMK8, was sequenced and analyzed in this study. It consists of 3337 bp with a G + C content of 33.11%. Sequence analysis of pMK8 revealed three putative open reading frames (ORFs). Based on homology, two of them were identified as genes encoding replication initiation (RepC) and mobilization (Mob) protein, respectively. Sequence analysis revealed a pT181 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the repC gene...
May 17, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29777101/supramolecularly-directed-rotary-motion-in-a-photoresponsive-receptor
#8
Sander J Wezenberg, Ben L Feringa
Stimuli-controlled motion at the molecular level has fascinated chemists already for several decades. Taking inspiration from the myriad of dynamic and machine-like functions in nature, a number of strategies have been developed to control motion in purely synthetic systems. Unidirectional rotary motion, such as is observed in ATP synthase and other motor proteins, remains highly challenging to achieve. Current artificial molecular motor systems rely on intrinsic asymmetry or a specific sequence of chemical transformations...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29777024/characterization-of-p-glycoprotein-humanized-mice-generated-by-chromosome-engineering-technology-its-utility-for-prediction-of-drug-distribution-to-the-brain-in-humans
#9
Yuki Yamasaki, Kaoru Kobayashi, Fuka Okuya, Naoyo Kajitani, Kanako Kazuki, Satoshi Abe, Shoko Takehara, Shingo Ito, Seiryo Ogata, Tatsuki Uemura, Sumio Ohtsuki, Genki Minegishi, Hidetaka Akita, Kan Chiba, Mitsuo Oshimura, Yasuhiro Kazuki
P-glycoprotein (P-gp), encoded by the MDR1 gene in humans and by the Mdr1a/1b genes in rodents, is expressed in numerous tissues and plays as an efflux pump to limit the distribution and absorption of many drugs. Owing to species differences of P-gp between humans and rodents, it is difficult to predict the impact of P-gp on pharmacokinetics and tissue distribution of P-gp substrates in humans from results of animal experiments. Therefore, we generated a novel P-gp humanized mouse model by using a mouse artificial chromosome (MAC) vector [designated human MDR1-MAC (hMDR1-MAC) mice]...
May 18, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29776931/shuffling-the-neutral-drift-of-unspecific-peroxygenase-in-saccharomyces-cerevisiae
#10
Javier Martin-Diaz, Carmen Paret, Eva García-Ruiz, Patricia Molina-Espeja, Miguel Alcalde
Unspecific peroxygenase (UPO) is a highly promiscuous biocatalyst and its selective mono(per)oxygenase activity makes it useful for many synthetic chemistry applications. Among the broad repertory of library creation methods for directed enzyme evolution, genetic drift allows neutral mutations to be accumulated gradually within a polymorphic network of variants. In this study, we conducted a campaign of genetic drift with UPO in Saccharomyces cerevisiae so that neutral mutations were simply added and recombined in vivo With low mutational loading and an activity threshold of 45% of the parent's native function, mutant libraries enriched in folded and active UPO variants were generated...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29776602/blurring-boundaries-receptor-tyrosine-kinases-as-functional-g-protein-coupled-receptors
#11
Caitrin Crudden, Takashi Shibano, Dawei Song, Naida Suleymanova, Ada Girnita, Leonard Girnita
Receptor tyrosine kinases (RTKs) such as the insulin-like growth factor type 1 receptor (IGF-1R) control important biological activities as well as being involved in pathological processes. Due to their supportive nature in many human cancers they have long been considered attractive therapeutic targets. However, lessons learnt from early targeting trials highlight that a simple "active versus inactive" state model with classical kinase-only signaling is overly simplistic and does not describe reality...
2018: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/29776380/use-of-designed-sequences-in-protein-structure-recognition
#12
Gayatri Kumar, Richa Mudgal, Narayanaswamy Srinivasan, Sankaran Sandhya
BACKGROUND: Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold...
May 9, 2018: Biology Direct
https://www.readbyqxmd.com/read/29776370/characterization-of-a-promiscuous-cadmium-and-arsenic-resistance-mechanism-in-thermus-thermophilus-hb27-and-potential-application-of-a-novel-bioreporter-system
#13
Immacolata Antonucci, Giovanni Gallo, Danila Limauro, Patrizia Contursi, Ana Luisa Ribeiro, Alba Blesa, José Berenguer, Simonetta Bartolucci, Gabriella Fiorentino
BACKGROUND: The characterization of the molecular determinants of metal resistance has potential biotechnological application in biosensing and bioremediation. In this context, the bacterium Thermus thermophilus HB27 is a metal tolerant thermophile containing a set of genes involved in arsenic resistance which, differently from other microbes, are not organized into a single operon. They encode the proteins: arsenate reductase, TtArsC, arsenic efflux membrane transporter, TtArsX, and transcriptional repressor, TtSmtB...
May 18, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29775936/from-hit-to-lead-structure-based-discovery-of-naphthalene-1-sulfonamide-derivatives-as-potent-and-selective-inhibitors-of-fatty-acid-binding-protein-4
#14
Ding-Ding Gao, Hui-Xia Dou, Hai-Xia Su, Ming-Ming Zhang, Ting Wang, Qiu-Feng Liu, Hai-Yan Cai, Hai-Peng Ding, Zhuo Yang, Wei-Liang Zhu, Ye-Chun Xu, He-Yao Wang, Ying-Xia Li
Fatty acid binding protein 4 (FABP4) plays a critical role in metabolism and inflammatory processes and therefore is a potential therapeutic target for immunometabolic diseases such as diabetes and atherosclerosis. Herein, we reported the identification of naphthalene-1-sulfonamide derivatives as novel, potent and selective FABP4 inhibitors by applying a structure-based design strategy. The binding affinities of compounds 16dk, 16do and 16du to FABP4, at the molecular level, are equivalent to or even better than that of BMS309403...
May 9, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29775897/the-gastric-mucosal-protective-effects-of-astragaloside-iv-in-mnng-induced-gpl-rats
#15
Tiantian Cai, Chengzhe Zhang, Ziming Zhao, Siyi Li, Haobin Cai, Xiaodong Chen, Dake Cai, Wei Liu, Yan Yan, Kaifeng Xie, Huafeng Pan, Xiaohui Zeng
Gastric Cancer is one of the most common types of cancer. And the occurrence of gastric carcinoma is an evolutionary histopathological stage. As a result, further research of GPL, which is a borderline of gastric cancer, is indispensable for preventing the formation and development of gastric carcinoma. Several studies have demonstrated a correlation between the expression of autophagy, apoptosis and Gastric cancer (GC). However, the effects of autophagy and apoptosis on human gastric cancer progression, particularly on gastric precancerous lesions (GPL), have not totally been investigated...
May 15, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29775855/dual-core-all-fiber-integrated-immunosensor-for-detection-of-protein-antigens
#16
Karol Wysokiński, Dawid Budnicki, Janusz Fidelus, Łukasz Szostkiewicz, Łukasz Ostrowski, Micha Murawski, Marcin Staniszewski, Magdalena Staniszewska, Marek Napierała, Tomasz Nasiłowski
An optical fiber interferometric microprobe for detection of specific proteins is presented in this paper. The microprobe is an all-fiber device, which is based on Michelson interferometer configuration, which allows for detection of protein antigens in an analyzed solution thanks to antibodies immobilized on the sensor surface. The interferometer is made of dual core fiber and has a precisely formed arm length difference, achieved by splicing a fragment of polarization maintaining fiber to one of the cores...
May 9, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29775653/atomic-structure-of-a-rationally-engineered-gene-delivery-vector-aav2-5
#17
Matthew Burg, Claire Rosebrough, Lauren M Drouin, Antonette Bennett, Mario Mietzsch, Paul Chipman, Robert McKenna, Duncan Sousa, Mark Potter, Barry Byrne, R Jude Samulski, Mavis Agbandje-McKenna
AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope. To confirm the design, the structure of the vector was determined to a resolution of 2.78 Å using cryo-electron microscopy and image reconstruction. The structure of the major viral protein (VP), VP3, was ordered from residue 219 to 736, as reported for other AAV structures, and the five AAV2...
May 15, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29775652/advances-and-prospects-of-bacillus-subtilis-cellular-factories-from-rational-design-to-industrial-applications
#18
REVIEW
Yang Gu, Xianhao Xu, Yaokang Wu, Tengfei Niu, Yanfeng Liu, Jianghua Li, Guocheng Du, Long Liu
Bacillus subtilis is the most characterized gram-positive bacterium that has significant attributes, such as growing well on cheap carbon sources, possessing clear inherited backgrounds, having mature genetic manipulation methods, and exhibiting robustness in large-scale fermentations. Till date, B. subtilis has been identified as attractive hosts for the production of recombinant proteins and chemicals. By applying various systems and synthetic biology tools, the productivity features of B. subtilis can be thoroughly analyzed and further optimized via metabolic engineering...
May 15, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29775616/amelioration-of-uvb-induced-oxidative-stress-and-inflammation-in-fat-1-transgenic-mouse-skin
#19
Hye-Won Yum, Seong Hoon Kim, Jing X Kang, Young-Joon Surh
ω-3 polyunsaturated fatty acids (PUFAs), which are abundant in some fish oils, are known to scavenge lipid peroxyl radicals and increase host immunoresponsiveness. As UVB-induced oxidative stress and inflammation have been implicated in apoptotic cell death, this study was designed to investigate the anti-inflammatory, anti-oxidative, and anti-apoptotic capacity of fat-1 transgenic mice capable of converting ω-6 to ω-3 PUFAs. Wild-type (WT) C57BL/6 mice and fat-1 mice were maintained on the AIN-93 diet supplemented with 10% safflower oil rich in ω-6 PUFAs for 5 weeks...
May 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29775277/cid-9998128-compound-is-a-potential-multi-target-drug-for-alzheimer-s-disease
#20
Nguyen Quoc Thai, Zuzana Bednarikova, Miroslav Gancar, Huynh Quang Linh, Chin-Kun Hu, Mai Suan Li, Zuzana Gazova
We have probed capability of small CID 9998128 compound as a potential multi-target drug for the Alzheimer's disease (AD) using in silico and in vitro experiments. By all-atom simulation and MM-PBSA method we have demonstrated that this compound strongly binds to both amyloid beta 42 (Aβ42 ) fibrils and β-secretase and the van der Waals interaction is dominating over the electrostatic interaction in binding affinity. A detailed analysis at the atomic level revealed that indazole in CID 99998128 structure made a major contribution to instability of all studied complexes...
May 18, 2018: ACS Chemical Neuroscience
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