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Protein design

Attila Kiss, Huaqing Shu, Ouafa Hamza, David Santer, Eva Verena Tretter, Shanglong Yao, Klaus Markstaller, Seth Hallström, Bruno K Podesser, Klaus Ulrich Klein
OBJECTIVES: Previous studies demonstrated that preconditioning with argon gas provided a marked reduction in inflammation and apoptosis and increased myocardial contractility in the setting of acute myocardial ischaemia-reperfusion (IR). There is substantial evidence that myocardial IR injury following cardioplegic arrest is associated with the enhancement of apoptosis and inflammation, which is considered to play a role in cardiac functional impairment. Therefore, the present study was designed to clarify whether preconditioning with argon gas enhances recovery of cardiac function following cardioplegic arrest...
March 13, 2018: European Journal of Cardio-thoracic Surgery
Qiaozhen Meng, Zhenling Peng, Jianyi Yang
Motivation: Coenzyme A (CoA)-protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA-binding residues prediction. Results: We developed three methods for the prediction of CoA- and CoA derivatives-binding residues, including an ab-initio method SVMpred, a template-based method TemPred, and a consensus-based method CoABind. In SVMpred, a comprehensive set of features are designed from two complementary sequence profiles and the predicted secondary structure and solvent accessibility...
March 14, 2018: Bioinformatics
Xi Wu, Xue Xue, Lihui Wang, Wenjing Wang, Jian Han, Xiaoxue Sun, Haotian Zhang, Yueyang Liu, Xiaohang Che, Jingyu Yang, Chunfu Wu
Autophagy, a cellular survival mechanism, is thought to allow the recycling of cellular breakdown products when cancer cells are subjected to chemotherapy, thus decreasing drug-induced apoptosis. Disulfiram (DSF), a drug widely used to control alcoholism, possesses anticancer activity by inducing apoptosis in vitro and in vivo in a copper (Cu)-dependent manner. Our previous studies proved that DSF/Cu exerts increased anti-tumor effects on non-small cell lung cancer (NSCLC) xenograft models, and inhibits NSCLC recurrence driven by ALDH-positive cancer stem cells...
March 13, 2018: European Journal of Pharmacology
David M Thal, Ziva Vuckovic, Christopher J Draper-Joyce, Yi-Lynn Liang, Alisa Glukhova, Arthur Christopoulos, Patrick M Sexton
G protein-coupled receptors (GPCRs) are the largest superfamily of cell surface receptor proteins and are important drug targets for many human diseases. In the last decade, remarkable progress has been made in the determination of atomic structures of GPCRs with over 200 structures from 53 unique receptors having been solved. Technological advances in protein engineering and X-ray crystallography have driven much of the progress to date. However, recent advances in cryo-electron microscopy have facilitated the structural determination of three new structures of active-state GPCRs in complex with heterotrimeric G protein...
March 13, 2018: Current Opinion in Structural Biology
Aniko Krumbholz, Martin Schönfelder, Hande Hofmann, Detlef Thieme
BACKGROUND: The endogenous glucocorticosteroid cortisol (F) and its metabolite cortisone (E) are known to be involved in stress adaption and anti-inflammatory and immune regulatory effects. The ratios of F to E in the matrices serum, hair and saliva are different. The shift of this ratio by the enzyme activity of 11β-hydroxysteroid-dehydrogenase, which inactivates cortisol, was often discussed. The aim of our study was to calculate the contribution of the plasma protein binding (PPB) to this shift...
February 26, 2018: Forensic Science International
Amporn Suphatrakul, Thaneeya Duangchinda, Natapong Jupatanakul, Kanjanawadee Prasittisa, Suppachoke Onnome, Jutharat Pengon, Bunpote Siridechadilok
Reporter virus is a versatile tool to visualize and to analyze virus infections. However, for flaviviruses, it is difficult to maintain the inserted reporter genes on the viral genome, limiting its use in several studies that require homogeneous virus particles and several rounds of virus replication. Here, we showed that flanking inserted GFP genes on both sides with ribosome-skipping 2A sequences improved the stability and the consistency of their fluorescent signals for dengue-virus-serotype 2 (DENV2) reporter viruses...
2018: PloS One
Clio A Andreae, Richard B Sessions, Mumtaz Virji, Darryl J Hill
Neisseria meningitidis is an antigenically and genetically variable Gram-negative bacterium and a causative agent of meningococcal meningitis and septicaemia. Meningococci encode many outer membrane proteins, including Opa, Opc, Msf, fHbp and NadA, identified as being involved in colonisation of the host and evasion of the immune response. Although vaccines are available for the prevention of some types of meningococcal disease, none currently offer universal protection. We have used sequences within the Neisseria PubMLST database to determine the variability of msf and opc in 6,500 isolates...
2018: PloS One
Xiangying Guan, Alok Upadhyay, Sudipto Munshi, Raj Chakrabarti
Across all families of enzymes, only a dozen or so distinct classes of non-natural small molecule activators have been characterized, with only four known modes of activation among them. All of these modes of activation rely on naturally evolved binding sites that trigger global conformational changes. Among the enzymes that are of greatest interest for small molecule activation are the seven sirtuin enzymes, nicotinamide adenine dinucleotide (NAD+)-dependent protein deacylases that play a central role in the regulation of healthspan and lifespan in organisms ranging from yeast to mammals...
2018: PloS One
Ognjen Perišić
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM...
March 16, 2018: Pharmaceuticals
María José Garcés Hernández, Miguel Klünder, Nayely Garibay Nieto, Juan Carlos López Alvarenga, Jenny Vilchis Gil, Samuel Flores Huerta, Rosa Quispe Siccha, Joselin Hernandez
OBJECTIVE: Visceral adiposity index (VAI) is a mathematical model associated with cardiometabolic risk in adults, but studies on children failed to support this association. Our group has proposed a pediatric VAI model using pediatric ranges, but it has not yet been evaluated and needs further adjustments. The objective of this study was to further adjust the proposed pediatric VAI by age, creating a new pediatric metabolic index (PMI), and assess the correlation of the PMI with insulin resistance indexes and hepatic enzymes...
March 2018: Endocrine Practice
Yutaka Ikeda, Yukio Nagasaki
Oxidative stress caused by reactive oxygen species (ROS) occurs as events in which living tissues contact certain materials. These events include cell cultures and implantation of materials. Because of the high reactivity of ROS, they damage cells by oxidizing DNA, lipids, and proteins. Conversely, ROS also act as signaling molecules regulating cellular morphology. In particular, mitochondrial ROS are involved in the regulation of cellular physiology, including differentiation, autophagy, metabolic adaptation, apoptosis, and immunity...
March 16, 2018: Biomedical Materials
Maria Luz Fernandez, Minu Sara Thomas, Bruno S Lemos, Diana M DiMarco, Amanda Missimer, Melissa Melough, Ock K Chun, Ana Gabriela Murillo, Hana Alyousef, Isabel Medina-Vera
BACKGROUND: Telomerase Activator 65 (TA-65), a compound extracted from Astragalus membranaceus has been used in Chinese traditional medicine for extending life span. Scarce information exists on the effects of TA-65 on parameters of metabolic syndrome (MetS). METHODS: We recruited 40 patients with MetS to determine the effects of TA-65 on dyslipidemias, hypertension, and oxidative stress in this at-risk population. The study was a double-blind, randomized crossover design in which patients were allocated to consume either 16 mg daily of a TA-65 supplement or a placebo for 12 weeks...
March 15, 2018: Current Pharmaceutical Design
Alice Ossoli, Chiara Pavanello, Eleonora Giorgio, Laura Calabresi, Monica Gomaraschi
Hypercholesterolemia is one of the main risk factors for the development of atherosclerosis. Among the various lipoprotein classes, however, high density lipoproteins (HDL) are inversely associated with the incidence of atherosclerosis, since they are able to exert a series of atheroprotective functions. The central role of HDL within the reverse cholesterol transport, their antioxidant and anti-inflammatory properties and their ability to preserve endothelial homeostasis are likely responsible for HDL-mediated atheroprotection...
March 15, 2018: Current Medicinal Chemistry
Angelica Nakagawa Lima, Ronaldo Junio de Oliveira, Antônio Sérgio Kimus Braz, Maurício Garcia de Souza Costa, David Perahia, Luis Paulo Barbour Scott
There are two different prion conformations: (1) the cellular natural (PrPC ) and (2) the scrapie (PrPSc ), an infectious form that tends to aggregate under specific conditions. PrPC and PrPSc are widely different regarding secondary and tertiary structures. PrPSc contains more and longer β-strands compared to PrPC . The lack of solved PrPSc structures precludes a proper understanding of the mechanisms related to the transition between cellular and scrapie forms, as well as the aggregation process. In order to investigate the conformational transition between PrPC and PrPSc , we applied MDeNM (molecular dynamics with excited normal modes), an enhanced sampling simulation technique that has been recently developed to probe large structural changes...
March 15, 2018: European Biophysics Journal: EBJ
T S M Carvalho, L S Sousa, F A Nogueira, D P Vaz, M M Saldanha, M V Triginelli, M F V S Pinto, N C Baião, L J C Lara
This work aimed at evaluating the effects of 4 digestible Met+Cys levels on the diet of commercial layers and their influence on the productive performance, quality, and amino acid profile of eggs and economic viability of the activity. A total of 576 white Lohmann LSL-Lite layers was distributed into 6 replicates of 24 birds for each diet. The experimental design was completely randomized, with 4 treatments defined by levels evaluated in the feed (0.465, 0.540, 0.581, and 0.647%). The productive performance was measured for 30 weeks...
March 13, 2018: Poultry Science
Yue Ma, Chunquan Zheng, Le Shi
Background: Chronic rhinosinusitis (CRS), commonly divided into CRS with nasal polyps (CRSwNP) and without nasal polyps (CRSsNP) is an inflammatory disease which mechanism remain unclear. Leucine-rich repeat kinase 2 (LRRK2) has been proved to be a negative regulator of inflammation response while its role in pathogenesis of CRS has yet to be revealed. This research study was designed to investigate the relationship between the expression level and biologic role of LRRK2 in CRS. Methods: Expression of LRRK2 mRNA and noncoding repressor of NFAT (NRON) were examined by qRT-PCR...
2018: Clinical and Translational Allergy
Dan Li, Peng Zhang
This study was designed to investigate the protective effect and possible molecular mechanism of liquiritin on oxybuprocaine-induced apoptosis of human corneal endothelial cells (HCECs). In this study, the effect of oxybuprocaine on the proliferation of HCEC-12 was detected using cell counting kit-8 (CCK-8). The inductive effect of oxybuprocaine on HCEC-12 apoptosis and protective effect of liquiritin against oxybuprocaine-induced HCEC-12 apoptosis were tested by Annexin V/propidium iodide (PI) staining and flow cytometry...
April 2018: Experimental and Therapeutic Medicine
Yun Chai, Miaomiao Qu, Meng Jin
This study was designed to evaluate the application effect of single balloon catheters and dinoprostone on promoting cervical ripening of pregnant women in late-term pregnancy and their influences on stress and inflammatory responses. A total of 160 pregnant women with indications of labor induction were included and randomly divided into the control (n=80) and observation (n=80) groups. Patients in the control group received labor induction by administration of dinoprostone at the vaginal vault, while those in the observation group received labor induction by domestic single balloon catheters...
April 2018: Experimental and Therapeutic Medicine
Alison Woods-Tör, David J Studholme, Volkan Cevik, Osman Telli, Eric B Holub, Mahmut Tör
The pathosystem of Arabidopsis thaliana and diploid biotrophic oomycete Hyaloperonospora arabidopsidis ( Hpa ) has been a model for investigating the molecular basis of Flor's gene-for-gene hypothesis. The isolates Hpa -Noks1 and Hpa -Cala2 are virulent on Arabidopsis accession RMX-A02 whilst an F1 generated from a cross between these two isolates was avirulent. The F2 progeny segregated 3,1 (avirulent, virulent), indicating a single major effect AVR locus in this pathogen. SNP-based linkage mapping confirmed a single AVR locus within a 14 kb map interval containing two genes encoding putative effectors...
2018: Frontiers in Plant Science
Qianqian Wang, Jiahui Xu, Ying Li, Jumin Huang, Zebo Jiang, Yuwei Wang, Liang Liu, Elaine Lai Han Leung, Xiaojun Yao
Protein arginine methyltransferase 5 (PRMT5) is able to regulate gene transcription by catalyzing the symmetrical dimethylation of arginine residue of histone, which plays a key role in tumorigenesis. Many efforts have been taken in discovering small-molecular inhibitors against PRMT5, but very few were reported and most of them were SAM-competitive. EPZ015666 is a recently reported PRMT5 inhibitor with a new binding site, which is different from S-adenosylmethionine (SAM)-binding pocket. This new binding site provides a new clue for the design and discovery of potent and specific PRMT5 inhibitors...
2018: Frontiers in Pharmacology
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