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Protein structure prediction

Tao Wu, Eva Brichtová, Jana Hudecová, Nikola Vršková, Jaroslav Šebestík, Petr Bouř
Lanthanide complexes are used as convenient spectroscopic probes for many biomolecules. Their binding to proteins is believed to be enhanced by the presence of histidine, but the strength of the interaction significantly varies across different systems. To understand the role of peptide length and sequence, short histidine-containing peptides were synthesized (His-Gly, His-Gly-Gly, His-Gly-Gly-Gly, Gly-His, Gly-His-Gly, His-His, and Gly-Gly-His) and circularly polarized luminescence (CPL) induced at the [Eu(DPA)3]3- complex was measured using the Raman optical activity (ROA) spectrometer...
April 14, 2018: Chemistry: a European Journal
Piyusha P Pagare, Mohini S Ghatge, Faik N Musayev, Tanvi M Deshpande, Qiukan Chen, Courtney Braxton, Solyi Kim, Jürgen Venitz, Yan Zhang, Osheiza Abdulmalik, Martin K Safo
Hypoxia-induced polymerization of sickle hemoglobin (Hb S) is the principal phenomenon that underlays the pathophysiology and morbidity associated with sickle cell disease (SCD). Opportunely, as an allosteric protein, hemoglobin (Hb) serves as a convenient and potentially critical druggable target. Consequently, molecules that prevent Hb S polymerization (Hb modifiers), and the associated erythrocyte sickling have been investigated-and retain significant interest-as a viable therapeutic strategy for SCD. This group of molecules, including aromatic aldehydes, form high oxygen affinity Schiff-base adducts with Hb S, which are resistant to polymerization...
April 6, 2018: Bioorganic & Medicinal Chemistry
Yanan Zong, Ning Liu, Shanshan Ma, Ying Bai, Fangxia Guan, Xiangdong Kong
Phenylketonuria (PKU) is the most common inherited metabolic disease, an autosomal recessive disorder affecting >10,000 newborns each year globally. It can be caused by over 1000 different naturally occurring mutations in the phenylalanine hydroxylase (PAH) gene. We analyzed three novel naturally occurring PAH gene variants: p.Glu178Lys (c.532G>A), p.Val245Met (c.733G>A) and p.Ser250Phe (c.749C>T). The mutant effect on the PAH enzyme structure and function was predicted by bioinformatics software...
April 10, 2018: Gene
Rabia Mazmouz, Insaf Essadik, Djemel Hamdane, Annick Méjean, Olivier Ploux
Cylindrospermopsin, a cytotoxin from cyanobacteria, is biosynthesized by a complex pathway, which involves CyrI, an iron and 2-oxoglutarate dependent hydroxylase that transforms 7-deoxy-cylindrospermopsin into cylindrospermopsin and its epimer, 7-epi-cylindrospermopsin, in the last step. The activity of CyrI from Oscillatoria sp. PCC 7926 depends on Fe(II) (Km  = 2.1 μM), and 2-oxoglutarate (Km  = 3.2 μM), and is strongly inhibited by 7-deoxy-cylindrospermopsin at concentration higher than 1 μM...
April 10, 2018: Archives of Biochemistry and Biophysics
Irini Doytchinova, Mariyana Atanasova, Iva Valkova, Georgi Stavrakov, Irena Philipova, Zvetanka Zhivkova, Dimitrina Zheleva-Dimitrova, Spiro Konstantinov, Ivan Dimitrov
The inhibition of the enzyme acetylcholinesterase (AChE) increases the levels of the neurotransmitter acetylcholine and symptomatically improves the affected cognitive function. In the present study, we searched for novel AChE inhibitors by docking-based virtual screening of the standard lead-like set of ZINC database containing more than 6 million small molecules using GOLD software. The top 10 best-scored hits were tested in vitro for AChE affinity, neurotoxicity, GIT and BBB permeability. The main pharmacokinetic parameters like volume of distribution, free fraction in plasma, total clearance, and half-life were predicted by previously derived models...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
Tianyi Qiu, Dingfeng Wu, Jingxuan Qiu, Zhiwei Cao
Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specific genes and associated with various diseases, which make it essential drug targets. Approaches which can predict the inhibition ability of compounds for different NR target should be particularly helpful for drug development. In this study, proteochemometric modelling was introduced to analysis the bioactivity between chemical compounds and NR targets...
April 12, 2018: Journal of Cheminformatics
Xin Cui, Yong-Xin Wang, Zhi-Wei Liu, Wen-Li Wang, Hui Li, Jing Zhuang
The tea plant is an important commercial horticulture crop cultivated worldwide. Yield and quality of this plant are influenced by abiotic stress. The bHLH family transcription factors play a pivotal role in the growth and development, including abiotic stress response, of plants. A growing number of bHLH proteins have been functionally characterized in plants. However, few studies have focused on the bHLH proteins in tea plants. In this study, 120 CsbHLH TFs were identified from tea plants using computational prediction method...
April 12, 2018: Functional & Integrative Genomics
Damien Ferhadian, Maud Contrant, Anne Printz-Schweigert, Redmond P Smyth, Jean-Christophe Paillart, Roland Marquet
Influenza A viruses (IAV) are responsible for recurrent influenza epidemics and occasional devastating pandemics in humans and animals. They belong to the Orthomyxoviridae family and their genome consists of eight (-) sense viral RNA (vRNA) segments of different lengths coding for at least 11 viral proteins. A heterotrimeric polymerase complex is bound to the promoter consisting of the 13 5'-terminal and 12 3'-terminal nucleotides of each vRNA, while internal parts of the vRNAs are associated with multiple copies of the viral nucleoprotein (NP), thus forming ribonucleoproteins (vRNP)...
2018: Frontiers in Microbiology
Mary Lilian Carabali-Isajar, Marisol Ocampo, Deisy Carolina Rodriguez, Magnolia Vanegas, Hernando Curtidor, Manuel Alfonso Patarroyo, Manuel Elkin Patarroyo
Mycobacterium tuberculosis is considered one of the most successful pathogens in the history of mankind, having caused 1.7 million deaths in 2016. The amount of resistant and extensively resistant strains has increased; BCG has been the only vaccine to be produced in more than 100 years though it is still unable to prevent the disease's most disseminated form in adults; pulmonary tuberculosis. The search is thus still on-going for candidate antigens for an antituberculosis vaccine. This paper reports the use of a logical and rational methodology for finding such antigens, this time as peptides derived from the Rv3587c membrane protein...
April 4, 2018: Bioorganic & Medicinal Chemistry
Dhanya T Jayaram, Samantha M Pustulka, Robert G Mannino, Wilbur A Lam, Christine K Payne
Nanoparticles used in cellular applications encounter free serum proteins that adsorb onto the surface of the nanoparticle, forming a protein corona. This protein layer controls the interaction of nanoparticles with cells. For nanomedicine applications, it is important to consider how intravenous injection and the subsequent shear flow will affect the protein corona. Our goal was to determine if shear flow changed the composition of the protein corona and if these changes affected cellular binding. Colorimetric assays of protein concentration and gel electrophoresis demonstrate that polystyrene nanoparticles subjected to flow have a greater concentration of serum proteins adsorbed on the surface, especially plasminogen...
April 9, 2018: Biophysical Journal
Makbule Guclin Ozsoy, Tansel Özyer, Faruk Polat, Reda Alhajj
BACKGROUND: Drug repositioning is the process of identifying new targets for known drugs. It can be used to overcome problems associated with traditional drug discovery by adapting existing drugs to treat new discovered diseases. Thus, it may reduce associated risk, cost and time required to identify and verify new drugs. Nowadays, drug repositioning has received more attention from industry and academia. To tackle this problem, researchers have applied many different computational methods and have used various features of drugs and diseases...
April 12, 2018: BMC Bioinformatics
Saowalak Onming, Wilawan Thongda, Chao Li, Orathai Sawatdichaikul, Nichanun McMillan, Sirawut Klinbunga, Eric Peatman, Supawadee Poompuang
Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36...
April 9, 2018: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
Ying Zhang, Jin Guo, Li He, Hong-Ying Zong, Guo-Bin Cai
Serine proteinase inhibitor (Serpin, SPI) is a vital superfamily of endogenous inhibitors that monitor proteolytic events active in a number of biological functions. In this study, we isolated a full length gene encoding a novel serine protease inhibitor of Schistosoma japonicum (SjSPI) and characterized its molecular properties. Our result showed that SjSPI contained an open reading frame of 1,218 bp, which encoded 405 amino acid residues. Chromosomal structure analysis showed that SjSPI gene was comprised of six exons separated by five introns...
April 9, 2018: Parasitology International
Muhammad Tanveer Khan, Sussie Dalvin, Qaiser Waheed, Frank Nilsen, Rune Male
The Salmon louse (Lepeophtheirus salmonis) is a marine ectoparasite of salmonid fish in the Northern Hemisphere and considered as a major challenge in aquaculture and a threat to wild populations of salmonids. Adult female lice produce a large number of lipid-rich eggs, however, the mechanism of maternal lipid transport into developing eggs during salmon louse reproduction has not been described. In the present study, a full-length L. salmonis lipophorin receptor (LsLpR) consisting of 16 exons was obtained by RACE and RT-PCR...
2018: PloS One
Andrew Ching-Yuet To, David Ho Ting Chu, Angela Ruoning Wang, Frances Cheuk-Yau Li, Alan Wai-On Chiu, Daisy Yuwei Gao, Chung Hang Jonathan Choi, Siu-Kai Kong, Ting-Fung Chan, King-Ming Chan, Kevin Y Yip
Background: Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses. The base complementation between the toehold switch and the trigger RNA also makes it sensitive to sequence variations. Design of toehold switches involves a series of considerations related to their sequence properties, structures and specificities...
April 10, 2018: Bioinformatics
Emily C Hartman, Christopher M Jakobson, Andrew H Favor, Marco J Lobba, Ester Álvarez-Benedicto, Matthew B Francis, Danielle Tullman-Ercek
Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering...
April 11, 2018: Nature Communications
Yimeng Li, Shu Shen, Liangbo Hu, Fei Deng, Just M Vlak, Zhihong Hu, Hualin Wang, Manli Wang
gp41 , one of the baculovirus core genes, encodes the only recognized tegument (O-glyco) protein of the occlusion-derived virion (ODV) phenotype so far. A previous study using a temperature-sensitive Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) mutant showed that GP41 plays a crucial role in budded virion (BV) formation. However, the precise function of GP41 in the baculovirus replication cycle remains unclear. In this study, AcMNPV GP41 was found to accumulate around the ring zone region (RZ) within the infected nucleus and finally assembled into both BV and ODV...
April 11, 2018: Journal of Virology
S-C Zou, J Jiang, J Song
OBJECTIVE: We aimed at exploring the role of IL-33 in mouse chronic obstructive pulmonary disease and its potential molecular mechanism. MATERIALS AND METHODS: The chronic obstructive pulmonary disease (COPD) mice model was established by cigarette smoking (CS). COPD mice were randomly assigned into PBS group and IL-33 antibody group. The peripheral blood and lung tissues of mice from two groups were collected for the following experiments. Pathological changes of the lung tissues in both groups were analyzed by hematoxylin and eosin (HE) staining...
March 2018: European Review for Medical and Pharmacological Sciences
Fabian Erdel, Karsten Rippe
Chromatin is partitioned on multiple length scales into subcompartments that differ from each other with respect to their molecular composition and biological function. It is a key question how these compartments can form even though diffusion constantly mixes the nuclear interior and rapidly balances concentration gradients of soluble nuclear components. Different biophysical concepts are currently used to explain the formation of "chromatin bodies" in a self-organizing manner and without consuming energy...
April 5, 2018: Biophysical Journal
Woo-Young Kim, Su-Jun Lee, Jungki Min, Kyung-Suk Oh, Dong-Hyun Kim, Heui-Soo Kim, Jae-Gook Shin
CYP4F2 is an enzyme involved in the formation of 20-hydroxyeicosatetraenoic acid (20-HETE) from arachidonic acid and metabolizes vitamin K into an inactive form. Our objectives were to identify new CYP4F2 genetic variants and to characterize the functional consequences of the conversion of arachidonic acid into 20-HETE. We used direct DNA sequencing to identify a total of 20 single-nucleotide polymorphisms (SNPs) including four coding variants, A27V, R47C, P85A, and V433M, in 50 randomly selected subjects. Of these, A27V and P85A were new...
April 2018: Prostaglandins, Leukotrienes, and Essential Fatty Acids
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