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https://www.readbyqxmd.com/read/27914300/structure-based-analysis-of-bacilli-and-plasmid-dihydrofolate-reductase-evolution
#1
Mona Alotaibi, Ben Delos Reyes, Tin Le, Phuong Luong, Faramarz Valafar, Robert P Metzger, Gary B Fogel, David Hecht
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database...
November 22, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27914139/genetic-variations-of-the-kiss1r-gene-in-korean-girls-with-central-precocious-puberty
#2
Yeon Joung Oh, Young Jun Rhie, Hyo Kyoung Nam, Hye Ryun Kim, Kee Hyoung Lee
The timing of puberty onset varies greatly among individuals, and much of this variation is modulated by genetic factors. This study aimed to identify the kisspeptin receptor (KISS1R) gene variations and to investigate the associations between these variations and central precocious puberty (CPP). Korean girls with CPP (n = 194) and their healthy controls (n = 99) were included in this study. The entire coding region and the exon-intron boundaries (exon 1 through 5) of the KISS1R gene were directly sequenced...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#3
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914060/a-protocol-for-the-design-of-protein-and-peptide-nanostructure-self-assemblies-exploiting-synthetic-amino-acids
#4
Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, Ruth Nussinov
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914057/bindml-bindml-detecting-protein-protein-interaction-interface-propensity-from-amino-acid-substitution-patterns
#5
Qing Wei, David La, Daisuke Kihara
Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914055/an-evolution-based-approach-to-de-novo-protein-design
#6
Jeffrey R Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914053/computational-protein-design-under-a-given-backbone-structure-with-the-abacus-statistical-energy-function
#7
Peng Xiong, Quan Chen, Haiyan Liu
An important objective of computational protein design is to identify amino acid sequences that stably fold into a given backbone structure. A general approach to this problem is to minimize an energy function in the sequence space. We have previously reported a method to derive statistical energies for fixed-backbone protein design and showed that it led to de novo proteins that fold as expected. Here, we present the usage of the program that implements this method, which we now name as ABACUS (A Backbone-based Amino aCid Usage Survey)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914050/multistate-computational-protein-design-with-backbone-ensembles
#8
James A Davey, Roberto A Chica
The ability of computational protein design (CPD) to identify protein sequences possessing desired characteristics in vast sequence spaces makes it a highly valuable tool in the protein engineering toolbox. CPD calculations are typically performed using a single-state design (SSD) approach in which amino-acid sequences are optimized on a single protein structure. Although SSD has been successfully applied to the design of numerous protein functions and folds, the approach can lead to the incorrect rejection of desirable sequences because of the combined use of a fixed protein backbone template and a set of rigid rotamers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#9
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#10
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914044/the-framework-of-computational-protein-design
#11
Ilan Samish
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein-protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914013/inhibitory-effect-of-homocysteine-on-rat-neural-stem-cell-growth-in-vitro-is-associated-with-reduced-protein-levels-and-enzymatic-activities-of-aconitase-and-respiratory-complex-iii
#12
Xu-Mei Zhang, Ya-Qian Zhao, Hai Yan, Huan Liu, Guo-Wei Huang
Increased blood plasma concentration of the sulphur amino acid homocysteine (Hcy) is considered as an independent risk factor of the neurodegenerative diseases. However, the detailed molecular mechanisms by which Hcy leads to neurotoxicity have yet to be clarified. Recent research has suggested that neurotoxicity of Hcy may involve negative regulation of neural stem cell (NSC) proliferation. In the current study, primary NSCs were isolated from neonatal rat brain hippocampus and the inhibition in cell growth was observed after exposure to l50 μM and 500 μM L-Hcy...
December 2, 2016: Journal of Bioenergetics and Biomembranes
https://www.readbyqxmd.com/read/27914004/hybrid-receptor-bound-mm-gbsa-per-residue-energy-based-pharmacophore-modelling-enhanced-approach-for-identification-of-selective-lta4h-inhibitors-as-potential-anti-inflammatory-drugs
#13
Patrick Appiah-Kubi, Mahmoud Soliman
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity...
December 2, 2016: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27913996/altered-gut-microbiota-composition-and-immune-response-in-experimental-steatohepatitis-mouse-models
#14
Mitsuaki Ishioka, Kouichi Miura, Shinichiro Minami, Yoichiro Shimura, Hirohide Ohnishi
BACKGROUND: Although several types of diet have been used in experimental steatohepatitis models, comparison of gut microbiota and immunological alterations in the gut among diets has not yet been performed. AIM: We attempted to clarify the difference in the gut environment between mice administrated several experimental diets. METHODS: Male wild-type mice were fed a high-fat (HF) diet, a choline-deficient amino acid-defined (CDAA) diet, and a methionine-choline-deficient (MCD) diet for 8 weeks...
December 2, 2016: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/27913980/complete-nucleotide-sequences-and-construction-of-full-length-infectious-cdna-clones-of-cucumber-green-mottle-mosaic-virus-cgmmv-in-a-versatile-newly-developed-binary-vector-including-both-35s-and-t7-promoters
#15
Chan-Hwan Park, Hye-Kyoung Ju, Jae-Yeong Han, Jong-Seo Park, Ik-Hyun Kim, Eun-Young Seo, Jung-Kyu Kim, John Hammond, Hyoun-Sub Lim
Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome...
December 2, 2016: Virus Genes
https://www.readbyqxmd.com/read/27913973/emergence-of-new-virulent-rabbit-hemorrhagic-disease-virus-strains-in-saudi-arabia
#16
Mahmoud M Ismail, Mahmoud H A Mohamed, Ibrahim M El-Sabagh, Mohamed A Al-Hammadi
Rabbit hemorrhagic disease is an acute fatal highly contagious viral infectious disease that causes high losses among rabbitries. The disease was first reported in China in 1984 and later on in Saudi Arabia in 1996. The aim of this study was to investigate the emergence and pathogenicity of new rabbit hemorrhagic disease virus (RHDV) strains in Saudi Arabia. The pathogenicity was confirmed by inoculation in susceptible rabbits. Three RHDV strains were detected by reverse transcriptase polymerase chain reaction (RT-PCR) using primers targeting VP60 capsid protein gene in infected rabbitries during 2012 and 2013...
December 2, 2016: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/27913948/branched-chain-amino-acids-administration-suppresses-endurance-exercise-related-activation-of-ubiquitin-proteasome-signaling-in-trained-human-skeletal-muscle
#17
Evgeny A Lysenko, Tatiana F Vepkhvadze, Egor M Lednev, Olga L Vinogradova, Daniil V Popov
We tested whether post exercise ingestion of branched-chain amino acids (BCAA < 10 g) is sufficient to activate signaling associated with muscle protein synthesis and suppress exercise-induced activation of mechanisms associated with proteolysis in endurance-trained human skeletal muscle. Nine endurance-trained athletes performed a cycling bout with and without BCAA ingestion (0.1 g/kg). Post exercise ACC(Ser79/222) phosphorylation (endogenous marker of AMPK activity) was increased (~3-fold, P < 0...
December 3, 2016: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/27913852/differential-effect-of-early-antibiotic-intervention-on-bacterial-fermentation-patterns-and-mucosal-gene-expression-in-the-colon-of-pigs-under-diets-with-different-protein-levels
#18
Chuanjian Zhang, Miao Yu, Yuxiang Yang, Chunlong Mu, Yong Su, Weiyun Zhu
The study aimed to evaluate the effects of early antibiotic intervention (EAI) on bacterial fermentation patterns and mucosal immune markers in the colon of pigs with different protein level diets. Eighteen litters of piglets at day (d) 7 were fed creep feed without or with growth promoting antibiotics until d 42. At d 42, pigs within each group were further randomly assigned to a normal- or low-crude protein (CP) diet. At d 77 and d 120, five pigs per group were slaughtered for analyzing colonic bacteria, metabolites, and mucosal gene expressions...
December 3, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#19
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913840/finding-direction-in-the-search-for-selection
#20
Grant Thiltgen, Mario Dos Reis, Richard A Goldstein
Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the species. Recently, a few methods have been developed to detect and characterize directional selection on a molecular level. Using the results of evolutionary simulations as well as HIV drug resistance data as models of directional selection, we compare two such methods with each other, as well as against a standard method for detecting diversifying selection...
December 2, 2016: Journal of Molecular Evolution
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