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Protein chemistry

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https://www.readbyqxmd.com/read/28534784/incorporation-of-solvent-effect-into-multi-objective-evolutionary-algorithm-for-improved-protein-structure-prediction
#1
Shangce Gao, Jiujun Cheng, Yuki Todo, Mengchu Zhou
The problem of predicting the three-dimensional structure of a protein from its one-dimensional sequence has been called the "holy grail of molecular biology", and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28533376/b12-dependent-photoresponsive-protein-hydrogels-for-controlled-stem-cell-protein-release
#2
Ri Wang, Zhongguang Yang, Jiren Luo, I-Ming Hsing, Fei Sun
Thanks to the precise control over their structural and functional properties, genetically engineered protein-based hydrogels have emerged as a promising candidate for biomedical applications. Given the growing demand for creating stimuli-responsive "smart" hydrogels, here we show the synthesis of entirely protein-based photoresponsive hydrogels by covalently polymerizing the adenosylcobalamin (AdoB12)-dependent photoreceptor C-terminal adenosylcobalamin binding domain (CarHC) proteins using genetically encoded SpyTag-SpyCatcher chemistry under mild physiological conditions...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28532301/heterotrimeric-g-protein-regulatory-circuits-in-plants-conserved-and-novel-mechanisms
#3
Sona Pandey
Article Addendum Efficient activation and deactivation of Gα protein is critical for the regulation of heterotrimeric G-protein mediated signaling pathways. While the core G-protein components and their activation/deactivation chemistries are broadly conserved throughout the eukaryotic evolution, their regulatory mechanisms seem to have been rewired in plants to meet specific needs. Plants such as Arabidopsis, which have a limited number of G-protein components and their regulators, offer a unique opportunity to dissect the mechanistic details of distinct signaling pathways...
May 22, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28532214/how-active-mechanics-and-regulatory-biochemistry-combine-to-form-patterns-in-development
#4
Peter Gross, K Vijay Kumar, Stephan W Grill
The development of organisms starting from their zygotic state involves a tight integration of the myriad biochemical signaling interactions with the mechanical forces that eventually pattern and shape the resulting embryo. In the past decade, it has become increasingly evident that several important developmental processes involve mechanical forces in an essential manner. In this review, we highlight the multifaceted role of mechanics in pattern formation, from protein and cell sorting to the generation of tissue shape...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28532078/enhancement-of-fibroblast-growing-on-the-mannosylated-surface-of-cellulose-membranes
#5
Simone Birkheur, Paula Cristina de Sousa Faria-Tischer, Cesar A Tischer, Elisângela Flávia Pimentel, Marcio Fronza, Denise Coutinho Endringer, Anna Paola Butera, Renato Márcio Ribeiro-Viana
Bacterial cellulose membrane is a biomaterial with high value in the biomedical field. Many groups have been making efforts to promote chemical modifications of its structure and, consequently, add new characteristics. Recently, our group has developed a methodology to insert monoester succinic acid in bacterial cellulose membrane without disrupting the microfibril network and bind a protein on it. Considering the role of carbohydrates in the molecular recognition process in biological events, we continued these studies by inserting covalently multiples copies of aryl monosaccharide to bacterial cellulose succinylated and to study the in vitro tissue compatibility using fibroblasts...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28530742/a-survey-of-the-different-roles-of-polyoxometalates-in-their-interaction-with-amino-acids-peptides-and-proteins
#6
Mina Arefian, Masoud Mirzaei, Hossein Eshtiagh-Hosseini, Antonio Frontera
One of the most attractive areas in inorganic chemistry is the synthesis of polyoxometalates (POMs) exhibiting new properties and applications. Since the impact of POMs in biochemistry and related fields of research has increased in the last few years, there has been a special interest in this topic. Significant progress in biological applications has been made where the interaction of POMs with amino acids, peptides and proteins is relevant. Versatile POMs play a series of different roles in the interaction with these biomolecules as described in this review...
May 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28529818/high-protein-fish-oil-diet-prevents-hepatic-steatosis-in-noncnzo10-mice-association-with-diet-genetics-regulated-micro-rnas
#7
Nikhil Adi, Jennipher Adi, Roberta Marques Lassance-Soares, Paul Kurlansky, Hong Yu, Keith A Webster
OBJECTIVE: NONcNZO10 (NZ10) mice are predisposed to obesity and develop type 2 diabetes (T2D) and hepatic steatosis even when maintained on a control diet (CD) of 6% fat. Studies were designed to determine whether this extreme susceptibility phenotype could be alleviated by diet and if so the molecular targets of diet. METHODS: NZ10 and SWR/J (SWR) control mice were fed a CD or a test diet of high protein and fish oil (HPO) for 19 weeks and then analyzed for steatosis, blood chemistry, hepatic gene and micro-RNA expression...
June 2016: Journal of Diabetes & Metabolism
https://www.readbyqxmd.com/read/28528390/colonization-by-nitrogen-fixing-frankia-bacteria-causes-short-term-increases-in-herbivore-susceptibility-in-red-alder-alnus-rubra-seedlings
#8
Daniel J Ballhorn, Jacob D Elias, M A Balkan, Rachel F Fordyce, Peter G Kennedy
Carbon allocation demands from root-nodulating nitrogen-fixing bacteria (NFB) can modulate the host plant's chemical phenotype, with strong bottom-up effects on herbivores. In contrast to well-studied rhizobia, the effects of other important NFB on plant chemistry and herbivory are much less understood. Here, combining field surveys in the Oregon Coast Range, USA with laboratory experiments, we analyzed how N2-fixing Frankia bacteria influenced plant growth, chemistry, and herbivory on Alnus rubra (red alder) seedlings...
May 20, 2017: Oecologia
https://www.readbyqxmd.com/read/28528213/optimal-electrostatic-interactions-between-substrate-and-protein-are-essential-for-radical-chemistry-in-ornithine-4-5-aminomutase
#9
Caitlyn Makins, Douglas A Whitelaw, Michael McGregor, Alix Petit, Robert G Mothersole, Kathleen E Prosser, Kirsten R Wolthers
Ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii is an adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a 1,2-amino shift, interconverting D-ornithine and 2S, 4R-diaminopentanoate. The reaction occurs via a radical-based mechanism whereby a PLP-bound substrate radical undergoes intramolecular isomerization via an azacyclopropylcarbinyl radical intermediate. Herein, we investigated the catalytic role of active site residues that form non-covalent interactions with PLP and/or substrate, D-ornithine...
May 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525262/serum-protein-adsorption-enhances-active-leukemia-stem-cell-targeting-of-mesoporous-silica-nanoparticles
#10
Michaela Beck, Tamoghna Mandal, Christian Buske, Mika Lindén
The functionalization of nanoparticles with a ligand targeting receptors overexpressed by the target cells is a commonly used strategy when aiming at nanoparticle-based, cell type-specific drug delivery. However, the influence of particle surface chemistry on the targetability has received much less attention. The surface charge is known to directly or indirectly affect the nanoparticle cellular uptake kinetics by influencing serum protein adsorption. Thus, it is fair to assume that both the specificity and cellular uptake kinetics of targeted nanoparticles are influenced by the nanoparticle charge, both of which are important parameters for controlling cell-specific drug delivery efficiency...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28523917/silica-nanoparticles-functionalized-with-zwitterionic-sulfobetaine-siloxane-for-application-as-a-versatile-antifouling-coating-system
#11
Brianna Rose Knowles, Pawel Wagner, Shane MacLaughlin, Michael J Higgins, Paul J Molino
The growing need to develop surfaces able to effectively resist biological fouling has resulted in the widespread investigation of nanomaterials with potential antifouling properties. However, the preparation of effective antifouling coatings is limited by the availability of reactive surface functional groups and our ability to carefully control and organise chemistries at a materials interface. Here, we present two methods of preparing hydrophilic low fouling surface coatings through reaction of silica nanoparticle suspensions and pre-deposited silica nanoparticle films with zwitterionic sulfobetaine...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28522160/complete-genome-of-a-metabolically-diverse-marine-bacterium-shewanella-japonica-kctc-22435-t
#12
Kyung Mo Kim, Hanna Choe, Byung Kwon Kim, Arshan Nasir
Shewanella japonica KCTC 22435(T) is a facultatively anaerobic, Gram-negative, mesophilic, rod-shaped bacterium isolated from sea water at the Pacific Institute of Bio-organic Chemistry of the Marine Experimental Station, Troitza Bay, Gulf of Peter the Great, Russia. Here, we report the complete genome of S. japonica KCTC 22435(T), which consists of 4,975,677bp (G+C content of 40.80%) with a single chromosome, 4036 protein-coding genes, 97 tRNAs and 8 rRNA operons. Genes detected in the genome reveal that the strain possesses a type II secretion system, cytochrome c family proteins with various numbers of heme-binding motifs, and metabolic pathways for utilizing diverse carbon sources, supporting the potential of KCTC 22435(T) to generate electricity in salinity culture conditions...
May 15, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28521765/inhibition-of-o-glcnacase-leads-to-elevation-of-o-glcnac-tau-and-reduction-of-tauopathy-and-cerebrospinal-fluid-tau-in-rtg4510-mice
#13
Nicholas B Hastings, Xiaohai Wang, Lixin Song, Brent D Butts, Diane Grotz, Richard Hargreaves, J Fred Hess, Kwok-Lam Karen Hong, Cathy Ruey-Ruey Huang, Lynn Hyde, Maureen Laverty, Julie Lee, Diane Levitan, Sherry X Lu, Maureen Maguire, Veeravan Mahadomrongkul, Ernest J McEachern, Xuesong Ouyang, Thomas W Rosahl, Harold Selnick, Michaela Stanton, Giuseppe Terracina, David J Vocadlo, Ganfeng Wang, Joseph L Duffy, Eric M Parker, Lili Zhang
BACKGROUND: Hyperphosphorylation of microtubule-associated protein tau is a distinct feature of neurofibrillary tangles (NFTs) that are the hallmark of neurodegenerative tauopathies. O-GlcNAcylation is a lesser known post-translational modification of tau that involves the addition of N-acetylglucosamine onto serine and threonine residues. Inhibition of O-GlcNAcase (OGA), the enzyme responsible for the removal of O-GlcNAc modification, has been shown to reduce tau pathology in several transgenic models...
May 18, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28521678/ipgk-pseaac-identify-lysine-phosphoglycerylation-sites-in-proteins-by-incorporating-four-different-tiers-of-amino-acid-pairwise-coupling-information-into-the-general-pseaac
#14
Li-Ming Liu, Yan Xu, Kuo-Chen Chou
BACKGROUND: Occurring at Lys residues, the PGK (lysine phosphoglycerylation) is a special kind of post-translational modification (PTM). It may invert the charge potential of the modified residue and change the protein structures and functions, causing various diseases in liver, brain, and kidney. OBJECTIVE: From the angles of both basic research and drug development, we are facing a critical challenging problem: for an uncharacterized protein sequence containing many Lys residues, which ones can be of phosphoglycerylation, and which ones cannot? METHOD: To address this problem, we have developed a predictor called iPGK-PseAAC by incorporating into the general PseAAC (pseudo amino acid composition) with four different tiers of amino acid pairwise coupling information, where tiers 1, 2, 3, and 4 refer to the amino acid pairwise couplings between all the 1st, 2nd, 3rd, and 4th most contiguous residues along a protein segment, respectively...
May 15, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28521066/optochemical-control-of-biological-processes-in-cells-and-animals
#15
Nicholas Ankenbruck, Taylor Courtney, Yuta Naro, Alexander Deiters
Achieving precise control of biological function represents a crucial tool for studying the mechanisms of cellular processes. Naturally, these processes occur in a strict spatially and temporally regulated fashion. In order to generate accurate models, the tools used to study these processes must also operate with high spatiotemporal resolution. To this end, the use of light as a conditional stimulus has found extensive applications for the activation and deactivation of small molecules, proteins, peptides, and oligonucleotides...
May 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28516207/enhancing-h2o2-resistance-of-an-esterase-from-pyrobaculum-calidifontis-by-structure-guided-engineering-of-the-substrate-binding-site
#16
Pengfei Zhou, Dongming Lan, Grzegorz Maria Popowicz, Xuping Wang, Bo Yang, Yonghua Wang
Green technologies are attracting increasing attention in industrial chemistry where enzymatic reactions can replace dangerous and environmentally unfriendly chemical processes. In situ enzymatic synthesis of peroxycarboxylic acid is an attractive alternative for several industrial applications although concentrated H2O2 can denature the biocatalyst, limiting its usefulness. Herein, we report the structure-guided engineering of the Pyrobaculum calidifontis esterase (PestE) substrate binding site to increase its stability and perhydrolysis activity...
May 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28515013/atomic-force-microscopy-from-red-blood-cells-to-immunohaematology
#17
REVIEW
Natasha Yeow, Rico F Tabor, Gil Garnier
Atomic force microscopy (AFM) offers complementary imaging modes that can provide morphological and structural details of red blood cells (RBCs), and characterize interactions between specific biomolecules and RBC surface antigen. This review describes the applications of AFM in determining RBC health by the observation of cell morphology, elasticity and surface roughness. Measurement of interaction forces between plasma proteins and antibodies against RBC surface antigen using the AFM also brought new information to the immunohaematology field...
May 11, 2017: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/28513597/thermophoretic-migration-of-vesicles-depends-on-mean-temperature-and-head-group-chemistry
#18
Emma L Talbot, Jurij Kotar, Lucia Parolini, Lorenzo Di Michele, Pietro Cicuta
A number of colloidal systems, including polymers, proteins, micelles and hard spheres, have been studied in thermal gradients to observe and characterize their driven motion. Here we show experimentally the thermophoretic behaviour of unilamellar lipid vesicles, finding that mobility depends on the mean local temperature of the suspension and on the structure of the exposed polar lipid head groups. By tuning the temperature, vesicles can be directed towards hot or cold, forming a highly concentrated region...
May 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28512386/oxidative-stress-biomarkers-establishment-of-reference-values-for-isoprostanes-aopp-and-npbi-in-cord-blood
#19
Mariangela Longini, Elisa Belvisi, Fabrizio Proietti, Francesco Bazzini, Giuseppe Buonocore, Serafina Perrone
Oxidative stress (OS) is a common pathogenic factor involved in the onset of several diseases in humans, from immunologic disorders to malignancy, being a serious public health problem. In perinatal period, OS has been associated with adverse outcome of pregnancy and neonatal diseases. Dangerous effects of OS are mediated by increased production of free radicals (FRs) following various mechanisms, such as hypoxia, ischemia reperfusion, hyperoxia, inflammation, mitochondrial dysfunction, Fenton chemistry, and prostaglandin metabolism...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/28512003/towards-a-sustainable-biobased-industry-highlighting-the-impact-of-extremophiles
#20
REVIEW
Anna Krüger, Christian Schäfers, Carola Schröder, Garabed Antranikian
The transition of the oil-based economy towards a sustainable economy completely relying on biomass as renewable feedstock requires the concerted action of academia, industry, politics and civil society. An interdisciplinary approach of various fields such as microbiology, molecular biology, chemistry, genetics, chemical engineering and agriculture in addition to cross-sectional technologies such as economy, logistics and digitalization is necessary to meet the future global challenges. The genomic era has contributed significantly to the exploitation of naturés biodiversity also from extreme habitats...
May 13, 2017: New Biotechnology
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