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Protein chemistry

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https://www.readbyqxmd.com/read/29792927/bacillus-subtilis-as-probiotic-candidate-for-red-sea-bream-growth-performance-oxidative-status-and-immune-response-traits
#1
Amr I Zaineldin, Sayed Hegazi, Shunsuke Koshio, Manabu Ishikawa, Abdulnasser Bakr, Abeer M S El-Keredy, Mahmoud A O Dawood, Serge Dossou, Weilong Wang, Zhang Yukun
The effects of dietary administration of Bacillus subtilis on the growth, digestive enzyme activity, blood chemistry, oxidative status and immune response of red sea bream (Pagrus major) were evaluated in the current study. Fish fed five different levels of B. subtilis at 0 (BS0), 1 × 104 (BS1), 1 × 106 (BS2), 1 × 108 (BS3) and 1 × 1010 (BS4) CFU kg-1 diet for 60 days. The obtained results showed that B. subtilis supplementation significantly improved growth performance (FBW, WG and SGR), feed utilization (FI, FCE, PER and PG) and whole-body protein content when compared to the control group (P < 0...
May 21, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29792801/developing-a-novel-sulfoxide-containing-ms-cleavable-homobifunctional-cysteine-reactive-cross-linker-for-studying-protein-protein-interactions
#2
Craig B Gutierrez, Sarah A Block, Clinton Yu, Stephanie M Soohoo, Alexander S Huszagh, Scott D Rychnovsky, Lan Huang
Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the mostly widely used cross-linking reagents are targeting lysines. While such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792689/selectivity-within-a-family-of-bacterial-phosphothreonine-lyases
#3
Kaitlin A Chambers, Nile S Abularrage, Rebecca A Scheck
Phosphothreonine lyases are bacterial effector proteins secreted into host cells to facilitate the infection process. This enzyme family catalyzes an irreversible elimination reaction that converts phosphothreonine or phosphoserine to dehydrobutyrine or dehydroalanine, respectively. Herein we report a study of substrate selectivity for each of the four known phosphothreonine lyases. This was accomplished using a combination of mass spectrometry and enzyme kinetics assays for a series of phosphorylated peptides derived from the mitogen activated protein kinase (MAPK) activation loop...
May 24, 2018: Biochemistry
https://www.readbyqxmd.com/read/29792672/biosynthesis-of-lincosamide-antibiotics-reactions-associated-with-degradation-and-detoxification-pathways-play-a-constructive-role
#4
Daozhong Zhang, Zhijun Tang, Wen Liu
Natural products typically are small molecules produced by living organisms. These products possess a wide variety of biological activities and thus have historically played a critical role in medicinal chemistry and chemical biology either as chemotherapeutic agents or as useful tools. Natural products are not synthesized for use by human beings; rather, living organisms produce them in response to various biochemical processes and environmental concerns, both internal and external. These processes/concerns are often dynamic and thus motivate the diversification, optimization, and selection of small molecules in line with changes in biological function...
May 24, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29792427/native-chemical-ligation-photodesulfurization-in-flow
#5
Timothy S Chisholm, Daniel Clayton, Luke J Dowman, Jessica Sayers, Richard J Payne
Native chemical ligation (NCL) combined with desulfurization chemistry has revolutionized the way in which large polypeptides and proteins are accessed by chemical synthesis. Herein, we outline the use of flow chemistry for the ligation-based assembly of polypeptides. We also describe the development of a novel photodesulfurization transformation that, when coupled with flow NCL, enables efficient access to native polypeptides on time scales up to 2 orders of magnitude faster than current batch NCL-desulfurization methods...
May 24, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29791796/tracking-of-engineered-bacteria-in-vivo-using-non-standard-amino-acid-incorporation
#6
Pichet Praveschotinunt, Noemie-Manuelle Dorval Courchesne, Ilona den Hartog, Chaochen Lu, Jessica J Kim, Peter Q Nguyen, Neel S Joshi
The rapidly growing field of microbiome research presents a need for better methods of monitoring gut microbes in vivo with high spatial and temporal resolution. We report a method of tracking microbes in vivo within the gastrointestinal tract by programming them to incorporate non-standard amino acids (NSAA) and labeling them via click chemistry. Using established machinery constituting an orthogonal translation system (OTS), we engineered Escherichia coli to incorporate p-azido-L-phenylalanine (pAzF) in place of the UAG (amber) stop codon...
May 23, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29791150/elastin-like-polypeptide-elp-charge-influences-self-assembly-of-elp-mcherry-fusion-proteins
#7
Carolyn E Mills, Zachary Michaud, Bradley D Olsen
Self-assembly of protein-polymer bioconjugates presents an elegant strategy for controlling nanostructure and orientation of globular proteins in functional materials. Recent work has shown that genetic fusion of globular protein mCherry to an elastin-like polypeptide (ELP) yields similar self-assembly behavior to these protein-polymer bioconjugates. In the context of studying protein-polymer bioconjugate self-assembly, the mutability of the ELP sequence allows several different properties of the ELP block to be tuned orthogonally while maintaining consistent polypeptide backbone chemistry...
May 23, 2018: Biomacromolecules
https://www.readbyqxmd.com/read/29791137/the-chemistry-of-lyophilized-blood-products
#8
Joseph Fernandez-Moure, Nuzhat Maisha, Erin B Lavik, Jeremy Cannon
With the development of new biologics and bioconjugates, storage and preservation have become more critical than ever before. Lyophilization is a method of cell and protein preservation by removing a solvent such as water from a substance followed by freezing. This technique has been used in the past and still holds promise for overcoming logistic challenges in safety net hospitals with limited blood banking resources, austere environments such as combat, and in mass casualty situations where existing resources may be outstripped...
May 23, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29791132/ptml-model-of-chembl-data-for-dopamine-targets-docking-synthesis-and-assay-of-new-plg-peptidomimetics
#9
Joana Ferreira da Costa, David Silva, Olga Caamaño, José M Brea, Maria Isabel Loza, Cristian R Munteanu, Alejandro Pazos, Xerardo García-Mera, Humbert González-Díaz
Predicting Drug-Protein Interactions (DPIs) for target proteins involved in Dopamine pathways is very important goal in medicinal chemistry. We can tackle this problem using Molecular Docking or Machine Learning (ML) models for one specific protein. Unfortunately, these models fail to account for large and complex Big Data sets of preclinical assays reported in public databases. This includes multiple conditions of assay like different experimental parameters, biological assays, target proteins, cell lines, organism of the target, organism of assay, etc...
May 23, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29790735/sensing-dna-through-dna-charge-transport
#10
Theodore J Zwang, Edmund C M Tse, Jacqueline K Barton
DNA charge transport chemistry involves the migration of charge over long molecular distances through the aromatic base pair stack within the DNA helix. This migration depends upon the intimate coupling of bases stacked one with another, and hence any perturbation in that stacking, through base modifications or protein binding, can be sensed electrically. In this review we describe the many ways DNA charge transport chemistry has been utilized to sense changes in DNA including the presence of lesions, mismatches, DNA-binding proteins, protein activity, and even reactions under weak magnetic fields...
May 23, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29790558/proteins-as-supramolecular-hosts-for-c-60-a-true-solution-of-c-60-in-water
#11
Matteo Di Giosia, Paul H H Bomans, Andrea Bottoni, Andrea Cantelli, Giuseppe Falini, Paola Franchi, Giuseppe Guarracino, Heiner Friedrich, Marco Lucarini, Francesco Paolucci, Stefania Rapino, Nico A J M Sommerdijk, Alice Soldà, Francesco Valle, Francesco Zerbetto, Matteo Calvaresi
Hybrid systems have great potential for a wide range of applications in chemistry, physics and materials science. Conjugation of a biosystem to a molecular material can tune the properties of the components or give rise to new properties. As a workhorse, here we take a C60@lysozyme hybrid. We show that lysozyme recognizes and disperses fullerene in water. AFM, cryo-TEM and high resolution X-ray powder diffraction show that the C60 dispersion is monomolecular. The adduct is biocompatible, stable in physiological and technologically-relevant environments, and easy to store...
May 23, 2018: Nanoscale
https://www.readbyqxmd.com/read/29788887/designing-peptidomimetics
#12
Juan J Perez
The concept of a peptidomimetic was coined about forty years ago. Since then, an enormous effort and interest has been devoted to mimic the properties of peptides with small molecules or pseudopeptides. The present report aims to review different approaches described in the past to succeed in this goal. Basically, there are two different approaches to design peptidomimetics: a medicinal chemistry approach, where parts of the peptide are successively replaced by non-peptide moieties until getting a non-peptide molecule and a biophysical approach, where a hypothesis of the bioactive form of the peptide is sketched and peptidomimetics are designed based on hanging the appropriate chemical moieties on diverse scaffolds...
May 21, 2018: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29786419/multifunctional-high-molecular-weight-post-translationally-modified-proteins-through-oxidative-cysteine-coupling-and-tyrosine-modification
#13
Brian M Seifried, James Cao, Bradley D Olsen
Glycoproteins and their mimics are challenging to produce via chemical or biological methods because of their long protein backbones and large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein, we demonstrate a new approach to protein bioconjugate synthesis that can approach the molar mass and functionalization densities of natural glycoproteins such as mucins and aggrecans. In this method, a tyrosine-enriched protein sequence is engineered and synthesized in E...
May 22, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29783836/a-y-shaped-three-arm-structure-for-probing-bivalent-interactions-between-protein-receptor-ligand-using-afm-and-spr
#14
Subhadip Senapati, Sudipta Biswas, Saikat Manna, Robert Ros, Stuart Lindsay, Peiming Zhang
The goal of this research was to develop linkage chemistry for the study of bivalent interactions between a receptor and its ligand using atomic force microscopy (AFM) and surface plasmon resonance (SPR). We conceived a three-arm structure composed of flexible chains connected to a large rigid core with orthogonal functional groups at their ends for formation and attachment (or immobilization) of bivalent ligands. To demonstrate the principle, we chose the well-known biotin-streptavidin interaction as a model system...
May 21, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29781242/photo-controlled-reversible-microtubule-assembly-mediated-by-cyclodextrin-derivative
#15
Ying-Ming Zhang, Ni-Yuan Zhang, Kui Xiao, Yu Liu, Qilin Yu
The design and construction of multistimuli-responsive supramolecular nanoassemblies that can mimic and regulate the fundamental biological processes has become a focus of interest in supramolecular chemistry. In this work, a perfect combination has been achieved between naturally occurring microtubule and artificially macrocyclic receptor. The self-assembling morphology of microtubules can be photo-tuned by the host-guest interaction of paclitaxel-modified β-cyclodextrin (PTX-CD) and photochromic arylazopyrazole (PTX-AAP)...
May 20, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29781014/cat-elcca-catalyzing-drug-discovery-through-click-chemistry
#16
Amanda L Garner
Click chemistry has emerged as a powerful tool in our arsenal for unlocking new biology. This includes its utility in both chemical biology and drug discovery. An emerging application of click chemistry is in the development of biochemical assays for high-throughput screening to identify new chemical probes and drug leads. This Feature Article will discuss the advancements in click chemistry that were necessary for the development of a new class of biochemical assay, catalytic enzyme-linked click chemistry assay or cat-ELCCA...
May 21, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29780551/protein-surface-functionalisation-as-a-general-strategy-for-facilitating-biomimetic-mineralisation-of-zif-8
#17
Natasha K Maddigan, Andrew Tarzia, David M Huang, Christopher J Sumby, Stephen G Bell, Paolo Falcaro, Christian J Doonan
The durability of enzymes in harsh conditions can be enhanced by encapsulation within metal-organic frameworks (MOFs) via a process called biomimetic mineralisation. Herein we show that the surface charge and chemistry of a protein determines its ability to seed MOF growth. We demonstrate that chemical modification of amino acids on the protein surface is an effective method for systematically controlling biomimetic mineralisation by zeolitic imidazolate framework-8 (ZIF-8). Reaction of surface lysine residues with succinic (or acetic) anhydride facilitates biomimetic mineralisation by increasing the surface negative charge, whereas reaction of surface carboxylate moieties with ethylenediamine affords a more positively charged protein and hinders the process...
May 14, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780502/the-impact-of-o-glycan-chemistry-on-the-stability-of-intrinsically-disordered-proteins
#18
Erica T Prates, Xiaoyang Guan, Yaohao Li, Xinfeng Wang, Patrick K Chaffey, Munir S Skaf, Michael F Crowley, Zhongping Tan, Gregg T Beckham
Protein glycosylation is a diverse post-translational modification that serves myriad biological functions. O -linked glycans in particular vary widely in extent and chemistry in eukaryotes, with secreted proteins from fungi and yeast commonly exhibiting O -mannosylation in intrinsically disordered regions of proteins, likely for proteolysis protection, among other functions. However, it is not well understood why mannose is often the preferred glycan, and more generally, if the neighboring protein sequence and glycan have coevolved to protect against proteolysis in glycosylated intrinsically disordered proteins (IDPs)...
April 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780280/generation-of-dynamic-combinatorial-libraries-using-hydrazone-functionalized-surface-mimetics
#19
Sarah H Hewitt, Andrew J Wilson
Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non-covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline-catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH4 OAc, at pH 6...
April 30, 2018: European Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29779667/terminal-alkyne-biosynthesis-in-marine-microbes
#20
Xuejun Zhu, Wenjun Zhang
The terminal alkyne is a readily derivatized functionality valued for its diverse applications in material synthesis, pharmaceutical science, and chemical biology. The synthetic biology routes to terminal alkynes are highly desired and yet underexplored. Some marine natural products contain a terminal alkyne functionality, and the discovery of the biosynthetic gene clusters for jamaicamide B and carmabin A marked the beginning of a new era in the understanding and engineering of terminal alkyne biosynthesis...
2018: Methods in Enzymology
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