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Protein chemistry

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https://www.readbyqxmd.com/read/28212487/interactions-between-membranes-and-metaphilic-polypeptide-architectures-with-diverse-sidechain-populations
#1
Michelle W Lee, Ming Han, Guilherme Volpe Bossa, Carly Snell, Ziyuan Song, Haoyu Tang, Lichen Yin, Jianjun Cheng, Sylvio May, Erik Luijten, Gerard C L Wong
At physiological conditions, most proteins or peptides can fold into relatively stable structures that present on their molecular surfaces specific chemical patterns partially smeared out by thermal fluctuations. These nanoscopically defined patterns of charge, hydrogen bonding, and/or hydrophobicity, along with their elasticity and shape stability (folded proteins have Young's moduli of ~1 × 10(8) Pa), largely determine and limit the interactions of these molecules, such as molecular recognition and allosteric regulation...
February 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28212462/climate-change-contaminant-interactions-in-marine-food-webs-towards-a-conceptual-framework
#2
Juan José Alava, William W L Cheung, Peter S Ross, Rashid U Sumaila
Climate change is reshaping the way in which contaminants move through the global environment, in large part by changing the chemistry of the oceans and affecting the physiology, health and feeding ecology of marine biota. Climate change-associated impacts on structure and function of marine food webs, with consequent changes in contaminant transport, fate and effects, is likely to have significant repercussions to those human populations that rely on fisheries resources for food, recreation or culture. Published studies on climate change-contaminant interactions with a focus on food web bioaccumulation were systematically reviewed to explore how climate change and ocean acidification may impact contaminant levels in marine food webs...
February 17, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28212442/ecto-5-nucleotidase-cd73-nt5e-vitamin-d-receptor-and-fgf23-gene-polymorphisms-may-play-a-role-in-the-development-of-calcific-uremic-arteriolopathy-in-dialysis-patients-data-from-the-german-calciphylaxis-registry
#3
Hansjörg Rothe, Vincent Brandenburg, Margot Haun, Barbara Kollerits, Florian Kronenberg, Markus Ketteler, Christoph Wanner
INTRODUCTION: Calciphylaxis/calcific uremic arteriolopathy affects mainly end-stage kidney disease patients but is also associated with malignant disorders such as myeloma, melanoma and breast cancer. Genetic risk factors of calciphylaxis have never been studied before. METHODS: We investigated 10 target genes using a tagging SNP approach: the genes encoding CD73/ ecto-5'-nucleotidase (purinergic pathway), Matrix Gla protein, Fetuin A, Bone Gla protein, VKORC1 (all related to intrinsic calcification inhibition), calcium-sensing receptor, FGF23, Klotho, vitamin D receptor, stanniocalcin 1 (all related to CKD-MBD)...
2017: PloS One
https://www.readbyqxmd.com/read/28208756/homocysteine-editing-thioester-chemistry-coenzyme-a-and-the-origin-of-coded-peptide-synthesis-%C3%A2
#4
REVIEW
Hieronim Jakubowski
Aminoacyl-tRNA synthetases (AARSs) have evolved "quality control" mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols...
February 9, 2017: Life
https://www.readbyqxmd.com/read/28206744/alkane-oxidation-methane-monooxygenases-related-enzymes-and-their-biomimetics
#5
Vincent C-C Wang, Suman Maji, Peter P-Y Chen, Hung Kay Lee, Steve S-F Yu, Sunney I Chan
Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation. Here, we review the progress made over the past two to three decades toward delineating the structures and functions of the catalytic sites in two MMOs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO)...
February 16, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28205401/computer-aided-drug-design-to-explore-cyclodextrin-therapeutics-and-biomedical-applications
#6
Azizeh Abdolmaleki, Fatemeh Ghasemi, Jahan B Ghasemi
Cyclodextrin (CD) is a subset of the macrocyclic structural class, which is an important class of small organic agents that are useful functional excipients. They have wide range application possibilities in different fields of sciences such as material preparation, medicine, analytical chemistry, and separation processes. They are used widely in pharmaceutical formulations and drug delivery for increasing the water solubility of low soluble drugs and drug candidates. Due to the ring structure, they behave differently than smaller molecules and may be capable of hitting new classes of targets...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28205291/molecular-dynamics-simulation-study-of-the-stay-or-leave-problem-for-two-magnesium-ions-in-gene-transcription
#7
Shaogui Wu
Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PPi )? This problem still remains obscure. In the present work, we studied the problem using all-atom molecular dynamics (MD) simulation combined with steered molecular dynamics (SMD) and umbrella sampling (US) simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups...
February 16, 2017: Proteins
https://www.readbyqxmd.com/read/28202724/chemistry-at-the-protein-mineral-interface-in-l-ferritin-assists-the-assembly-of-a-functional-%C3%AE-3-oxo-tris-%C3%AE-2-peroxo-triiron-iii-cluster
#8
Cecilia Pozzi, Silvia Ciambellotti, Caterina Bernacchioni, Flavio Di Pisa, Stefano Mangani, Paola Turano
X-ray structures of homopolymeric L-ferritin obtained by freezing protein crystals at increasing exposure times to a ferrous solution showed the progressive formation of a triiron cluster on the inner cage surface of each subunit. After 60 min exposure, a fully assembled (μ(3)-oxo)Tris[(μ(2)-peroxo)(μ(2)-glutamato-κO:κO')](glutamato-κO)(diaquo)triiron(III) anionic cluster appears in human L-ferritin. Glu60, Glu61, and Glu64 provide the anchoring of the cluster to the protein cage. Glu57 shuttles incoming iron ions toward the cluster...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28199365/click-chemistry-approach-to-study-mycoloylated-proteins-evidence-for-porb-and-porc-porins-mycoloylation-in-corynebacterium-glutamicum
#9
Hanane Issa, Emilie Huc-Claustre, Thamila Reddad, Nolwenn Bonadé Bottino, Maryelle Tropis, Christine Houssin, Mamadou Daffé, Nicolas Bayan, Nathalie Dautin
Protein mycoloylation is a recently identified, new form of protein acylation. This post-translational modification consists in the covalent attachment of mycolic acids residues to serine. Mycolic acids are long chain, α-branched, β-hydroxylated fatty acids that are exclusively found in the cell envelope of Corynebacteriales, a bacterial order that includes important genera such as Mycobacterium, Nocardia or Corynebacterium. So far, only 3 mycoloylated proteins have been identified: PorA, PorH and ProtX from C...
2017: PloS One
https://www.readbyqxmd.com/read/28199119/engineering-a-catalytically-efficient-recombinant-protein-ligase
#10
Renliang Yang, Yee Hwa Wong, Giang K T Nguyen, James P Tam, Julien Lescar, Bin Wu
Breaking and forming peptidyl bonds are fundamental biochemical reactions in protein chemistry. Unlike proteases that are abundantly available, fast-acting ligases are rare. OaAEP1 is an enzyme isolated from the cyclotide-producing plant oldenlandia affinis that displayed weak peptide cyclase activity, despite having a similar structural fold with other asparaginyl endopeptidases (AEP). Here we report the first atomic structure of OaAEP1, at a resolution of 2.56 Å, in its pre-activation form. Our structure and biochemical analysis of this enzyme reveals its activation mechanism as well as structural features important for its ligation activity...
February 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28199101/fungal-identification-using-molecular-tools-a-primer-for-the-natural-products-research-community
#11
Huzefa A Raja, Andrew N Miller, Cedric J Pearce, Nicholas H Oberlies
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi...
February 15, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28199055/photo-induced-click-chemistry-for-dna-surface-structuring-via-direct-laser-writing
#12
Ljiljana Fruk, Antonina Kerbs, Patrick Mueller, Michael Kaupp, Ishtiaq Ahmed, Alexander S Quick, Doris Abt, Martin Wegener, Christof M Niemeyer, Christopher Barner-Kowollik
Oligonucleotides containing photo-caged dienes were prepared and shown to react quantitatively in a light-induced Diels-Alder cycloaddition with functional maleimides in aqueous solution within minutes. Due to its high yield and fast rate, the reaction was exploited for DNA surface patterning with sub-micrometer resolution employing direct laser writing (DLW). Functional DNA arrays were written via direct laser writing (DLW) in variable patterns, which were further encoded with fluorophores and proteins through DNA directed immobilisation...
February 15, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28198622/a-cell-penetrant-manganese-superoxide-dismutase-mnsod-mimic-is-able-to-complement-mnsod-and-exerts-an-antiinflammatory-effect-on-cellular-and-animal-models-of-inflammatory-bowel-diseases
#13
Emilie Mathieu, Anne-Sophie Bernard, Nicolas Delsuc, Elodie Quévrain, Géraldine Gazzah, Barry Lai, Florian Chain, Philippe Langella, Maria Bachelet, Joelle Masliah, Philippe Seksik, Clotilde Policar
Inorganic complexes are increasingly used for biological and medicinal applications, and the question of the cell penetration and distribution of metallodrugs is key to understanding their biological activity. Oxidative stress is known to be involved in inflammation and in inflammatory bowel diseases for which antioxidative defenses are weakened. We report here the study of the manganese complex Mn1 mimicking superoxide dismutase (SOD), a protein involved in cell protection against oxidative stress, using an approach in inorganic cellular chemistry combining the investigation of Mn1 intracellular speciation using mass spectrometry and of its quantification and distribution using electron paramagnetic resonance and spatially resolved X-ray fluorescence with evaluation of its biological activity...
February 15, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28196299/activity-based-probes-for-the-ubiquitin-conjugation-deconjugation-machinery-new-chemistries-new-tools-and-new-insights
#14
REVIEW
David S Hewings, John A Flygare, Matthew Bogyo, Ingrid E Wertz
The reversible post-translational modification of proteins by ubiquitin and ubiquitin-like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity-based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme-catalyzed manner...
February 14, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28195700/discovery-and-characterization-of-a-potent-and-specific-peptide-ligand-targeting-endothelial-progenitor-cells-and-endothelial-cells-for-tissue-regeneration
#15
Dake Hao, Wenwu Xiao, Ruiwu Liu, Priyadarsini Kumar, YuanPei Li, Ping Zhou, Fuzheng Guo, Diana L Farmer, Kit S Lam, Fengshan Wang, Aijun Wang
Endothelial progenitor cells (EPCs) and endothelial cells (ECs) play a vital role in endothelialization and vascularization for tissue regeneration. Various EPC/EC targeting biomolecules have been investigated to improve tissue regeneration with limited success often due to their limited functional specificity and structural stability. One-Bead-One-Compound (OBOC) combinatorial technology is an ultra-high throughput chemical library synthesis and screening method suitable for ligand discovery against a wide range of biological targets, such as integrins...
February 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28195695/o-glcnacylation-of-%C3%AE-synuclein-at-serine-87-reduces-aggregation-without-affecting-membrane-binding
#16
Yuka E Lewis, Ana Galesic, Paul M Levine, Cesar A De Leon, Natalie Lamiri, Caroline K Brennan, Matthew R Pratt
The aggregation of neurodegenerative-disease associated proteins can be affected by many factors, including a variety of posttranslational modifications. One such modification, O-GlcNAcylation, has been found on some of these aggregation prone proteins, including α-synuclein, the major protein that plays a causative role in synucleinopathies like Parkinson's disease. We previously used synthetic protein chemistry to prepare α-synuclein bearing an homogeneous O-GlcNAc modification at threonine 72 and showed that this modification inhibits protein aggregation...
February 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28194957/highly-selective-and-large-scale-mass-spectrometric-analysis-of-4-hydroxynonenal-modification-via-fluorous-derivatization-and-fluorous-solid-phase-extraction
#17
Wenjuan Yuan, Ying Zhang, Yun Xiong, Tao Tao, Yi Wang, Jun Yao, Lei Zhang, Guoquan Yan, Huimin Bao, Haojie Lu
Modification of proteins with 4-hydroxynonenal (HNE) is known to alter the function of proteins and regulate the associated biological processes in eukaryotic cells. The development of mass spectrometry (MS) makes high-throughput analysis of HNE modification accessible. However, the identification of HNE modification is still hampered by the low frequency of this modification. Therefore, only a limited number of HNE modification sites have been identified. The enrichment of HNE-modified peptides is critical for the MS analysis of this modification because of its low abundance...
February 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28194953/click-chemistry-reagent-for-identification-of-sites-of-covalent-ligand-incorporation-in-integral-membrane-proteins
#18
Melissa M Budelier, Wayland W L Cheng, Lucie Bergdoll, Zi-Wei Chen, Jeff Abramson, Kathiresan Krishnan, Mingxing Qian, Douglas F Covey, James W Janetka, Alex S Evers
Identifying sites of protein-ligand interaction is important for structure-based drug discovery and understanding protein structure-function relationships. Mass spectrometry (MS) has emerged as a useful tool for identifying residues covalently modified by ligands. Current methods use database searches that are dependent on acquiring interpretable fragmentation spectra (MS2) of peptide-ligand adducts. This is problematic for identifying sites of hydrophobic ligand incorporation in integral membrane proteins (IMPs), where poor aqueous solubility and ionization of peptide-ligand adducts and collision-induced adduct loss hinder the acquisition of quality MS2 spectra...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193150/maleimide-scavenging-enhances-determination-of-protein-s-palmitoylation-state-in-acyl-exchange-methods
#19
Charlotte H Hurst, Dionne Turnbull, Fiona Plain, William Fuller, Piers A Hemsley
S-palmitoylation (S-acylation) is emerging as an important dynamic post-translational modification of cysteine residues within proteins. Current assays for protein S-palmitoylation involve either in vivo labeling or chemical cleavage of S-palmitoyl groups to reveal a free cysteine sulfhydryl that can be subsequently labeled with an affinity handle (acyl-exchange). Assays for protein S-palmitoylation using acyl-exchange chemistry therefore require blocking of non-S-palmitoylated cysteines, typically using N-ethylmaleimide (NEM), to prevent non-specific detection...
February 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28193002/organic-cyanide-decorated-sers-active-nanopipettes-for-quantitative-detection-of-hemeproteins-and-fe-3-in-single-cells
#20
Sumaira Hanif, Hailing Liu, Ming Chen, Pir Muhammad, Yue Zhou, Jiao Cao, Saud Asif Ahmed, Jingjuan Xu, Xinghua Xia, Hongyuan Chen, Kang Wang
It is challenging to develop a robust nanoprobe for real-time operational and accurate detection of heavy metals in single cells. Fe-CN coordination chemistry has been well studied to determine the structural characteristics of hemeproteins by different techniques. However, the frequently used cyanide ligands are inorganic molecules that release cyanide anion under particular conditions and cause cyanide poisoning. In the present study, organic cyanide (4-mercaptobenzonitrile, MBN) was utilized for the first time in developing a facile nanoprobe based on surface-enhanced Raman scattering (SERS) for quantitative detection of hemeproteins (oxy-Hb) and trivalent iron (Fe(3+)) ions...
February 7, 2017: Analytical Chemistry
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