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Biochemistry

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https://www.readbyqxmd.com/read/28206750/synthetic-riboswitches-from-plug-and-pray-towards-plug-and-play
#1
Maja Etzel, Mario Mörl
In synthetic biology, metabolic engineering as well as gene therapy there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28206745/atomistic-molecular-dynamics-simulations-of-mitochondrial-dna-polymerase-gamma-novel-mechanisms-of-function-and-pathogenesis
#2
Liliya Euro, Outi Haapanen, Tomasz Rog, Ilpo Vattulainen, Anu Suomalainen, Vivek Sharma
DNA polymerase gamma (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report first atomistic classical molecular dynamics (MD) simulations of human Pol γ replicative complex...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28206738/defective-rnps-mistakes-in-rna-processing-and-diseases
#3
Mia K Mihailovic, Angela Chen, Juan C Gonzalez-Rivera, Lydia M Contreras
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA-targeting from traditional protein-targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight of the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28182405/blip-ii-employs-differential-hotspot-residues-to-bind-structurally-similar-staphylococcus-aureus-pbp2a-and-class-a-%C3%AE-lactamases
#4
Carolyn J Adamski, Timothy Palzkill
The interaction of β-lactamase inhibitory protein II (BLIP-II) with β-lactamases serves as a model system to investigate the principles underlying protein-protein interactions. Previous studies have focused on identifying the determinants of binding affinity and specificity between BLIP-II and class A β-lactamases. However, interactions between BLIP-II and other bacterial proteins have yet to be explored. Here, we provide evidence that BLIP-II binds penicillin binding protein 2a (PBP2a) from methicillin-resistant Staphylococcus aureus (MRSA) with a KD in the low micromolar range...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28145684/alanine-501-mutations-in-penicillin-binding-protein-2-from-neisseria-gonorrhoeae-structure-mechanism-and-effects-on-cephalosporin-resistance-and-biological-fitness
#5
Joshua Tomberg, Alena Fedarovich, Leah R Vincent, Ann E Jerse, Magnus Unemo, Christopher Davies, Robert A Nicholas
Resistance of Neisseria gonorrhoeae to expanded-spectrum cephalosporins such as ceftriaxone and cefixime has increased markedly in the past decade. The primary cephalosporin resistance determinant is a mutated penA gene, which encodes the essential peptidoglycan transpeptidase, penicillin-binding protein 2 (PBP2). Decreased susceptibility and resistance can be conferred by mosaic penA alleles containing upward of 60 amino acid changes relative to wild-type PBP2, or by nonmosaic alleles with relatively few mutations, the most important of which occurs at Ala501 located near the active site of PBP2...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28124899/selenomethionine-quenching-of-tryptophan-fluorescence-provides-a-simple-probe-of-protein-structure
#6
Matthew D Watson, Ivan Peran, Junjie Zou, Osman Bilsel, Daniel P Raleigh
Fluorescence spectroscopy, relying on intrinsic protein fluorophores, is one of the most widely used methods for studying protein folding, protein-ligand interactions, and protein dynamics. Tryptophan is usually the fluorophore of choice, given its sensitivity to its environment and having the highest quantum yield of the natural amino acids; however, changes in tryptophan fluorescence can be difficult to interpret in terms of specific structural changes. The introduction of quenchers of tryptophan fluorescence can provide information about specific structures, particularly if quenching is short-range; however, the most commonly employed quencher is histidine, and it is effective only when the imidazole side chain is protonated, thus limiting the pH range over which this approach can be employed...
February 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28199095/interrelationship-among-the-fe-his-bond-strengths-oxygen-affinities-and-intersubunit-hydrogen-bonding-changes-upon-ligand-binding-in-%C3%AE-subunit-of-human-hemoglobin-the-alkaline-bohr-effect
#7
Shigenori Nagatomo, Miki Okumura, Kazuya Saito, Takashi Ogura, Teizo Kitagawa, Masako Nagai
Regulation of oxygen affinity of human adult hemoglobin (Hb A) at high pH, known as the alkaline Bohr effect, is essential to its physiological function. In this study structural mechanisms of the alkaline Bohr effect and pH-dependent O2 affinity changes are investigated with (1)H NMR, and visible- and UV-resonance Raman spectra of mutant Hbs, Hb M Iwate (αH87Y) and Hb M Boston (αH58Y). It was found that even though the O2 binding to the α subunits is forbidden in the mutant Hbs, the O2 affinity became higher at alkaline pH than at neutral pH and concomitantly, the Fe-His stretching frequency of the β subunits was shifted to higher values...
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28199087/expression-purification-and-properties-of-a-human-arachidonoyl-specific-isoform-of-diacylglycerol-kinase
#8
William Jennings, Sejal Doshi, Prasanta Kumar Hota, Aaron Prodeus, Stephanie Black, Richard M Epand
Diacylglycerol kinase epsilon (DGKε) catalyzes the phosphorylation of diacylglycerol producing phosphatidic acid. DGKε demonstrates exquisite specificity for the acyl chains of diacylglycerol. This contributes to the specificity of the PI-cycle for lipid intermediates containing particular acyl chains. Dysregulation of DGKε perturbs lipid signaling and biosynthesis, which has been linked to epilepsy, Huntington's disease and heart disease. Recessive loss-of-function mutations in the DGKε gene cause atypical hemolytic uremic syndrome...
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28198613/the-discovery-of-a-%C3%AE-lactone-synthetase
#9
Frank M Raushel
No abstract text is available yet for this article.
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28198610/disentangling-nanonets-human-%C3%AE-defensin-6-targets-candida-albicans-virulence
#10
Lynette Cegelski
No abstract text is available yet for this article.
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28165720/intein-promoted-cyclization-of-aspartic-acid-flanking-the-intein-leads-to-atypical-n-terminal-cleavage
#11
Christopher J Minteer, Nicolle M Siegart, Kathryn M Colelli, Xinyue Liu, Robert J Linhardt, Chunyu Wang, Alvin V Gomez, Julie N Reitter, Kenneth V Mills
Protein splicing is a post-translational reaction facilitated by an intein, or intervening protein, which involves the removal of the intein and the ligation of the flanking polypeptides, or exteins. A DNA polymerase II intein from Pyrococcus abyssi (Pab PolII intein) can promote protein splicing in vitro on incubation at high temperature. Mutation of active site residues Cys1, Gln185, and Cys+1 to Ala results in an inactive intein precursor, which cannot promote the steps of splicing, including cleavage of the peptide bond linking the N-extein and intein (N-terminal cleavage)...
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28165218/perfluoro-tert-butyl-homoserine-is-a-helix-promoting-highly-fluorinated-nmr-sensitive-aliphatic-amino-acid-detection-of-the-estrogen-receptor%C3%A2-coactivator-protein-protein-interaction-by-19-f-nmr
#12
Caitlin M Tressler, Neal J Zondlo
Highly fluorinated amino acids can stabilize proteins and complexes with proteins, via enhanced hydrophobicity, and provide novel methods for identification of specific molecular events in complex solutions, via selective detection by (19)F NMR and the absence of native (19)F signals in biological contexts. However, the potential applications of (19)F NMR in probing biological processes are limited both by the strong propensities of most highly fluorinated amino acids for the extended conformation and by the relatively modest sensitivity of NMR spectroscopy, which typically constrains measurements to mid-micromolar concentrations...
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28196325/decoding-of-o-linked-glycosylation-by-mass-spectrometry
#13
SriHariRaju Mulagapati, Veerendra Koppolu, T Shantha Raju
Protein glycosylation (N-, and O- linked) plays an important role in many biological processes including the protein structure and function. However, the structural elucidation of glycans, specifically O-linked glycans remains a major challenge and is often overlooked during protein analysis. Recently, mass spectrometry (MS) is maturing as a powerful technology for high-quality analytical characterization of O-linked glycans. This article summarizes the recent developments and insights of MS based glycomics technology, which focus on mucin type O-glycan analysis...
February 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28187685/geometric-patterns-for-neighboring-bases-near-the-stacked-state-in-nucleic-acid-strands
#14
Ada Anna Sedova, Nilesh K Banavali
Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in non-helical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and presence or absence of a protein environment...
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28186725/small-molecules-engage-hot-spots-through-cooperative-binding-to-inhibit-a-tight-protein-protein-interaction
#15
Degang Liu, David Xu, Min Liu, William Eric Knabe, Cai Yuan, Donghui Zhou, Mingdong Huang, Samy O Meroueh
Protein-protein interactions drive every aspect of cell signaling, yet there exist only few small-molecule inhibitors of these interactions. Despite our ability to identify critical residues known as hot spots, little is known about how to effectively engage them to disrupt protein-protein interactions. Here, we take advantage of the ease of preparation and stability of pyrrolinone 1, a small-molecule inhibitor of the tight uPAR•uPA interaction, to synthesize more than 40 derivatives and explore their effect on the protein-protein interaction...
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28186720/cuprizone-intoxication-induces-cell-intrinsic-alterations-in-oligodendrocyte-metabolism-independent-of-copper-chelation
#16
Alexandra Taraboletti, Tia Louise Walker, Robin Avila, He Huang, Joel Caporoso, Erendra Manandhar, Thomas C Leeper, David A Modarelli, Satish Medicetty, Leah P Shriver
Cuprizone intoxication is a common animal model used to test myelin regenerative therapies to treat diseases such as multiple sclerosis. Mice fed this copper chelator develop reversible, region-specific oligodendrocyte loss and demyelination. While the cellular changes influencing the demyelinating process have been explored in this model, there is no consensus on the biochemical mechanisms of toxicity in oligodendrocytes and if this damage arises from the chelation of copper in vivo. Here we have identified an oligodendroglial cell line that displays sensitivity to cuprizone toxicity and performed global metabolomic profiling to determine biochemical pathways altered by this treatment...
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28186409/correction-to-structural-and-enzymatic-analysis-of-tumor-targeted-antifolates-that-inhibit-glycinamide-ribonucleotide-formyltransferase
#17
Siobhan M Deis, Arpit Doshi, Zhanjun Hou, Larry H Matherly, Aleem Gangjee, Charles E Dann
No abstract text is available yet for this article.
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28186407/x-ray-absorption-spectroscopy-reveals-an-organometallic-ni-c-bond-in-the-co-treated-form-of-acetyl-coa-synthase
#18
Mehmet Can, Logan J Giles, Stephen W Ragsdale, Ritimukta Sarangi
Acetyl CoA synthase (ACS) is a key enzyme in the Wood-Ljungdahl pathway of anaerobic CO2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni-CO, methyl-Ni, acetyl-Ni) intermediates. Here we report the first direct structural evidence for the proposed metal-carbon bond. We describe the preparation of highly active metal-replete enzyme and near quantitative generation of the kinetically competent carbonylated intermediate. This advance has enabled a combination of Ni- and Fe-K-edge XAS and EXAFS experiments along with DFT calculations...
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28183176/retraction-of-%C3%AE-amyloid-and-%C3%AE-synuclein-cooperate-to-block-snare-dependent-vesicle-fusion
#19
Bong-Kyu Choi, Jae-Yeol Kim, Moon-Yong Cha, Inhee Mook-Jung, Yeon-Kyun Shin, Nam Ki Lee
No abstract text is available yet for this article.
February 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28125218/identification-of-a-ligand-binding-site-on-the-staphylococcus-aureus-dnag-primase-c-terminal-domain
#20
Jonathan Catazaro, Jessica Periago, Matthew D Shortridge, Bradley Worley, Andrew Kirchner, Robert Powers, Mark A Griep
The interface between the DnaG primase C-terminal domain (CTD) and the N-terminal domain of DnaB helicase is essential for bacterial DNA replication because it allows coordinated priming of DNA synthesis at the replication fork while the DNA is being unwound. Because these two proteins are conserved in all bacteria and distinct from those in eukaryotes, their interface is an attractive antibiotic target. To learn more about this interface, we determined the solution structure and dynamics of the DnaG primase CTD from Staphylococcus aureus, a medically important bacterial species...
February 9, 2017: Biochemistry
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