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Biochemistry

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https://www.readbyqxmd.com/read/28333446/quantification-of-membrane-protein-self-association-with-a-high-throughput-compatible-fluorescence-assay
#1
Junbei Li, Xiaoyan Jade Qiu
For many membrane proteins, self-association serves both structural and functional roles. Studies of such association can be simplified by switching to micelles as the membrane-mimicking environment. But native interaction is not preserved in all detergents. The selection of suitable conditions for biochemical experiments would be greatly facilitated by a quantitative high-throughput assay. Here we showed that the fluorescence polarization (FP) reduction, resulted from homo-FRET and measured in a high-throughput compatible format, can be used to determine both association states and constants for membrane proteins in micelles...
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28333436/replication-protein-a-blocks-the-way
#2
Eric C Greene
No abstract text is available yet for this article.
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28332826/packaged-and-free-stmv-rna-genomes-adopt-distinct-conformational-states
#3
Bridget C Larman, Elizabeth A Dethoff, Kevin M Weeks
The RNA genomes of viruses likely undergo multiple functionally important conformational changes during their replication cycles, changes that are poorly understood at present. We used two complementary in-solution RNA structure probing strategies (SHAPE-MaP and RING-MaP) to examine the structure of the RNA genome of satellite tobacco mosaic virus inside authentic virions and in a capsid-free state. Both RNA states feature similar three-domain architectures in which each major replicative function - translation, capsid coding, and genome synthesis - fall into distinct domains...
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28332820/kinetic-landscape-of-a-peptide-bond-forming-prolyl-oligopeptidase
#4
Clarissa Melo Czekster, James H Naismith
Prolyl oligopeptidase B from Galerina marginata (GmPOPB) has recently been discovered as a peptidase capable of breaking and forming peptide bonds to yield a cyclic peptide. Despite the relevance of prolyl oligopeptidases in human biology and disease, a kinetic analysis pinpointing rate-limiting steps for a member of this enzyme family is not available. Macrocyclase enzymes are currently exploited to produce cyclic peptides with potential therapeutic applications. Cyclic peptides are promising drug-like molecules due to their stability and conformational rigidity...
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28304156/probing-the-time-dependency-of-cyclooxygenase-1-inhibitors-by-computer-simulations
#5
Yasmin Shamsudin Khan, Hugo Gutiérrez-de-Terán, Johan Åqvist
Time-dependent inhibition of the cyclooxygenases (COX) by a range of nonsteroidal anti-inflammatory drugs has been described since the first experimental assays of COX were performed. Slow tight-binding inhibitors of COX-1 bind in a two-step mechanism in which the EI → EI* transition is slow and practically irreversible. Since then, various properties of the inhibitors have been proposed to cause or affect the time dependency. Conformational changes in the enzyme have also been proposed to cause the time dependency, but no particular structural feature has been identified...
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28300394/an-asymmetric-conformational-change-in-lacy
#6
Irina Smirnova, Vladimir Kasho, Xiaoxu Jiang, H Ronald Kaback
Galactoside/H(+) symport by the lactose permease of Escherichia coli (LacY) involves reciprocal opening and closing of periplasmic and cytoplasmic cavities so that sugar- and H(+)-binding sites become alternatively accessible to either side of the membrane. After reconstitution into proteoliposomes, LacY with the periplasmic cavity sealed by cross-linking paired-Cys residues does not bind sugar from the periplasmic side. However, reduction of the S-S bond restores opening of the periplasmic cavity and galactoside binding...
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28326765/a-change-in-the-rate-determining-step-of-polymerization-by-the-k289m-dna-polymerase-beta-cancer-associated-variant
#7
Khadijeh S Alnajjar, Beatriz Garcia-Barboza, Amirsoheil Negahbani, Maryam Nakhjiri, Boris A Kashemirov, Charles E McKenna, Myron F Goodman, Joann B Sweasy
K289M is a variant of DNA polymerase β (pol β) that was previously identified in colorectal cancer. The expression of this variant leads to a 16-fold increase in mutation frequency at a specific site <i>in vivo</i> and a reduction in fidelity <i>in vitro</i> in a sequence context-specific manner. Previous work shows that this reduction in fidelity results from decreased discrimination against incorrect nucleotide incorporation at the level of polymerization. To probe the transition state of the K289M mutator variant of pol β, single turnover kinetics experiments were performed using β,γ-CXY dGTP analogues with a wide range of leaving group monoacid dissociation constants (p<i>K</i><sub>a4</sub>), including a corresponding set of novel β,γ-CXY dCTP analogues...
March 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28304160/nucleosome-histone-tail-conformation-and-dynamics-impacts-of-lysine-acetylation-and-a-nearby-minor-groove-benzo-a-pyrene-derived-lesion
#8
Iwen Fu, Yuqin Cai, Nicholas E Geacintov, Yingkai Zhang, Suse Broyde
Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored...
March 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28323419/the-role-of-sufs-is-restricted-to-fes-cluster-biosynthesis-in-escherichia-coli
#9
Martin Bühning, Angelo Valleriani, Silke Leimkühler
In Escherichia coli two different systems have been identified that are important for the coordinate formation of Fe-S clusters, namely the ISC and SUF systems. The ISC system is the housekeeping Fe-S machinery, which provides Fe-S clusters for numerous cellular proteins. The IscS protein of this system was additionally revealed to be the primary sulfur donor for numerous sulfur-containing molecules with important biological functions, among which are the molybdenum cofactor (Moco) and thiolated nucleosides in tRNA...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28322549/vitamin-c-modulates-the-immunotoxic-effect-of-17-alpha-methyltestosterone-in-nile-tilapia
#10
Haitham G Abo-Al-Ela, Abeer F El-Nahas, Shawky Mahmoud, Essam M Ibrahim
The synthetic androgen, 17 alpha-methyltestosterone (MT), is profusely used and practically needed in the production of all-male Nile tilapia fry; however, such androgenic hormones badly disrupt the immune system. This study aimed to alleviate or counteract the immunotoxic effect of MT using vitamin C (ascorbic acid, vit C). Our results show that the highest phagocytic activity (PA), phagocytic index (PI) and lysozyme activity were detected in the vit C group and the MT plus vit C group. Furthermore, PA and PI were significantly suppressed, but lysozyme activity was stronger in the MT group than the control...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28319368/comparative-analysis-reveals-furoyl-in-vivo-selective-hydroxyl-acylation-analyzed-by-primer-extension-reagents-form-stable-ribosyl-ester-adducts
#11
Dalen Chan, Chao Feng, Yuran Zhen, Ryan A Flynn, Robert C Spitale
RNA molecules depend on structural elements that are critical for cellular function. Chemical methods for probing RNA structure have emerged as a necessary component of characterizing RNA function. As such, understanding the limitations and idiosyncrasies of these methods is essential for their utility. Selective hydroxyl acylation has emerged as a common method for analyzing RNA structure. Ester products as a result of 2'-hydroxyl acylation can then be identified through reverse transcription or mutational enzyme profiling...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28287260/probing-for-and-quantifying-agonist-hydrogen-bonds-in-%C3%AE-6%C3%AE-2-nicotinic-acetylcholine-receptors
#12
Michael R Post, Henry A Lester, Dennis A Dougherty
Designing subtype-selective agonists for neuronal nicotinic acetylcholine receptors is a challenging and significant goal aided by intricate knowledge of each subtype's binding patterns. We previously reported that in α6β2 receptors, acetylcholine makes a functional cation-π interaction with Trp149, but nicotine and TC299423 do not, suggesting a distinctive binding site. This work explores hydrogen binding at the backbone carbonyl associated with α6β2 Trp149. Substituting residue i + 1, Thr150, with its α-hydroxy analogue (Tah) attenuates the carbonyl's hydrogen bond accepting ability...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28225601/rationalizing-the-binding-kinetics-for-the-inhibition-of-the-burkholderia-pseudomallei-fabi1-enoyl-acp-reductase
#13
Carla Neckles, Sandra Eltschkner, Jason E Cummings, Maria Hirschbeck, Fereidoon Daryaee, Gopal R Bommineni, Zhuo Zhang, Lauren Spagnuolo, Weixuan Yu, Shabnam Davoodi, Richard A Slayden, Caroline Kisker, Peter J Tonge
There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the drug-target residence time require knowledge of both the ground and transition states on the inhibition reaction coordinate, and we have determined the structure-kinetic relationship for 22 ethyl- or hexyl-substituted diphenyl ethers that are slow-binding inhibitors of bpFabI1, the enoyl-ACP reductase FabI1 from Burkholderia pseudomallei...
March 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28319664/reduction-of-folate-by-dihydrofolate-reductase-from-thermotoga-maritima
#14
E Joel Loveridge, Lukas Hroch, Robert L Hughes, Thomas Williams, Rhidian L Davies, Antonio Angelastro, Louis Y P Luk, Giovanni Maglia, Rudolf K Allemann
Mammalian dihydrofolate reductases (DHFR) catalyse the reduction of folate more efficiently than the equivalent bacterial enzymes, despite typically having similar efficiencies for the reduction of their natural substrate dihydrofolate. In contrast, we show here that DHFR from the hyperthermophilic bacterium Thermotoga maritima is able to catalyse reduction of folate to tetrahydrofolate with a similar efficiency to reduction of dihydrofolate under saturating conditions. NMR and mass spectrometry experiments showed no evidence for production of free dihydrofolate during either the EcDHFR- or TmDHFR-catalysed reductions of folate, suggesting that both enzymes perform the two reduction steps without release of the partially reduced substrate...
March 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28318265/cytoskeletal-like-filaments-of-camkii-are-formed-in-a-regulated-and-zn2-dependent-manner
#15
Laurel Hoffman, Lin Li, Emil Alexov, Hugo Sanabria, Melvin Neal Waxham
Ca2+-Calmodulin-dependent protein kinase II (CaMKII) is highly abundant in neurons, where its concentration reaches that typically found for cytoskeletal proteins. Functional reasons for such a high concentration are not known, but given the multitude of known binding partners for CaMKII, a role as a scaffolding molecule has been proposed. In this report, we provide experimental evidence that demonstrates a novel structural role for CaMKII. We discovered that CaMKII forms filaments that can extend for several microns in the presence of certain divalent cations (Zn2+, Cd2+ and Cu2+) but not with others (Ca2+, Mg2+, Co2+ and Ni2+)...
March 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28277678/unravelling-the-non-native-low-spin-state-of-the-cytochrome-c-cardiolipin-complex-evidence-of-the-formation-of-a-his-ligated-species-only
#16
Lisa Milazzo, Lorenzo Tognaccini, Barry D Howes, Federica Sinibaldi, Maria C Piro, Maria Fittipaldi, Maria C Baratto, Rebecca Pogni, Roberto Santucci, Giulietta Smulevich
The interaction between cytochrome c (Cyt c) and cardiolipin (CL) plays a vital role in the early stages of apoptosis. The binding of CL to Cyt c induces a considerable increase in its peroxidase activity that has been attributed to the partial unfolding of the protein, dissociation of the Met80 axial ligand, and formation of non-native conformers. Although the interaction between Cyt c and CL has been extensively studied, there is still no consensus regarding the conformational rearrangements of Cyt c that follow the protein-lipid interaction...
March 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28316240/heme-gazing-illuminating-eukaryotic-heme-trafficking-dynamics-and-signaling-with-fluorescent-heme-sensors
#17
David A Hanna, Osiris Martinez-Guzman, Amit Ram Reddi
Heme (iron protoporphyrin IX) is an essential protein prosthetic group and signaling molecule required for most life on Earth. All heme dependent processes require the dynamic and rapid mobilization of heme from sites of synthesis or uptake to hemoproteins present in virtually every subcellular compartment. The cytotoxicity and hydrophobicity of heme necessitates that heme mobilization is carefully controlled to mitigate the deleterious effects of this essential toxin. Indeed, a number of disorders, including certain cancers, cardiovascular diseases, and aging and age-related neurodegenerative diseases, are tied to defects in heme homeostasis...
March 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28291355/the-conformation-of-the-epidermal-growth-factor-receptor-transmembrane-domain-dimer-dynamically-adapts-to-the-local-membrane-environment
#18
Eduard V Bocharov, Pavel E Bragin, Konstantin V Pavlov, Olga V Bocharova, Konstantin S Mineev, Anton A Polyansky, Pavel E Volynsky, Roman G Efremov, Alexander S Arseniev
The epidermal growth factor receptor (EGFR) family is an important class of receptor tyrosine kinases, mediating a variety of cellular responses in normal biological processes and in pathological states of multicellular organisms. Different modes of dimerization of the human EGFR transmembrane domain (TMD) in different membrane mimetics recently prompted us to propose a novel signal transduction mechanism based on protein-lipid interaction. However, the experimental evidence for it was originally obtained with slightly different TMD fragments used in the two different mimetics, compromising the validity of the comparison...
March 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28290671/mobility-and-core-protein-binding-patterns-of-disordered-c-terminal-tails-in-%C3%AE-tubulin-isotypes
#19
Yoann Laurin, Joel Eyer, Charles H Robert, Chantal Prevost, Sophie Sacquin-Mora
Although they play a significant part in the regulation of microtubule structure, dynamics, and function, the disordered C-terminal tails of tubulin remain invisible to experimental structural methods and do not appear in the crystallographic structures that are currently available in the Protein Data Bank. Interestingly, these tails concentrate most of the sequence variability between tubulin isotypes and are the sites of the principal post-translational modifications undergone by this protein. Using homology modeling, we developed two complete models for the human αI/βI- and αI/βIII-tubulin isotypes that include their C-terminal tails...
March 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28296385/theoretical-studies-on-the-electronic-absorption-spectra-of-thiamin-diphosphate-in-pyruvate-decarboxylase
#20
Mirko Paulikat, Cindy Wechsler, Kai Tittmann, Ricardo A Mata
Electronic absorption spectra are often times used to identify reaction intermediates or substrates/products in enzymatic systems, as long as absorption bands can be unequivocally assigned to the species under study. The latter task is far from trivial given the transient nature of some states and the complexity of the surrounding environment around the active site. In order to identify unique spectral fingerprints, controlled experiments on model compounds have been used in the past, but even these can sometimes be unreliable...
March 15, 2017: Biochemistry
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