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https://www.readbyqxmd.com/read/28651101/competitive-ligands-facilitate-dissociation-of-the-complex-of-bifunctional-inhibitor-and-protein-kinase
#1
Taavi Ivan, Erki Enkvist, Hedi Sinijarv, Asko Uri
Dissociation of the complex of a ligand and a protein usually follows the kinetic profile of the first order process and the rate of dissociation is not affected by the presence of competitive ligands. We discovered that dissociation of the complex between a bifunctional ligand and a protein kinase (the catalytic subunit of cAMP-dependent protein kinase), an enzyme possessing 2 different substrate binding sites, was accelerated (facilitated) over 50-fold in the presence of competitive ligands at higher concentrations...
June 20, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28651056/significantly-improved-protein-folding-thermodynamics-using-a-dispersion-corrected-water-model-and-a-new-residue-specific-force-field
#2
Hao-Nan Wu, Fan Jiang, Yun-Dong Wu
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature-dependence of folding/unfolding equilibrium, and overly collapsed unfolded or disordered states. For the later problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage and the GB1 hairpin)...
June 26, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28648524/molecular-modelling-of-biomolecules-by-paramagnetic-nmr-and-computational-hybrid-methods
#3
REVIEW
Kala Bharath Pilla, Kari Gaalswyk, Justin L MacCallum
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modelling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures...
June 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28647789/probing-slow-timescale-dynamics-in-proteins-using-methyl-1-h-cest
#4
Tairan Yuwen, Rui Huang, Lewis E Kay
Although (15)N- and (13)C-based chemical exchange saturation transfer (CEST) experiments have assumed an important role in studies of biomolecular conformational exchange, (1)H CEST experiments are only beginning to emerge. We present a methyl-TROSY (1)H CEST experiment that eliminates deleterious (1)H-(1)H NOE dips so that CEST profiles can be analyzed robustly to extract methyl proton chemical shifts of rare protein conformers. The utility of the experiment, along with a version that is optimized for (13)CHD2 labeled proteins, is established through studies of exchanging protein systems...
June 24, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28645097/raman-spectroscopy-differentiates-between-sensitive-and-resistant-multiple-myeloma-cell-lines
#5
Domenico Franco, Sebastiano Trusso, Enza Fazio, Alessandro Allegra, Caterina Musolino, Antonio Speciale, Francesco Cimino, Antonella Saija, Fortunato Neri, Marco S Nicolò, Salvatore P P Guglielmino
Current methods for identifying neoplastic cells and discerning them from their normal counterparts are often nonspecific and biologically perturbing. Here, we show that single-cell micro-Raman spectroscopy can be used to discriminate between resistant and sensitive multiple myeloma cell lines based on their highly reproducible biomolecular spectral signatures. In order to demonstrate robustness of the proposed approach, we used two different cell lines of multiple myeloma, namely MM.1S and U266B1, and their counterparts MM...
June 15, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28644630/expanding-the-therapeutic-potential-of-the-iron-chelator-deferasirox-in-the-development-of-aqueous-stable-ti-iv-anticancer-complexes
#6
Sergio A Loza-Rosas, Alexandra M Vázquez-Salgado, Kennett I Rivero, Lenny J Negrón, Yamixa Delgado, Josué A Benjamín-Rivera, Angel L Vázquez-Maldonado, Timothy B Parks, Charlene Munet-Colón, Arthur D Tinoco
The recent X-ray structure of titanium(IV)-bound human serum transferrin (STf) exhibiting citrate as a synergistic anion reveals a difference in Ti(IV) coordination versus iron(III), the metal endogenously delivered by the protein to cells. This finding enriches our bioinspired drug design strategy for Ti(IV)-based anticancer therapeutics, which applies a family of Fe(III) chelators termed chemical transferrin mimetic (cTfm) ligands to inhibit Fe bioavailability in cancer cells. Deferasirox, a drug used for iron overload disease, is a cTfm ligand that models STf coordination to Fe(III), favoring Fe(III) binding versus Ti(IV)...
June 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28644379/physical-forces-may-cause-the-hoxd-gene-cluster-elongation
#7
Spyros Papageorgiou
Hox gene collinearity was discovered be Edward B. Lewis in 1978. It consists of the Hox1, Hox2, Hox3 ordering of the Hox genes in the chromosome from the telomeric to the centromeric side of the chromosome. Surprisingly, the spatial activation of the Hox genes in the ontogenetic units of the embryo follows the same ordering along the anterior-posterior embryonic axis. The chromosome microscale differs from the embryo macroscale by 3 to 4 orders of magnitude. The traditional biomolecular mechanisms are not adequate to comprise phenomena at so divergent spatial domains...
June 23, 2017: Biology
https://www.readbyqxmd.com/read/28640620/using-complementary-nmr-data-sets-to-detect-inconsistencies-and-model-flaws-in-the-structure-determination-of-human-interleukin-4
#8
Lorna J Smith, Wilfred F van Gunsteren, Niels Hansen
The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather non-trivial task due to (i) the limited number of data compared to degrees of freedom of a protein, (ii) the uncertainty inherent to the function connecting an observable quantity to molecular structure, (iii) the finite quality of biomolecular models and force fields used in structure refinement, and (iv) the conformational freedom of a protein in aqueous solution, which requires extensive conformational sampling and appropriate conformational averaging when calculating or restraining to sets of NMR data...
June 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28640608/numerical-diculties-computing-electrostatic-potentials-near-interfaces-with-the-poisson-boltzmann-equation
#9
Marcia Oliveira Fenley, Alexander H Boschitsch, Robert C Harris
Many researchers compute surface maps of the electrostatic potential with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of electrostatic potential, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of the electrostatic potential) at the surface...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640560/integration-of-biomolecules-with-metal-organic-frameworks
#10
REVIEW
Jia Zhuang, Allison P Young, Chia-Kuang Tsung
Owing to the progressive development of metal-organic-frameworks (MOFs) synthetic processes and considerable potential applications in last decade, integrating biomolecules into MOFs has recently gain considerable attention. Biomolecules, including lipids, oligopeptides, nucleic acids, and proteins have been readily incorporated into MOF systems via versatile formulation methods. The formed biomolecule-MOF hybrid structures have shown promising prospects in various fields, such as antitumor treatment, gene delivery, biomolecular sensing, and nanomotor device...
June 22, 2017: Small
https://www.readbyqxmd.com/read/28639674/transition-from-disordered-aggregates-to-ordered-lattices-kinetic-control-of-the-assembly-of-a-computationally-designed-peptide
#11
Yu Tian, Huixi Violet Zhang, Kristi L Kiick, Jeffery G Saven, Darrin J Pochan
Natural biomolecular self-assembly typically occurs under a narrow range of solution conditions, and the design of sequences that can form prescribed structures under a range of such conditions would be valuable in the bottom-up assembly of predetermined nanostructures. We present a computationally designed peptide that robustly self-assembles into regular arrays under a wide range of solution pH and temperature conditions. Controling the solution conditions provides the opportunity to exploit a simple and reproducible approach for altering the pathway of peptide solution self-assembly...
June 22, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28639650/mechanisms-of-h-and-co-loss-from-the-uracil-nucleobase-following-low-energy-electron-irradiation
#12
Mark A Fennimore, Tolga N V Karsili, Spiridoula Matsika
Ionising radiation in cells generates secondary low energy electrons (LEEs) which can induce biomolecular damage when incident upon a particular biomolecule. Notable biomolecules include those contained within double-stranded DNA and RNA helices, which upon exposure to LEEs, may form reactive intermediate products that show detriment to their specific structures and functions. Such damaging processes are understood to proceed via dissociative electron attachment (DEA). Using anion resonance stabilisation methods, coupled to state-of-the-art electronic structure methods, and reaction path mapping, the work presented herein highlights the detailed mechanisms associated with molecular elimination of CO and H from the uracil nucleobase following LEE irradiation - providing a rationale for earlier experiments...
June 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28639539/foreskin-and-the-molecular-politics-of-risk
#13
Aaron T Norton
In this paper, I examine disputes over recent claims that male circumcision reduces HIV risk to suggest a complicated relationship between risk individualization and categorization. Whereas randomized controlled trials (RCTs) conducted in sub-Saharan Africa appear to have provided key evidence for the World Health Organization's endorsement of male circumcision as an HIV prevention strategy, RCTs alone did not provide evidence for the underlying causal mechanism. For that, medical authorities have turned to histo-immunological studies of the foreskin's biomolecular vulnerability to HIV, thus molecularizing risk...
June 1, 2017: Social Studies of Science
https://www.readbyqxmd.com/read/28636761/molecular-tools-for-facilitative-carbohydrate-transporters
#14
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28632260/visualization-of-the-protein-corona-towards-a-biomolecular-understanding-of-nanoparticle-cell-interactions
#15
Maria Kokkinopoulou, Johanna Simon, Katharina Landfester, Volker Mailänder, Ingo Lieberwirth
The use of nanocarriers in biology and medicine is complicated by the current need to understand how nanoparticles interact in complex biological surroundings. When nanocarriers come into contact with serum, proteins immediately adsorb onto their surface, forming a protein corona which defines their biological identity. Although the composition of the protein corona has been widely determined by proteomics, its morphology still remains unclear. In this study we show for the first time the morphology of the protein corona using transmission electron microscopy...
June 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28632153/fabrication-and-characterization-of-plasmonic-nanopores-with-cavities-in-the-solid-support
#16
Bita Malekian, Kunli Xiong, Gustav Emilsson, Jenny Andersson, Cecilia Fager, Eva Olsson, Elin M Larsson-Langhammer, Andreas B Dahlin
Plasmonic nanostructures are widely used for various sensing applications by monitoring changes in refractive index through optical spectroscopy or as substrates for surface enhanced Raman spectroscopy. However, in most practical situations conventional surface plasmon resonance is preferred for biomolecular interaction analysis because of its high resolution in surface coverage and the simple single-material planar interface. Still, plasmonic nanostructures may find unique sensing applications, for instance when the nanoscale geometry itself is of interest...
June 20, 2017: Sensors
https://www.readbyqxmd.com/read/28630667/evaluation-of-radical-scavenging-system-in-amoeba-chaos-carolinense-during-nutrient-deprivation
#17
Yuru Deng, Edlyn Li-Hui Lee, Ketpin Chong, Zakaria A Almsherqi
The frequent appearance of non-lamellar membrane arrangements such as cubic membranes (CMs) in cells under stressed or pathological conditions points to an intrinsic cellular response mechanism. CM represents highly curved, three-dimensional nano-periodic structures that correspond to mathematically well-defined triply periodic minimal surfaces. Specifically, cellular membrane may transform into CM organization in response to pathological, inflammatory and oxidative stress conditions. CM organization, thus, may provide an advantage to cope with various types of stress...
August 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28629749/a-distinct-biomolecular-profile-identifies-monoclonal-mast-cell-disorders-in-patients-with-idiopathic-anaphylaxis
#18
Melody C Carter, Avanti Desai, Hirsh D Komarow, Yun Bai, Sarah T Clayton, Alicia S Clark, Karina N Ruiz-Esteves, Lauren M Long, Daly Cantave, Todd M Wilson, Linda M Scott, Olga Simakova, Mi-Yeon Jung, Jamie Hahn, Irina Maric, Dean D Metcalfe
BACKGROUND: Clonal mast cell disorders are known to occur in a subset of patients with systemic reactions to Hymenoptera stings. This observation has prompted the question as to whether clonal mast cell disorders also occur in patients with idiopathic anaphylaxis (IA). OBJECTIVE: We sought to determine the prevalence of clonal mast cell disorders among patients with IA, criteria to identify those patients who require a bone marrow biopsy and whether the pathogenesis of IA involves a hyper-responsive mast cell compartment...
June 16, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28627759/vibrational-biospectroscopy-characterises-biochemical-differences-between-cell-types-used-for-toxicological-investigations-and-identifies-alterations-induced-by-environmental-contaminants
#19
Kelly A Heys, Richard F Shore, M Glória Pereira, Francis L Martin
The use of cell-based assays is essential in reducing the number of vertebrates used in the investigation of chemical toxicities and in regulatory toxicology assessment. An important factor in obtaining meaningful results which can be accurately extrapolated is the use of biologically appropriate cell lines. In this preliminary study, ATR-FTIR spectroscopy with multivariate analysis was used to assess the fundamental biomolecular differences between a commonly used cell line, MCF-7 cells, and an environmentally relevant cell line derived from Mallard (Anas platyrhynchos) dermal fibroblasts...
June 19, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28620800/non-uniform-sampling-in-biomolecular-nmr
#20
EDITORIAL
Martin Billeter
No abstract text is available yet for this article.
June 15, 2017: Journal of Biomolecular NMR
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