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Ming Guo, Xiaowang Lu, Yan Wang, Peter E Brodelius
The binding properties of pentacyclic triterpenoid isomeric drugs, i.e. ursolic acid (UA) and oleanolic acid (OA), to bovine lactoferrin (BLF) have been studied by molecule modeling, fluorescence spectroscopy, UV-visible absorbance spectroscopy and infrared spectroscopy (IR). Molecular docking, performed to reveal the possible binding mode or mechanism, suggested that hydrophobic interaction and hydrogen bonding play important roles to stabilize the complex. The results of spectroscopic measurements showed that the two isomeric drugs both strongly quenched the intrinsic fluorescence of BLF through a static quenching procedure although some differences between UA and OA binding strength and non-radiation energy transfer occurred within the molecules...
October 18, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Zahra Aghili, Saba Taheri, Hojjat Alizadeh Zeinabad, Leila Pishkar, Ali Akbar Saboury, Arash Rahimi, Mojtaba Falahati
Herein, the interaction of hen egg white lysozyme (HEWL) with iron nanoparticle (Fe NP) was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV) to HEWL (8.57±0.54 mV) can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV). In addition, dynamic light scattering (DLS) study revealed that addition of Fe NP (92.95±6.11 nm) to HEWL (2.68±0.37 nm) increases suspension potential of protein/nanoparticle system (51...
2016: PloS One
Fan-Ching Chien, Yang-Hong Dai, Chiung Wen Kuo, Peilin Chen
Flexible polymer nanopillar substrates were used to systematically demonstrate cell alignment and migration guided by the directional formation of focal adhesions. The polymer nanopillar substrates were constructed to various height specifications to provide an extensive variation of flexibility; a rectangular arrangement created spatial confinement between adjacent nanopillars, providing less spacing in the horizontal and vertical directions. Three polymer nanopillar substrates with the diameter of 400 nm and the heights of 400, 800, and 1200 nm were fabricated...
October 24, 2016: Nanotechnology
Yiqian Cui, Junyou Shi, Zili Wang
The centers and radii of radial basis functions (RBFs) greatly affect the approximation capability of RBF networks (RBFNs). Traditional statistics-based approaches are widely used, but they may lack adaptivity to different data structures. Quantum clustering (QC), derived from quantum mechanics and the Schrödinger equation, demonstrates excellent capability in finding the structure and conformity toward data distribution. In this paper, a novel neural networks model called quantum local potential function networks (QLPFNs) is proposed...
October 20, 2016: IEEE Transactions on Neural Networks and Learning Systems
Deb P Jaisi, Hui Li, Adam F Wallace, Prajwal Paudel, Mingjing Sun, Avula Balakrishna, Bob N Lerch
Degradation of glyphosate in the presence of Mn oxide and UV light was analyzed using phosphate oxygen isotope ratios and density function theory (DFT). Preference of C-P or C-N bond cleavage was found to vary with changing glyphosate:Mn oxide ratios indicating the potential role of sorption-induced conformational changes on the composition of intermediate degradation products. Isotope data confirmed that one oxygen atom derived solely from water was incorporated into the released phosphate during glyphosate degradation and this might suggest similar nucleophilic substitution at P centers and C-P bond cleavage both in Mn oxide- and UV light-mediated degradation...
October 24, 2016: Journal of Agricultural and Food Chemistry
Karen Druart, Julien Bigot, Edouard Audit, Thomas Simonson
Multistate protein design explores sidechain mutations with the backbone allowed to sample a small, predetermined library of conformations. To achieve Boltzmann sampling of sequences and conformations, we use a hybrid Monte Carlo (MC) scheme: a trial hop between backbone models is followed by a short MC segment where sidechain rotamers adjust to the new backbone, before applying a Metropolis-like acceptance test. The theoretical form and a practical approximation for the acceptance test are derived. We then compute backbone conformational free energies for two SH2 and SH3 proteins using different routes and protocols, and verify that for simple test problems, the free energy behaves like a state function, a hallmark of Boltzmann sampling...
October 24, 2016: Journal of Chemical Theory and Computation
Monika B Dolinska, Nicole Kus, Katie Farney, Paul T Wingfield, Brian P Brooks, Yuri V Sergeev
: Oculocutaneous albinism Type 1 (OCA1) is an autosomal recessive disorder caused by mutations in the tyrosinase gene. Two subtypes of OCA1 have been described: severe OCA1A with complete absence of tyrosinase activity and less severe OCA1B with residual tyrosinase activity. Here, we characterize the recombinant human tyrosinase intra-melanosomal domain and mutant variants, which mimic genetic changes in both subtypes of OCA1 patients. Proteins were prepared using site-directed mutagenesis, expressed in insect larvae, purified by chromatography, and characterized by enzymatic activities- tryptophan fluorescence, and Gibbs free energy changes...
October 24, 2016: Pigment Cell & Melanoma Research
Antonietta Franco, Richard N Kitsis, Julie A Fleischer, Evripidis Gavathiotis, Opher S Kornfeld, Guohua Gong, Nikolaos Biris, Ann Benz, Nir Qvit, Sara K Donnelly, Yun Chen, Steven Mennerick, Louis Hodgson, Daria Mochly-Rosen, Gerald W Dorn
Mitochondria are dynamic organelles, remodeling and exchanging contents during cyclic fusion and fission. Genetic mutations of mitofusin (Mfn) 2 interrupt mitochondrial fusion and cause the untreatable neurodegenerative condition, Charcot Marie Tooth disease type 2A (CMT2A). It has not been possible to directly modulate mitochondrial fusion, in part because the structural basis of mitofusin function is incompletely understood. Here we show that mitofusins adopt either a fusion-constrained or fusion-permissive molecular conformation directed by specific intramolecular binding interactions, and demonstrate that mitofusin-dependent mitochondrial fusion can be regulated by targeting these conformational transitions...
October 24, 2016: Nature
Yunxiang Zang, Mingliang Jin, Huping Wang, Zhicheng Cui, Liangliang Kong, Caixuan Liu, Yao Cong
The eukaryotic chaperonin TRiC (or CCT) assists in the folding of 10% of cytosolic proteins. Here we present two cryo-EM structures of Saccharomyces cerevisiae TRiC in a newly identified nucleotide partially preloaded (NPP) state and in the ATP-bound state, at 4.7-Å and 4.6-Å resolution, respectively. Through inner-subunit eGFP tagging, we identified the subunit locations in open-state TRiC and found that the CCT2 subunit pair forms an unexpected Z shape. ATP binding induces a dramatic conformational change on the CCT2 side, thereby suggesting that CCT2 plays an essential role in TRiC allosteric cooperativity...
October 24, 2016: Nature Structural & Molecular Biology
Alejandro Parrales, Atul Ranjan, Swathi V Iyer, Subhash Padhye, Scott J Weir, Anuradha Roy, Tomoo Iwakuma
Stabilization of mutant p53 (mutp53) in tumours greatly contributes to malignant progression. However, little is known about the underlying mechanisms and therapeutic approaches to destabilize mutp53. Here, through high-throughput screening we identify statins, cholesterol-lowering drugs, as degradation inducers for conformational or misfolded p53 mutants with minimal effects on wild-type p53 (wtp53) and DNA contact mutants. Statins preferentially suppress mutp53-expressing cancer cell growth. Specific reduction of mevalonate-5-phosphate by statins or mevalonate kinase knockdown induces CHIP ubiquitin ligase-mediated nuclear export, ubiquitylation, and degradation of mutp53 by impairing interaction of mutp53 with DNAJA1, a Hsp40 family member...
October 24, 2016: Nature Cell Biology
Vivek Verma, Amy C Moreno, Steven H Lin
Radiation therapy (RT) as part of multidisciplinary oncologic care has been marked by profound advancements over the past decades. As part of multimodality therapy for esophageal cancer (EC), a prime goal of RT is to minimize not only treatment toxicities, but also postoperative complications and hospitalizations. Herein, discussion commences with the historical approaches to treating EC, including seminal trials supporting multimodality therapy. Subsequently, the impact of RT techniques, including three-dimensional conformal RT, intensity-modulated RT, and proton beam therapy, is examined through available data...
October 21, 2016: Journal of Clinical Medicine
Igor V Ukrainets, Lidiya A Petrushova, Svitlana V Shishkina, Lina A Grinevich, Galina Sim
In order to obtain and then test pharmocologically any possible conformers of the new feasible analgesic N-benzyl-4-hydroxy-1-methyl-2,2-dioxo-1H-2λ⁶,1-benzothiazine-3-carboxamide, its 4-O-sodium salt was synthesized using two methods. X-ray diffraction study made possible to determine that, depending on the chosen synthesis conditions, the above-mentioned compound forms either monosolvate with methanol or monohydrate, where organic anion exists in the form of three different conformers. Pharmacological testing of the two known pseudo-enantiomeric forms of the original N-benzylamide and of the two solvates of its sodium salt was performed simultaneously under the same conditions and in equimolar doses...
October 19, 2016: Scientia Pharmaceutica
Wojciech Pulawski, Michal Jamroz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane...
October 24, 2016: Journal of Chemical Information and Modeling
Brian P Charrette, Mark A Boerneke, Thomas Hermann
Crystal structure analysis revealed key interactions of a 2-amino-benzimidazole viral translation inhibitor that captures an elongated conformation of an RNA switch target in the internal ribosome entry site (IRES) of hepatitis C virus (HCV). Here, we have designed and synthesized quinazoline derivatives with improved shape complementarity at the ligand binding site of the viral RNA target. A spiro-cyclopropyl modification aimed at filling a pocket in the back of the RNA binding site led to a fivefold increase of ligand affinity while a slightly more voluminous dimethyl substitution at the same position did not improve binding...
October 24, 2016: ACS Chemical Biology
Yuanyuan Zhou, Miao Li, Yijing Guo, Heng Lu, Jinsheng Song, Zhishan Bo, Hua Wang
With the efficient synthesis of the crucial dibenzopyran building block, a series of PDBPTBT polymers containing different alkyl side chains and/or fluorine substitution were designed and synthesized via the microwave assisted Suzuki polycondensation. Quantum chemistry calculations based on density functional theory indicated that different substitutions have significant impacts on the planarity and rigidity of the polymer backbones. Interestingly, the alkyloxy chains of PDBPTBT-4 tend to stay in the same plane with the benzothiadiazole unit, but the others appear to be out of plane...
October 24, 2016: ACS Applied Materials & Interfaces
Heinrich Krobath, Tao Chen, Hue Sun Chan
Volumetric properties of proteins bear directly on their biological functions in hyperbaric environments and are useful in general as a biophysical probe. To gain insight into conformation-dependent protein volume, we developed an implicit-solvent atomic chain model that transparently embodies two physical origins of volume. First, a fundamental geometric term capturing the van der Waals volume of the protein and the particulate, finite-size nature of the water molecules, modeled together by the volume encased by the protein's molecular surface...
October 24, 2016: Biochemistry
Andreas Link, Christa E Müller
Together forever? Functional selection was applied to finally achieve separation of the analgesic properties of opiods from serious side effects such as potentially lethal respiratory depression. A Gi-biased μ-opioid-receptor agonist (PZM21) was identified that stabilizes previously unexplored receptor conformations. This compound relieves pain in mice without causing hypoventilation or addiction.
October 24, 2016: Angewandte Chemie
Patrick S Walsh, Karl N Blodgett, Carl McBurney, Samuel H Gellman, Timothy S Zwier
Gas-phase single-conformation spectroscopy is used to study Ac-Gln-Gln-NHBn in order to probe the interplay between sidechain hydrogen bonding and backbone conformational preferences. This small, amide-rich peptide offers many possibilities for backbone-backbone, sidechain-backbone, and sidechain-sidechain interactions. The major conformer observed experimentally features a type-I β-turn with a canonical 10-membered ring C=O-H-N hydrogen bond between backbone amide groups. In addition, the C=O group of each Gln sidechain participates in a seven-membered ring hydrogen bond with the backbone NH of the same residue...
October 24, 2016: Angewandte Chemie
Tonya Deen, Theresa Terna, Elizabeth Kim, Brian Leahy, Wende Fedder
PURPOSE: The purpose of this study was to describe the impact a Stroke Nurse Navigation Program has on concurrent chart reviews and patient compliance post discharge. DESIGN: Phase I: Concurrent chart review of The Joint Commission Primary Stroke Center core measures for ischemic stroke patients. Phase II: Longitudinal study of 100 ischemic stroke patients discharged to home. METHODS: Telephone surveys were conducted at prescribed intervals posthospital discharge (Phase II)...
October 24, 2016: Rehabilitation Nursing: the Official Journal of the Association of Rehabilitation Nurses
J S Kłos, J-U Sommer
We study the conformational properties of dendrimers with flexible spacers in solutions over a wide range of concentrations from dilute solutions to melts. By combining large scale computer simulations using the bond fluctuation model with scaling arguments we identify the semi-dilute regime of dendrimers which is controlled by the concentration behavior of the linear spacers. Associated with this observation we find that the decrease in the size of flexible dendrimers is accompanied by increasing interpenetration between the molecules with increasing concentration of the solution...
October 24, 2016: Soft Matter
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