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Kinetic chain

Makusu Tsutsui, Takanori Morikawa, Kazumichi Yokota, Masateru Taniguchi
Understanding and control of heat dissipation is an important challenge in nanoelectronics wherein field-accelerated hot carriers in current-carrying ballistic systems release a large part of the kinetic energy into external bulk phonon baths. Here we report on a physical mechanism of this remote heat dissipation and its role on the stability of atomic contacts. We used a nano-fabricated thermocouple to directly characterize the self-heating in a mechanically-configurable Au junction. We found more pronounced heat dissipation at the current downstream that signifies the electron-hole asymmetry in Au nanocontacts...
May 18, 2018: Scientific Reports
Fabio C Zegarra, Dirar Homouz, Yossi Eliaz, Andrei G Gasic, Margaret S Cheung
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α/β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β-barrel α-spectrin Src-homology 3 domain (SH3) protein...
March 2018: Physical Review. E
Erika N Bentz, Rosana Maria Lobayan, Henar Martinez, Pilar Redondo, Antonio Largo
A computational kinetics study of the antioxidant activity of tryptamine toward HO● and HOO● radicals in water at 298 K has been carried out. Density functional methods have been employed for the quantum chemical calculations and conventional transition state theory was used for rate constants evaluation. Different mechanisms have been considered: radical adduct formation (RAF), single electron transfer (SET), and hydrogen atom transfer (HAT). For the reaction of tryptamine with the hydroxyl radical nearly all channels are diffusion controlled, and the overall rate constant is very high, 6...
May 18, 2018: Journal of Physical Chemistry. B
Wenhao Dai, Jing Zhang, Xiangdan Meng, Jie He, Kai Zhang, Yu Cao, Dongdong Wang, Haifeng Dong, Xueji Zhang
As important modulators of gene expression, microRNAs (miRNAs) have been identified as promising biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. Here we report a facile, multiple and sensitive miRNA detection method that uses conventional gel electrophoresis and catalytic hairpin assembly (CHA) system without any complex nanomaterials or enzymatic amplification. Methods: In this study, three pairs of hairpin probes are rationally designed with thermodynamically and kinetically preferable feasibility for the CHA process...
2018: Theranostics
Olivier Dangles, Pascale Goupy, Michel Carail, Alexandre Giuliani, Denis Duflot, Catherine Caris-Veyrat
Carotenoids are important natural pigments and micronutrients contributing to health prevention by several mechanisms, including their electron-donating (antioxidant) activity. In this work, a large series of carotenoids, including 11 carotenes and 14 xanthophylls, has been investigated by wavelength-resolved atmospheric pressure photoionization mass spectrometry (DISCO line of SOLEIL synchrotron), thus allowing the experimental determination of their ionization energy (IE) for the first time. On the other hand, the carotenoids have been also investigated for their ability to inhibit the heme iron-induced peroxidation of linoleic acid in mildly acidic micelles, a simple but relevant chemical model of oxidative stress in the gastric compartment...
May 17, 2018: Journal of Physical Chemistry. B
Meng-Jun Hu, Xiao-Xia Shao, Hao-Zheng Li, Wei-Han Nie, Jia-Hui Wang, Ya-Li Liu, Zeng-Guang Xu, Zhan-Yun Guo
Relaxin family peptides perform a variety of biological functions by binding and activating relaxin family peptide receptor 1-4 (RXFP1-4), four A-class G protein-coupled receptors. In the present work, we developed a novel ligand binding assay for RXFP3 and RXFP4 based on NanoLuc complementation technology (NanoBiT). A synthetic ligation version of the low-affinity small complementation tag (SmBiT) was efficiently ligated to the A-chain N terminus of recombinant chimeric agonist R3/I5 using recombinant circular sortase A...
May 16, 2018: Amino Acids
Chin-Wei Huang, Kao-Min Lin, Te-Yu Hung, Yao-Chung Chuang, Sheng-Nan Wu
BACKGROUND/AIMS: Rotenone (Rot) is known to suppress the activity of complex I in the mitochondrial chain reaction; however, whether this compound has effects on ion currents in neurons remains largely unexplored. METHODS: With the aid of patch-clamp technology and simulation modeling, the effects of Rot on membrane ion currents present in mHippoE-14 cells were investigated. RESULTS: Addition of Rot produced an inhibitory action on the peak amplitude of INa with an IC50 value of 39...
May 11, 2018: Cellular Physiology and Biochemistry
Hamid Reza Mokhtarinia, Azadeh Hosseini, Azam Maleki-Ghahfarokhi, Charles Philip Gabel, Majid Zohrabi
BACKGROUND: There are various instruments and methods to evaluate spinal health and functional status. Whole-spine patient reported outcome (PRO) measures, such as the Spine Functional Index (SFI), assess the spine from the cervical to lumbo-sacral sections as a single kinetic chain. The aim of this study was to cross-culturally adapt the SFI for Persian speaking patients (SFI-Pr) and determine the psychometric properties of reliability and validity (convergent and construct) in a Persian patient population...
May 15, 2018: Health and Quality of Life Outcomes
Jing Wu, Chenqian Cheng, Gaoyuan Liu, Ping Zhang, Tao Chen
Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm...
May 14, 2018: Journal of Chemical Physics
Satish C Kalhan
Starch, a major source of carbohydrates in human nutrition, is extensively hydrolyzed in the gastrointestinal tract of children and adults. A small fraction of the ingested starch reaches the cecum and colon where it is fermented by the gut microbiome into short-chain fatty acids (SCFA) and other products. Recent data in humans and in animal models have demonstrated the extensive effects of short-chain fatty acids on whole body energy metabolism, appetite, insulin resistance, fatty acid oxidation, fat accretion, obesity, and diabetes...
June 2018: Journal of Pediatric Gastroenterology and Nutrition
Xiuyuan Li, Natalia Sevillano, Florencia La Greca, Lindsay Deis, Yu-Chen Liu, Marc C Deller, Irimpan I Mathews, Tsutomu Matsui, David E Cane, Charles S Craik, Chaitan Khosla
Catalytic modules of assembly-line polyketide synthases (PKSs) have previously been observed in two very different conformations-an "extended" architecture and an "arch-shaped" architecture-although the catalytic relevance of neither has been directly established. By the use of a fully human naïve antigen-binding fragment (Fab ) library, a high-affinity antibody was identified that bound to the extended conformation of a PKS module, as verified by X-ray crystallography and tandem size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS)...
May 18, 2018: Journal of the American Chemical Society
Miaomiao Zhang, Xiaopeng Guo, Yue Gao, Dong Lu, Wenjian Li
Whether telomere structure integrity is related to radiosensitivity is not well investigated thus far. In this study, we investigated the relation between telomere instability and radiation-induced accelerated senescence. Partial knockdown of DNA-dependent catalytic subunit of protein kinase (DNA-PKcs) in human breast cancer cell line MCF-7 was established by small interfering RNA. Radiosensitivity of control and DNA-PKcs knockdown MCF-7 cells was analyzed by clonogenetic assay. Cell growth was measured by real-time cell electronic sensing...
April 2018: Dose-response: a Publication of International Hormesis Society
Francisco M Hernández-Maya, María P Cañizares-Macías
β-glucosidase from almonds was immobilized on a polydimethylsiloxane (PDMS) microdevice by covalent chain using 3-aminopropyltrietoxysilane and glutaraldehyde. Enzymatic activity was evaluated using p-nitro-phenyl-β-D-glucopyranoside dissolved in a 0.01 M pH 5.0 phosphate solution at 45 °C measuring the reaction product (p-nitrophenol) at 410 nm. The microdevice consisted of two parts: the one part where the enzymatic reaction was carried out and a second part where pH was adjusted at 10, with NaOH...
August 1, 2018: Talanta
Matthew S Kimber, Evan Mallette
S-(+)-1-amino-2-propanol dehydrogenase (APDH) is a short chain dehydrogenase/reductase associated with the incompletely characterized Rhodococcus and Mycobacterium bacterial microcompartment (RMM). We enzymatically characterized the APDH from M. smegmatis, and showed it is highly selective, with a low-micromolar Km for S-(+)-1-amino-2-propanol, and specificity for NADP(H). A paralogous enzyme from a non-microcompartment associated operon in the same organism was also shown to have similar activity. We determined the structure of APDH in both apo form (at 1...
May 14, 2018: Biochemistry
Gustavo Pierdominici-Sottile, Rodrigo Cossio-P Eacute Rez, Isabel Da Fonseca, Karina Kizjakina, John J Tanner, Pablo Sobrado
Galactose is an abundant monosaccharide found exclusively in mammals as galactopyranose (Galp), the six-membered ring form of this sugar. In contrast, galactose appears in many pathogenic microorganisms as the five-membered ring form, galactofuranose (Galf). Galf biosynthesis begins with the conversion of UDP-Galp to UDP-Galf catalyzed by the flavoenzyme UDP-galactopyranose mutase (UGM). Because UGM is essential for the survival and proliferation of several pathogens, there is interest in understanding the catalytic mechanism to aid inhibitor development...
May 14, 2018: Biochemistry
An T Ta, Govind A Hegde, Brian D Etz, Anna G Baldwin, Yuan Yang, Jenifer C Shafer, Mark Peter Jensen, C Mark Maupin, Shubham Vyas
Actinide-Lanthanide Separation (ALSEP) has been a topic of interest in recent years as it has been shown to selectively extract problematic metals from spent nuclear fuel. However, the process suffers from slow kinetics prohibiting it from being applied to nuclear facilities. In effort to improve the process, many fundamental studies have been performed, but the majority have only focused on the thermodynamics of separation. Therefore, to understand the mechanism behind the ALSEP process, molecular dynamics (MD) simulations were utilized to obtain the dynamics and solvation characteristics for an organic extractant, 2-ethylhexylphosphonic acid mono-2-ethylhexyl ester (HEHEHP)...
May 14, 2018: Journal of Physical Chemistry. B
Andrei V Astashkin, Jinghui Li, Huayu Zheng, Yubin Miao, Changjian Feng
The FMN-heme interdomain electron transfer (IET) in nitric oxide synthase (NOS) is a key stage of the electron transport chain, which supplies the catalytic heme site(s) with the NADPH-derived electrons. While there is a recognition that this IET depends on both the electron tunneling and the conformational dynamics, the detailed mechanism remains unclear. In this work, the IET kinetics were measured by laser flash photolysis for a bidomain oxygenase/FMN (oxyFMN) construct of human inducible NOS (iNOS) over the ionic strength range from 0...
March 26, 2018: Journal of Inorganic Biochemistry
Yajie Qian, Gang Xue, Jiabin Chen, Jinming Luo, Xuefei Zhou, Pin Gao, Qi Wang
While the widely used β-lactam antibiotics, such as cephalosporins, are known to be susceptible to oxidation by sulfate radical (SO4 - ), comprehensive study about SO4 - -induced oxidation of cephalosporins is still limited, such as the impact of water matrices, and the structure and antibacterial activity of transformation products. Herein, the oxidation of cefalexin (CFX), a most frequently detected cephalosporin, was systematically investigated by thermally activated persulfate (PS). CFX oxidation followed pseudo-first-order kinetics, and SO4 - dominantly contributed to the overall oxidation of CFX...
May 3, 2018: Journal of Hazardous Materials
Ipsita Chakraborty, Kaustuv Mukherjee, Priyadarsi De, Rangeet Bhattacharyya
Thermo-responsive polymers exhibit coil-globule transition in aqueous solution where the polymer undergoes from the coil-like morphology to a globular form with the change of temperature. Such transitions also reflect changes in the solvent dynamics captured by various spectroscopic methods. In this work, we construct a phenomenological model to capture the dynamics of the NMR relaxation of water molecules of an aqueous solution of thermo-responsive polymers which are known to form hydrogen bonds with the solvent water molecules...
May 11, 2018: Journal of Physical Chemistry. B
Jacob Schäfer, Hannah Dawitz, Martin Ott, Pia Ädelroth, Peter Brzezinski
Respiration in Saccharomyces cerevisiae is regulated by small proteins such as the respiratory supercomplex factors (Rcf). One of these factors (Rcf1) has been shown to interact with complexes III (cyt. bc1 ) and IV (cytochrome c oxidase, CytcO) of the respiratory chain and to modulate the activity of the latter. Here, we investigated the effect of Rcf1 deletion on the functionality of CytcO, purified using a protein C-tag on core subunit 1 (Cox1). Specifically, we measured the kinetics of ligand binding to the CytcO catalytic site, the O2 -reduction activity and changes in light absorption spectra...
May 7, 2018: Biochimica et Biophysica Acta
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