Experimental and theoretical study of the thermal decomposition of ethyl acetate during fast pyrolysis

The thermal decomposition of ethyl acetate was experimentally studied in a newly designed fast pyrolysis set-up. The results were compared to theoretical calculations and literature values in order to proof the experimental concept. The reaction was carried out in a free fall tubular reactor with a residence time of 0.15 s. The identification and quantification of products stream composition was performed online using a GC-TCD/FID. First, an overview of the reaction rate at feed volumes of 0.25, 0.50 and 0.75 mL was obtained at reaction temperature between 400 to 600 degrees C in intervals of 50 degrees C. As a result mass transfer limitation for feeds larger than 0.5 mL were identified. For the second approach, a constant feed volume of 0.25 mL and temperatures between 420 to 550 degrees C were investigated. Using the experimental results, a global kinetic model is proposed for the thermal decomposition of ethyl acetate into ethylene and acetic acid through a first order unimolecular reaction. Also, theoretical calculations were performed at wB97XD/6-311++G(d,p) level. A concerted mechanism through a six-membered transition state was identified in the reaction path. The theoretical and experimental activation energy values lie within the literature values between 193 and 213 kJ/mol. 2020 The Authors. Published by Elsevier B.V. on behalf of Institution of Chemical Engineers. This is an open access article under the CC BY-NC -ND license (http://creativecommons.orgilicenseseby-nc-nd/450/)

A Branched Kinetic Scheme Describes the Mechanochemical Coupling of Myosin Va Processivity in Response to Substrate

Myosin Va is a double-headed cargo-carrying molecular motor that moves processively along cellular actin filaments. Long processive runs are achieved through mechanical coordination between the two heads of myosin Va, which keeps their ATPase cycles out of phase, preventing both heads detaching from actin simultaneously. The biochemical kinetics underlying processivity are still uncertain. Here we attempt to define the biochemical pathways populated by myosin Va by examining the velocity, processive run-length, and individual steps of a Qdot-labeled myosin Va in various substrate conditions (i.e., changes in ATP, ADP, and Pi) under zero load in the single-molecule total internal reflection fluorescence microscopy assay. These data were used to globally constrain a branched kinetic scheme that was necessary to fit the dependences of velocity and run-length on substrate conditions. Based on this model, myosin Va can be biased along a given pathway by changes in substrate concentrations. This has uncovered states not normally sampled by the motor, and suggests that every transition involving substrate binding and release may be strain-dependent. © 2012 Biophysical Society

Tracking Ca2+ ATPase intermediates in real time by x-ray solution scattering

Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2] E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca2+ and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate “instructs” the host to change its shape after complexation, while CS asserts that a guest “selects” the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the first time describe the way by which twisted capsule M-1, encompassing two conformers M-1(+) and M-1(−), trap CX4 (X=Cl, Br) to give CX4⊂M-1(+) and CX4⊂M-1(−), with all four states being in thermal equilibrium. With the assistance of 2D EXSY, we found that CBr4 would, at its lower concentrations, bind M-1 via a M-1(+)→M-1(−)→CBr4⊂M-1(−) pathway corresponding to conformational selection. For M-1 complexing CCl4 though, data from 2D EXSY measurements and 1D NMR line-shape analysis suggested that lower CCl4 concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive, we reason that our work sets the stage for characterizing the dynamics of a wide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents, catalysts and chemosensors akin to those found in nature

Aplysinopsins - Marine Indole Alkaloids: Chemistry, Bioactivity and Ecological Significance

Aplysinopsins are tryptophan-derived marine natural products isolated from numerous genera of sponges and scleractinian corals, as well as from one sea anemone and one nudibranch. Aplysinopsins are widely distributed in the Pacific, Indonesia, Caribbean, and Mediterranean regions. Up to date, around 30 analogues occurring in Nature have been reported. Natural aplysinopsins differ in the bromination pattern of the indole ring, variation in the structure of the C ring, including the number and position of N-methylation, the presence and configuration of the C-8-C-1′ double bond, and the oxidation state of the 2-aminoimidazoline fragment. Aplysinopsins can also occur in the form of dimers. This review summarizes 30 years’ research on aplysinopsins. The origin, isolation sources, chemistry, bioactivity, and ecological functions of aplysinopsins are comprehensively reviewed

Protein mechanics probed using simple molecular models

Background: Single-molecule experimental techniques such as optical tweezers or atomic force microscopy are a direct probe of the mechanical unfolding/folding of individual proteins. They are also a means to investigate free energy landscapes. Protein force spectroscopy alone provides limited information; theoretical models relate measurements to thermodynamic and kinetic properties of the protein, but do not reveal atomic level information. By building a molecular model of the protein and probing its properties through numerical simulation, one can gauge the response to an external force for individual interatomic interactions and determine structures along the unfolding pathway. In combination, single-molecule force probes and molecular simulations contribute to uncover the rich behavior of proteins when subjected to mechanical force. Scope of review: We focus on how simplified protein models have been instrumental in showing how general properties of the free energy landscape of a protein relate to its response to mechanical perturbations. We discuss the role of simple protein models to explore the complexity of free energy landscapes and highlight important conceptual issues that more chemically accurate models with all-atom representations of proteins and solvent cannot easily address. Major conclusions: Native-centric, coarse-grained models, despite simplifications in chemical detail compared to all-atom models, can reproduce and interpret experimental results. They also highlight instances where the theoretical framework used to interpret single-molecule data is too simple. However, these simple models are not able to reproduce experimental findings where non-native contacts are involved. General significance: Mechanical forces are ubiquitous in the cell and it is increasingly clear that the way a protein responds to mechanical perturbation is important