Redox and Conformational Equilibria and Dynamics of Cytochrome c at High Electric Fields

Cytochrome c (Cyt‐c) adsorbed in the electrical double layer of the Ag electrode/electrolyte interface has been studied by stationary and time‐resolved surface‐enhanced resonance Raman spectroscopy to analyse the effect of strong electric fields on structure and reaction equilibria and dynamics of the protein. In the potential range between +0.1 and ?0.55 V (versus saturated calomel electrode), the adsorbed Cyt‐c forms a potential‐dependent reversible equilibrium between the native state B1 and a conformational state B2. The redox potentials of the bis‐histidine‐coordinated six‐coordinated low‐spin and five‐coordinated high‐spin substates of B2 were determined to be ?0.425 and ?0.385 V, respectively, whereas the additional six‐coordinated aquo‐histidine‐coordinated high‐spin substate was found to be redox‐inactive. The redox potential for the conformational state B1 was found to be the same as in solution in agreement with the structural identity of the adsorbed B1 and the native Cyt‐c. For all three redox‐active species, the formal heterogeneous electron transfer rate constants are small and of the same order of magnitude (3–13 s^?1), which implies that the rate‐limiting step is largely independent of the redox‐site structure. These findings, as well as the slow and potential‐dependent transitions between the various conformational (sub‐)states, can be rationalized in terms of an electric field‐induced increase of the activation energy for proton‐transfer steps linked to protein structural reorganisation. Further increasing the electric field strength by shifting the electrode potential above +0.1 V leads to irreversible structural changes that are attributed to an unfolding of the polypeptide chain.     

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level.     

Medium-size polarized basis sets for high-level-correlated calculations of molecular electric properties

Summary The first-order polarized basis sets for the use in high-level-correlated investigations of molecular electric properties have been generated for Pb, Bi, Po, and At. The performance of the standard [10.17.14.5/13.11.8.2] and extended [20.17.14.9/13.11.8.4] basis sets has been examined in nonrelativistic and quasirelativistic calculations for atoms and simple closed-shell hydrides. The relativistic contributions to electric dipole properties of those systems have been evaluated by using the recently developed quasirelativistic scheme. The predicted dipole polarizability of At is in good agreement with the results of other relativistic calculations. The calculated quasirelativistic dipole moments of BiH₃ (–0.499 a.u.), PoH₂ (–0.207 a.u.), and AtH (+0.036 a.u.) involve a significant relativistic contribution which amounts to —0.230 a.u., –0.177 a.u., and –0.097 a.u., respectively. The basis set details append this paper. They are also available as a part of the basis set library of the MOLCAS system.     

结晶PET驻极体的分子运动与陷阱性质

半晶性的聚对苯二甲酸乙二醇酯(PET)存在不同尺寸运动单元的多重形式的分子运动,而且PET等高聚物前结构欠序、晶界和杂质等缺陷还使电子价带与导带间的禁带中出现局域能级(陷阱),并成为捕获载流子的中心,从而影响载流子的输运性质。分子运动和陷阱     

Living Cationic Ring-Opening Polymerization of Hetero Diels–Alder Adducts to Give Multifactor-Controlled and Fast-Photodegradable Vinyl Polymers

Precise control of multiple structural parameters associated with vinyl polymers is important for producing materials with the desired properties and functions. While the development of living polymerization methods has provided a way to control the various structural parameters of vinyl polymers, the concomitant control of their sequence and regioregularity remains a challenging task. To overcome this challenge, herein, we report the living cationic ring-opening polymerization of hetero Diels–Alder adducts. The scalable and modular synthesis of the cyclic monomers was achieved by a one-step protocol using readily available vinyl precursors. Subsequently, living polymerization of the cyclic monomers was examined, allowing the synthesis of vinyl polymers while controlling multiple factors, including molecular weight, dispersity, alternating sequence, head-to-head regioregularity, and end-group functionality. The living characteristics of the developed method were further demonstrated by block copolymerization. The synthesized vinyl polymers exhibited unique thermal properties and underwent fast photodegradation even under sunlight.     

Front Cover: Enhancement of dielectrophoresis-based particle collection from high conducting fluids due to partial electrode insulation

Dielectrophoresis (DEP) is a successful method to recover nanoparticles from different types of fluid. The DEP force acting on these particles is created by an electrode microarray that produces a nonuniform electric field. To apply DEP to a highly conducting biological fluid, a protective hydrogel coating over the metal electrodes is required to create a barrier between the electrode and the fluid. This protects the electrodes, reduces the electrolysis of water, and allows the electric field to penetrate into the fluid sample. We observed that the protective hydrogel layer can separate from the electrode and form a closed domed structure and that collection of 100 nm polystyrene beads increased when this occurred. To better understand this collection increase, we used COMSOL Multiphysics software to model the electric field in the presence of the dome filled with different materials ranging from low-conducting gas to high conducting phosphate-buffered saline fluids. The results suggest that as the electrical conductivity of the material inside the dome is reduced, the whole dome acts as an insulator which increases electric field intensity at the electrode edge. This increased intensity widens the high-intensity electric field factor zone resulting in increased collection. This informs how dome formation results in increased particle collection and provides insight into how the electric field can be intensified to the increase collection of particles. These results have important applications for increasing the recovery of biologically-derived nanoparticles from undiluted physiological fluids that have high conductance, including the collection of cancer-derived extracellular vesicles from plasma for liquid biopsy applications.     

Component reconstruction in the primary space of spectra and concentrations. Alternating regression and related direct methods

A set of methods that extract the spectral components in a chromatographic run is considered. The methods do not need libraries of previously known spectra or retention times. The methods have been developed for two-dimensional spectra but they can also be used for chromatographic analyses with a single-channel detector. The methods are direct; they do not use principal components as the starting point. Alternating regression (AR) remains in the primary space of spectra and concentrations during the calculations. Random numbers are used as the starting spectra. Regression is used to solve first for the concentrations, then for the spectra. The method uses two kinds of constraints: all spectra and concentrations are forced to be positive; and all concentration profiles are forced to a unimodal shape with a single local maximum. It is assumed that all observations are a linear sum of components. Compact alternating regression (CAR) is a new variant of the basic AR. The idea is to replace multiplication of a large matrix by two multiplications of smaller matrices. This typically speeds up the iterations by a factor of ten. AR and CAR have been successfully used with combined techniques such as gas chromatography—mass spectrometry and liquid chromatography with UV—visible detection. The reliability of the solution is checked by repeatedly injecting noise and performing the analysis several times. This produces estimates of confidence intervals. AR and CAR have recently been extended to handle single-dimensional signals. Examples are single-channel detectors such as the flame ionization detector in gas or liquid chromatography with a fixed-wavelength UV detector. A batch of samples is used as the observation matrix. As a result, one obtains both the concentrations and the elution shapes of individual chromatographic peaks.     

双电层相互作用时胶体表面电位的分布及电荷密度的计算

本文以实验为基础,运用计算机数值解解出双电层相互作用时平面胶体表面电位ψ随距离X的分布,依据作者导出的双电层相互作用时胶体表面阴离子负吸附方程,计算出胶体表面外Hclmhotz面(OHP)处的表面电荷密度σ_δ;讨论了双电层相互作用程度(ψ_d/ψ_δ)对胶体表面电位分布及其表面电荷密度的影响。     

Electric parameters of photosystem II particles — electric light scattering study

Electric light scattering and microelectrophoresis were applied to investigate the electric moments (permanent dipole moment and electric polarizability and electrophoretic mobility of envelope-free chloroplasts and photosystem II (PS II particles. The effect of the removal of the extrinsic polypeptides (18, 24 and 33 kDa) on the electric moments was also studied. A significant difference was observed between the orientation behaviour of chloroplasts and PS II preparations. The data indicate that the permanent and induced dipole moments contribute to the orientation of the PS II particles, whereas chloroplasts possess induced dipole moment only.

NaCl and Tris treatments of PS II preparations influence both the transverse permanent dipole moment and the electric polarizability of PS II particles. The increase in the electrophoretic mobility of PS II particles on removal of the extrinsic proteins corresponds to an increase in the electric polarizability value, demonstrating its interfacial nature.