Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L?1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Probing the Subunit-Subunit Interaction of the Tetramer of E. coli KDO8P Synthase by Electrospray Ionization Mass Spectrometry

Escherichia coli 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation reaction between D-arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P and inorganic phosphate (Pi). This enzyme exists as a tetramer in solution, which is important for catalysis. Two different states of the enzyme were obtained: i) PEP-bound and ii) PEP-unbound. The effect of the substrates and products on the overall structure of KDO8P synthase in both PEP-bound and unbound states was examined using electrospray ionization mass spectrometry. The analysis of our data showed that the complexes of the PEP-unbound enzyme with PEP (or Pi) favored the formation of monomers, while the complexes with A5P (or KDO8P) mainly favored dimers. The PEP-bound enzyme was found to exist in the monomer and dimer with a small amount of the tetramer, whereas the PEP-unbound form primarily exists in the monomer and dimer, and no tetramer was observed, suggesting that the bound PEP have a role in stabilization of the tetrameric structure. Taken together, the results imply that the addition of the substrates or products to the unbound enzyme may alter the subunit-subunit interactions and/or conformational change of the protein at the active site, and this study also demonstrates that the electrospray ionization mass spectrometric method may be a powerful tool in probing the subunit-subunit interactions and/or conformational change of multi-subunit protein upon binding to ligand.     

Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2 ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.     

Self-assembled structures of a semi-rigid polyanion in aqueous solutions and hydrogels

Poly(2,2’-disulfonyl-4,4’-benzidine terephthalamide) (PBDT), a kind of liquid-crystalline (LC) molecule, has high molecular weight, negative charge and a semi-rigid structure. The aqueous solution of PBDT shows nematic liquid crystalline state above a critical PBDT concentration, CLC*, of 2 wt%-3wt%. Different from the flexible polyelectrolyte, PBDT shows a variety of self-assembling structures in aqueous solution with and without salt due to the semi-rigid nature and highly charged property. In addition, the hydrogels with ordered structure are developed by polymerizing a cationic monomer N-[3-(N,N-dimethylamino) propyl] acrylamide methyl chloride quarternary (DMAPAA-Q) in the presence of a small amount of PBDT below the CLC*. During the polymerization of cationic monomer, the polycations form a complex with semi-rigid PBDT through electrostatic interaction; these complexes self-assemble into ordered structures that are frozen in the hydrogel. Several different structures, including the anisotropic, dual network-like structure, and cylindrically symmetric structure, with various length scales from micrometer to millimeter, are observed. The hydrogels with ordered liquid crystalline assemblies and particular optical properties should promise applications in many fields, such as in bionics, tissue engineering, and mechano-optical sensors.     

Impact of Carbon Chain Structures in the Backbone on the Flexibility of Modified Polyarylene Sulfide Resins:Molecular Dynamics Simulations and Mesoscopic Analysis

In the domain of high-performance engineering polymers, the enhancement of mechanical flexibility in poly(phenylene sulfide)(PPS)resins has long posed a significant challenge. A novel molecular structure, designated as PP-He-IS, wherein imide rings and an aliphatic hexylene chain are covalently incorporated into the PPS backbone to enhance its flexibility, is introduced in this study. Molecular dynamics(MD) simulations are employed to systematically explore the effects of diversifying the backbo...     

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.     

NOVEL HYPERBRANCHED POLY（PHENYLENE OXIDE）S WITH PHENOLIC TERMINAL GROUPS： EFFECTS OF REACTION TIME AND CORE MOLECULES ON THE MOLECULAR WEIGHT AND POLYDISPERSITY

A novel hyperbranched poly（phenylene oxide） （HPPO） with phenolic terminal groups was prepared from 4-bromo-4＇,4＂-dihydroxytriphenylmethane as AB2 monomer in dimethylsulfoxide （DMSO） via a modified Ullmann reaction. The molecular weight and polydispersity （PD） of the resulting polymers increased with increasing reaction time. In the presence of core molecules （bisphenol A and 1,3,5-trihydroxybenzene）, which have the similar molecular backbones to the reactive monomer, the molecular weight could be controlled by varying the core-to-monomer ratio. Incorporation of a very small amount of core molecules could lead to a higher molecular weight as compared with that without the addition of core molecules. However, when the core content reached certain extent, the molecular weight would decrease with the further increase in the core content. A new similar behavior of control over the PD was also obtained. The resulting polymers were characterized by ^1H-NMR, ^13C-NMR, FT-IR, and GPC.     

Non-fullerene acceptor pre-aggregates enable high efficiency pseudo-bulk heterojunction organic solar cells

Pseudo-bulk heterojunction(BHJ)fabricated by sequential casting of donor and acceptor layers has been recently demonstrated as a superior structure to prepare organic solar cells(OSCs)with enhanced efficiency compared to the conventional BHJ OSCs cast from a common solution of donors and acceptors.However,molecular diffusion and aggregation within the pseudo-BHJ layer bring great challenges to fully realize the advantage of pseudo-BHJ structure.Herein,a solution-incubated pre-aggregation strategy is employed to tune the nanoscale aggregates of non-fullerene acceptor(NFA)BTP-e C11 and N3 to substantially enhance device power-conversion efficiency(PCE).NFA pre-aggregates are incubated in solutions via aging or adding antisolvent,and then sequentially cast onto D18 fibrillar network,which then penetrate to form a pseudo-BHJ structure with appropriate domain sizes to ensure superior charge mobilities.While the conventional pseudo-BHJ OSCs obtain inferior PCEs below 17%compared with normal BHJ OSCs,NFA pre-aggregates help to achieve remarkable PCEs of 17.7%and 17.5%for D18/BTP-e C11 and D18/N3 pseudo-BHJ OSCs.This work demonstrates that the solution-incubated nanoscale pre-aggregation is an efficient approach to regulate molecular diffusion and aggregation to guarantee high performance pseudo-BHJ OSCs.     

Density functional theory (DFT) and ab initio investigations of the electronic and molecular structures of the monomer and the dimer of trimethylaluminium

The electronic and molecular structures of the monomer and dimer of trimethylalu-minium have been studied using density functional theory and ab initio MP2 method. The optimized geometry of the monomer Al(CH3)3 is of C3h symmetry, whereas that of the dimer [A1(CH3)3]2 contains a carbon-bridged four-membered ring structure with C2h symmetry. The hydrogen-bridged six-membered ring structure is found to be unstable. The calculated dimerization energy for the four-membered ring structure is 78 kJ/mol, in close proximity to the experimental value of 85.27 kJ/mol.     

Dynamical and allosteric regulation of photoprotection in light harvesting complex Ⅱ

Major light-harvesting complex of photosystem Ⅱ(LHCⅡ) plays a dual role in light-harvesting and excited energy dissipation to protect photodamage from excess energy. The regulatory switch is induced by increased acidity, temperature or both. However,the molecular origin of the protein dynamics at the atomic level is still unknown. We carried out temperature-jump time-resolved infrared spectroscopy and molecular dynamics simulations to determine the energy quenching dynamics and conformational changes of LHCⅡ trimers. We found that the spontaneous formation of a pair of local α-helices from the 310-helix E/loop and the C-terminal coil of the neighboring monomer, in response to the increased environmental temperature and/or acidity, induces a scissoring motion of transmembrane helices A and B, shifting the conformational equilibrium to a more open state, with an increased angle between the associated carotenoids. The dynamical and allosteric conformation change leads to close contacts between carotenoid lutein 1 and chlorophyll pigment 612, facilitating the fluorescence quenching. Based on these results, we suggest a unified mechanism by which the LHCⅡ trimer controls the dissipation of excess excited energy in response to increased temperature and acidity, as an intrinsic result of intense sun light in plant photosynthesis.     

Theoretical methods for excited state dynamics of molecules and molecular aggregates

This contribution provides a summary of proposed theoretical and computational studies on excited state dynamics in molecular aggregates, as an important part of the National Natural Science Foundation (NNSF) Major Project entitled "Theoretical study of the low-lying electronic excited state for molecular aggregates". This study will focus on developments of novel methods to simulate excited state dynamics of molecular aggregates, with the aim of understanding several important chemical physics processes, and providing a solid foundation for predicting the opto-electronic properties of organic functional materials and devices. The contents of this study include: (1) The quantum chemical methods for electronic excited state and electronic couplings targeted for dynamics in molecular aggregates; (2) Methods to construct effective Hamiltonian models, and to solve their dynamics using system-bath approaches; (3) Non-adiabatic mixed quantum-classic methods targeted for molecular aggregates; (4) Theoretical studies of charge and energy transfer, and related spectroscopic phenomena in molecular aggregates.     

Catalytic Mechanism of Cytochrome P450 2D6 for 4-Hydroxylation of Aripiprazole： A QM/MM Study

Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports.     

PRELIMINARY CRYSTALLOGRAPHIC STUDIES ON THE COENZYME BINDING TO GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM Palinurus versicolor

The three forms of glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor muscle, namelyapo native enzyme, apo calboxymethylated enzyme and the enzyme carrying two fluorescent NAD deriva-tives per tetramer have been crystallized. The space groups and unit cell dimensions of these crystals areisomorphous to each other and to those of three corresponding holo-enzymes saturated with NAD~+ reportedin a previous paper suggesting that binding of coenzyme to the apo enzymes does not lead to significantconformational changes involving domain movement as demonstrated in the case of glyceraldehyde-3-phos-phate dehydrogenase from Bacillus stearothermophilus.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Preparation and Structure of a New Coagulation Factor XI Catalytic Domain for Drug Discovery

Human blood coagulation factor XI (FXI) is a key enzyme in the amplification phase of blood coagulation cascade,and is recognized as an important target for anti-coagulant deve-lopment in recent years.We designed a new mutant form of FXIa catalytic domain rhFXI 370～607 (N73Q-N113Q-C123S),and report here the facile preparation,protein crystallization,and crystal structure of this protein.We highlight a few unique structural features of FXIa after comparison with the trypsin family serine proteases at sequence and structural levels.This work provides a foundation to develop new small molecular FXIa inhibitors with increased potency and specificity.     

Structural Transition Dynamics in Carbon Electrode-Based Single-Molecule Junctions

Monitoring the structural transitions of individual molecules is of great significance because it helps to in depth explore the properties of molecules and provide diverse possibilities for molecular applications in the fields of chemistry,biology and material science.This review summarizes the strategy of using single-molecule electrical approaches to study molecular structure transitions at the single-molecule level in real time.Specifically,through the use of stable single-molecule devices for real-time electrical monitoring,the process of molecular structure transitions of a single molecule can be investigated,which helps to explore the nature of molecules in chemical and biological systems.In particular,the detection methods have been extended to the investigation of biological macromolecules for monitoring the conformational changes of nucleotide chains in different systems,such as double helix DNA,aptamer and DNA enzyme.In the end,we discuss the future challenges of probing structural transitions of single molecules,and provide prospects for further breakthroughs in this field.     

Soluble and degradable polyimides with phenyl-2-pyridyl ether structure: Synthesis and characterization

A diamine monomer o-phenylenedioxybis(5-amino-2-pyridine) was synthesized via reduction of a dinitro compound o-phenylenedioxybis(5-nitro-2-pyridine), producing a series of new polyimides from this diamine and various commercially available aromatic dianhydrides via conventional two-stage processes. The resulting polyimides are able to form tough and transparent films, with decomposition temperatures in the range of 529–551 °C, and can be dissolved in organic polar solvents. Meanwhile, these polyimides can be degraded in a hydrazine hydrate medium, a degradation mechanism proposed by analyzing the degradation products suggests that the degradable properties could be attributed to the phenyl-2-pyridyl ether structure in the polymer. In addition, the transformation of the compound structure from dinitro compound to damine monomer in the synthetic process is discussed in respect to X-ray structure.     

STUDIES ON THE SYMMETRY OF QUATERNARY STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYLASE FROM SORGHUM LEAVES

Studies on the symmetry of quaternary structure of PEP carboxylase from sorghum leaves were carried out by means of chemical crosslinking with bifunctional reagents (diimidoesters) and subsequent SDS polyacrylamide gel electrophoresis.Results showed that the four identical subunits of the enzyme are associated isologously: i.e. the quaternary structure of the enzyme has a D_2 symmetry.The patterns of PEP carboxylase crosslinked with suberic dimethylimidate varied in the presence of various ligands.Substrate PEP, Mg~(2+) (required for catalysis of the enzyme), PEP plus Mg~(2+) and the inhibitor malate increased the extent of crosslinking of the enzyme in varying degrees, indicating that binding of these ligands to the enzyme gave rise to changes in the subunit interactions.However,the extent of crosslinking of PEP carboxylase with suberic dimethylimidate decreased greatly in the presence of the activator G6P. Meanwhile, the enzyme remains a tetrameric form either in the absence or in the presence of G6P.     

INTERNAL BOUNDARY VALUE PROBLEM OF GRAVIMETRY AND ITS APPLICATION

As a deepening and extension of Theory of Unified Representation of Gravitational Field~([1]), this paper covers two aspects as follows: in theory, we go into the fundamental structure of the internal problem and put emphasis on seeking the solution of the disturbing potential in spectral domain and establishing a spectral structure form of anomalous density; and in application, according to the given form we try to take a look at the distribution charateristics of anomalous densities of lithosphere about 30—40 km deep in the continent of China in illustration of evaluating practical trustworthiness of the present theory. Calculations done here are based on earth gravity model DQM84D~([2]) and show that this theory seems to be convincing.