Insights into trehalose synthesis provided by the structure of the retaining glucosyltransferase OtsA

Trehalose is a nonreducing disaccharide that plays a major role in many organisms, most notably in survival and stress responses. In Mycobacterium tuberculosis, it plays a central role as the carbohydrate core of numerous immunogenic glycolipids including "cord factor" (trehalose 6,6'-dimycolate). The classical pathway for trehalose synthesis involves the condensation of UDP-glucose and glucose-6-phosphate to afford trehalose-6-phosphate, catalyzed by the retaining glycosyltransferase OtsA. The configurations of two anomeric positions are set simultaneously, resulting in the formation of a double glycoside. The three-dimensional structure of the Escherichia coli OtsA, in complex with both UDP and glucose-6-phosphate, reveals the active site at the interface of two beta/alpha/beta domains. The overall structure and the intimate details of the catalytic machinery reveal a striking similarity to glycogen phosphorylase, indicating a strong evolutionary link and suggesting a common catalytic mechanism.     

Electronic and mechanical properties of 5d transition metal mononitrides via first principles

The electronic and mechanical properties of 5d transition metal mononitrides from LaN to AuN are systematically investigated by use of the density-functional theory. For each nitride, six structures are considered, i.e., rocksalt, zinc blende, CsCl, wurtzite, NiAs and WC structures. Among the considered structures, rocksalt structure is the most stable for LaN, HfN and AuN, WC structure for TaN, NiAs structure for WN, wurtzite structure for ReN, OsN, IrN and PtN. The most stable structure for each nitride is mechanically stable. The formation enthalpy increases from LaN to AuN. For LaN, HfN and TaN, the formation enthalpy is negative for all the considered structures, while from WN to AuN, except wurtzite structure in ReN, the formation enthalpy is positive. The calculated density of states shows that they are all metallic. ReN in NiAs structure has the largest bulk modulus, 418 GPa. The largest shear modulus 261 GPa is from TaN in WC structure. Trends are discussed.     

A partition function algorithm for nucleic acid secondary structure including pseudoknots

Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications.     

Rovibrational eigenenergy structure of the [H,C,N] molecular system

The vibrational-rotational eigenenergy structure of the [H,N,C] molecular system is one of the key features needed for a quantum mechanical understanding of the HCN?HNC model reaction. The rotationless vibrational structure corresponding to the multidimensional double well potential energy surface is well established. The rotational structure of the bending vibrational states up to the isomerisation barrier is still unknown. In this work the structure of the rotational states for low and high vibrational angular momentum is described from the ground state up to the isomerisation barrier using hot gas molecular high resolution spectroscopy and rotationally assigned ab initio rovibronic states. For low vibrational angular momentum the rotational structure of the bending excitations splits in three regions. For J < 40 the structure corresponds to that of a typical linear molecule, for 40 < J < 60 has an approximate double degenerate structure and for J > 60 the splitting of the e and f components begins to decrease and the rotational constant increases. For states with high angular momentum, the rotational structure evolves into a limiting structure for v(2) > 7--the molecule is locked to the molecular axis. For states with v(2) > 11 the rotational structure already begins to accommodate to the lower rotational constants of the isomerisation states. The vibrational energy begins to accommodate to the levels above the barrier only at high vibrational excitations of v(2) > 22 just above the barrier whereas this work shows that the rotational structure is much more sensitive to the double well structure of the potential energy surface. The rotational structure already experiences the influence of the barrier at much lower energies than the vibrational one.     

Architecture of intracellular networks in plant matrices

Pectin is an integral component of plant cell walls. It is believed to form an interconnected network structure independent of the cellulose–xyloglucan network structure. Pectin gels are often used as a model for the pectin network structure within the plant cell wall. The middle lamella pectin can be extracted with chelating agents and is believed to be associated through cooperative binding of calcium ions in the so-called egg-box junction zones. Although a great deal is known about the nature of the junction zones in pectin gels, less is known about the long-range structure within calcium-set gels. Two plausible alternative models for long-range order in these gels are a pseudo rubber-like structure and a fibrous network structure. Atomic force microscopy studies of calcium-induced gel precursors, and fragments released from gels, suggest that association leads to a branched fibrous structure within the gels. Enzymatic de-esterification of high methoxy pectin in the presence of calcium ions can induce gelation of the pectin. Thus pectin gel networks may provide a model for a self-assembled network structure within the middle lamella region of the plant cell wall.     

Symmetry operation measures

We introduce a new mathematical tool for quantifying the symmetry contents of molecular structures: the Symmetry Operation Measures. In this approach, we measure the minimal distance between a given structure and the structure which is obtained after applying a selected symmetry operation on it. If the given operation is a true symmetry operation for the structure, this distance is zero; otherwise it gives an indication of how different the transformed structure is from the original one. Specifically, we provide analytical solutions for measures of all the improper rotations, S n p, including mirror symmetry and inversion, as well as for all pure rotations, C n p. These measures provide information complementary to the Continuous Symmetry Measures (CSM) that evaluate the distance between a given structure and the nearest structure which belongs to a selected symmetry point-group.     

The first solution structure of a paramagnetic copper(II) protein: the case of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803.

The NMR solution structure of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803 is here reported. The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross-peaks, 18 1D NOEs, 26 T(1) values, 96 dihedral angle constraints, and 18 H-bonds. The detection of broad hyperfine-shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root-mean-square deviation from the mean structure for the solution structure family is 0.72 +/- 0.14 and 1.16 +/- 0.17 A for backbone and heavy atoms, respectively. The structure is overall quite satisfactory and represents a breakthrough, in that it includes paramagnetic copper proteins among the metalloproteins for which solution structures can be afforded. The comparison with the available X-ray structure of a triple mutant is also performed.     

Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.     

Structure of cationized glycine, gly.m (m = be, mg, ca, sr, ba), in the gas phase: intrinsic effect of cation size on zwitterion stability

Interactions between divalent metal ions and biomolecules are common both in solution and in the gas phase. Here, the intrinsic effect of divalent alkaline earth metal ions (Be, Mg, Ca, Sr, Ba) on the structure of glycine in the absence of solvent is examined. Results from both density functional and Moller-Plesset theories indicate that for all metal ions except beryllium, the salt-bridge form of the ion, in which glycine is a zwitterion, is between 5 and 12 kcal/mol more stable than the charge-solvated structure in which glycine is in its neutral form. For beryllium, the charge-solvated structure is 5-8 kcal/mol more stable than the salt-bridge structure. Thus, there is a dramatic change in the structure of glycine with increased metal cation size. Using a Hartree-Fock-based partitioning method, the interaction between the metal ion and glycine is separated into electrostatic, charge transfer and deformation components. The charge transfer interactions are more important for stabilizing the charge-solvated structure of glycine with beryllium relative to magnesium. In contrast, the difference in stability between the charge-solvated and salt-bridge structure for magnesium is mostly due to electrostatic interactions that favor formation of the salt-bridge structure. These results indicate that divalent metal ions dramatically influence the structure of this simplest amino acid in the gas phase.     

对功能高分子课程教学的思考

功能高分子的设计思想是功能高分子课程的灵魂 ,它以高分子物理学所研究的结构与性能之间关系为基础。结构与性能之间的关系是贯穿功能高分子课程始末的主线。功能高分子材料有三种设计途径 ,即化学结构设计、聚集态结构设计和复合结构设计     

Modeling the local structure and energetics of protozeolitic nanoclusters in hydrothermally stable aluminosilicate mesostructures

The density functional theory (DFT) method is used to investigate the structure and bonding of silica and aluminosilicate nanoclusters containing five- and six-membered oxygen rings. The clusters, which are derived from the BEA zeolite structure, are considered as models of the protozeolitic clusters that are incorporated into the pore walls of steam stable aluminosilicate mesostructures assembled from zeolite seeds. Two locally different Br?nsted acid sites in the aluminosilicate structure are identified for the adsorption of a water molecule. The sterically more open acid site is favored for water binding. The stability of the aluminosilicate structure in the presence of H2O molecule is studied by breaking an Al-O bond and inserting a water molecule into the five-membered ring structure. We find that an excitation energy at least 18 times larger than the room-temperature thermal energy is needed to break the stable five-membered ring structure, implying a high hydrothermal stability and acidity for this aluminosilicate structure.     

Comparative study of the high-pressure behavior of As,Sb, and Bi

The high-pressure behavior of the heavier group 15 elements As, Sb, and Bi was investigated by means of ab initio density functional calculations employing pseudopotentials and a plane wave basis set. The high-pressure structural sequence of these elements is distinguished by the occurrence of the Bi-III structure, which is a complex, incommensurately modulated, host-guest structure. We approximated this structure by a supercell which reproduced the experimentally established pressure stability ranges of the host-guest structure for the different elements extremely well. With pressure we find an increasing admixture of d states (s-d hybridization) in the occupied levels of the electronic structure of As, Sb, and Bi. However, the s-d mixing remains at a low level. Thus, the emergence of a complex intermediate pressure structure cannot be explained by a pressure-induced altered valence state for these elements. Instead, it is argued that the Bi-III structure is a consequence of a delicate interplay between the electrostatic and the band energy contribution to the total energy. In the intermediate pressure range of heavier group 15 elements, both important parts of the total energy account equally for structural stability.     

Automated search for new thermoelectric materials: the case of LiZnSb

An automated band structure calculation based on the inorganic crystal structure database and the augmented plane wave method for electronic structure calculations is presented. Using a rigid band approach and semiclassic Boltzmann theory the band structures are analyzed and a large number of compounds are screened for potential interesting thermoelectric properties. We thereby propose LiZnSb as a potential new thermoelectric material. The k-space structure of the lowest conduction band of LiZnSb is analyzed in detail, and excellent thermoelectric properties are expected for this material. Furthermore the lattice dynamics are calculated, and anisotropic lattice thermal conduction is predicted.     

Quantum control by means of hamiltonian structure manipulation

A traditional quantum optimal control experiment begins with a specific physical system and seeks an optimal time-dependent field to steer the evolution towards a target observable value. In a more general framework, the Hamiltonian structure may also be manipulated when the material or molecular 'stockroom' is accessible as a part of the controls. The current work takes a step in this direction by considering the converse of the normal perspective to now start with a specific fixed field and employ the system's time-independent Hamiltonian structure as the control to identify an optimal form. The Hamiltonian structure control variables are taken as the system energies and transition dipole matrix elements. An analysis is presented of the Hamiltonian structure control landscape, defined by the observable as a function of the Hamiltonian structure. A proof of system controllability is provided, showing the existence of a Hamiltonian structure that yields an arbitrary unitary transformation when working with virtually any field. The landscape analysis shows that there are no suboptimal traps (i.e., local extrema) for controllable quantum systems when unconstrained structural controls are utilized to optimize a state-to-state transition probability. This analysis is corroborated by numerical simulations on model multilevel systems. The search effort to reach the top of the Hamiltonian structure landscape is found to be nearly invariant to system dimension. A control mechanism analysis is performed, showing a wide variety of behavior for different systems at the top of the Hamiltonian structure landscape. It is also shown that reducing the number of available Hamiltonian structure controls, thus constraining the system, does not always prevent reaching the landscape top. The results from this work lay a foundation for considering the laboratory implementation of optimal Hamiltonian structure manipulation for seeking the best control performance, especially with limited electromagnetic resources.     

Stabilization centers in various proteins

Interactions among residues together with their interactions with the surrounding medium determine the unique structure of globular proteins. An algorithm was recently developed to locate residues participating in cooperative long-range interactions, called stabilization center residues, that are primarily responsible for preventing the decay of the 3D structure. While our statistical analysis showed that interactions of stabilization center residues hardly influence the formation of the various secondary structure elements, the distribution of the stabilization center residues is rather uneven among the secondary structure elements. Here we analyzed the frequency and distribution of the stabilization center residues and their interacting pairs in secondary structure classes to learn about the effect of secondary structure on the formation and properties of stabilization centers and about the types of interactions responsible for stabilization of proteins of various secondary structure classes. It was found that residues from the same secondary structure tend to interact with each other in the stabilization centers of all classes. It is also suggested that the folding-unfolding equilibrium is governed by different principles for class all-α than for the rest of the classes. Received: 24 April 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998     

How to determine structures when single crystals cannot be grown: opportunities for structure determination of molecular materials using powder diffraction data

Many crystalline solids cannot be prepared as single crystals of sufficient size and/or quality for structure determination to be carried out using single crystal X-ray diffraction techniques. In such cases, when only polycrystalline powders of a material are available, it is necessary instead to tackle structure determination using powder X-ray diffraction. This article highlights recent developments in the opportunities for determining crystal structures directly from powder diffraction data, focusing on the case of molecular solids and giving particular attention to the most challenging stage of the structure determination process, namely the structure solution stage. In particular, the direct-space strategy for structure solution is highlighted, as this approach has opened up new opportunities for the structure determination of molecular solids. The article gives an overview of the current state-of-the-art in structure determination of molecular solids from powder diffraction data. Relevant fundamental aspects of the techniques in this field are described, and examples are given to highlight the application of these techniques to determine crystal structures of molecular materials.     

Liquid structure of vanadium tetrachloride from neutron diffraction study

Assuming the separation of the intermolecular scattering function into the radial and angular parts and using Egelstaffet al’s orientational model for tetrachlorides, the structure of liquid vanadium tetrachloride has been studied. It has been observed that such a separation is approximate for this liquid and the introduction of a third correction term is required to account for the molecular structure function. The chlorine-chlorine partial structure and effective angleaveraged intermolecular chlorine-chlorine potential in the liquid has been evaluated. Without taking the third correction term, introduced to generate theoretically the molecular structure function, the centre structure function has been obtained in an approximate way from the experimentally observed molecular structure function and from it the centre radial distribution function, centre direct correlation function and the angle-averaged vanadium-vanadium effective potential has been evaluated.     

Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation

In the present letter, we directly compare neutron structure factors calculated from force field (FF)-based molecular dynamics simulations with experimental structure factors for water, methanol, and tetrahydrofuran (THF). For water, the difference in the measured structure factors is more significant than differences between the FFs. It is shown that the inclusion of electronic polarization in the force field improves the agreement with experiment for the more-polar methanol, whereas the results are comparable for the additive and polarizable FF models of the less-polar THF. The data presented here confirm that comparing the calculated scattering profiles from FF-based MD simulations to measured neutron structure factors is a promising method for FF validation and development.     

A hierarchic sparse matrix data structure for large-scale Hartree-Fock/Kohn-Sham calculations

A hierarchic sparse matrix data structure for Hartree-Fock/Kohn-Sham calculations is presented. The data structure makes the implementation of matrix manipulations needed for large systems faster, easier, and more maintainable without loss of performance. Algorithms for symmetric matrix square and inverse Cholesky decomposition within the hierarchic framework are also described. The presented data structure is general; in addition to its use in Hartree-Fock/Kohn-Sham calculations, it may also be used in other research areas where matrices with similar properties are encountered. The applicability of the data structure to ab initio calculations is shown with help of benchmarks on water droplets and graphene nanoribbons.