Ab initio and molecular dynamics studies of solid β-HMX: effects of hydrostatic pressure and high temperature

Using first-principles density functional theory and classical molecular dynamics (MD), the structural, electronic and mechanical properties of the energetic material β-HMX have been studied. The crystal structure optimised by the local density approximation calculations compares reasonably with the experimental data. Electronic band structure and density of states indicate that β-HMX is an insulator with a band gap of 3.059 eV. The pressure effect on the crystal structure and physical properties has been investigated in the range of 0–40 GPa. The crystal structure and electronic properties change slightly as the pressure increases from 0 to 2.5 GPa; when the pressure is above 2.5 GPa, further increment of the pressure results in significant changes in crystal structure. There is a larger compression along the b-axis than along the a- and c-axes. Isothermal–isobaric MD simulations on β-HMX were performed in the temperature range of 5–400 K. Phase transition at 360 K, corresponding to a volume interrupt, was found. The computed thermal expansion coefficients show anisotropic behaviour with a slightly larger expansion along the b- and c-axes than along the a-axis. In the temperature range of 5–360 K, β-HMX possesses good plasticity and its stiffness decreases with increasing the temperature.     

Differentiation of adenine non-planarity in valence molecular orbitals

Two molecular orbitals: MO7 (29a) and MO13 (23a) have been identified using dual space analysis (DSA) as the signatures of adenine non-planarity (C₁ point group symmetry). The non-planarity of adenine has been demonstrated to be from the attachment of the amino group (NH₂) to purine rings as well as the non-rigid deformability of the purine ring of adenine. Orbital 29a (3a″ in the planar case), a π-like orbital, is the direct result of the attachment of the amino group to the purine ring. Orbital 23a (23a′ in the planar case) is the result of the deformability of the purine ring in non-planar adenine (NP) and will be experimentally challenging to resolve.     

股骨近端三维有限元模型评价髋部骨折患者骨密度

目的：探究骨密度与老年髋部骨折股骨近端三维有限元模型密度的关系。方法：选取8 例老年髋部骨折,其中4 例股骨颈骨 折,4 例股骨转子间骨折;左侧肢体3 例,右侧肢体5 例。分别测定腰椎骨密度和双侧髋关节CT 资料,运用Mimics软件和abaqus 软件对健侧股骨近端进行重建和计算出该模型的密度。结果：股骨转子间骨折组腰椎骨密度为(-4.05± 0.24) g/cm2,三维有限元模 型密度为[(1.15± 0.02)× 106],均低于股骨颈骨折组的(-3.15± 0.54) g/cm2,[(1.34± 0.06)× 106],两组比较差异均有统计学意义（均 P<0.05）。腰椎的骨密度与三维有限元模型密度成线性正相关（r=0.881,P=0.004）。结论：骨密度与老年髋部骨折股骨近端三维有限 元模型密度成线性正相关的关系,可为进一步用有限元分析法探讨老年髋部骨折部位与骨密度的关系提供理论依据。     

Purification and characterization of peridinin-chlorophyll a-proteins from the marine dinoflagellates Glenodinium sp. and Gonyaulax polyedra

Summary A peridinin-chlorophyll a-protein complex (PCP) was obtained in large quantity from the marine dinoflagellates, Glenodinium sp. and Gonyaulax polyedra. The chromoproteins have similar molecular weights, 35,500 for Glenodinium sp. and 34,500 for G. polyedra. The proteins from the PCP complex of Glenodinium sp. dissociated from the chromophore on treatment with 1% sodium dodecyl sulfate (SDS) at room temperature. The protein component was a single subunit with a molecular weight of 15,500. Proteins from the PCP complex of G. polyedra were composed of a single polypeptide with a molecular weight of about 32,000. Two peridinin-chlorophyll a-proteins from Glenodinium sp. accounted for 70% of the PCP complex and had isoelectric points of 7.4 and 7.3. The PCP complex from G. polyedra was dominated by a single chromoprotein with an isoelectric point of 7.2 Chromophore analysis indicated the presence of only peridinin and chlorophyll a in a molar ratio approaching 4:1. Other pigments characteristically found in dinoflagellates were absent. Fluorescence excitation spectra of purified PCP indicated an efficient energy transfer from peridinin to chlorophyll a, an observation that lends support to the reported role of peridinin as an accessory pigment in photosynthetic oxygen evolution. In several other brown colored dinoflagellates examined, PCP representtd less than 20% of the total peridinin. However, no PCP could be isolated from cultures of Amphidinium carterae (PY-1). This study provides further evidence that PCP is a normal component of most peridinin-containing dinoflagellates, and functions as a light-harvesting component of the dinoflagellate chloroplast. No fucoxanthin-containing analog of PCP was detected in the chrysophyte, Cricosphera carterae and the dinoflagellate Glenodinium foliaceum.Abbreviations PCP peridinin-chlorophyll a-protein complex - PCP's peridinin-chlorophyll a-proteins - SDS sodium dodecyl sulfate - pl isoelectric point - DEAE diethylaminoethyl cellulose - TLC thin layer chromatography - A optical absorbance at a designated wavelength - SIO (F.T. Haxo), Scripps Institution of Oceanography collection     

On the mechanism of oxygen activation by tetrahydropterin and dihydroflavin-dependent monooxygenases

A brief critical survey of the current theories of molecular oxygen activation in the hydroxylation of aromatic compounds by dihydroflavin- and tetrahydropterin-dependent monooxygenases is presented. A reinterpretation of the available data has resulted in the proposal of a new mechanistic hypothesis. It is suggested that the dihydroflavin (or tetrahydropterin) cofactor interacts with ground-state molecular oxygen to give a C_4a-C_10a singlet perepoxy dihydroflavin (or a C_4a-C_8a perepoxy tetrahydropterin) intermediate which functions as the oxenoid reagent in this class of biological hydroxylations.     

On the Mathematical Reconstruction of Two Dimensional Plants

A set of 10, chosen medicinal plants (some of them with a reputation as remedies for tuberculosis) has been investigated through Partitioned Iterated Function Systems-Semi Fractals with Angle (PIFS-SFA) coding, Lempel, Ziv, Welch with quantization and noise (LZW-QN) compression, and surface density statistics (f(α)-SDS) discrimination techniques. The final outcomes of this quantitative analysis were, firstly: the linear ordering of the plants in question accompanied by the hope that it reflects their medical significance, secondly: the mathematical representation of each of the plants, and thirdly: the impressive compression achieved, leading to remarkable computer memory saving, and still permitting successful pattern recognition i.e., proper identification of the plant from the compressed image.     

Predicting protein pKa by environment similarity

A statistical method to predict protein pK_a has been developed by using the 3D structure of a protein and a database of 434 experimental protein pK_a values. Each pK_a in the database is associated with a fingerprint that describes the chemical environment around an ionizable residue. A computational tool, MoKaBio, has been developed to identify automatically ionizable residues in a protein, generate fingerprints that describe the chemical environment around such residues, and predict pK_a from the experimental pK_a values in the database by using a similarity metric. The method, which retrieved the pK_a of 429 of the 434 ionizable sites in the database correctly, was crossvalidated by leave‐one‐out and yielded root mean square error (RMSE) = 0.95, a result that is superior to that obtained by using the Null Model (RMSE 1.07) and other well‐established protein pK_a prediction tools. This novel approach is suitable to rationalize protein pK_a by comparing the region around the ionizable site with similar regions whose ionizable site pK_a is known. The pK_a of residues that have a unique environment not represented in the training set cannot be predicted accurately, however, the method offers the advantage of being trainable to increase its predictive power. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Combined multispectroscopic and molecular docking investigation on the interaction between delphinidin‐3‐O‐glucoside and bovine serum albumin

Anthocyanin is one of the flavonoid phytopigments with specific health benefits. The interaction between delphinidin‐3‐O‐glucoside (D3G) and bovine serum albumin (BSA) was investigated by fluorescence spectroscopy, synchronous fluorescence spectroscopy, three‐dimensional fluorescence spectroscopy, ultraviolet‐visible absorption spectroscopy, circular dichroism spectroscopy and molecular modeling. D3G effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites and binding constant K_a were determined, and the hydrogen bonds and van der Waals forces played major roles in stabilizing the D3G–BSA complex. The distance r between donor and acceptor was obtained as 2.81 nm according to Förster's theory. In addition, the effects of pH and metal ions on the binding constants were discussed. The results studied by synchronous fluorescence, three‐dimensional fluorescence and circular dichroism experiments indicated that the secondary structures of the protein has been changed by the addition of D3G and the α‐helix content of BSA decreased (from 56.1% to 52.4%). Furthermore, the study of site marker competitive experiments and molecular modeling indicated that D3G could bind to site I of BSA, which was in the large hydrophobic cavity of subdomain IIA. Copyright © 2014 John Wiley & Sons, Ltd.     

'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve

Background  

The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as S = a ²+ c ²+t ²+g ², where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than 1/3 for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius r = 1/ contains almost all points corresponding to various genomes, implying that S <r ². The distribution of the points P obtained by S was studied using the Z-curve.     

cPPB‐aE is discovered from photosynthetic benthic dinoflagellates

Although chlorophyll degradation pathways in higher plants have been well studied, little is known about the mechanisms of chlorophyll degradation in microalgae. In this article, we report the occurrence of a chlorophyll a derivative that has never been discovered in photosynthetic organisms. This chlorophyll derivative emits no fluorescence and has a peculiar absorbance peak at 425, 451, 625, and 685 nm. From these features, it was identified as 13²,17³‐cyclopheophorbide a enol (cPPB‐aE), reported as a degradation product of chlorophyll a derived from prey algal cells in heterotrophic protists. We discovered cPPB‐aE in six benthic photosynthetic dinoflagellates that are phylogenetically separated into four clades based on SSU rDNA molecular phylogeny. This is the first report of this chlorophyll derivative in photosynthetic organisms and we suggest that the derivative is used to quench excess light energy.     

Comparison of tomato root distributions by minirhizotron and destructive sampling

Calibration of minirhizotron data against root length density (RLD) was carried out in a field trial where three drip irrigation depths: surface (R0) and subsurface, 0.20 m (RI) and 0.40 m depth (RII) and two processing tomato cultivars: `Brigade' (CI) and `H3044' (CII) were imposed. For each treatment three minirhizotron tubes were located at 10, 37.5 and 75 cm of the way from one plant row to the next. Roots intersecting the minirizotrons walls were expressed as root length intensity (L _a) and number of roots per unit of minirhizotron wall area (N _ra). Root length density (RLD) was calculated from core samples taken for each minirhizotron tube at two locations: near the top of the minirhizotron (BI) and 15 cm apart from it, facing the minirhizotron wall opposite the plant row (BII). Minirhizotron data were regressed against RLD obtained at BI and BII and with their respective means. The results show that for all the situations studied, better correlations were obtained when RLD was regressed with L _a than with N _ra. Also was evident that the relationship between L _a and RLD was strongly influenced by the location of soil coring. RLD was correlated with L _a trough linear and cubic equations, having the last ones higher determination coefficients. For instance at 10 cm from the plant row when values from the top layer (0–40 cm) were analysed separately, L _a was significantly regressed with RLD measured at BII and described by the equations: RLD = 0.5448 + 0.0071 L _a (R ² = 0.51) and RLD = 0.4823 + 0.0074L _a + 8×10^–5 L _a ² – 5×10^–7 L _a ³ (R ² = 0.61). Under the 40 cm depth the highest coefficients of determination for the linear and cubic equations were respectively 0.47 and 0.88, found when L _a was regressed with RLD measured at BI. For minirhizotrons located at 75 cm from the plant row and for location BI it was possible to analyse jointly data from all depths with coefficients of determination of 0.45 and 0.59 for the linear and cubic equations respectively.     

Minor but key chlorophylls in Photosystem II

A ‘metal-free’ chlorophyll (Chl) a, pheophytin (Phe) a, functions as the primary electron acceptor in PS II. On the basis of Phe a/PS II = 2, Phe a content is postulated as an index for estimation of the stoichiometry of pigments and photosystems. We found Phe a in a Chl d-dominant cyanobacterium Acaryochloris marina, whereas Phe d was absent. The minimum Chl a:Phe a ratio was 2:2, indicating that the primary electron donor is Chl a, accessory is Chl d, and the primary electron acceptor is Phe a in PS II of A. marina. Chl d was artificially formed by the treatment of Chl a with papain in aqueous organic solvents. Further, we will raise a key question on the mechanisms of water oxidation in PS II.     

Synthesis,molecular docking,binding free energy calculation and molecular dynamics simulation studies of benzothiazol-2-ylcarbamodithioates as Staphylococcus aureus MurD inhibitors

Abstract

A new series of benzothiazol-2-ylcarbamodithioate functional compounds 5a-f has been designed, synthesized and characterized by spectral data. These compounds were screened for their in vitro antibacterial activity against strains of Staphylococcus aureus (NCIM 5021, NCIM 5022 and methicillin-resistant isolate 43300), Bacillus subtilis (NCIM 2545), Escherichia coli (NCIM 2567), Klebsiella pneumoniae (NCIM 2706) and Psudomonas aeruginosa (NCIM 2036). Compounds 5a and 5d exhibited significant activity against all the tested bacterial strains. Specifically, compounds 5a and 5d showed potent activity against K. pneumoniae (NCIM 2706), while compound 5a also displayed potent activity against S. aureus (NCIM 5021). Compound 5d showed minimum IC₅₀ value of 13.37?μM against S. aureus MurD enzyme. Further, the binding interactions of compounds 5a-f in the catalytic pocket have been investigated using the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. A 30?ns molecular dynamics simulation of 5d/modeled S. aureus MurD enzyme was performed to determine the stability of the predicted binding conformation.     

Perspectives of data analysis of enzyme inhibition and activation,Part 1: Use of the three‐dimensional Km′ V′I coordinate system for data analysis of enzyme inhibition and activation

The possibility of construction of the three‐dimensional (unfolded and folded) K_m′ V′I rectangular coordinate systems convenient for vector representation of inhibited and activated enzymatic reactions as well as of a two‐dimensional K_m′ V′ scalar rectangular coordinate system convenient for diagrammatic representation of enzymatic reactions is considered. The perspectives of using the properties of the three‐dimensional L vectors and their scalar L projections for data analysis of enzyme inhibition and activation are analyzed. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:97–100, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20273     

MolMod – an open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de and contains intermolecular force fields for over 150 pure fluids at present. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programmes ms2 and ls1 mardyn, GROMACS, and LAMMPS. To characterise the semantics associated with the numerical database content, a force field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the database were generally optimised such as to yield good representations of experimental data of the vapour–liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.     

Predicting protein folding rate change upon point mutation using residue‐level coevolutionary information

Change in folding kinetics of globular proteins upon point mutation is crucial to a wide spectrum of biological research, such as protein misfolding, toxicity, and aggregations. Here we seek to address whether residue‐level coevolutionary information of globular proteins can be informative to folding rate changes upon point mutations. Generating residue‐level coevolutionary networks of globular proteins, we analyze three parameters: relative coevolution order (rCEO), network density (ND), and characteristic path length (CPL). A point mutation is considered to be equivalent to a node deletion of this network and respective percentage changes in rCEO, ND, CPL are found linearly correlated (0.84, 0.73, and ?0.61, respectively) with experimental folding rate changes. The three parameters predict the folding rate change upon a point mutation with 0.031, 0.045, and 0.059 standard errors, respectively. Proteins 2016; 84:3–8. © 2015 Wiley Periodicals, Inc.     

Mode‐coupling Smoluchowski dynamics of a double‐stranded DNA oligomer

The local dynamics of a double‐stranded DNA d(TpCpGpCpG)₂ is obtained to second order in the mode‐coupling expansion of the Smoluchowski diffusion theory. The time correlation functions of bond variables are derived and the ¹³C‐nmr spin–lattice relaxation times T₁ of different ¹³C along the chains are calculated and compared to experimental data from the literature at three frequencies. The DNA is considered as a fluctuating three‐dimensional structure undergoing rotational diffusion. The fluctuations are evaluated using molecular dynamics simulations, with the ensemble averages approximated by time averages along a trajectory of length 1 ns. Any technique for sampling the configurational space can be used as an alternative. For a fluctuating three‐dimensional (3D) structure using the three first‐order vector modes of lower rates, higher order basis sets of second‐rank tensor are built to give the required mode coupling dynamics. Second‐ and even first‐order theories are found to be in close agreement with the experimental results, especially at high frequency, where the differences in T₁ for ¹³C in the base pairs, sugar, and backbone are well described. These atomistic calculations are of general application for studying, on a molecular basis, the local dynamics of fluctuating 3D structures such as double‐helix DNA fragments, proteins, and protein–DNA complexes. © 1999 John Wiley & Sons, Inc. Biopoly 50: 613–629, 1999