Molecular Dynamics Study on Protein and it's Water Structure at High Pressure

Abstract

We have performed NPT molecular dynamics simulations (Langevin Piston Method) on two types of solvated proteins-‘denaturation-unfavorable’ protein (insulin) and ‘denaturation-favorable protein’ (ribonuclease A) at high pressure (from 1 bar up to 20 kbar). The method is based on the extended system formalism introduced by Andersen, where the deterministic equations of motion for the piston degree of freedom are replaced by Langevin equation. We report the structural changes of proteins (ribonuclease A and insulin) and water molecules through radius of gyration, solvent accessible surface area, hydrogen bond pattern, and the topology of water clusters connected by the hydrogen bonded circular network. The solvent accessibility of ribonuclease A is mainly decreased by hydrophilic residues rather than hydrophobic residues under high pressure. From the results of hydrogen bond analysis, we have found that α-helix is more stable than β-sheet under high pressure. In addition, from the analysis of the water cluster, we have observed that for ribonuclease A, 5-membered ring structure is more favorable than 6-membered ring at higher pressure. However, for insulin, the ratio of 5 to 6-ring is constant over the pressure ranges for which we have performed MD simulation. This indicates that the water structure around insulin does not change under high pressure.     

Ecotoxicity of Imidacloprid to Aquatic Organisms: Derivation of Water Quality Standards for Peak and Long-Term Exposure

The neonicotinoid insecticide imidacloprid is among the pesticides that most frequently exceed current water quality standards in Dutch surface waters. Recent research shows that effects of imidacloprid on water organisms occur at concentrations below these standards. Mayflies appear to be particularly sensitive with chronic No Observed Effect Concentrations in the nanogram per liter range. The aim of this study was to derive updated water quality standards in accordance with the methodology of the European Water Framework Directive by evaluating the available recent literature on acute and chronic ecotoxicity of imidacloprid to aquatic organisms in laboratory and semi-field experiments. It is concluded that the standard for long-term exposure should be lowered to 8.3 nanograms per liter; the standard for short-term concentration peaks can be maintained at the current value of 0.2 micrograms per liter. The European Commission set restrictions to the use of imidacloprid-based products to reduce the risks for bees and the Dutch national authorities issued emission reduction measures to protect aquatic life. Future monitoring data will ultimately reveal if these measures are sufficient to meet the newly proposed standards.     

Kinetic and Thermodynamic Solubility Values of Some Bioactive Compounds

Thermodynamic solubility is a decisive physicochemical property in drug development. The Chasing Equilibrium method offers an alternative to the classical procedures to measure the solubility of compounds with acid–base properties. The method is fast and yields accurate results. In this work, the solubility of several compounds including acids and bases was determined through the Chasing Equilibrium approach. A study of experimental conditions in terms of sample weight was performed to measure solubilities. The study shows that only a limited range of weights, depending on the nature and solubility of the compounds, is adequate to obtain reliable results.     

Solubility of Saturated Fatty Acids in Water at Elevated Temperatures

The solubility in water of saturated fatty acids with even carbon numbers from 8 to 18 was measured in the temperature range of 60 to 230°C and at a pressure of 5 or 15 MPa. The pressure had no significant effect on the solubility. The solubility of the fatty acids increased with increasing temperature. At temperatures higher than about 160°C, the logarithm of the solubility in mole fraction was linearly related to the reciprocal of the absolute temperature for each fatty acid, indicating that the water containing solubilized fatty acid molecules formed a regular solution at the higher temperatures. The enthalpy of a solution of the fatty acids in water, which was evaluated from the linear relationship at the given temperatures, increased linearly with the carbon number of the fatty acid.     

Discrimination in resolving systems. III: Pseudoephedrine-mandelic acid

(+)-(1S;2S)-Pseudoephedrine and racemic mandelic acid form three distinct diastereomeric salts from solutions in 95% ethanol. The least-soluble phase, a hemihydrate, contains the (2R)-mandelate. A salt phase of intermediate solubility is the unsolvated double salt, containing both the (2R)- and the (2S)-mandelate. The most-soluble salt phase contains the (2S)-mandelate. Mandelate configuration and order of solubility (based on the heats of fusion) is inverted from that found in the same system synthesized from chiral base and acid, and then crystallized from benzene solution. The (2R)-mandelate hemihydrate (−H₂O at 349.5K, mp 391K), monoclinic, P2₁, a = 6.788(5), b = 29.415(35), c = 9.488(10)Å, β = 108.91(8)°, Z = 4 (2 ion-pairs/asymmetric unit). Intermediate double salt (2S)- and (2R)-mandelate, mp 377.6K, anorthic, P1, a = 7.758(4), b = 9.966(5), c = 13.366(6)Å, α = 72.99(4), β = 79.98(4), γ = 70.51(4)°, Z = 1 (2 ion-pairs/asymmetric unit). The (2S)-mandelate (mp 386.2K), orthorhombic, P2₁2₁2₁, a = 7.079(6), b = 13.443(10), c = 18.820(14)Å, Z = 4 is identical to a salt made from a combination of enantiomeric moieties from benzene solution. While differing from ephedrine mandelates in configuration at one center, solubilities of pseudoephedrine mandelates in 95% ethanol are much larger. A comparison of molecular structure (non-polar and H-bonding) regions of pseudoephedrine and ephedrine mandelates shows similarities and differences that are tentatively linked to crystal properties. This study reemphasizes the necessity for consistency in solvent use in resolution and in phase identification and comparison because the phases produced are frequently dependent upon the solvent. Chirality 10:325–337, 1998. © 1998 Wiley-Liss, Inc.     

Affinity to the Nicotinic Acetylcholine Receptor and Insecticidal Activity of Chiral Imidacloprid Derivatives with a Methylated Imidazolidine Ring

Four imidacloprid derivatives with an asymmetrically methylated imidazolidine ring were synthesized. Their affinity to the nicotinic acetylcholine receptor of housefly Musca domestica and insecticidal activity against the housefly were measured. The compound with a 5R-methylated imidazolidine ring demonstrated intrinsic activity comparable to that of the unsubstituted compound. Most of the compounds were synergized by oxygenase inhibitors.     

不同晶型甘氨酸在水中溶解度的测定与关联

不同晶型甘氨酸溶解度的测定对研究甘氨酸结晶及多晶型现象具有重要意义。采用激光动态法测定了15~80℃范围内α型和γ型甘氨酸在纯水中的溶解度数据,并且采用Apelb lat溶解度经验方程对实验数据进行了关联,回归了溶解度经验方程的参数,关联效果令人满意。实验结果表明,在水中α和γ甘氨酸溶解度均随温度升高而变大;在相同温度下,热力学亚稳的α型甘氨酸比稳态的γ型甘氨酸溶解度大。     

Relation between Electronic Structure and Hydroxylation of Aromatic Compounds by Microorganisms

The π-electron distribution of various aromatic compounds has been calculated by a molecular orbital method.

The reaction of hydroxylation was assumed to be radical type.

Relation between electronic structures and mono-hydroxylation of aromatic compounds by microorganisms was investigated.

A distinct parallelism was ruled out between the electronic structure and hydroxylation of aromatic compounds.

Hydroxylation of aromatic compounds occurred where the superdelocalizability Sr (R) showed large value.     

Adsorption of Five Model Organic Compounds on a Peat at Different Stages of Drying

Acridine orange (AO), dinitrobenzoic acid (DNB), bromocresol green (BCG), bromophenol blue (BPB), and methylene blue (MB) were chosen as model aromatic compounds of different polarity, charge, and solubility in water to examine the effects of solute properties on hydrophobic adsorption. These compounds show strict structural similarities to some herbicides and other potential xenobiotic pollutants and exhibit distinct absorption maxima in the visible region, which allows for their easy determination. A well-decomposed peat (medisaprist) at four different stages of drying was used to determine compound adsorption/desorption influences based on the degree of hydrophobicity and charge density of an organic surface. Adsorption and desorption isotherms were investigated using the batch equilibration method and determining the concentration of free chemicals by UV-Vis spectrophotometry. AO had a high tendency of adsorption and was strongly sorbed on peat samples that had been air-dried for 12 months. The lower Freundlich coefficient values found for MB when compared with AO at all the drying stages of the peat indicated that electrostatic attraction has a secondary contribution to sorption. On the contrary, the higher energy that must be spent to break solute-solvent interactions in the case of charged or polar molecules is one of the main factors in determining the position of the equilibrium. For a given solute, K_f values varied with the degree of hydrophobicity and the charge density of the surface, but again solute-solvent interactions appear to be much more important in the overall energy balance of hydrophobic pollutants than the electrostatic sorbate-sorbent interactions. A change in the solution pH does not improve the adsorption of the relatively polar DNB molecule, but sorption increases strongly for BCG and BPB when these molecules are in non-dissociated forms. The larger increase in BPB sorption observed on H⁺ saturated peat suggests that the degree of interaction increases with the suppression of the negative charge, but charge repulsion has a small effect in preventing adsorption of molecules bearing hydrophobic groups such as BCG. Desorption results differed depending on the chemical structure of the compound examined. For example, with AO there was no desorption from the more hydrophobic peat surfaces. A negative hysteresis was observed for DNB; the magnitude of hysteresis, evaluated using the ratio of Freundlich coefficients for adsorption and desorption, increased with the drying stage of the sorbent and was larger on oven-dried samples.     

Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.)

Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis depicts the involvement of six amino acids in hydrogen bonding (AGP-SThr422-AGP-LMet138, AGP- SArg420-AGP-LGly47, AGP-SSer259-AGP-LSer306, AGP-SGlu241-AGP-LIle311, AGPSGln113- AGP-LGlu286 and AGP-SGln70-AGP-LLys291). Fifteen amino acids of small subunit were able to make hydrophobic contacts with seventeen amino acids of large subunit. Furthermore, decrease in the solvent accessible surface area in the amino acids involved in interaction were also reported. All the distances were formed in between 2.27 to 3.78Å. The present study focussed on heterodimeric structure of (AGPase). This predicted complex not only enhance our understanding of the interaction mechanism between these subunits (AGP-L and AGP-S) but also enable to further study to obtain better variants of this enzyme for the improvement of the plant yield.     

Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations, we investigate the preferential binding of metal ion such as Na⁺ and molecular ions such as tetramethyl ammonium (TMA⁺) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO⁺) to double-stranded DNA. The thermodynamic driving force for a particular molecular ion-DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO⁺. The ion binding processes are found to be entropically favourable. In addition, the contribution of hydrophobic effects towards the entropic stabilisation (in case of TMA⁺) and the effect of hydrogen bonding contributing to enthalpic stabilisation (in case of CHO⁺) have also been investigated.     

Internal Water Molecules as Mobile Polar Groups for Light-Induced Proton Translocation in Bacteriorhodopsin and Rhodopsin as Studied by Difference FTIR Spectroscopy

FTIR spectroscopy is advantageous for detecting changes in polar chemical bonds that participate in bacteriorhodopsin function. Changes in H-bonding of Asp85, Asp96, the Schiff base, and internal water molecules around these residues upon the formation of the L, M, and N photo-intermediates of bacteriorhodopsin were investigated by difference FTIR spectroscopy. The locations and the interactions of these water molecules with the amino acid residues were further revealed by use of mutant pigments. The internal water molecules in the cytoplasmic domain probably work as mobile polar groups in an otherwise apolar environment and act to stabilize the L intermediate, and carrying a proton between the Schiff base and the proton acceptor or donor. Similar internal water molecules were shown to be present in bovine rhodopsin.     

Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation

Solvation energy calculation is one of the main difficulties for the estimation of protein-ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein-ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of protein-ligand binding free energy predictions. The ASP set, designed to handle both proteins and organic compounds and derived from experimental n-octanol/water partition coefficient (log P) data, contains 100 atom types (united model that treats hydrogen atoms implicitly) or 119 atom types (all-atom model that treats hydrogen atoms explicitly). By using this unified ASP set, an algorithm was developed for solvation energy calculation and was further integrated into a score function for predicting protein-ligand binding affinity. The score function reproduced the absolute binding free energies of a test set of 50 protein-ligand complexes with a standard error of 8.31 kJ/mol. As a byproduct, a conformation-dependent log P calculation algorithm named ASPLOGP was also implemented. The predictive results of ASPLOGP for a test set of 138 compounds were r = 0.968, s = 0.344 for the all-atom model and r = 0.962, s = 0.367 for the united model, which were better than previous conformation-dependent approaches and comparable to fragmental and atom-based methods. ASPLOGP also gave good predictive results for small peptides. The score function based on the ASP model can be applied widely in protein-ligand interaction studies and structure-based drug design.     

单氰胺对葡萄休眠过程中冬芽水分和碳水化合物的影响

以酿酒葡萄品种'赤霞珠'和'霞多丽'为材料,对其冬芽休眠进程和休眠过程中冬芽水分和碳水化合物含量的变化进行分析.结果表明,(1)在陕西杨陵地区气候条件下,'霞多丽'、'赤霞珠'分别在12月20日和1月9日达到深度休眠,随后开始休眠解除阶段.(2)在芽休眠过程中,两个品种冬芽的总水分含量、自由水含量和淀粉含量均随休眠的加深而降低,随休眠的解除而增加,而冬芽的束缚水含量、束缚水/自由水比值、可溶性糖含量均在休眠加深阶段持续上升,在休眠解除阶段逐渐降低.(3)单氰胺处理后,两品种冬芽中自由水含量显著增加,束缚水的比例同时显著降低,且'赤霞珠'的变化幅度大于'霞多丽',但其总水分、可溶性糖和淀粉等含量在休眠过程中无显著变化.(4)葡萄冬芽中的水分含量及存在状态、可溶性糖含量和淀粉含量的变化与其休眠进程密切相关;单氰胺处理能够增加冬芽自由水含量,降低其束缚水含量,从而有效打破葡萄休眠.     

HIV-1整合酶核心区野生型和F185K突变型活性和溶解性的比较及分子动力学模拟分析

表达纯化了野生型(WT)及F185K突变型HIV-1整合酶核心区蛋白(IN_C),并对二者的溶解性和活性进行了比较．实验结果表明：F185K 突变后IN_C溶解性显著提高,活性有一定程度降低．对WT和F185K IN_C体系进行了1800 ps的分子动力学模拟．模拟结果表明：F185K IN_C功能loop区柔性和蛋白质整体运动性降低,使蛋白质活性降低,F185K突变后盐桥网络的变化驱动了IN_C局部构象改变,引起IN_C表面的部分疏水残基被包埋,亲水残基暴露,相对亲水溶剂可接近面积增大,同时,突变后IN_C与水之间形成氢键的数量增加,与水之间作用加强,以上变化使IN_C溶解性提高．分子动力学模拟与实验结果相吻合．为理解蛋白质溶解性和对蛋白质进行可溶性改造提供了一定的理论依据．     

Solubility of proteins

A theory is presented on the solubility of proteins, in the hydrated as well as in the dry state, and in water as well as in organic solvents. To this effect, colloidal stability is assimilated with the solubility of the proteins, considered as hydrated entities. By means of a surface thermodynamic approach it can be shown that an increase in size of a hydrated protein must lead to insolubility, even in the absence of any change in a protein's surface properties. This can be substantiated experimentally by comparing the surface properties of immune complexes with those of their constituent immunoglobulins, as well as by comparing some of the properties of intact tobacco mosaic virus with those of its monomeric capsid subunits. Insolubilization of proteins by means of charge interactions as well as by dehydration is studied; an explanation is given of why precipitation caused by charge interactions is more likely to lead to partial irreversible denaturation than precipitation caused by protein-protein interactions brought about by partial dehydration (e.g., by salting-out). A link is established between the smallness (or even the negative value) of the interfacial tension between given proteins and various solvents and their solubility in these solvents. The energy of hydration of proteins can also be measured, and the differences between the free energies of interaction of dried and hydrated proteins with water point toward the additional processes underlying the solubilization, i.e., toward the conformational change of a protein in the process of becoming hydrated. The parameter of conformational change of a protein, while becoming hydrated, appears to be more closely linked to its degree of hydration than to its hydration energy.     

Conserved positions for ribose recognition: importance of water bridging interactions among ATP,ADP and FAD-protein complexes

Analysis of the spatial arrangement of protein and water atoms that form polar interactions with ribose has been performed for a structurally non-redundant dataset of ATP, ADP and FAD-protein complexes. The 26 ligand-protein structures were separated into two groups corresponding to the most populated furanose ring conformations (N and S-domains). Four conserved positions were found for S-domain protein-ligand complexes and five for N-domain complexes. Multiple protein folds and secondary structural elements were represented at a single conserved position. The following novel points were revealed: (i) Two complementary positions sometimes combine to describe a putative atomic spatial location for a specific conserved binding spot. (ii) More than one third of the interactions scored were water-mediated. Thus, conserved spatial positions rich in water atoms are a significant feature of ribose-protein complexes.     

PMR Study on the Absolute Structure of Kanamycins and Related Compounds

The antioxidant behaviors of vitamin E and its analogues, 2, 2, 5, 7, 8-pentamethyl-6-hydroxychroman and l, 2-diacyl-sn-glycero-3-phospho-2?-(hydroxyethyl)-2?, 5?, 7?, 8?-tetramethyl-6?-hydroxychro-man, were studied in unilamellar vesicles. The two analogues scavenged aqueous radicals generated from azo compounds more efficiently than vitamin E. On the other hand, vitamin E scavenged the lipid peroxyl radicals preferentially. It is concluded that the superior antioxidant activity of vitamin E is attributed to its location suitable for breaking the chain propagation reaction.     

北京土石山区典型植物水分来源

在季节性干旱区,水分是限制植物生长的关键因子.为了分析比较北京山区群落植物的水分利用特征,本文利用稳定同位素(D/H、¹⁸O/¹⁶O)技术,探讨典型群落植物侧柏、荆条、构树和胡枝子的水分来源及其对各水源的利用比率.结果表明: 群落内4种植物的水分来源不同,侧柏主要吸收利用40～60、60～80和80～100 cm深度的土壤水,对这3层的利用率在23.3%～25.9%,对表层0～20和20～40 cm的利用率分别为12.3%和13.0%;荆条主要吸收利用60～80和80～100 cm深度的土壤水,利用率分别为51.9%和25.2%,对其他土壤水利用较少;构树主要吸收利用表层0～20 cm和20～40 cm土壤水,利用率分别为47.5%和36.8%;胡枝子对5个水源层水分均有利用,对0～20、20～40和40～60 cm深度土壤水的利用率在21.4%～22.8%,对60～80和80～100 cm深度土壤水的利用率分别为15.2%和18.3%.侧柏和胡枝子的水分利用深度相似,两个树种混交可能会造成较大的水分竞争;荆条和构树的水分利用深度恰好互补,适宜混交.研究结果可为恢复受损生态环境的最佳植物种组合方式提供参考.