A Monte Carlo simulation of chemical reactions

A computer-based algorithm to solve complex chemical rate equations is introduced. A simple Monte Carlo sampling method is used to generate chemical reactions in numbers proportional to reaction probabilities, and a second-order Runge-Kutta method is used to calculate time. The method is compared with a closed form mathematical solution for a simple chemical system, and it is compared with a numerical integration of the rate equations for a more complicated system.     

Differential analysis of major natural cytokinins by enzyme immunoassay

An immunochemical method for quantitative differential analysis of major types of natural cytokinins in plant tissues subjected to minimal treatment, without purification or chemical modification of hormones, is proposed. This method is recommended for use in biology, medicine, and agriculture for determination of low-molecular-weight compounds having similar chemical structures but various biological activities.     

匹拉米洞法、邻联甲苯胺法和联苯胺法检测林麝便隐血的比较

圈养林麝(Moschusberezovskii)长期受困于消化道类疾病,尤其是肠道炎症性疾病患病率和死亡率一直居高不下。粪便检测是评估野生动物消化系统是否存在出血情况的有效方法之一,并且在圈养林麝肠道健康状况评估及肠道炎症性疾病临床诊断等方面提供了一定的诊断依据。粪便隐血在消化道出血诊断中有广泛的临床诊断价值。基于此,本研究用新鲜的林麝血液进行稀释,来探究匹拉米洞法、邻联甲苯胺法和联苯胺法三种方法对林麝血液浓度的灵敏度范围。检测结果显示,匹拉米洞法的最低敏感性检测浓度为0.05 mg/L,敏感性范围远大于邻联甲苯胺法(0.40 mg/L)和联苯胺法(100.00 mg/L)。分别利用三种检测方法对林麝粪便潜血进行检测,比较检测结果的阳性率,结果显示,匹拉米洞法的检测效果优于其他两种方法,阳性率分别为匹拉米洞法检测法10.13%、邻联甲苯胺法检测法2.56%和联苯胺法检测法0,差异有诊断学意义(P <0.05)。而且在操作上,匹拉米洞法更加简便快捷。故在诊断林麝消化道出血时,采用匹拉米洞法进行林麝便隐血的检测更加准确便捷。     

Determination of the preferred tautomeric form histamine by 13C nmr spectroscopy.

The pH-dependent 13C chemical shifts for histamine indicate an approximate 4: 1 preference for the N-H tautomer of the imidazole ring, similar to that previously deduced for L-histidine. It is concluded that the 13C chemical shift method is a complimentary technique to the method of determining tautomer preference from pK values. Factors determining the tautomer preference in histamine and L-histidine are discussed.     

Validation of archived chemical shifts through atomic coordinates

The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per‐atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per‐entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries ( http://www.ebi.ac.uk/pdbe/nmr/vasco ) and hope this data will aid the development of new chemical shift‐based methods in NMR. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Prediction of peak overlap in NMR spectra

Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.     

Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information on the residual secondary structure elements in the acid-denatured state of an acyl-coenzyme A binding protein. This method reveals a clear correlation between the carbon secondary chemical shifts and the amide secondary chemical shifts 3-5 residues away in the primary sequence. These findings strongly suggest transient formation of short helix-like segments, and identify unique sequence segments important for protein folding.     

Direct observation of long-strand DNA conformational changing in microchannel flow and microfluidic hybridization assay

Conformational control of macromolecules is useful for efficient chemical and biochemical reactions. This article reports a direct observation method for macromolecules, such as long-strand DNA, in microchannel flow as well as a simple method for stretching DNA strands by microfluidics. Stretching and orientation of DNA molecules by control of flow within a microchannel was observed by optical microscopy. This DNA stretching is explained by coil-stretch transition of polymer molecules. This technique is useful for creating chemical reactions with macromolecules. It offers high selectivity and efficiency that are impossible to achieve in bulk solution. We also demonstrate that our microfluidic stretching method can accomplish efficient hybridization of long-strand DNA. This method will be useful for direct hybridization assay of long-strand DNA.     

Specific chemical labeling of DNA fragments.

We describe a simple method for specific chemical labeling of DNA fragments at their 3'-termini. The procedure includes enzymatic addition of 4-thiouridine, followed by reaction in mild non-denaturing conditions with the highly reactive alpha-haloacetamido derivatives of several chemical labels. The attached reporter molecule can be removed by extended treatment with beta-mercaptoethanol. Among the potential applications of this labeling method is the study of specific protein-DNA interactions in solution.     

植物-微生物联合修复化学农药污染土壤的研究进展

化学农药的高毒性、生物积累性和扩散性极易对环境及人类健康造成危害,环境中化学农药的去除尤为重要。植物-微生物联合修复技术因其高效、环境友好和修复成本低等优点受到越来越多的关注,植物-微生物联合修复化学农药污染土壤是一种很有前景的方法。植物为根际和内生细菌提供养分,而细菌通过化学农药的降解和解毒来支持植物生长。本文综述了影响化学农药在植物体内吸收和转运的因素以及植物-微生物修复技术的原理,并讨论了植物与微生物在化学农药污染土壤修复中的协同效应,并对植物-微生物联合修复法在化学农药污染土壤修复中的应用前景进行了展望。     

A combination method of chemical with enzyme reactions for identification of membrane proteins

A simple method for effective analysis of various proteins has been developed, including membrane proteins, with LC-MS/MS, using CNBr and acetic acid cleavage in one reaction for the digestion of both the M/ and /D/ positions within the target proteins. This dual chemical reaction has been compared with traditional CNBr or an acid cleavage method using a rat kidney membrane fraction and it showed an advantage of the dual reaction with respect to a high number of peptides detected and a high protein recovery. Furthermore, when this dual chemical reaction was combined with trypsin digestion, the number of proteins surprisingly increased approximately 3.0 times more than in the cases with the trypsin digestion only. It was also 1.9 times more than in cases dealing with Tube-Gel trypsin digestion, which is one of the most efficient digestion methods. In addition, it was shown that this dual chemical reaction could be applied to an in-gel digestion. Using the combination of the chemical and enzyme reaction, 172 proteins including 95 membrane proteins were identified. This indicated that this method is one of the efficient systems in single MS/MS analysis. In particular, many membrane proteins identified in this study were detected by a new combination, but not by a traditional trypsin digestion method.     

Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH

Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970–2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins. Temperature has a non-negligible effect on the ¹³C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary structure in disordered proteins.     

Statistical prediction of protein chemical interactions based on chemical structure and mass spectrometry data

MOTIVATION: Prediction of interactions between proteins and chemical compounds is of great benefit in drug discovery processes. In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability. RESULTS: We describe a novel method for predicting protein-chemical interaction using SVM. We utilize very general protein data, i.e. amino acid sequences, and combine these with chemical structures and mass spectrometry (MS) data. MS data can be of great use in finding new chemical compounds in the future. We assessed the validity of our method in the dataset of the binding of existing drugs and found that more than 80% accuracy could be obtained. Furthermore, we conducted comprehensive target protein predictions for MDMA, and validated the biological significance of our method by successfully finding proteins relevant to its known functions. AVAILABILITY: Available on request from the authors.     

A New Version of the Insertion Particle Method for Determining the Chemical Potential by Monte Carlo Simulation

A new version of the test particle method for determining the chemical potential by Monte Carlo simulations is proposed. The method, applicable to any fluid at any density, combines the Widom's test particle insertion method with the ideas of the scaled particle theory, gradual insertion method and multistage sampling. Its applicability is exemplified by evaluating the chemical potential of the hard sphere fluid at a very high density in semi-grand-canonical and grand-canonical ensembles. A theory estimating the efficiency (i.e. statistical errors) of the method is proposed and the results are compared with the Widom's and gradual insertion methods, and the analytic results.     

Some evidence of the nature of the Golgi-Cox deposit and its biochemical origin

Summary Evidence obtained from simple chemical tests suggests that the black deposit in Golgi-Cox impregnated nerve cells which have been submitted to alkalinisation is black mercuric sulphide. Some sulphydryl and disulphide containing compounds may prove to be useful chemical models for studying the mechanism of this histological method.     

Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins

Despite the many protein structures solved successfully by nuclear magnetic resonance (NMR) spectroscopy, quality control of NMR structures is still by far not as well established and standardized as in crystallography. Therefore, there is still the need for new, independent, and unbiased evaluation tools to identify problematic parts and in the best case also to give guidelines that how to fix them. We present here, quantum chemical calculations of NMR chemical shifts for many proteins based on our fragment-based quantum chemical method: the adjustable density matrix assembler (ADMA). These results show that (13)C chemical shifts of reasonable accuracy can be obtained that can already provide a powerful measure for the structure validation. (1)H and even more (15)N chemical shifts deviate more strongly from experiment due to the insufficient treatment of solvent effects and conformational averaging.     

HS-SPME-GC / MS 在大熊猫尿液化学成分检测中的应用

尿液在大熊猫化学通讯过程中具有重要作用。对大熊猫尿液中化学成分的检测是揭示大熊猫尿液中化学物质组成及其功能的关键。本实验通过使用顶空固相微萃取技术(Headspace-solid phase microextraction,HSSPME)对大熊猫尿液样品进行前期处理,继而利用气相色谱- 质谱联用技术(Gas chromatography-mass spectrometry,GC / MS)对大熊猫尿液中化学成分进行检测。共检测到56 个峰,通过在NIST (National Institute of Standards
and Technology)质谱库中进行检索,初步推定出其中的38 种物质。除此之外,还对HS - SPME 萃取头的净化方法进行了探索和改进。结果表明,顶空固相微萃取技术结合气相色谱- 质谱联用技术能够应用于大熊猫尿液中挥发性与半挥发性化合物的检测,并且能够得到较好的实验结果,为揭示大熊猫化学通讯机理提供基础。     

Melting of cross-linked DNA IV. Methods for computer modeling of total influence on DNA melting of monofunctional adducts, intrastrand and interstrand cross-links formed by molecules of an antitumor drug

A theoretical method is developed for calculation of melting curves of covalent complexes of DNA with antitumor drugs. The method takes into account all the types of chemical modifications of the double helix caused by platinum compounds and DNA alkylating agents: 1) monofunctional adducts bound to one nucleotide; 2) intrastrand cross-links which appear due to bidentate binding of a drug molecule to two nucleotides that are included into the same DNA strand; 3) interstrand cross-links caused by bidentate binding of a molecule to two nucleotides of different strands. The developed calculation method takes into account the following double helix alterations at sites of chemical modifications: 1) a change in stability of chemically modified base pairs and neighboring ones, that is caused by all the types of chemical modifications; 2) a change in the energy of boundaries between helical and melted regions at sites of chemical modification (local alteration of the factor of cooperativity of DNA melting), that is caused by all the types of chemical modifications, too; 3) a change in the loop entropy factor of melted regions that include interstrand cross-links; 4) the prohibition of divergence of DNA strands in completely melted DNA molecules, which is caused by interstrand cross-links only. General equations are derived, and three calculation methods are proposed to calculate DNA melting curves and the parameters that characterize the helix-coil transition.