An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

分子力场进展

分子力学（简称ＭＭ）是近年来化学家常用的一种计算方法。与量子力学从头计算和半经验方法相比，用分子力学处理大分子可以大大节省计算时间，而且，在大多数情况下，用分子力学方法计算得到的分子几何构型参数与实验值之间的差值可在实验误差范围之内。所以，分子力学是研究生物化学体系的有效和可行的手段。分子力学的核心是分子力场。本文介绍了分子力场的量子力学背景、分子力场和光谱力场之间的关系。分子力场的一般形式、分力     

土壤中烃类污染物的超临界流体萃取

采用超临界流体萃取技术提取环境样品中的烃类污染物，以色谱－质谱联用仪测定了萃取物的化学成分，考察了影响萃取效率的主要因素。比传统的索氏萃取能更有效地从复杂环境样品中萃取分析物。     

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH₂)₂COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation. Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002     

Molecular mechanics (MM3) calculations on lithium amide compounds

The MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6-31G* and/or DFT (B3LYP/6-31G*, B3-PW91/6-31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations.     

Conformational analysis of 5,6-dihydropyrimidine and its derivatives

The equilibrium geometry and inversion barriers of 5,6-dihydropyrimidine, 6,7-dihydroazolopyrimidines with node nitrogen atoms and their alkyl (Me, Et, Prⁱ, Bu^t) and phenyl derivatives were calculated using a molecular mechanics approach. Annelation with azole cycles and the introduction of substituents have a slight effect on the equilibrium conformation of the dihydrocycle (distorted sofa). Alkyl substutuents at saturated carbons have an essentially equatorial orientation in 5,6-dihydropyridimine derivatives and are axial in the annelated analogs. On the other hand, the equatorial conformers are more stable in phenyl derivatives of dihydroazolopyrimidines. Factors determining the relative stability of conformers were analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 487–491, March, 1995.     

磺酰胺类常咯啉的分子力学参数的确定

应用量子化学ＭＮＤＯ程序及分子力学ＭＭＰ２程序，确定了一些未知磺酰胺类常咯啉的分子力学参数。应用这些参数计算了几个晶体结构已知的磺酰胺类化合物，与真实结构比较，计算结果令人满意。由此说明确定的分子力学参数用于计算磺酰胺类化合物时的正确性和可行性。     

The complete symmetrization of quantum operators: new thoughts on an old problem

The complete symmetrization with respect to x, p _x,... of the operators associated with dynamical properties can sometimes lead to results different from those obtained by the conventional quantum formalism based on the rule op (A ²)=(op A)². For example, angular momentum operators M _z ² and M ² are modified by the additive constants ²/2 and 3 ²/2 respectively (M ²0 for electron in the ground state of H atom, rotator never at rest, but spectra unchanged); the average quadratic dispersion of energy is different from zero. These results can be interpreted by assuming that the system is never strictly isolated but communicates with the other systems of the universe by means of electromagnetic interactions. Quantum mechanics would give only average values over a sufficiently long time and would exhibit a quasi-ergodic character. Examples supporting this possibility are given, in particular that of arsines for which quantum forecasts correspond to average values over one year.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

Analysis of trace elements and their physico-chemical forms in natural waters

Trace elements in natural waters can be present in different physico-chemical forms, varying in size, charge and density properties. Knowledge of speciation is essential for understanding the transport, distribution, and biological uptake of trace elements in the environment. The development of techniques to provide reliable information on physico-chemical forms has, therefore, become a challenge within Analytical Chemistry.When selecting analytical methods for the determination of total concentrations or fractions of trace elements in natural waters, no exclusion of species should occur, or at least it must be accounted for. Furthermore, the determination limits must be sufficiently low to allow the actual concentrations to be determined with reasonable precision and accuracy. For very low concentrations, preconcentration techniques are applicable, provided the chemical yield of the spike represents that of the original species present. For methods meeting these criteria, the suitability for routine analysis should be considered.When the physico-chemical forms of trace elements are to be determined, the fractionation should take placein situ or shortly after sampling. As the concentrations involved in speciation studies may be extremely low, there is an increasing awareness of potential sources of errors influencing analytical results. Sample collection and separation/fractionation/concentration procedures prior to analysis are, therefore, essential within Analytical Chemistry, and the whole procedure must be taken into account when interpreting the results. There are, however, several requirements which should be met by techniques applicable for speciation purposes. In general, size fractionation techniques (e.g.in situ hollow fibre ultrafiltration) should be applied prior to the addition of any chemical reagents (charge fractionation techniques).     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.