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81.
Julie A. Braatz Michael B. Bass Rick L. Ornstein 《Journal of computer-aided molecular design》1994,8(5):607-622
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. 相似文献
82.
83.
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 相似文献
84.
O. V. Shishkin A. S. Polyakova S. N. Desenko D. V. Orlov S. V. Lindeman Yu. T. Struchkov 《Russian Chemical Bulletin》1995,44(3):470-474
The equilibrium geometry and inversion barriers of 5,6-dihydropyrimidine, 6,7-dihydroazolopyrimidines with node nitrogen atoms and their alkyl (Me, Et, Pri, But) 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. 相似文献
85.
André Julg 《Theoretical chemistry accounts》1988,74(4):323-330
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 相似文献
86.
Pablo A. Molina R. Steven Sikorski Jan H. Jensen 《Theoretical chemistry accounts》2003,109(3):100-107
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 Nδ1−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 Hɛ1 (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 Hδ1 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. 相似文献
87.
Ivan Bernal D. C. Levendis Richard Fuchs G. M. Reisner Juanita M. Cassidy 《Structural chemistry》1997,8(4):275-285
The crystal structure of 4-cyclopropylacetanilide was investigated at room temperature (21C) and at –100C in order to determine the orientation of the phenyl ring with respect to the cyclopropane moiety and the effect of this substituent on the stereochemistry of the three-membered ring. The compound was chosen because it is one of the few species containing a simple phenyl ring as the sole cyclopropane ring substituent and whose crystals are suitable for X-ray diffraction at room temperature. The substance crystallizes in space groupP2l/c at either temperature (no phase transitions) with cell constants: (at 21C)a=9.725(2),b=10.934(3), andc=9.636(2) å,=106.13(1);V=984.21 å3 andd(calc;z=4)=1.182 g cm–3. The relevant parameters for the –100C structure area=9.557(4),b=10.980(2), andc=9.641(2) å,=106.34(3);V=970.76 å3 and d(calc;z=4)=1.199 g cm–3. Final values wereR(F)=0.042, Rw=0.035, using unit weights, and its nonhydrogen atoms were used to phase the low-temperature data, whose final discrepancy indices wereR(F)=0.051,R
w
=0.061. The phenyl substituent is almost exactly in the bisecting conformation with respect to the C-C-C angle at the point of attachment to cyclopropane and conjugative effects are clearly evident in the lengths of the cyclopropane ring [1.494(3), 1.498(3), and 1.474(4) å, the later being the distal bond]. If one omits the terminal methylene fragments at C10 and C11, the atoms comprising the acetanilide fragment and the substituted carbon of the cyclopropane ring lie in a nearly perfect plane. Molecular mechanics as well as semiempirical (AM1) calculations were carried out in order to determine the structure of the energy-minimized configurations in the two computational environments. The molecular conformations thus obtained are close to that experimentally observed from the X-ray diffraction experiment. In both theoretical models, the lowest energy conformation is that in which the plane of the phenyl ring bisects the cyclopropane C-C-C angle as was experimentally observed. Finally, the shape of the conformational barrier as a function of the orientation of the plane of the phenyl ring was computed, giving a maximum barrier to rotation of 2.2 kcal/mol. Similar calculations were carried out for two other aryl cyclopropanes, whose rings (naphthalene and anthracene) cannot adopt the bisecting position. Comparisons of experimental geometrical parameters as well as of the barriers to rotation are presented.on leave at the University of Houston, 1995–1996. 相似文献
88.
通过分子模拟方法研究了手性金属配合物[Rh(bpy)2Chrysi]^3+(bpy=2,2’-bipyridineChrysi=5,6-chrysenequinonediimine)对包含C:T错配碱基对的B-DNA序列的识别作用.结合类似的针对含G:A错配的和正常的B-DNA序列的识别作用研究,发现配合物I-Rh(bpy)zChrysi]^3+可以对错配B-DNA序列进行序列特异性的识别.能量对比计算结果表明,该经典插入识别作用倾向于在错配碱基对附近进行,其中△-[Rh(bpy)2chrysi]^3+比其手性异构体更占优势.这同Barton教授工作组的实验结果是一致的.另外插入作用倾向于在错配序列中的正常双碱基对C3A4/G3T4(错配碱基对附近)中从小沟进行.与该配合物对含G:A错配的和正常的B-DNA序列的识别作用不同的是,对包含C:T错配碱基对的B-DNA序列的识别作用倾向于从小沟进行.这一点可能源于C:T碱基对结构的不同. 相似文献
89.
We expose and discussPenrose's thesis: Nature produces harnessable noncomputable processes, but none at the classical level. We then suggest a partial counterexample to it, based on aGedanken experiment about an undecidable family of integrable Hamiltonian systems that could lead to a sort of idealized solution to the Halting problem for Turing machines.1. Partially supported by a Fulbright/CNPq-Brazil grant. Permanent address after November 5, 1990: Center for the Study of Mathematical Theories of Communication, IDEA/School of Communications, Federal University of Rio de Janeiro, Av. Pasteur 250, 22290 Rio de Janeiro, RJ Brazil. 相似文献
90.
Marek Czachor 《Foundations of Physics Letters》1991,4(4):351-361
A mobility phenomenon is typical for a large class of non-linear evolutions. It is shown that the mobility can be responsible for a malignant form of quantum mechanical non separability of two correlated systems. An explicit example based on Weinberg's non linear quantum mechanics is considered. We show that in such a theory a transfer of information without a transfer of energy is possible and discuss physical roots of this phenomenon. In Polchinski's approach this effect is not present.1 Permanent address: Laboratory of Dielectrics and Organic Semiconductors, Technical University of Gdask, Gdask, Poland. 相似文献