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1.
Roman G. Efremov Gérard Vergoten Alexander S. Arseniev 《Theoretical chemistry accounts》1999,101(1-3):73-76
We present a “hydrophobic template” method enabling recognition of α-helix bundles in membrane channels from sequence analysis.
Inspection of hydrophobic properties of pore-forming helices in proteins with known structure (A-B5 toxins) permits delineation of a common polarity motif: two hydrophobic surface stretches separated by polar areas. The bundles
are stabilized by nonpolar interhelical contacts. A number of transmembrane segments were checked for presence of this motif,
and it was detected for pore-forming helices of several ion transporters (segments M2 of acetylcholine and GABAA receptors, α5 peptide of δ-endotoxin), which reveal five α-helix bundle architecture. Applications of the method to modeling
of membrane channels are discussed.
Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998 相似文献
2.
Tru Huynh Gabriel Musat Jean-Michel Neumann Jeremy C. Smith Alain Sanson 《Theoretical chemistry accounts》1999,101(1-3):82-86
Annexin molecules consist of a symmetrical arrangement of four domains of identical folds but very different sequences. Nuclear
magnetic resonance (NMR) experiments on the isolated domains of annexin I in aqueous solution have indicated that domain 1
retains its native structure whereas domain 2 unfolds. Therefore these two domains constitute interesting models for comparative
simulations of structural stability using molecular dynamics. Here we present the preliminary results of molecular dynamics
simulations of the isolated domain 1 in explicit water at 300 K, using two different simulation protocols. For the first,
domain 1 was embedded in a 46 ? cubic box of water. A group-based non-bonded cut-off of 9 ? with a 5–9 ? non-bonded switching
function was used and a 2 fs integration step. Bonds containing hydrogens were constrained with the SHAKE algorithm. These
conditions led to unfolding of the domain within 400 ps at 300 K. In the second protocol, the domain was embedded in a 62 ?
cubic box of water. An atom-based non-bonded cut-off of 8–12 ? using a force switching function for electrostatics and a shifting
function for van der Waals interactions were used with a 1 fs integration step. This second protocol led to a native-like
conformation of the domain in accord with the NMR data which was stable over the whole trajectory (∼2 ns). A small, but well-defined
relaxation of the structure, from that observed for the same domain in the entire protein, was observed. This structural relaxation
is described and methodological aspects are discussed.
Received: 10 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
3.
Molecular mechanics calculations were performed with the JUMNA program on d(GCGTGOGTGCG) · d(CGCACTCACGC) where “O” is a
modified abasic site: 3-hydroxy-2-(hydroxymethyl)tetrahydrofuran. From energy minimizations, for intrahelical or extrahelical
positions of the unpaired thymine, various structures with different curvatures were obtained. Dynamical properties of this
abasic sequence were also investigated through the controlled studies of DNA bending. Poisson-Boltzmann calculations were
used to mimic the electrostatic effect of solvent on this sequence. The lowest energy structures show an acceptable agreement
with experimental data.
Received: 1 June 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998 相似文献
4.
Roman G. Efremov Dmitry E. Nolde Gérard Vergoten Alexander S. Arseniev 《Theoretical chemistry accounts》1999,101(1-3):170-174
A recently developed implicit solvation model is applied to Monte Carlo simulations of peptides in bilayer-mimetic and polar
environments. The model employs the formalism of atomic solvation parameters and reproduces experimental data. Solvent effects
on the␣structure of the following peptides were studied: 20-residue poly-Leu and poly-Val, transmembrane helix A of bacteriorhodopsin,
magainin2. It was shown that a␣membrane-like environment considerably promotes α-helix formation (all the peptides were found
to be α-helical), while simulations in water reveal helix distortion. Consistency of the results with experimental data and
further implications of the model are discussed.
Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998 相似文献
5.
H. O. Bertrand A. Pullman K. Zakrzewska B. Hartmann S. Fermandjian 《Theoretical chemistry accounts》1999,101(4):269-273
Phosphorothioate DNAs, have emerged as a new class of potent drugs. They are obtained by the replacement of the anionic oxygens
of the phophodiester backbone by sulphur. A set of parameters has been developed for the FLEX force field implemented in JUMNA
10.0 to take into account the influence of sulphur on the structure of the DNA double helix. The consistency of our parameters
was tested by modelling a phosphorothioate oligomer namely d(GC)8. d(GC)8. Results, obtained on both R-pS and S-pS diastereoisomers, were compared to the phosphodiester counterpart and are in agreement with available experimental data.
Thus, our set of parameters seems suitable for further molecular modelling of other phosphorothioate oligomers.
Received: 15 July 1998 / Accepted: 8 September 1998 / Published online: 10 December 1998 相似文献
6.
Gerald Löffler 《Theoretical chemistry accounts》1999,101(1-3):163-169
We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the
electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic
potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for
the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant,
conformational flexibility and solvation effects on the electrostatic potential at these eight points.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998 相似文献
7.
Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability
of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular
systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results
are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared
deviations from experimental structures and now provide believable structural insight into a variety of processes such as
the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation
and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate
to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald
methods are becoming the de facto standard.
Received: 9 April 1998 / Accepted: 21 May 1998 / Published online: 13 August 1998 相似文献
8.
To obtain a highly selective material for the antibiotic chloramphenicol, which has several harmful side effects in humans,
different molecularly imprinted polymers (MIPs) were prepared. In order to avoid a major traditional drawback associated with
MIPs of residual template bleeding, molecules that are structurally related to chloramphenicol were used as templates for
polymer synthesis. Chromatographic evaluation indicated that the employed template imparted a significant influence on the
recognition properties of the corresponding polymer. A strong retention of chloramphenicol under nonpolar elution conditions
(k = 68.03, IF = 17.72) and under aqueous elution conditions (k = 92.44, IF = 1.35) was achieved. After chromatographic evaluation, the MIP was utilized as the recognition sorbent in a
solid-phase extraction to determine chloramphenicol using either an organic or aqueous washing solvent. Recoveries of nearly
100% from the chloramphenicol standard solution and nearly 90% from honey samples spiked with chloramphenicol were attained.
Furthermore, the applicability of the MIP for sample cleanup was demonstrated. 相似文献
9.
Krzysztof A. Olszewski Lisa Yan David J. Edwards 《Theoretical chemistry accounts》1999,101(1-3):57-61
SeqFold is a fold recognition program based on sequence-similarity detection aided by predicted secondary structure [1–3].
Critical validation and evaluation of SeqFold fold recognition performance based on the latest Critical Assessment of protein
Structure Prediction (CASP2) targets has been performed. It has revealed that four out of seven CASP2 threading targets were
assigned a correct fold using this method. SeqFold has also been applied to the problem of fold recognition for leptin. Mice
with a defective leptin gene are extremely obese and diabetic. Leptin does not exhibit clear sequence homology to any protein
with known structure. SeqFold predicts that leptin belongs to the class of short-chain four-helical cytokines. The structure
of leptin, which has recently been solved by X-ray crystallography, reveals that leptin is a long-chain four-helical cytokine.
The 3D model of leptin demonstrates that SeqFold alignment-based homology modeling captures essential features of the leptin
structure.
Received: 25 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
10.
Jianwei Che Tahir Çağın William A. Goddard III 《Theoretical chemistry accounts》1999,102(1-6):346-354
We present a general approach for describing chemical processes (bond breaking and bond formation) in materials using force
fields (FF) that properly describe multiple bonds at small distances while describing nonbond (Coulomb and van der Waals)
interactions at long distances. This approach is referred to as the generalized extended empirical bond-order dependent FF.
In this paper we use the Brenner empirical bond-order dependent FF for the short-range interactions and report applications
on the energetics and structures of graphite crystal, dynamics of molecular crystals, and distortions of bucky tubes.
Received: 7 August 1998 / Accepted: 26 October 1998 / Published online: 16 March 1999 相似文献
11.
The molecular structures of the model systems of the polaron and the bipolaron in poly-para-phenylene (PPP) were calculated
by an ab initio molecular orbital (MO) method with fairly sophisticated approximations. The calculated models are monocations,
dications, monoanions and dianions of biphenyl, para-terphenyl, para-quaterphenyl, para-quinquephenyl and para-hexaphenyl.
The calculations show that the longer the PPP oligomer is, the stronger is the tendency to take on a non-planar twisting structure.
This was accounted for by the combination of repulsions between proximate ortho-hydrogen atoms with resonance interactions
between benzene π MOs. The magnitude of the resonance interactions was assessed by using the symmetry of benzene π MOs as
well as an analytical Hückel solution of the π MO for polyene. In addition, negatively charged polarons and bipolarons were
found to have a stronger tendency to take on a planar structure than positively charged ones. This result was also explained
by comparing the benzene π HOMO with the benzene π LUMO.
Received: 30 June 1998 / Accepted: 9 September 1998 / Published online: 23 February 1999 相似文献
12.
A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras
and Morokuma that is used to perform combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations,
frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology
is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and
MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be
cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We
describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system,
thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to
perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have
examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability
of thermochemical data derived from IMOMM frequency calculations.
Received: 11 May 1998 / Accepted: 14 August 1998 / Published online: 16 November 1998 相似文献
13.
The rational function optimization algorithm is one of the widely used methods to search stationary points on surfaces. However,
one of the drawbacks of this method is the step reduction procedure to deal with the overstepping problem. We present and
comment on a method such that the step obtained from the solution of the rational function equations possesses the desired
correct length. The analysis and discussion of the method is mainly centered on the location and optimization of transition
states.
Received: 18 June 1998 / Accepted: 17 September 1998 / Published online: 23 November 1998 相似文献
14.
A large-scale one-centre expansion with a radial B-spline basis set is implemented for bound and continuum states. A Kohn-Sham
hamiltonian is employed with Hartree and exchange-correlation potentials calculated from the SCF electron density taken from
a previous LCAO calculation. An inverse iteration method is used to obtain the continuum wavefunction, from which the cross
section and asymmetry parameter are calculated. The convergence with respect to angular momentum and cut-off radius is analysed
for N2. The relevance of multipolar contributions even at large distances is shown and suggestions for further improvements are
given. In order to show that the present method is suitable to treat systems of moderate size, the (CH3)3N molecule has also been calculated and the results are compared with experiment.
Received: 19 May 1998 / Accepted: 20 August 1998 / Published online: 7 December 1998 相似文献
15.
D. Sy C. Durand S. Hugot C. Savoye C. Swenberg M. Charlier M. Spotheim-Maurizot 《Theoretical chemistry accounts》1999,101(1-3):114-120
Sequence-dependent variations of DNA structure modulate radiation-induced strand breakage. Thiols reduce breakage by scavenging
damaging radiolytic OH
.
and repairing sugar radicals. As shown by sequencing gel electrophoresis, WR-1065 radioprotection is modulated by sequence,
whereas that of WR-151326, a larger thiol, is more evenly distributed. Molecular modelling was performed on complexes of a
53 bp oligonucleotide (belonging to a natural restriction fragment) with one molecule of WR-1065 or WR-151326. Energy minimised
structures exhibit a broadening of the minor groove of an AAATT motif upon WR-1065 binding, and a narrowing of the groove
upon WR-151326 binding. Consequently, the accessibility to OH˙ of H4′ (whose abstraction leads to strand breakage) increases near WR-1065, whereas it decreases near WR-151326. This modifies
locally the otherwise homogeneous radioprotection. The effect of WR-151326 strengthens the protection at all tested binding
sites, whereas that of WR-1065 diminishes it in some regions, in good agreement with the observed radioprotection distribution.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 11 November 1998 相似文献
16.
Whether a semiconductor has a direct or an indirect band gap is important in determining physical properties such as photoconductivity
and electroluminescence. For one-dimensional conjugated polymeric semiconductors, as well as organic molecular crystals, we
show how the band gap type (direct or indirect) is determined by the shapes of the HOMO and the LUMO of constituent monomeric
conjugated molecules. The connectivity of the monomer units, and the topology of orbital interaction determine the band gap
type. Pairing symmetry in the π electronic system of even alternant hydrocarbons allows the immediate prediction of the band
gap type, direct or indirect, by examining only the structures of the monomer units and their connectivity in polymers or
molecular stacks.
Received: 29 June 1998 / Accepted: 3 September 1998 / Published online: 8 February 1999 相似文献
17.
Renato Colle Raffaele Montagnani Oriano Salvetti 《Theoretical chemistry accounts》1999,101(4):262-268
A molecular fragment approach is used to compute ionization potentials, transition energies and electron affinities of pyrrole
oligomers. The calculations of these quantities include correlation energy contributions evaluated by integrating a functional
of the two-particle Hartree-Fock density matrix. Pyrrole oligomers with chains of up to 16 rings are explicitly treated and
the calculated quantities extrapolated to the limit of an infinitely long chain, to predict polymer properties. The theoretical
results compare favorably with data on gas-phase ionization potentials deduced from experimental oxidation potentials, and
with optical absorption peaks recorded in solution or on solid films. The large discrepancy between electron affinities obtained
from the eigenvalues of an independent-particle frozen-orbital calculation and those obtained from separate, correlated calculations
on the neutral system and the negative ion in shown.
Received: 24 March 1998 / Accepted: 2 September 1998 / Published online: 7 December 1998 相似文献
18.
A new method for the evaluation of one- and two-centre magnetic and electric multipole integrals for Slater-type functions
is presented. The method is strictly analytical in that no approximations of any kind are involved. Two simple functions,
ℐ1
aug and ℐ2
aug, are introduced, which employ only functions that are well known in electronic structure theory. With the use of augmentation
exponents these functions apply to multipole integrals as well as other one-electron integrals, such as nuclear attraction
integrals. The proposed method includes the analytic determination of derivatives of the integrals with respect to atomic
displacements. Some illustrative test calculations are presented and compared to results from the literature.
Received: 20 April 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999 相似文献
19.
Paul G. Mezey 《Theoretical chemistry accounts》1999,102(1-6):279-284
A simple proof is presented for a fundamental topological property of catchment regions of potential energy hypersurfaces:
each catchment region C(λ,i), representing a chemical species and its conformational range on the potential energy hypersurface, is simply k-connected for each dimension k=1,2,…3N−6−λ, where λ is the index of the catchment region. The consequences of this property on the structure of the fundamental
group of reaction mechanisms (the one-dimensional homotopy group of reaction paths) is discussed.
Received: 8 July 1998 / Accepted: 6 October 1998 / Published online: 23 February 1999 相似文献
20.
Interest in the transmembrane receptors tyrosine kinase of the erbB family is high due to the involvement of some of the
members in human cancers. The original oncogenic alleles of neu discovered in rat neuroectodermal tumors lead to single Val664Glu
substitution within the predicted transmembrane domain. Identical substitution at the homologous position 659 constitutively
activates the oncogenic potential of the human ErbB-2 receptor by enhanced receptor dimer formation. The precise molecular
details of receptor dimerization are still unknown and to acquire more knowledge of the mechanisms involved, molecular dynamics
simulations are undertaken to study transmembrane dimer association. Transmembrane helices are predicted to associate in left-handed
coiled-coil structures stabilized by Glu-Glu interhelix hydrogen bonds in the mutated form. The internal dynamics reveals
π helix deformations which modify the helix-helix interface. Predicted models agree with those suggested from polarized IR
and magic-angle spinning NMR spectroscopy.
Received: 24 April 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998 相似文献