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PubMedDate not supplied

[Modeling of the 3D structure of the HIV-Haiti immunodominant epitope].

The 3D structure for the HIV-Haiti immunodominant epitope was computed in terms of NMR spectroscopy data using the theoretical procedure including a probabilistic approach in conjunction with molecular mechanics algorithms and quantum chemical methods. The immunogenic crown of the virus protein gp120 was shown to form in solution a prevalent conformation whose geometric parameters match the double beta-turn IV-IV. Two structures observed in crystal were found in the ensemble of the best-energy conformations of the HIV-Haiti principal neutralizing epitope. From a comparison of simulated structures with those computed previously for the HIV-Thailand and HIV-MN isolates, it was concluded that the immunogenic tip of gp120 gives rise to similar spatial backbone forms in different HIV-1 strains but has some inherent conformational flexibility of its individual amino acid residues. The differences in local fragment structures revealed in three isolates of HIV-1 are supposed to be important for the specificity of its binding with neutralizing antibodies.

Computational Biology↗
PubMed2006

Extension of molecular electronic structure methods to the solid state: computation of the cohesive energy of lithium hydride.

We describe a simple strategy for calculating the cohesive energy of certain kinds of crystal using readily available quantum chemistry techniques. The strategy involves the calculation of the electron correlation energies of a hierarchy of free clusters, and the cohesive energy E(coh) is extracted from the constant of proportionality between these correlation energies and the number of atoms in the limit of large clusters. We apply the strategy to the LiH crystal, using the MP2 and CCSD(T) schemes for the correlation energy, and show that for this material E(coh) can be obtained to an accuracy of approximately 30 meV per ion pair. Comparison with the experimental value, after correction for zero-point energy, confirms this accuracy.

Algorithms↗
PubMedDate not supplied

[Cell molecular computer. VII. Cell biophysics and realistic or information physics (1)].

Living organisms measure many parameters in order to have orientation in the outer medium. That is why biophysics cannot use the ordinary laws of physics and must take into account the influence on the phenomena to be studied not only of a measurement but also of a calculation process in the real physical and biophysical device predicting the future. Science taking into account the effects of the calculating process-realistical or informative (RI) physics-has different (laws) for different times, distances and numbers of measuring and predicting parameters. RI-physics deals with unreproducible events and considers only such time intervals and distances for which the prediction can be made on the basis of earlier measurements and calculations according to the laws with optimal difficulty. It is suggested that the living cell uses the laws which are close to these optimal (limiting) laws of RI-physics. Physics and quantum mechanics can be considered as a limiting case of RI-physics. In this case values of distances and times are large enough and the number of simultaneously measured independent parameters is such that the heat effect of the calculating device would become negligible. Molecular cell computer (MCC) [I] cannot calculate the interaction of a great quantity of different molecules, using the equations of quantum mechanics because the expense of the (price of action) would be very large and both MCC and the surrounding world could change.

Cell Physiological Phenomena↗
PubMed2006

How the stabilization of INK4 tumor suppressor 3D structure evaluated by quantum chemical and molecular mechanics calculations corresponds well with experimental results: interplay of association enthalpy, entropy, and solvation effects.

The folding free energy of the INK4c tumor suppressor core, consisting of 10 helices, was determined as the sum of gas-phase interaction enthalpy, gas-phase interaction entropy, and dehydration and hydration free energy. The interaction energy and the hydration free energy were determined using the nonempirical density functional theory (DFT) method, augmented by a dispersion-energy correction term, the semiempirical density-functional tight-binding method covering the dispersion energy, and the density functional theory/conductor-like screening model (DFT/COSMO) procedure, whereas the interaction entropy was calculated with the empirical Cornell et al. force field. Alternatively, all contributions were evaluated consistently using empirical methods. All the values of the interaction energy of helix pairs are stabilizing, and the dominant stabilizing terms stem from the London dispersion energy and, in the case of charged systems, the electrostatic energy. The stabilization energy of the core, determined as the difference of the energy of the core and 10 separate helices, amounts to approximately 450 kcal/mol. Systematically, the difference in the hydration free energy of a helix pair and its separate components is smaller in magnitude than the interaction energy, and it is negative for some pairs while positive for others. The average total free energy of a core formation amounts to -29.6 kcal/mol (yielded by scaled quantum-chemical methods) and +13.9 kcal/mol (resulting from empirical methods). These values are considerably smaller than their single components, which are dominated by the interaction energy. The computationally predicted interval encloses the experimental value of the folding free energy (-2.8 kcal/mol).

Amino Acid Motifs↗
PubMed2005

Quantum-dot-based cell motility assay.

Because of their favorable physical and photochemical properties, colloidal CdSe/ZnS-semiconductor nanocrystals (commonly known as quantum dots) have enormous potential for use in biological imaging. In this report, we present an assay that uses quantum dots as markers to quantify cell motility. Cells that are seeded onto a homogeneous layer of quantum dots engulf and absorb the nanocrystals and, as a consequence, leave behind a fluorescence-free trail. By subsequently determining the ratio of cell area to fluorescence-free track area, we show that it is possible to differentiate between invasive and noninvasive cancer cells. Because this assay uses simple fluorescence detection, requires no significant data processing, and can be used in live-cell studies, it has the potential to be a powerful new tool for discriminating between invasive and noninvasive cancer cell lines or for studying cell signaling events involved in migration.

Adenocarcinoma↗
PubMed2006

Aging correlation functions of the interrupted fractional Fokker-Planck propagator.

The authors explore aging in a general semi-Markov process with arbitrary waiting time distributions and discuss the role of trapping phenomenon in glasses in determining the waiting time distributions. In certain limits, they obtain a two-time propagator for the fractional Fokker-Planck equation through coordination, but one can generalize the construction to incorporate cutoffs in the aging of the system, i.e., the interrupted aging. The construction allows the incorporation of cutoffs in the aging of the system, and the exploration of signatures of aging effects in systems that eventually achieve equilibrium. Cutoffs in aging effects are illustrated for interrupted fractional diffusion in a harmonic potential and for the on-time probability of a quantum dot system.

Algorithms↗
PubMed1976

Analysis of pairs of individual Ia-E.P.S.P.S in single motoneurones.

1. Recordings of individual e.p.s.p.s evoked by the action of single medial gastrocnemius Ia fibres have been made from medial gastrocnemius motoneurones. In many motoneurones the action of two Ia fibres has been observed and the properties of the e.p.s.p.s compared. 2. For sixty-three pairs of averaged e.p.s.p.s, each from the same motoneurone, the ratio of half-widths was plotted against the ratio of rise times. These results were compared with theoretical values derived from the Rall compartmental model. It was found that variations in synaptic current time courses and differences in the termination of localized synaptic terminals were not sufficient to account for all the data. 3. Amplitude and rise time were inversely related but the correlation coefficient was very low. For pairs of e.p.s.p.s in the same motoneurone the e.p.s.p. with the fast rise time was larger than that with the slow rise time in forty-eight of sixty-three cases. 4. In a given motoneurone individual e.p.s.p.s evoked by the action of different Ia fibres did not vary greatly in amplitude. The ratio of peak amplitudes was less than 3 for 86% of the pairs of e.p.s.p.s examined, and the maximum was 4-8. 5. Amplitude histograms were constructed for individual e.p.s.p.s at thirty-three synapses. Twenty-two of them could be shown to satisfy the Poisson law. The others satisfied the binomial law or neither. 6. Within a given motoneurone the amplitude of an e.p.s.p. is closely related to the mean number of quanta released but not to the amplitude of the unit e.p.s.p. produced by the action of a single quantum of transmitter.

Animals↗
PubMed2003

Excitations in one-dimensional S = 1/2 quantum antiferromagnets.

The transition from dimerized to uniform phases is studied in terms of spectral weights for spin chains using continuous unitary transformations. The spectral weights in the S=1 channel are computed perturbatively around the limit of strong dimerization. We find that the spectral weight is concentrated mainly in the subspaces with a small number of elementary triplets (triplons), even for vanishing dimerization. So, besides spinons, triplons may be used as elementary excitations in spin chains. We conclude that there is no necessity to use fractional excitations in low-dimensional, undoped, or doped quantum antiferromagnets.

Journal Article↗
PubMed2006

Experimental and theoretical electron density study of estrone.

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.

Computer Simulation↗
PubMed2006

A computational study of the deacylation mechanism of human butyrylcholinesterase.

To investigate the mechanism of the deacylation reaction in the active site of human butyrylcholinesterase (BuChE), we carried out quantum mechanical (QM) calculations on cluster models of the active site built from a crystallographic structure. The models consisted of the substrate butyrate moiety, the catalytic triad of residues (Ser198, Glu325, and His438), the "oxy-anion hole" (Gly116, Gly117, and Ala199), the side chain of Glu197, four water molecules, the side chain of Ser225, and the peptide linkage between Val321 and Asn322. Analyses of the equilibrium geometries, electronic properties, and energies of the QM models gave insights into the catalytic mechanism. In addition, the QM calculations provided the data required to build a molecular mechanics representation of the reactive BuChE region that was employed in molecular dynamics simulations followed by molecular-mechanics-Poisson-Boltzmann (MM-PB) calculations. Subsequently, we combined the QM energies with average MM-PB energies to estimate the free energy of the reactive structures in the enzyme. The rate-determining step corresponds to the formation of a tetrahedral intermediate with a free-energy barrier of approximately 14.0 kcal/mol. The modulation of the BuChE activity, exerted by either neutral molecules (glycerol, GOL) or a second butyrylcholine (CHO) molecule bound to the cation-pi site, does not involve any significant allosteric effect. Interestingly, the presence of GOL or CHO stabilizes a product complex formed between a butyric acid molecule and BuChE. These results are in consonance with the crystallographic structure of BuChE, in which the catalytic Ser198 interacts with a butyric fragment, while the cation-pi site is occupied by one GOL molecule.

Acylation↗
PubMed1996

Mixed quantum mechanical/molecular mechanical simulations of chemical reactions in solution and in enzymes by the classical trajectory mapping approach.

We present a practical hybrid quantum mechanical/molecular mechanical approach to study chemical reactions in solution and in enzymes. In this method, referred to as the "Classical Trajectory Mapping" method, trajectories are calculated on the classical potential surfaces and, by using the classical surfaces as a reference state for the actual quantum mechanical ground state potential, the free energy profile of the chemical reaction is obtained by the free energy perturbation technique. This method was applied to proton-transfer reactions both in aqueous solution and in papain. The encouraging results indicate the applicability of our method to chemical reactions in the condensed phase and the biological systems.

Calorimetry↗
PubMed2002

A novel approach for the sequential backbone assignment of larger proteins: selective intra-HNCA and DQ-HNCA.

Sequential assignment of backbone resonances in larger proteins can be achieved by recording two or more complementary triple-resonance NMR spectra of deuterated proteins. For such proteins, higher fields and experiments based on the TROSY method provide the needed resolution and sensitivity. However, increasingly rapid carbonyl relaxation at the high magnetic field strengths required by TROSY techniques renders assignment strategies that rely on sequential HN(CO)CA-type experiments much less efficient for proteins >40 kDa. Here we present two complementary new experiments, which allow backbone assignments with good sensitivity for larger deuterated proteins. A 3D intra-HNCA experiment provides uniquely the intraresidue connection, while a 3D DQ-HNCA experiment, which detects a (13)C(alpha)(i)()(13)C(alpha)(i-1)() double-quantum (DQ) coherence, contains the sequential information. The experiments work well at high magnetic fields, and their utility is demonstrated on a protein with a correlation time of 28 ns ( approximately 60 kDa). For larger proteins the sensitivity is predicted through simulations which suggest that the approach should work for proteins with correlation times >50 ns.

Carbon Isotopes↗
PubMed2006

Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.

The dependence of the (13)C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel beta-sheet model peptide represented by the amino acid sequence Ac-(Ala)(3)-X-(Ala)(12)-NH(2) where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel beta-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the (13)C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel beta-sheet, there is (i) good agreement between computed and observed (13)C(alpha) and (13)C(beta) chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed (13)C(alpha) and (13)C(beta) chemical shifts as a function of chi(1) for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed (13)C(alpha) chemical shifts on chi(xi) (with xi > or = 2) compared to chi(1) for eleven out of seventeen residues. Our results suggest that predicted (13)C(alpha) and (13)C(beta) chemical shifts, based only on backbone (phi,psi) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into account.

Amino Acid Sequence↗
PubMed2005

Efficient multipole model and linear scaling of NDDO-based methods.

Fast growth of computational costs with that of the system's size is a bottleneck for the applications of traditional methods of quantum chemistry to polyatomic molecular systems. This problem is addressed by the development of linear (or almost linear) scaling methods. In the semiempirical domain, it is typically achieved by a series of approximations to the self-consistent field (SCF) solution. By contrast, we propose a route to linear scalability by modifying the trial wave function itself. Our approach is based on variationally determined strictly local one-electron states and a geminal representation of chemical bonds and lone pairs. A serious obstacle previously faced on this route were the numerous transformations of the two-center repulsion integrals characteristic for the neglect of diatomic differential overlap (NDDO) methods. We pass it by replacing the fictitious charge configurations usual for the NDDO scheme by atomic multipoles interacting through semiempirical potentials. It ensures invariance of these integrals and improves the computational efficiency of the whole method. We discuss possible schemes for evaluating the integrals as well as their numerical values. The method proposed is implemented for the most popular modified neglect of diatomic overlap (MNDO), Austin model 1 (AM1), and PM3 parametrization schemes of the NDDO family. Our calculations involving well-justified cutoff procedures for molecular interactions unequivocally show that the proposed scheme provides almost linear scaling of computational costs with the system's size. The numerical results on molecular properties certify that our method is superior with respect to its SCF-based ancestors.

Journal Article↗
PubMed2002

Modeling enzyme reactivity in organic solvents and water through computer simulations.

In this article, we review how molecular modeling techniques can be used to shed light on how water and organic solvents influence the reactivity of enzymes. The application of thermodynamics-based models allowed the first qualitative predictions on the selectivity of many reaction types. However, it was with the application of quantum mechanical/molecular mechanical (QM/MM) methods that quantitative models of actual reactivity patterns could be realistically formulated.

Computer Simulation↗
PubMedDate not supplied

[Organization of the background activity of rabbit visual cortex neurons].

Algorithm of calculation of consitent approximation to real entropy and redundancy which helps to understand the connection of two or more related states was realized by means of electronic computer BECM-6. Different laws of changes of information estimates dependeing on the number of approximation and the pitch of temporary quantum of messages corresponded to every type of cell impulsation of rabbits' visual cortex--arrhithimical, grouping and regular. The connections between the laws of impulse succession organization and some of its parameters were revealed. The results of studying the models of casual and deterministic pulse trains were compared.

Animals↗
PubMed2004

An algorithm for the study of DNA sequence evolution based on the genetic code.

Recent studies of the quantum-mechanical processes in the DNA molecule have seriously challenged the principle that mutations occur randomly. The proton tunneling mechanism causes tautomeric transitions in base pairs resulting in mutations during DNA replication. The meticulous study of the quantum-mechanical phenomena in DNA may reveal that the process of mutagenesis is not completely random. We are still far away from a complete quantum-mechanical model of DNA sequence mutagenesis because of the complexity of the processes and the complex three-dimensional structure of the molecule. In this paper we have developed a quantum-mechanical description of DNA evolution and, following its outline, we have constructed a classical model for DNA evolution assuming that some aspects of the quantum-mechanical processes have influenced the determination of the genetic code. Conversely, our model assumes that the genetic code provides information about the quantum-mechanical mechanisms of mutagenesis, as the current code is the product of an evolutionary process that tries to minimize the spurious consequences of mutagenesis. Based on this model we develop an algorithm that can be used to study the accumulation of mutations in a DNA sequence. The algorithm has a user-friendly interface and the user can change key parameters in order to study relevant hypotheses.

Algorithms↗
PubMed2006

Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements.

Knowledge of (13)C chemical shift anisotropy (CSA) tensors in nucleotide bases is important for interpretation of NMR relaxation data in terms of local dynamic properties of nucleic acids and for analysis of residual chemical shift anisotropy (RCSA) resulting from weak alignment. CSA tensors for protonated nucleic acid base carbons have been derived from measurements on a uniformly (13)C-enriched helical A-form RNA segment and a helical B-form DNA dodecamer at natural (13)C abundance. The magnitudes of the derived CSA principal values are tightly restricted by the magnetic field dependencies of the (13)C transverse relaxation rates, whereas the tensor orientation and asymmetry follow from quantitative measurements of interference between (13)C-{(1)H} dipolar and (13)C CSA relaxation mechanisms. Changes in the chemical shift between the isotropic and aligned states, Deltadelta, complement these measurements and permit cross-validation. The CSA tensors are determined from the experimental Deltadelta values and relaxation rates, under the assumption that the CSA tensor of any specific carbon in a given type of base is independent of the base position in either the RNA or DNA helix. However, the experimental data indicate that for pyrimidine C(6) carbons in A-form RNA the CSA magnitude is considerably larger than in B-form DNA. This result is supported by quantum chemical calculations and is attributed in part to the close proximity between intranucleotide C(6)H and O(5)' atoms in RNA. The magnitudes of the measured CSA tensors, on average, agree better with previous solid-state NMR results obtained on powdered nucleosides than with prior results from quantum chemical calculations on isolated bases, which depend rather strongly on the level of theory at which the calculations are carried out. In contrast, previously computed orientations of the chemical shift tensors agree well with the present experimental results and exhibit less dependence on the level of theory at which the computations are performed.

Anisotropy↗