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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↗
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↗
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↗
PubMedDate not supplied

Software tools and databases for bacterial systematics and their dissemination via global networks.

The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic 'Authority Files' are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.

Amino Acid Sequence↗
PubMed1994

Influence of slight sequence changes on the free energy of a single stranded ribonucleic acid molecule.

Single-stranded ribonucleic acid molecules take a variety of secondary structures. The free energy (g) of a given secondary structure of a molecule is calculated from the Boltzmann weighted summation over the states of this molecule taking this secondary structure. Likewise, the free energy (G) of a molecule is calculated from the summation over the states of this molecule, which takes various secondary structures. The g-value can be evaluated by Salser's method (1977, Cold Spring Harbor Symp. Quantum Biol. 42, 985-1002). By use of these values, the G-value can also be obtained. Computer studies utilizing this method reveal that there is a particular class of molecules whose G-values tend to increase when the sequences are slightly changed. As far as we examined, such molecules take few secondary structures that fulfill the following two conditions simultaneously: (i) The g-value is close to that of the optimal secondary structure. (ii) The structure is very different from the optimal secondary structure. Here, the optimal secondary structure means the one with the lowest g-value among all the secondary structures taken by the molecule.

Base Sequence↗
PubMed1990

Theoretical calculations on calcium channel drugs: is electron transfer involved mechanistically?

Theoretical studies were done on calcium channel drugs in order to gain insight into the mode of action. Empirical force field calculations with nifedipine, a calcium channel antagonist, indicate that the E-conformation at the ring juncture is lower in energy than the Z-conformation. This energy difference is only 0.2 kcal/mol when the esters in the 3- and 5-positions of the dihydropyridine (DHP) ring are both synperiplanar (sp, sp). Molecular orbital calculations on the ground and excited states in the Z-conformation with the esters in the (ap, sp) conformation show a low lying excited state with substantial intramolecular electron transfer (ET) character. This excited state is only 1.8 eV higher in energy than the ground state and corresponds to a transfer of approximately 0.3 electron from the DHP ring to the nitrobenzene moiety. We suggest that ET may play an important role in the mechanism of action, either intramolecular or, as previously proposed, intermolecular, along with lipophilicity and steric effects.

Calcium Channel Blockers↗
PubMedDate not supplied

Information and artifact in computed tomography image statistics.

In conventional computed tomography images only the average CT number, which is a first-order statistical parameter, is used to characterize the tissues by giving an estimate of tissue density. Second order statistical parameters such as the signal variance and cross-correlation function have also been used to obtain additional information to discriminate between certain tissues and lesions. However, the contribution of quantum noise to the signal variance and cross-correlation function creates, for the conventional CT patient dose, a background signal often larger than the signal containing the information about tissue structure. The misleading information, called "artifacts", in second-order image statistics caused by quantum noise, is studied.

Information Theory↗
PubMed1994

Structure-function studies of DNA damage using ab initio quantum mechanics and molecular dynamics simulation.

Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic structure calculations on the lesions in isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG)2 with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

Base Sequence↗
PubMed1990

Solution behavior of methyl beta-xylobioside: conformational flexibility revealed by n.m.r. measurements and theoretical calculations.

The conformations of methyl beta-xylobioside in solution have been determined by n.m.r. spectroscopy. Interglycosidic 3JC,H values and the chemical shifts of the 13C resonances were measured at various temperatures in the range 238-378 K for solutions in 1,4-dioxane, methanol, methyl sulfoxide, and water. The temperature and solvent dependencies of the data obtained suggest conformational flexibility. Quantum-chemical PCILO calculations, with evaluation of the solvent effects, and molecular mechanics calculations revealed the existence of 7 low-energy regions for which the geometries and energies were determined. The computed abundances of conformers and averaged J values accord with the experimental data.

Carbohydrate Conformation↗
PubMed1986

Molecular determinants for the agonist activity of 2-methylhistamine and 4-methylhistamine at H2-receptors.

A model for drug action at the histamine H2-receptor has been evaluated computationally for the agonists 2- and 4-methylhistamine. Based on molecular properties calculated for molecular structures optimized with ab initio quantum mechanical methods, the activities of these compounds and their potencies relative to histamine are found to be explained by the previously proposed model. Recognized in the N3-H tautomeric form of their monocations, both compounds exhibit a change in ring tautomeric preference when the cationic side chain is neutralized. This change makes possible their participation in a proposed proton relay event that was postulated to initiate the receptor response of H2-agonists. The relative concentrations of the mono- and dication forms of the molecules in equimolar concentrations of histamine and the two derivatives are calculated from the values of the molecular electrostatic potentials at the ring protonation sites. Because the monocation is the species recognized at the H2-receptor, the reduced potency of 2-methylhistamine relative to histamine and to the 4-methyl derivative is explained by the finding that 2-methylhistamine will have the lowest concentration of the recognized species. The rank order of potencies obtained from the ratio of monocationic species of the molecules is in agreement with experimental results.

Methylhistamines↗
PubMed1988

Role of primary and secondary protein structure in neurotransmitter receptor activation mechanisms.

A proton transfer triggered by a ligand interacting with the receptor had been suggested as the initial step in the activation of a receptor for the neurotransmitter serotonin (5-hydroxy-tryptamine; 5-HT). To evaluate the role of the receptor macromolecule in modulating the primary molecular event in ligand-mediated activation, the process of proton transfer was analysed in the environment of a protein model for the 5-HT receptor. In the absence of a detailed receptor structure, the enzyme actinidin was chosen as the model for the receptor based on criteria obtained from structure-activity considerations on the ligands. The first simulation of a mechanism for receptor activation was performed on this model using methods of theoretical chemistry to study the effect of specific structural elements. The premise is that the role of the elements of secondary structure of soluble proteins (e.g. actinidin) in determining structure-function relations in these macromolecules is maintained when these elements are part of membrane-bound receptor proteins. Results from the calculations of the effects of the six alpha helices of actinidin on the proton transfer process from the imidazolium side chain of His 162 to the thiol side chain of Cys 25 in the protein show that the helices contribute in different ways to modulate the energy of proton transfer. The largest helix, A1, opposes the proton transfer through the effect of the helix dipole. The charged residues (primary structure) in helix A3 favor the proton transfer, and mask the effect of its helix dipole (secondary structure) which opposes the transfer. The direction of the proton transfer simulated for the activation mechanism is opposite to that assumed in the catalytic process of the thiol protease, and the entire protein environment opposes the transfer. This supports the specific role of the ligand in triggering the proton transfer as a response to its binding.

Computer Graphics↗