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Biomedical subjects

A Kremen

Publications and source records attributed to A Kremen.

9 recordsLinked to original sources
PubMed1994

Ribosomes as molecular energy machines.

The idea that ribosomes operate as biological molecular energy machines offers an alternative description to that based on the assumption that the functionally important motions in ribosomes are only coupled to thermal degrees of freedom. The alternative model assumes that the energy gained in GTP cleavage generates in the ribosomal complex a localized metastable region temporarily not interacting with thermal motions. The metastable region may move along a definite pathway and in distinct sites promote irreversible logical operations involved in polypeptide biosynthesis. The new alternative represents a more complex and advanced algorithm offering advantages in speed, accuracy, more sophisticated control, and better resistance to various kinds of noise.

Animals↗
PubMed1992

Critical analysis of objections against the biological molecular energy machines.

In the past, two important objections against McClare's idea of biological molecular energy machines were raised. One of the criticisms was concerned with the origin of energy gained in ATP cleavage and with an interpretation of McClare's "excited vibrational state." The former argument reveals a failure of the critics to comprehend McClare's approach. As to the excited vibrational state, it can be identified with nonequilibrium conformational states of the unit rather than with a single vibrational mode. The other criticism based on Brillouin's energy cost of measurement argued that reversible operation of biological molecular energy machines would be virtually impossible. Using propagation velocities of deformations of the unit's structure (instead of velocity of light), the objections against reversibility are invalidated even in the framework of the critic's approach. McClare's idea and relevant definitions are thus physically correct.

Adenosine Triphosphate↗
PubMed1992

Plausible view on the biological molecular energy machines.

A qualitative picture of operation modes of biological molecular energy machines is presented. It is suggested that there is mutual control between the flow of molecular energy stored in a biological molecular energy machine and the sequence of nonequilibrium conformational states through which the machine passes in doing work. If the structure of the conformational space is favorable, the set of trajectories in this space decomposes into two families, each of which accomplishes another task. This divergence of trajectories enables to distinguish molecular objects according to differences in interaction between the machine and the object, i.e., to perform a measurement on a molecular object and process the object according to the result of that measurement.

Adenosine Triphosphate↗
PubMed1984

Logical elements in living cells.

Recognition processes with enhanced accuracy (as performed by structures like enzymes or ribosomes) are investigated using elementary ideas of statistical mechanics and related concepts of thermodynamics. The analysis starts from a formal definition of recognition and provides a correspondence with appropriate physical properties of the macromolecular logical elements. Transitions of the recognizing system between different modifications are a necessary feature of a more exacting recognition process. Rearrangement steps provide the process with higher accuracy by performing two physical operations: (1) rearranging the phase space of the system so that the "correct" states be better separated from the "wrong" states and the probability of occupation of the "correct" states be enhanced, (2) directing the process toward the more favourable modifications thus formed. Both operations are related to changes in the physical properties of the recognizing system. These changes can be expressed as differences of macromolecular Gibbs energy levels; if ligand binding or release participate in a step, directivity of the step depends also on the actual chemical potentials of the ligands in solution. The two operations just mentioned resemble two basic operations known to be necessary in electronic digital networks: directivity of control and signal standardization. An analysis of the entire reaction catalysed by a macromolecular logical element takes into account the requirements imposed by the logical functions as well as the need that the chemical potential of the product be not restricted to very low values. To satisfy these conditions, the reaction must be supported by a so-called non-specific reaction, usually implemented by the cleavage reaction of a nucleoside triphosphate.

Catalysis↗
PubMed1982

Information-theoretic significance of Gibbs energy supply to editing mechanisms.

If a branched multistep editing mechanism is implemented by an enzyme with a single site for the specific substrates, there is no reason to believe that the number of testing steps is fixed and cannot be controlled by some external factors. The paper considers the mechanisms of single- or multistep editing done in response to various factors, particularly to the value of displacement from the reaction equilibrium. To avoid a complicated analysis of a fully specified case, which would be likely to obscure the general significant features, the operating modes of those mechanisms are estimated using the method of minimizing associated information gains. It turns out that sufficiently far from equilibrium the variable mechanisms can essentially operate just as well as the fixed multistep mechanisms.

Binding Sites↗
PubMed1976

Regulation and biosynthesis of secondary metabolites. XVIII. Adenylate level and chlorotetracycline production in Streptomyces aureofaciens.

The relationship was studied between the energy metabolism of the actinomycete Streptomyces aureofaciens and the biosynthesis of chlorotetracycline by this organism. The energy charge values in a culture of low-production strain were almost identical with those of a production variant but the total sum of adenylates was about 10 times higher. In the stationary growth phase both strains evinced a drop in energy charge values followed by a rise to the original level. An increase in the concentration of inorganic phosphate in fermentation medium caused a suppression of antibiotic formation in the lowproduction strain and further rise in the total adenylate level. The expression of the energy charge in Streptomyces aureofaciens acquires a complex character owing to the participation, apart from the adenylate system, of high-molecular polyphosphates as energy donors and the probable lack of a regulating mechanism such as the adenylate kinase reaction.

Adenine Nucleotides↗