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Biomedical subjects

N Agmon

Publications and source records attributed to N Agmon.

15 recordsLinked to original sources
PubMed2001

Experimental evidence for a kinetic transition in reversible reactions.

We provide a first experimental verification of a theoretical prediction of a kinetic transition in a reversible binding reaction, AB right harpoon over left harpoon A+B, driven by the difference in effective lifetimes of the bound and the unbound states. We consider the kinetics of excited-state proton transfer to solvent from a photoacid whose conjugate anionic base possesses an extremely short unbound anion lifetime. Its solvent variation relative to the overall dissociation rate coefficient induces a transition in the kinetics, from power law to exponential.

Journal Article↗
PubMed2000

Rigorous derivation of the long-time asymptotics for reversible binding

Using an iterative solution in Laplace-Fourier space, we supply a rigorous mathematical proof for the long-time asymptotics of reversible binding in one dimension. The asymptotic power law and its concentration dependent prefactor result from diffusional and many-body effects which, unlike for the corresponding irreversible reaction and in classical chemical kinetics, play a dominant role in shaping the approach to equilibrium.

Journal Article↗
PubMed1997

Trehalose prevents myoglobin collapse and preserves its internal mobility.

A quantitative model, which involves diffusion on a temperature-dependent potential, is utilized to analyze the time-dependence of geminate CO recombination to sperm whale myoglobin in a trehalose glass and the accompanying spectral shifts. Most of the recombination is inhomogeneous. This is due to higher geminate reactivity rather than slower protein relaxation. A fraction of the hemes undergoes relaxation with a concomitant increase in the barrier height for recombination. The activation energy for conformational diffusion (relaxation) is considerably lower than in glycerol/water. "Protein collapse", manifested in glycerol/water by a decrease in the equilibrium conformational separation between the bound and deoxy states, is completely prevented in trehalose. We postulate that the high internal viscosity in glycerol/water is due to dehydration of the heme pocket. Trehalose prevents the escape of the few vital internal water molecules and thus preserves the internal lability of the protein. This might be important in understanding the ability of trehalose to protect against the adverse effects of dehydration.

Animals↗
PubMed1997

Collective binding properties of receptor arrays.

Binding kinetics of receptor arrays can differ dramatically from that of the isolated receptor. We simulate synaptic transmission using a microscopically accurate Brownian dynamics routine. We study the factors governing the rise and decay of the activation probability as a function of the number of transmitter molecules released. Using a realistic receptor array geometry, the simulation reproduces the time course of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor-mediated excitatory postsynaptic currents. A consistent interpretation of experimentally observed synaptic currents in terms of rebinding and spatial correlations is discussed.

Animals↗
PubMed1995

Geometric and many-particle aspects of transmitter binding.

We investigate the various reactivity patterns possible when several transmitter molecules, released at one side of a synaptic gap, diffuse and bind reversibly to a single receptor at the other end. In the framework of a one-dimensional approximation, the complete time, reactivity, concentration and gap-width dependence are determined, using a rigorous theoretical and computational approach to the many-body aspects of this problem. The time dependence of the survival probability is found to consist of up to four phases. These include a short delay followed by gaussian, power-law, and exponential decay phases. A rigorous expression is derived for the long-time exponent and approximate expressions are obtained for describing the short-time gaussian phase.

Acetylcholine↗
PubMed1994

The transition from inhomogeneous to homogeneous kinetics in CO binding to myoglobin.

Heme proteins react inhomogeneously with ligands at cryogenic temperatures and homogeneously at room temperature. We have identified and characterized a transition from inhomogeneous to homogeneous behavior at intermediate temperatures in the time dependence of CO binding to horse myoglobin. The turnover is attributed to a functionally important tertiary protein relaxation process during which the barrier increases dynamically. This is verified by a combination of theory and multipulse measurements. A likely biological significance of this effect is in the autocatalysis of the ligand release process.

Animals↗
PubMed1988

Reactive line-shape narrowing in low-temperature inhomogeneous geminate recombination of CO to myoglobin.

The temporal shift in the near-IR absorption peak of myoglobin (Mb) following flash photolysis of MbCO at cryogenic temperatures appears to be due largely to an inhomogeneous reactive process rather than to relaxation. This conclusion, which follows from a new analysis of the experimental data, is based on the following three points: First, at very low temperatures (60 K) a transient line-narrowing effect can be detected. Second, there is a universal, temperature-independent, correlation between spectral shift and survival probability in the rebinding kinetics, and third, the same quantitative model which accounts for rebinding accounts semiquantitatively for the temporal shift in the peak. A fit to the model indicates that the inhomogeneous broadening of the near-IR peak in myoglobin is 15-20% of the total width. The same rebinding process which governs the loss of intensity of this peak is therefore most likely responsible for the shift in its center wavelength.

Animals↗
PubMed1985

A diffusion Michaelis-Menten mechanism: continuous conformational change in enzymatic kinetics.

We present a simple model which extends the Michaelis-Menten mechanism by incorporating a continuous protein conformational change in enzymatic catalysis. This model can represent a quantitative version for "rack" or "induced fit" mechanisms. In the steady-state it leads to an equation of the Michaelis-Menten form, but with the catalytic step at the active site showing strong dependence on solvent viscosity. We suggest that a careful examination of solvent viscosity effects on enzymatic activity may serve as a test for the conformational change hypothesis.

Binding Sites↗