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Biomedical subjects

K Sneppen

Publications and source records attributed to K Sneppen.

At least 19 recordsLinked to original sources
PubMed2002

Epigenetics as a first exit problem.

We develop a framework to discuss the stability of epigenetic states as first exit problems in dynamical systems with noise. We consider in particular the stability of the lysogenic state of the lambda prophage. The formalism defines a quantitative measure of robustness of inherited states.

Bacteriophage lambda↗
PubMed2001

Thermodynamical implications of a protein model with water interactions.

We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: (1) binding energy of folding relative to the orientational energy of bound water, (2) ratio of degrees of freedom between the folded and unfolded protein chain, and (3) the number of water molecules that can access the hydrophobic parts of the protein interior upon unfolding. By increasing the number of water molecules in the model, the separation between the two peaks in the heat capacity curve comes closer, which is more consistent with experimental data. In the end we show that if we, as a speculative assumption, assign only two distinct energy levels for the bound water molecules, better correspondence with experiments can be obtained.

Animals↗
PubMed2001

Hydrogen bonds in polymer folding.

We studied the thermodynamics of a homopolymeric chain with both van der Waals and directed hydrogen bond interaction. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give rise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated states. The consequences of this transition for protein folding and, in particular, for the problem of prions are discussed.

Hydrogen Bonding↗
PubMed2000

Robustness as an evolutionary principle.

We suggest simulating evolution of complex organisms using a model constrained solely by the requirement of robustness in its expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence for dynamical features in the evolved networks is found that can be related to biological observables.

Animals↗
PubMed2000

Thermodynamics of heat-shock response.

Production of heat-shock proteins is induced when a living cell is exposed to a rise in temperature. The heat-shock response of protein DnaK synthesis in E.coli for temperature shifts T-->T+DeltaT and T-->T-DeltaT is measured as a function of the initial temperature T. We observe a reversed heat shock at low T. The magnitude of the shock increases when one increases the distance to the temperature T0 approximately 23 degrees C, thereby mimicking the nonmonotonous stability of proteins at low temperature. This suggests that stability related to hot as well as cold unfolding of proteins is directly implemented in the biological control of protein folding.

Escherichia coli↗
PubMed2000

Pathways in two-state protein folding.

Thermodynamic measurements of proteins indicate that the folding to the native state takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of proteins indicate that folding is guided through some sequence of contact bindings. We discuss the possibility of reconciling a two-state folding event with a sequential folding process in a schematic model of protein folding. We propose a new dynamical transition temperature that is lower than the temperature at which proteins in equilibrium unfold. This is in qualitative agreement with observations of in vivo protein folding activity quantified by chaperone concentration in Escherichia coli. Finally, we discuss our framework in connection with the unfolding of proteins at low temperatures.

Biophysical Phenomena↗
PubMed1995

Evolution as a self-organized critical phenomenon.

We present a simple mathematical model of biological macroevolution. The model describes an ecology of adapting, interacting species. The environment of any given species is affected by other evolving species; hence, it is not constant in time. The ecology as a whole evolves to a "self-organized critical" state where periods of stasis alternate with avalanches of causally connected evolutionary changes. This characteristic behavior of natural history, known as "punctuated equilibrium," thus finds a theoretical explanation as a self-organized critical phenomenon. The evolutionary behavior of single species is intermittent. Also, large bursts of apparently simultaneous evolutionary activity require no external cause. Extinctions of all sizes, including mass extinctions, may be a simple consequence of ecosystem dynamics. Our results are compared with data from the fossil record.

Adaptation, Biological↗