Structural distribution of stability in a thermophilic enzyme

Stability parameters for individual residues in Thermus thermophilus cysteine-free RNase H were determined by native state hydrogen exchange, thus providing a unique comparison of regional thermodynamics between thermophilic and mesophilic homologues. The general distribution of stability in the thermophilic protein is similar to that of its mesophilic homologue, with a proportional increase in stability for almost all residues. As a consequence, the residue-specific stabilities of the two proteins are remarkably similar under conditions where their global stabilities are the same. These results indicate that T. thermophilus RNase H is stabilized in a delocalized fashion, preserving a finely tuned balance of stabilizing interactions throughout the structure. Therefore, although protein stability can be altered by single amino acid substitution, evolution for optimal function may require more subtle and delocalized mechanisms.

The origins of stability of spontaneous vesicles

Equilibrium unilamellar vesicles are stabilized by one of two distinct mechanisms depending on the value of the bending constant. Helfrich undulations ensure that the interbilayer potential is always repulsive when the bending constant, K, is of order kBT. When K ≫ kBT, unilamellar vesicles are stabilized by the spontaneous curvature that picks out a particular vesicle radius; other radii are disfavored energetically. We present measurements of the bilayer elastic constant and the spontaneous curvature, Ro, for three different systems of equilibrium vesicles by an analysis of the vesicle size distribution determined by cryo-transmission electron microscopy and small-angle neutron scattering. For cetyltrimethylammonium bromide (CTAB)/sodium octyl sulfonate catanionic vesicles, K = .7 kBT, suggesting that the unilamellar vesicles are stabilized by Helfrich-undulation repulsions. However, for CTAB and sodium perfluorooctanoate (FC7) vesicles, K = 6 kBT, suggesting stabilization by the energetic costs of deviations from the spontaneous curvature. Adding electrolyte to the sodium perfluorooctanoate/CTAB vesicles leads to vesicles with two bilayers; the attractive interactions between the bilayers can overcome the cost of small deviations from the spontaneous curvature to form two-layer vesicles, but larger deviations to form three and more layer vesicles are prohibited. Vesicles with a discrete numbers of bilayers at equilibrium are possible only for bilayers with a large bending modulus coupled with a spontaneous curvature.

The challenge of paleoecological stasis: reassessing sources of evolutionary stability.

The paleontological record of the lower and middle Paleozoic Appalachian foreland basin demonstrates an unprecedented level of ecological and morphological stability on geological time scales. Some 70-80% of fossil morphospecies within assemblages persist in similar relative abundances in coordinated packages lasting as long as 7 million years despite evidence for environmental change and biotic disturbances. These intervals of stability are separated by much shorter periods of ecological and evolutionary change. This pattern appears widespread in the fossil record. Existing concepts of the evolutionary process are unable to explain this uniquely paleontological observation of faunawide coordinated stasis. A principle of evolutionary stability that arises from the ecosystem is explored here. We propose that hierarchical ecosystem theory, when extended to geological time scales, can explain long-term paleoecological stability as the result of ecosystem organization in response to high-frequency disturbance. The accompanying stability of fossil morphologies results from "ecological locking," in which selection is seen as a high-rate response of populations that is hierarchically constrained by lower-rate ecological processes. When disturbance exceeds the capacity of the system, ecological crashes remove these higher-level constraints, and evolution is free to proceed at high rates of directional selection during the organization of a new stable ecological hierarchy.

Stability and dynamics in a hyperthermophilic protein with melting temperature close to 200°C

The rubredoxin protein from the hyperthermophilic archaebacterium Pyrococcus furiosus was examined by a hydrogen exchange method. Even though the protein does not exhibit reversible thermal unfolding, one can determine its stability parameters—free energy, enthalpy, entropy, and melting temperature—and also the distribution of stability throughout the protein, by using hydrogen exchange to measure the reversible cycling of the protein between native and unfolded states that occurs even under native conditions.

Use of spacecraft data to derive regions on Mars where liquid water would be stable

Combining Viking pressure and temperature data with Mars Orbital Laser Altimeter topography data, we have computed the fraction of the martian year during which pressure and temperature allow for liquid water to be stable on the martian surface. We find that liquid water would be stable within the Hellas and Argyre basin and over the northern lowlands equatorward of about 40°. The location with the maximum period of stable conditions for liquid water is in the southeastern portion of Utopia Planitia, where 34% of the year liquid water would be stable if it were present. Locations of stability appear to correlate with the distribution of valley networks.

Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage

Predicted highly expressed (PHX) and putative alien genes determined by codon usages are characterized in the genome of Deinococcus radiodurans (strain R1). Deinococcus radiodurans (DEIRA) can survive very high doses of ionizing radiation that are lethal to virtually all other organisms. It has been argued that DEIRA is endowed with enhanced repair systems that provide protection and stability. However, predicted expression levels of DNA repair proteins with the exception of RecA tend to be low and do not distinguish DEIRA from other prokaryotes. In this paper, the capability of DEIRA to resist extreme doses of ionizing and UV radiation is attributed to an unusually high number of PHX chaperone/degradation, protease, and detoxification genes. Explicitly, compared with all current complete prokaryotic genomes, DEIRA contains the greatest number of PHX detoxification and protease proteins. Other sources of environmental protection against severe conditions of UV radiation, desiccation, and thermal effects for DEIRA are the several S-layer (surface structure) PHX proteins. The top PHX gene of DEIRA is the multifunctional tricarboxylic acid (TCA) gene aconitase, which, apart from its role in respiration, also alerts the cell to oxidative damage.

Types of evolutionary stability and the problem of cooperation.

The evolutionary stability of cooperation is a problem of fundamental importance for the biological and social sciences. Different claims have been made about this issue: whereas Axelrod and Hamilton's [Axelrod, R. & Hamilton, W. (1981) Science 211, 1390-1398] widely recognized conclusion is that cooperative rules such as "tit for tat" are evolutionarily stable strategies in the iterated prisoner's dilemma (IPD), Boyd and Lorberbaum [Boyd, R. & Lorberbaum, J. (1987) Nature (London) 327, 58-59] have claimed that no pure strategy is evolutionarily stable in this game. Here we explain why these claims are not contradictory by showing in what sense strategies in the IPD can and cannot be stable and by creating a conceptual framework that yields the type of evolutionary stability attainable in the IPD and in repeated games in general. Having established the relevant concept of stability, we report theorems on some basic properties of strategies that are stable in this sense. We first show that the IPD has "too many" such strategies, so that being stable does not discriminate among behavioral rules. Stable strategies differ, however, on a property that is crucial for their evolutionary survival--the size of the invasion they can resist. This property can be interpreted as a strategy's evolutionary robustness. Conditionally cooperative strategies such as tit for tat are the most robust. Cooperative behavior supported by these strategies is the most robust evolutionary equilibrium: the easiest to attain, and the hardest to disrupt.