Interbasin motion approach to dynamics of conformationally constrained peptides

On the Origin of the Chemical Barrier and Tunneling in Enzymes

This paper presents both a review of some recent results from our group and experimental groups, and some new theoretical results all of which are helping to form a more physically rigorous picture of the process of enzymatic catalysis. A common classical picture of enzymatic catalysis is the transition state tight binding model. Schwartz and Schramm1 have recently argued from both theoretical and experimental results that this picture is incorrect. We now investigate what the nature of barriers might be in enzymatic reactions, and what this viewpoint might imply for tunneling in a hydrogen transfer enzyme. For lactate dehydrogenase we conclude that the enzymes role in catalysis is at least partially to hunt through configuration space for those configurations that minimize chemical free energy barriers. Those configurations do not seem to be stable basins on the free energy surface, and in fact the overall free energy barrier to reaction may well largely be due to this stochastic hunt - both probabilistically and energetically. We suggest further computations to test this hypothesis.

Master equation methods in gas phase chemical kinetics

In this article, we discuss the application of master equation methods to problems in gas phase chemical kinetics. The focus is on reactions that take place over multiple, interconnected potential wells and on the dissociation of weakly bound free radicals. These problems are of paramount importance in combustion chemistry. To illustrate specific points, we draw on our experience with reactions we have studied previously.

Molecular crowding effects on protein stability

The volume fraction occupied by the dry matter of the cell can be as large as 40%, of which more than half (approximately 60%) are proteins. Thus, cellular proteins and protein assemblies occupy a large volume that can have a profound effect on their own native-state stabilities and on their unfolding/refolding rates. In addition, macromolecular crowding can change the properties of a significant fraction of the water in the cell. We review features of the molecular crowding effect which are relevant for describing the microscopic mechanism of thermal injuries.

Effects of crowding on the thermal stability of heterogeneous protein solutions

Crowding can substantially affect the transition of a protein between its native (N) and unfolded (U) states via volume exclusion effects. Also, it influences considerably the aggregation (A) of unfolded proteins. To examine the details, we developed an approach for computing the kinetic rates of the process N <--> U --> A in which the concentration of the protein is explicitly taken into account. We then compute the relative change with temperature of the protein denaturation for various fractional volume occupancies and partition of proteins in solution. The analysis indicates that, in protein solutions in which the average distance between proteins is comparable with the radius of gyration of an unfolded protein, steric effects increase the stability of the proteins which are in compact, native states. In heterogeneous protein solutions containing various types of proteins with different thermal stabilities, the unfolding of the most thermolabile proteins will increase the stability of the other proteins. The results shed light on the way proteins change the thermal stability of a cell as they unfold and aggregate. This study may be valuable in questions related to the dynamics of thermal injuries.

The relative thermal stability of tissue macromolecules and cellular structure in burn injury

When tissue is subjected to higher than physiological temperatures, protein and cell organelle structures can be altered resulting in cell death and subsequent tissue necrosis. A burn injury can be stratified into three main zones, coagulation, stasis and edema, which correlate with the extent of heat exposure and thermal properties of the tissue. While there has been considerable effort to characterize the time-temperature dependence of the injury, relatively little attention has been paid to the other important variable, the thermal susceptibility of the tissue. In the present study, we employ a standard physical chemistry approach to predict the level of denaturation at supraphysiological temperatures of 12 vital proteins as well as RNA, DNA and cell membrane components. Melting temperatures and unfolding enthalpies of the cellular components are used as input experimental parameters. This approach allows us to establish a relation between the level of denaturation of critical cellular components and clinical manifestations of the burn through the characteristic zones of the injury. Specifically, we evaluate the degree of molecular alteration for characteristic temperature profiles at two different depths (Mid-Dermis and Dermis-Fat interface) of 80 degrees C; 20s contact burn. The results of this investigation suggest that the thermal alteration of the plasma membrane is likely the most significant cause of the tissue necrosis. The lipid bilayer and membrane-bound ATPases show a high probability of thermal damage (almost 100% for the former and 85% for the latter) for short heat exposure times. These results suggest that strategies to minimize the damage in a burn injury might focus on the stabilization of the cellular membrane and membrane-bound ATPases. Further work will be required to validate these predictions in an in vivo model.

Archetypal energy landscapes: Dynamical diagnosis

Recent studies have identified several motifs for potential energy surfaces corresponding to distinct dynamic and thermodynamic properties. The corresponding disconnectivity graphs were identified as "palm tree," "willow tree," and "banyan tree" patterns. In the present contribution we present a quantitative analysis of the relation between the topography and dynamics for each of these motifs. For the palm tree and willow tree forms we find that the arrangement of the stationary points in the monotonic sequences with respect to the global minimum is the most important factor in establishing the kinetic properties. However, the results are somewhat different for motifs involving a rough surface with several deep basins (banyan tree motif), with large barriers relative to the energy differences between minima. Here it is the size of the barrier for escape from the region relative to the barriers at the bottom that is most important. The present results may be helpful in distinguishing between the dynamics of "structure seeking" and "glass forming" systems.

Dielectric modulation of biological water

We show that water constrained by vicinal hydrophobes undergoes a librational dynamics that lowers the dielectric susceptibility and induces a "redshift" of the relaxation frequency in the hydration shell. The results shed light on the way proteins enhance their intramolecular interactions as they fold or associate.

How much can an intermediate state influence competing reactive pathways?

A molecule undergoing reaction may form a short-lived intermediate. Under certain conditions, the rate at which the reaction proceeds toward the product state via the intermediate may exceed that of a simple, direct path. The competition of two alternative reactive pathways is analyzed here in terms of a stochastic model. The approach allows one to diagnose this competition as a function of the energy of the intermediate relative to the barrier heights of the potential surface and values of the reactive vibrational modes. The result has applications to a variety of problems in chemical physics, ranging from the "lock-and-key" mechanism for the enzymatic activity to control of temporal evolution of complex systems by optimal laser fields.