Top-down free-energy minimization on protein potential energy landscapes

The hierarchical properties of potential energy landscapes have been used to gain insight into thermodynamic and kinetic properties of protein ensembles. It also may be possible to use them to direct computational searches for thermodynamically stable macroscopic states, i.e., computational protein folding. To this end, we have developed a top-down search procedure in which conformation space is recursively dissected according to the intrinsic hierarchical structure of a landscape's effective-energy barriers. This procedure generates an inverted tree similar to the disconnectivity graphs generated by local minima-clustering methods, but it fundamentally differs in the manner in which the portion of the tree that is to be computationally explored is selected. A key ingredient is a branch-selection algorithm that takes advantage of statistically predictive properties of the landscape to guide searches down the tree branches that are most likely to lead to the physically relevant macroscopic states. Using the computational folding of a β-hairpin-forming peptide as an example, we show that such predictive properties indeed exist and can be used for structure prediction by free-energy global minimization.

Ion channels gated by heat

All animals need to sense temperature to avoid hostile environments and to regulate their internal homeostasis. A particularly obvious example is that animals need to avoid damagingly hot stimuli. The mechanisms by which temperature is sensed have until recently been mysterious, but in the last couple of years, we have begun to understand how noxious thermal stimuli are detected by sensory neurons. Heat has been found to open a nonselective cation channel in primary sensory neurons, probably by a direct action. In a separate study, an ion channel gated by capsaicin, the active ingredient of chili peppers, was cloned from sensory neurons. This channel (vanilloid receptor subtype 1, VR1) is gated by heat in a manner similar to the native heat-activated channel, and our current best guess is that this channel is the molecular substrate for the detection of painful heat. Both the heat channel and VR1 are modulated in interesting ways. The response of the heat channel is potentiated by phosphorylation by protein kinase C, whereas VR1 is potentiated by externally applied protons. Protein kinase C is known to be activated by a variety of inflammatory mediators, including bradykinin, whereas extracellular acidification is characteristically produced by anoxia and inflammation. Both modulatory pathways are likely, therefore, to have important physiological correlates in terms of the enhanced pain (hyperalgesia) produced by tissue damage and inflammation. Future work should focus on establishing, in molecular terms, how a single ion channel can detect heat and how the detection threshold can be modulated by hyperalgesic stimuli.