Folding transition and

CROSS-TALK BETWEEN FOLDING TRANSITION AND HELIX-COIL... 

Figure 71. Emission spectra of 23 (n = 12) (open diamonds) excited in the broad absorption band peaked at 270—300 nm area diagnostic of its helical content (Aex = 288 nm, 0.5 //M 23 [n = 12] in 50 50 v/v THF/methanol.) The folded peak at 400 nm decreases at higher T. A spectral/lattice model prediction (solid line) describes the folding transition and equilibrium constant near quanti tatively. Insets show representative unfolded and folded conformations (side chains omitted for clarity).410...

An exact knowledge of the microcanonical entropy, or the density of the states, of a protein model in both the native and nonnative states is crucial for a precise characterization of the folding process of the model, such as whether the folding is first-order or gradual, whether the model can fold uniquely to the native structure, whether there is a discontinuity in the order parameter of the conformation in the folding transition, and so on. Once the microscopic entropy function is accurately determined, the statistical mechanics of the protein folding problem is solved. The accurate determination of the entropy function of protein models by the ESMC method requires a proper treatment of the computational problems discussed in Section IV. 

Recently there has been considerable interest in the phase transition of polymerized (tethered) membranes with attractive interactions [1-4]. In a pioneer work [1], Abraham and Nelson found by molecular dynamics simulations that the introduction of attractive interactions between monomers leads to a collapsed membrane with fractal dimension 3 at a sufficiently low temperature. Subsequently, Abraham and Kardar [2] showed that for open membranes with attractive interactions, as the temperature decreases, there exists a well-defined sequence of folding transitions and then the membrane ends up in the collapsed phase. They also presented a Landau theory of the transition. Grest and Petsche [4] extensively carried out molecular dynamics simulations of closed membranes. They considered flexible membranes the nodes of the membrane are connected by a linear chain of n monomers. For short monomer chains, n = 4, there occurs a first-order transition from the high-temperature flat phase to... 

Biological macromolecules (hke all except the smallest molecules) are flexible and move ceaselessly. Atomic fluctuations and side-chain motions have ampH-tudes of 1-500 pm and characteristic times ranging from 1 fs to 0.1 s. Rigid body motions, such as the motions of helices and subunits, have amplitudes of 0.1 -1.0 pm and characteristic times of 1 ns to 1 s. Folding transitions and the formation of quaternary structure from large structures have amplitudes greater than 0.5 nm and occur over a time span of from 100 ns to several hours. 

DA d Avignon, GL Bretthorst, ME Holtzer, A Holtzer. Thermodynamics and kinetics of a folded-folded transition at vahne-9 of a GCN4-hke leucine zipper. Biophys I 76 2752-2759, 1999. 

These results are plausible since according to Sand a two-fold concentration of a component yields a four-fold transition time. Now, these features show, in contrast to the net separation and pure additivity of polarographic waves and their diffusion-limited currents as concentration functions, that in chrono-potentiometry the transition times of components in mixtures are considerably increased by the preceding transition times of any other more reactive component, which complicates considerably the concentration evaluation of chronopotentiograms. 

Pan, Y. P. Daggett, V., Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor. 2 Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding, Biochemistry 2001,40, 2723-2731. 

In contrast to carbon, which forms structures derived from both sp2 and sp3 bonds, silicon is unable to form sp2 related structures. Since one out of four sp3 bonds of a given atom is pointing out of the cage, the most stable fullerene-like structure in this case is a network of connected cages. This kind of network is realized in alkali metal doped silicon clathrate (19), which were identified to have a connected fullerene-like structure (20). In these compounds, Si polyhe-dra of 12 five-fold rings and 2 or 4 more six-fold rings share faces, and form a network of hollow cage structures, which can accommodate endohedral metal atoms. Recently, the clathrate compound (Na,Ba), has been synthesized and demonstrated a transition into a superconductor at 4 K (21). The electronic structure of these compounds is drastically different from that of sp3 Si solid (22). 

---