Single intrinsic dynamics

Melittin, which is an amphipathic peptide from honeybee venom, consists of 26 amino acid residues and adopts different conformations from a random coil, to an a-helix, and to a self-assembled tetramer under certain aqueous environments see Fig. 9. We have carried out our systematic studies of the hydration dynamics in these three conformations using a single intrinsic tryptophan ( W19) as a molecular probe. The folded a-helix melittin was formed with lipid interactions to mimic physiological membrane-bound conditions. The self-assembled tetramer was prepared under high-salt concentration (NaCl = 2 M). The tryptophan emission of three structures under three different aqueous environments is 348.5 nm, 341 nm, and 333.5 nm, which represents different exposures of aqueous solution from complete in random-coil, to locating at the lipid surface of a nanochannel (50 A in diameter) in a-helix and to partially buried in tetramer. Figure 10 shows... 

NMR is probably the single most powerful technique to study a large variety of structural and dynamic problems in supramolecular chemistry. The strength of the technique derives from its atomic-scale resolution and its sensitivity to subtle changes in the environment of individual atoms when the corresponding molecules participate in supramolecular assemblies. NMR is intrinsically sensitive to dynamic processes in a wide range of timescales, and therefore extremely appropriate to study the intrinsically dynamic... 

In SEC, universal calibration is often utilized to characterize a molecular weight distribution. For a universal calibration curve, one must determine the product of log(intrinsic viscosity molecular weight), or log([7j] M). The universal calibration method originally described by Benoit et al. (9) employs the hydro-dynamic radius or volume, the product of [tj] M as the separation parameter. The calibration curves for a variety of polymers will converge toward a single curve when plotted as log([7j] M) versus elution volume (VJ, rather than plotted the conventional way as log(M) versus V, (5). Universal calibration behavior is highly dependent on the absence of any secondary separation effects. Most failures of universal calibration are normally due to the absence of a pure size exclusion mechanism. 

Mechanistic Ideas. The ordinary-extraordinary transition has also been observed in solutions of dinucleosomal DNA fragments (350 bp) by Schmitz and Lu (12.). Fast and slow relaxation times have been observed as functions of polymer concentration in solutions of single-stranded poly(adenylic acid) (13 14), but these experiments were conducted at relatively high salt and are interpreted as a transition between dilute and semidilute regimes. The ordinary-extraordinary transition has also been observed in low-salt solutions of poly(L-lysine) (15). and poly(styrene sulfonate) (16,17). In poly(L-lysine), which is the best-studied case, the transition is detected only by QLS, which measures the mutual diffusion coefficient. The tracer diffusion coefficient (12), electrical conductivity (12.) / electrophoretic mobility (18.20.21) and intrinsic viscosity (22) do not show the same profound change. It appears that the transition is a manifestation of collective particle dynamics mediated by long-range forces but the mechanistic details of the phenomenon are quite obscure. 

Grubisic et al. (3) showed that for many polymers a single calibration curve can be drawn through a plot of the product of intrinsic viscosity and molecular weight ( [7/] M) vs. retention volume. This relationship certainly supports the model of molecular separation based on hydro-dynamic volume since [77] M is proportional to the hydrodynamic volume of the molecule in solution. Hence, molecular weights of the two polymers (calibration standard polymer and sample) which have identical retention volume under identical GPC analytical conditions can be expressed in terms of each other by combining the Grubisic relationship ... 

Contemporary theories go beyond and treat solvation dynamics in detail. In Section III we review many recent papers in this field [62-73,136-142], A key result is that the rate of a charge transfer reactions should be a function of the microscopic dynamics of the specific solvent. In fact, in the case of very small intrinsic charge transfer activation barrier, the rate is predicted to be roughly equal to the rate of solvation (i.e., rf1 for a solvent with a single relaxation (td) time). This result was first derived over 20 years ago by... 

We recently developed a systematic method that uses the intrinsic tryptophan residue (Trp or W) as a local optical probe [49, 50]. Using site-directed mutagenesis, tryptophan can be mutated into different positions one at a time to scan protein surfaces. With femtosecond temporal and single-residue spatial resolution, the fluorescence Stokes shift of the local excited Trp can be followed in real time, and thus, the location, dynamics, and functional roles of protein-water interactions can be studied directly. With MD simulations, the solvation by water and protein (residues) is differentiated carefully to determine the hydration dynamics. Here, we focus our own work and review our recent systematic studies on hydration dynamics and protein-water fluctuations in a series of biological systems using the powerful intrinsic tryptophan as a local optical probe, and thus reveal the dynamic role of hydrating water molecules around proteins, which is a longstanding unresolved problem and a topic central to protein science. 

---