Dynamics of stiff polymer chains

Mediating the slow dynamics of polyacrylates by small molecule-bridged hydrogen bonds

This report studied the changes in the slow dynamics of polyacrylate by adding a hindered phenol (CA) capable of forming three intermolecular hydrogen bonds (inter-HBs) per molecule with the polymer chain. The CA molecule apparently diminishes the slow modes (with lower peak temperatures and peak heights) of the polyacrylate, although it has a higher glass transition temperature (T_g) than the acrylic matrix, and the rigid CA-bridged HB network significantly amplifies the α-relaxation near T_g (with higher peak temperatures and peak heights). Consequently, the mixtures exhibit a diminishing slow mode that gradually merges with the prominent α-peak with increasing CA loadings. The anomalous dynamics concerning the opposite behaviors of the slow mode and α-relaxation was further rationalized in terms of dissociation of inter-HBs when the temperature is higher than T_g, together with the small molecule-alleviated macromolecular connectivity. This work provides essential insights into the slow dynamics of such HB-driven hybrids, and paves the way for tailoring the viscous flow properties of the hybrid material from a molecular level perspective.

How important are fluctuations in the treatment of internal friction in polymers?

The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on preaveraging internal friction. By comparison with Brownian dynamics simulations of an exact coarse-grained model that incorporates fluctuations in internal friction, the accuracy of the preaveraged model predictions is examined both at and away from equilibrium. While the two models predict intrachain autocorrelations that approach each other for long enough chain segments, they differ in their predictions for shorter segments. Furthermore, the two models differ qualitatively in their predictions for the chain extension and viscosity in shear flow, which is taken to represent a prototypical out-of-equilibrium condition.

Viscosity scaling for the glassy phase of protein folding

Although commendable progress has been made in the understanding of the physics of protein folding, a key unresolved issue is whether Kramers' diffusion model of chemical reactions is generally applicable to activated barrier crossing events during folding. To examine the solvent viscosity effect on the folding transition of native-like trapped intermediates, laser flash photolysis has been used to measure the microsecond folding kinetics of a natively folded state of CO-liganded ferrocytochrome c (M-state) in the 1-250 cP range of glycerol viscosity at pH 7.0, 20 degrees C. The single rate coefficient for the folding of the M-state to the native state of the protein (i.e., the M --> N folding process) decreases initially when the solvent viscosity is low (<10 cP), but saturates at higher viscosity, indicating that Kramers model is not general enough for scaling the viscosity dependence of post-transition folding involving glassy dynamics. Analysis based on the Grote-Hynes idea of time dependent friction in conjunction with defect diffusion dynamics can account for the observed non-Kramers scaling.

Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy

Long-range conformational changes in proteins are ubiquitous in biology for the transmission and amplification of signals; such conformational changes can be triggered by small-amplitude, nanosecond protein domain motion. Understanding how conformational changes are initiated requires the characterization of protein domain motion on these timescales and on length scales comparable to protein dimensions. Using neutron spin-echo spectroscopy (NSE), normal mode analysis, and a statistical-mechanical framework, we reveal overdamped, coupled domain motion within DNA polymerase I from Thermus aquaticus (Taq polymerase). This protein utilizes correlated domain dynamics over 70 angstroms to coordinate nucleotide synthesis and cleavage during DNA synthesis and repair. We show that NSE spectroscopy can determine the domain mobility tensor, which determines the degree of dynamical coupling between domains. The mobility tensor defines the domain velocity response to a force applied to it or to another domain, just as the sails of a sailboat determine its velocity given the applied wind force. The NSE results provide insights into the nature of protein domain motion that are not appreciated by conventional biophysical techniques.

Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin

Understanding the mechanisms of protein folding requires knowledge of both the energy landscape and the structural dynamics of a protein. We report a neutron-scattering study of the nanosecond and picosecond dynamics of native and the denatured alpha-lactalbumin. The quasielastic scattering intensity shows that there are alpha-helical structure and tertiary-like side-chain interactions fluctuating on sub-nanosecond time-scales under extremely denaturing conditions and even in the absence of disulfide bonds. Based on the length-scale dependence of the decay rate of the measured correlation functions, the nanosecond dynamics of the native and the variously denatured proteins have three dynamic regimes. When 0.05<Q<0.5 A(-1) (where the scattering vector, Q, is inversely proportional to the length-scale), the decay rate, Gamma, shows a power law relationship, Gamma proportional to Q(2.42+/-0.08), that is analogous to the dynamic behavior of a random coil. However, when 0.5<Q<1.0 A(-1), the decay rate exhibits a Gamma proportional to Q(1.0+/-0.2) relationship. The effective diffusion constant of the protein decreases with increasing Q, a striking dynamic behavior that is not found in any chain-like macromolecule. We suggest that this unusual dynamics is due to the presence of a strongly attractive force and collective conformational fluctuations in both the native and the denatured states of the protein. Above Q>1.0 A(-1) is a regime that displays the local dynamic behavior of individual residues, Gamma proportional to Q(1.8+/-0.3). The picosecond time-scale dynamics shows that the potential barrier to side-chain proton jump motion is reduced in the molten globule and in the denatured proteins when compared to that of the native protein. Our results provide a dynamic view of the native-like topology established in the early stages of protein folding.

Harmonic analysis of DNA dynamics in a viscous medium

The harmonic dynamics of normal modes of double-stranded DNA in a viscous fluid are investigated. The model DNA consists of two backbone-supported DNA strands coiling around a common helix axis with base stacking, sugar puckering, interstrand hydrogen bonding, and intrastrand sugar-base interactions assigned values based on published data. Assuming that the DNA bases are shielded from direct bombardment by the solvent, analytical solutions are obtained. The dissipation and fluctuation of the normal modes of the bases moving along the spirals display the effect of the medium indirectly through interactions with the backbone. The dynamics of the backbone are found to be overdamped with the characteristic damping times extending to the picosecond region for disturbance in position and to the sub-picosecond region for disturbance in velocity. In addition to the dynamic mode of a rigid rod, the motions of the bases are coupled to the motions of the backbone with comparable amplitudes for disturbance in position. For disturbance in velocity, however, the bases are effectively at rest, not being able to follow the motions of the backbone. The angular frequencies of the underdamped vibrational modes, identified as the ringing modes of the bases with the backbone effectively at rest, are insensitive to the viscosity and lie in the low frequency region of the Raman spectrum. These findings indicate that the backbone of DNA plays a significant role in modulating the dynamics of double-stranded DNA in an overdamping environment. This modulation of the dynamics of the motions of the bases in DNA by environmental impediments to molecular motion is briefly discussed in connection with protein- and drug- DNA interactions as well as gene regulation.