Rotational diffusion of two-segmented macromolecules with a ball–socket joint: A kinetic theory approach

Electron-nuclear interactions as probes of domain motion in proteins

Long range interactions between nuclear spins and paramagnetic ions can serve as a sensitive monitor of internal motion of various parts of proteins, including functional loops and separate domains. In the case of interdomain motion, the interactions between the ion and NMR-observable nuclei are modulated in direction and magnitude mainly by a combination of overall and interdomain motions. The effects on observable parameters such as paramagnetic relaxation enhancement (PRE) and pseudocontact shift (PCS) can, in principle, be used to characterize motion. These parameters are frequently used for the purpose of structural refinements. However, their use to probe actual domain motions is less common and is lacking a proper theoretical treatment from a motional perspective. In this work, a suitable spin Hamiltonian is incorporated in a two body diffusion model to produce the time correlation function for the nuclear spin-paramagnetic ion interactions. Simulated observables for nuclei in different positions with respect to the paramagnetic ion are produced. Based on these simulations, it demonstrated that both the PRE and the PCS can be very sensitive probes of domain motion. Results for different nuclei within the protein sense different aspects of the motions. Some are more sensitive to the amplitude of the internal motion, others are more sensitive to overall diffusion rates, allowing separation of these contributions. Experimentally, the interaction strength can also be tuned by substitution of different paramagnetic ions or by varying magnetic field strength (in the case of lanthanides) to allow the use of more detailed diffusion models without reducing the reliability of data fitting.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

Brownian dynamics simulations of needle chain and nugget chain polymer models—rigid constraint conditions versus infinitely stiff springs

It is well known that orientational correlations appear in polymer chain models when the subunits are linked by ball-socket joints implemented as rigid constraint conditions. These correlations do not appear when the subunits are connected by springlike potential forces, even in the limit of infinitely stiff springs. In a widely used class of algorithms for Brownian dynamics simulations, inertia effects are ignored. However, in the recently introduced needle chain and nugget chain algorithms, the rigid constraint correlations depend on the mass and moment of inertia. This inconsistency does not appear in the bead-rod (Kramers) polymer chain model, which also has orientational correlations introduced by rigid constraint conditions. Explicit expressions for the correlation functions are given for thermodynamic equilibrium states. Analytical expressions for the associated forces ("metric forces") and simulation results showing how the rigid constraint correlations influence dynamical properties, are also presented. Further we discuss the physical relevance of these correlations and show via simulations that their influence on stationary and dynamical properties depend significantly on chain length. We further show that if the metric forces are removed, algorithms designed with rigid constraint conditions describe a chain of segments connected by infinitely stiff springs. Finally we show that the results presented here for needle chains are relevant also for the bead-rod (Kramers) chain model, making it possible to simulate a bead-spring chain with infinitely stiff springs.