Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations.

Predicting and controlling the properties of amphiphile aggregate mixtures require understanding the arrangements and dynamics of the constituent molecules. To explore these topics, we study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms to describe the dynamics. NMR relaxation rates, which depend on relative motions of interacting atom pairs, are influenced by wide distributions of dynamic time scales. We find that relative motions of neighboring atom pairs are rapid and liquidlike but are subject to structural constraints imposed by micelle morphology. Relative motions of distant atom pairs are slower than nearby atom pairs because changes in distances and angles are smaller when the moving atoms are further apart. Large numbers of atom pairs undergoing these slow relative motions contribute to predominantly negative cross-relaxation rates. For spherical micelles, but not for cylindrical micelles, cross-relaxation rates are positive only for surfactant tail atoms connected to the hydrophilic headgroup. This effect is related to the lower packing density of these atoms at the hydrophilic-hydrophobic boundary in spherical vs cylindrical arrangements, with correspondingly rapid and less constrained motion of atoms at the boundary.

Role of Diffusion in Unfolding and Translocation of Multidomain Titin I27 Substrates by a Clp ATPase Nanomachine.

Degradation of multidomain substrate proteins (SPs) by AAA+ nanomachines takes place processively from the tagged terminal. Ring-shaped ATPase components, such as ClpY, apply repetitive mechanical forces to effect domain unfolding and translocation of polypeptide segments through a narrow central channel. We study these mechanisms through atomistic Langevin dynamics simulations of C-terminal-tagged SPs in allosteric ClpY cycles. We find that monomeric SPs are processed through single unfolding pathways and fast timescales, whereas multimeric SPs involve branched pathways and slower timescales. These distinct mechanisms are attributed to the slower rotational diffusion of the C-terminal domain in multidomain SPs that hinders access to the soft mechanical direction. In the geometry specific to laser optical tweezers experiments, involving a restrained SP N-terminal, a single unfolding pathway is found for both monomeric and tetrameric SPs as pulling is applied along the N-C direction. Non-native interactions modulate unfolding of unrestrained monomers by weakening the C-terminal interface but do not contribute significantly to unfolding of restrained SPs. On the basis of these results, we propose that the interplay of restricted SP dynamics and ATPase kinetics underlies partitioning of multidomain SPs into completely degraded products and undegraded fragments comprising folded domains.

Asymmetric Conformational Transitions in AAA+ Biological Nanomachines Modulate Direction-Dependent Substrate Protein Unfolding Mechanisms.

Powerful AAA+ biological nanomachines, such as ClpY, form hexameric ring structures, which selectively process abnormal proteins targeted for degradation by unfolding and threading them through a narrow central channel. The molecular details of this process are not yet fully understood. We perform Langevin dynamics simulations using a coarse-grained model of substrate proteins (SPs), Titin I27 and its V13P variant, threading through the ClpY pore. We probe the effect of ClpY surface heterogeneity and changes in pore width on SP orientation and the direction of applied force during SP unfolding. We contrast mechanisms of SP unfolding in a restrained geometry, as in single-molecule force spectroscopy experiments, and in an unrestrained geometry, as in the in vivo degradation process. In open pore configurations, unfolding of unrestrained SPs occurs via an unzipping mechanism, which involves force application along a weak mechanical direction. In the partially closed pore, unfolding occurs via a shearing mechanism, with force application along a strong mechanical direction. By contrast, unfolding of the restrained I27 is limited to a shearing mechanism due to application of force along the strong mechanical direction. We propose that Clp nanomachine plasticity underlies direction-dependent pulling mechanisms that enable versatile SP remodeling actions.