The hemoprotein myoglobin is a model system to study protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes taking place in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 fs with the C-, F- and H-helices moving away from the heme and the E- and A-helices moving toward it. These collective movements are predicted by quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, the calculations support predictions that an immediate collective response of the protein takes place upon ligand dissociation due to coupling of vibrational modes of the heme to global modes of the protein

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation.Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraint should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" (BioEn) method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of singlemolecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Water confined into the interior channels of narrow carbon nanotubes or transmembrane proteins forms collectively oriented molecular wires held together by tight hydrogen bonds. Here, we explore the thermodynamic stability and dipolar orientation of such 1D water chains from nanoscopic to macroscopic dimensions. We show that a dipole lattice model accurately recovers key properties of 1D confined water when compared to atomically detailed simulations. In a major reduction in computational complexity, we represent the dipole model in terms of effective Coulombic charges, which allows us to study pores of macroscopic lengths in equilibrium with a water bath (or vapor). We find that at ambient conditions, the water chains filling the tube are essentially continuous up to macroscopic dimensions. At reduced water vapor pressure, we observe a 1D Ising-like filling/emptying transition without a true phase transition in the thermodynamic limit. In the filled state, the chains of water molecules in the tube remain dipole-ordered up to macroscopic lengths of Ϸ0.1 mm, and the dipolar order is estimated to persist for times up to Ϸ0.1 s. The observed dipolar order in continuous water chains is a precondition for the use of nanoconfined 1D water as mediator of fast long-range proton transport, e.g., in fuel cells. For water-filled nanotube bundles and membranes, we expect anti-ferroelectric behavior, resulting in a rich phase diagram similar to that of a 2D Coulomb gas.1D confinement ͉ antiferro-electric ͉ carbon nanotubes ͉ proton transfer ͉ phase transition T he 1D wires formed by water in molecularly narrow pores are central to the function of many biomolecules, offer new possibilities for technological applications, and provide model systems to study the unique properties of dimensionally confined fluids (1). Proteins filled by water wires, such as aquaporins and gramicidin A, mediate the transport of water, protons, or ions across biological membranes (2, 3). Inspired in part by biology, narrow water-filled pores have been suggested as promising building blocks for high-selectivity/high-flux membranes in molecular separation devices and fuel cells (4-8). As an example of the rich properties of nanoscopically confined fluids, 1D water wires in carbon nanotubes have been found to exhibit first-order like drying transitions (9).Carbon nanotubes provide nearly ideal systems to study water in 1D confinement. Their smooth interior cavity surface interacts in a relatively nonspecific way with water molecules, confining them to a narrow, almost cylindrical volume. In pores with subnanometer diameters, the water molecules arrange themselves in a single-file structure, linked by hydrogen bonds. Such ordered chains of water molecules were found to permit rapid water flow (4, 9), and mediate proton transfer with mobilities exceeding those in bulk water (10-13).A key factor for the unique properties of 1D confined water is the nearly perfect molecular order, both translationally and orientationally, with uninterrupted chains of wate...

Water molecules confined to pores with sub-nanometer diameters form single-file hydrogen-bonded chains. In such nanoscale confinement, water has unusual physical properties that are exploited in biology and hold promise for a wide range of biomimetic and nanotechnological applications. The latter can be realized by carbon and boron-nitride nanotubes which confine water in a relatively non-specific way and lend themselves to the study of intrinsic properties of single-file water. As a consequence of strong water-water hydrogen bonds, many characteristics of single-file water are conserved in biological and synthetic pores despite differences in their atomistic structure. Charge transport and orientational order in water chains depend sensitively on and are mainly determined by electrostatic effects. Thus, mimicking functions of biological pores with apolar pores and corresponding external fields gives insight into the structure-function relation of biological pores and allows the development of technical applications beyond the molecular devices found in living systems. In this Perspective, we revisit results for single-file water in apolar pores, and examine the similarities and the differences between these simple systems and water in more complex pores.