We present experimental evidence for a long-range protein-protein interaction in purple membrane (PM). The interprotein dynamics were quantified by measuring the spectrum of the acoustic phonons in the 2D bacteriorhodopsin (BR) protein lattice using
inelastic neutron scattering. Phonon energies of about 1 meV were determined. The data are compared to an analytical model, and the effective spring constant for the interaction between neighboring protein trimers are determined to be k=53 N/m. Additional, optical-like excitations at 0.45 meV were found and assigned to intraprotein dynamics between neighboring BR monomers.
Neutrons and x-rays are coherent probes, and their coherent properties are used in scattering experiments. Only coherent scattering probes can elucidate collective molecular motions. While phonons in crystals were studied for half a century now, the
study of collective molecular motions in soft-matter and biology is a rather new but upcoming field. Collective dynamics often determine material properties and interactions, and are crucial to establish dynamics-function relations. We review properties of neutrons and x-rays and derive the origin of coherent and incoherent scattering. Taking molecular motions in membranes and proteins as example, the difference between coherent and incoherent dynamics is discussed, and how local and collective motions can be accessed in x-ray and neutron scattering experiments. Matching of coherent properties of the scattering probe may become important in soft-matter and biology because of (1) the missing long ranged order and (2) the large length scales involved. It is likely to be important in systems, where fluctuating nanoscale domains strongly determine material properties. Inelastic scattering can provide very local structural information in disordered systems. Inelastic neutron scattering experiments point to a coexistence of short-lived nanoscale gel and fluid domains in phospholipid bilayers in the range of the gel-fluid phase transition, which may be responsible for critical behavior and determine elastic properties.
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of membrane compos
ition and properties and of structure and dynamics of the surrounding hydration water on protein function is an upcoming hot topic, which can be addressed by modern experimental and computational techniques. Correlated molecular motions might play a crucial role for the understanding of, for instance, transport processes and elastic properties, and might be relevant for protein function. Experimentally that involves determining dispersion relations for the different molecular components, i.e., the length scale dependent excitation frequencies and relaxation rates. Only very few experimental techniques can access dynamical properties in biological materials on the nanometer scale, and resolve dynamics of lipid molecules, hydration water molecules and proteins and the interaction between them. In this context, inelastic neutron scattering turned out to be a very powerful tool to study dynamics and interactions in biomolecular materials up to relevant nanosecond time scales and down to the nanometer length scale. We review and discuss inelastic neutron scattering experiments to study membrane elasticity and protein-protein interactions of membrane embedded proteins.
The nanoscale fluctuation dynamics of semi dilute high molecular weight polymer solutions of Polyethylenoxide (PEO) in D2O under non-equilibrium flow conditions were studied by the neutron spin-echo technique. The sample cell was in contraction flow
geometry and provided a pressure driven flow with a high elongational component that stretched the polymers most efficiently. The experiments suggest that the mobility on the scale of a few monomers, comparable to the Kuhn segment length, becomes highly anisotropic and is enhanced perpendicular to the flow direction. Diffraction data show a weak structural correlation along the chains on a length scale of about 17 Angstroems, which might be related to the Kuhn length in this system.
We report a high energy-resolution neutron backscattering study, combined with in-situ diffraction, to investigate slow molecular motions on nanosecond time scales in the fluid phase of phospholipid bilayers of 1,2-dimyristoyl-sn-glycero-3-phoshatidy
lcholine (DMPC) and DMPC/40% cholesterol (wt/wt). A cooperative structural relaxation process was observed. From the in-plane scattering vector dependence of the relaxation rates in hydrogenated and deuterated samples, combined with results from a 0.1 microsecond long all atom molecular dynamics simulation, it is concluded that correlated dynamics in lipid membranes occurs over several lipid distances, spanning a time interval from pico- to nanoseconds.
We use a long, all-atom molecular dynamics (MD) simulation combined with theoretical modeling to investigate the dynamics of selected lipid atoms and lipid molecules in a hydrated diyristoyl-phosphatidylcholine (DMPC) lipid bilayer. From the analysis
of a 0.1 $mu$s MD trajectory we find that the time evolution of the mean square displacement, [delta{r}(t)]^2, of lipid atoms and molecules exhibits three well separated dynamical regions: (i) ballistic, with [delta{r}(t)]^2 ~ t^2 for t < 10 fs; (ii) subdiffusive, with [delta{r}(t)]^2 ~ t^{beta} with beta<1, for 10 ps < t < 10 ns; and (iii) Fickian diffusion, with [delta{r}(t)]^2 ~ t for t > 30 ns. We propose a memory function approach for calculating [delta{r}(t)]^2 over the entire time range extending from the ballistic to the Fickian diffusion regimes. The results are in very good agreement with the ones from the MD simulations. We also examine the implications of the presence of the subdiffusive dynamics of lipids on the self-intermediate scattering function and the incoherent dynamics structure factor measured in neutron scattering experiments.
