Structural flexibility of a helical peptide regulates vibrational energy transport properties

Applying ultrafast vibrational spectroscopy, we find that vibrational energy transport along a helical peptide changes from inefficient but mostly ballistic below approximately 270 K into diffusive and significantly more efficient above. On the basis of molecular dynamics simulations, we attribute this change to the increasing flexibility of the helix above this temperature, similar to the glass transition in proteins. Structural flexibility enhances intramolecular vibrational energy redistribution, thereby refeeding energy into the few vibrational modes that delocalize over large parts of the structure and therefore transport energy efficiently. The paper outlines concepts how one might regulate vibrational energy transport properties in ultrafast photobiological processes, as well as in molecular electronic devices, by engineering the flexibility of their components.     

Influence of nanotopography on phospholipid bilayer formation on silicon dioxide

We have investigated the effect of well-defined nanoscale topography on the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid vesicle adsorption and supported phospholipid bilayer (SPB) formation on SiO2 surfaces using a quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). Unilamellar lipid vesicles with two different sizes, 30 and 100 nm, were adsorbed on pitted surfaces with two different pit diameters, 110 and 190 nm, as produced by colloidal lithography, and the behavior was compared to results obtained on flat surfaces. In all cases, complete bilayer formation was observed after a critical coverage of adsorbed vesicles had been reached. However, the kinetics of the vesicle-to-bilayer transformation, including the critical coverage, was significantly altered by surface topography for both vesicle sizes. Surface topography hampered the overall bilayer formation kinetics for the smaller vesicles, but promoted SPB formation for the larger vesicles. Depending on vesicle size, we propose two modifications of the precursor-mediated vesicle-to-bilayer transformation mechanism used to describe supported lipid bilayer formation on the corresponding flat surface. Our results may have important implications for various lipid-membrane-based applications using rough or topographically structured surfaces.     

Around Solomon’s Descent Algebras

We study different problems related to the Solomon’s descent algebra Σ(W) of a finite Coxeter group (W,S): positive elements, morphisms between descent algebras, Loewy length... One of the main result is that, if W is irreducible and if the longest element is central, then the Loewy length of Σ(W) is equal to . Presented by Alain Verschoren.     

Atomistic insights into rhodopsin activation from a dynamic model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.     

Protein folding kinetics under force from molecular simulation

Despite a large number of studies on the mechanical unfolding of proteins, there are still relatively few successful attempts to refold proteins in the presence of a stretching force. We explore refolding kinetics under force using simulations of a coarse-grained model of ubiquitin. The effects of force on the folding kinetics can be fitted by a one-dimensional Kramers theory of diffusive barrier crossing, resulting in physically meaningful parameters for the height and location of the folding activation barrier. By comparing parameters obtained from pulling in different directions, we find that the unfolded state plays a dominant role in the refolding kinetics. Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces.     

Spectroscopic characterization of molybdenum dinitrogen complexes containing a combination of di- and triphosphine coligands: 31P NMR analysis of five-spin systems

The three molybdenum-N2 complexes [Mo(N2)(dpepp)(depe)] (1), [Mo(N2)(dpepp)(dppe)] (2), and [Mo(N2)(dpepp)(1,2-dppp)] (3), all of which contain a combination of a bi- and a tridentate phosphine ligand, were prepared and investigated by vibrational and (31)P NMR spectroscopy. As a tridentate ligand bis(2-diphenylphosphinoethyl)phenylphosphine (dpepp) has been employed. The three different bidentate ligands are 1,2-bis(diethylphosphino)ethane (depe), 1,2-bis(diphenylphosphino)ethane (dppe), and R-(+)-1,2-bis(diphenylphosphino)propane (1,2-dppp). N-N as well as metal-N vibrations of 1-3 are identified and interpreted in terms of the geometric and electronic structures of the complexes. (31)P NMR spectra are recorded and fully analyzed. Moreover, correlation spectroscopy (COSY)-45 measurements are performed to determine the relative signs of coupling constants. Special attention is directed to a detection of different isomers and their (31)P NMR, as well as vibrational spectroscopic properties. The implications of the results for the area of synthetic nitrogen fixation with phosphine complexes are discussed.     

Short-time transport properties in dense suspensions: from neutral to charge-stabilized colloidal spheres

We present a detailed study of short-time dynamic properties in concentrated suspensions of charge-stabilized and of neutral colloidal spheres. The particles in many of these systems are subject to significant many-body hydrodynamic interactions. A recently developed accelerated Stokesian dynamics (ASD) simulation method is used to calculate hydrodynamic functions, wave-number-dependent collective diffusion coefficients, self-diffusion and sedimentation coefficients, and high-frequency limiting viscosities. The dynamic properties are discussed in dependence on the particle concentration and salt content. Our ASD simulation results are compared with existing theoretical predictions, notably those of the renormalized density fluctuation expansion method of Beenakker and Mazur [Physica A 126, 349 (1984)], and earlier simulation data on hard spheres. The range of applicability and the accuracy of various theoretical expressions for short-time properties are explored through comparison with the simulation data. We analyze, in particular, the validity of generalized Stokes-Einstein relations relating short-time diffusion properties to the high-frequency limiting viscosity, and we point to the distinctly different behavior of de-ionized charge-stabilized systems in comparison to hard spheres.     

Maximum Caliber: a variational approach applied to two-state dynamics

We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same spirit that Maximum Entropy is a variational principle for equilibrium statistical mechanics. The central idea is to compute a dynamical partition function, a sum of weights over all microscopic paths, rather than over microstates. We illustrate the method on the simple problem of two-state dynamics, A<-->B, first for a single particle, then for M particles. Maximum Caliber gives a unified framework for deriving all the relevant dynamical properties, including the microtrajectories and all the moments of the time-dependent probability density. While it can readily be used to derive the traditional master equation and the Langevin results, it goes beyond them in also giving trajectory information. For example, we derive the Langevin noise distribution rather than assuming it. As a general approach to solving nonequilibrium statistical mechanics dynamical problems, Maximum Caliber has some advantages: (1) It is partition-function-based, so we can draw insights from similarities to equilibrium statistical mechanics. (2) It is trajectory-based, so it gives more dynamical information than population-based approaches like master equations; this is particularly important for few-particle and single-molecule systems. (3) It gives an unambiguous way to relate flows to forces, which has traditionally posed challenges. (4) Like Maximum Entropy, it may be useful for data analysis, specifically for time-dependent phenomena.     

Influence of the remanent polarisation on the liquid crystal alignment in composite films of ferroelectric poly(vinylidene fluoride-trifluoroethylene) and a cyanobiphenyl-based liquid crystal

Polymer-dispersed liquid crystals (PDLCs) of ferroelectric poly(vinylidene fluoride-trifluoroethylene) and nematic 4-cyano-4?-n-hexylbiphenyl (6CB) or 4-cyano-4?-n-pentylbiphenyl (5CB) were prepared to study the effect of the remanent polarisation of the polymer on the liquid crystal alignment. We measured the macroscopic alignment of the liquid crystal molecules in the thickness direction by means of Infrared Transition-Moment Orientational Analysis. Electrical poling at 100 V/µm caused an increased order parameter up to 0.15. After subsequent annealing above the nematic-to-isotropic phase-transition temperature, the order parameter was reduced to 0.02. Nevertheless, the order parameter was still higher than for non-poled film indicating a slight orientation in thickness direction. Both values are lower than those expected from model calculations. In agreement with dielectric measurements, we attribute this result to the shielding effect of mobile charge carriers within the liquid crystal inclusions.