Noise effects in two different biological systems

We investigate the role of the colored noise in two biological systems: (i) adults of Nezara viridula (L.) (Heteroptera: Pentatomidae), and (ii) polymer translocation. In the first system we analyze, by directionality tests, the response of N. viridula individuals to subthreshold signals plus noise in their mating behaviour. The percentage of insects that react to the subthreshold signal shows a nonmonotonic behaviour, characterized by the presence of a maximum, as a function of the noise intensity. This is the signature of the non-dynamical stochastic resonance phenomenon. By using a “soft” threshold model we find that the maximum of the input-output cross correlation occurs in the same range of noise intensity values for which the behavioural activation of the insects has a maximum. Moreover this maximum value is lowered and shifted towards higher noise intensities, compared to the case of white noise. In the second biological system the noise driven translocation of short polymers in crowded solutions is analyzed. An improved version of the Rouse model for a flexible polymer is adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and the effects of a Lennard-Jones potential between all beads. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion in the presence of thermal fluctuations and a colored noise source. At low temperatures or for strong colored noise intensities the translocation process of the polymer chain is delayed. At low noise intensity, as the polymer length increases, we find a nonmonotonic behaviour for the mean first translocation time of the polymer centre of inertia. We show how colored noise influences the motion of short polymers, by inducing two different regimes of translocation in the dynamics of molecule transport.     

Active membranes studied by X-ray scattering

In view of recent theories of “active” membranes, we have studied multilamellar phospholipid membrane stacks with reconstituted transmembrane protein bacteriorhodopsin (BR) under different illumination conditions by X-ray scattering. The light-active protein is considered as an active constituent which drives the system out of equilibrium and is predicted to change the collective fluctuation properties of the membranes. Using X-ray reflectivity, X-ray non-specular (diffuse) scattering, and grazing incidence scattering, we find no detectable change in the scattering curves when changing the illumination condition. In particular the intermembrane spacing d remains constant, after eliminating hydration-related artifacts by design of a suitable sample environment. The absence of any observable non-equilibrium effects in the experimental window is discussed in view of the relevant parameters and recent theories.     

Interactions between isolated nucleosome core particles: A tail-bridging effect?

Interactions between isolated nucleosome core particles are studied as a function of the monovalent salt concentration by osmometry and by electrophoretic mobility measurements. The data are compared to the measurements performed on the protein-free DNA fragments and also analysed using the conventional theoretical approach. At low salt, an electrostatic screening effect accounts for the variation of the second virial coefficient whereas the simple hard-core contribution becomes predominant at high salt. In the intermediate range, an attraction occurs. In the light of previous results (Mangenot et al. Biophys. J. 82, 345 (2002)), we show that the flexible basic proteic tails are responsible for this attraction. A tail-bridging effect is discussed. Received 4 October 2001     

Surfaces with quenched and annealed disordered charge distributions

We consider surfaces with disordered charge distribution. The disorder can be caused by mobile charges, as for example in mixed lipid bilayers, or by weakly charged surfaces where charge regulation takes place (e.g. carboxyl groups). Using Monte-Carlo simulation methods we find for quenched as well as annealed disordered charge distributions counterion densities close to the surface that are significantly larger than for ordered regularly spaced surface ions. Our field-theoretic results agree well with results obtained from Monte-Carlo simulations of the system. Furthermore, we obtain expressions for the effective interaction between charged colloids and charged rods close to a charged surface and discuss the effect of the surface-ion mobility and polarization charges on the interaction. In general, polarization effects as well as surface-ion mobility lead to a weakening of the effective interaction between charged objects.     

Specific biomembrane adhesion --Indirect lateral interactions between bound receptor molecules

We studied biomembrane adhesion using the micropipet aspiration technique. Adhesion was caused by contact site A, a laterally mobile and highly specific cell adhesion molecule from Dictyostelium discoideum, reconstituted in lipid vesicles of DOPC (L-α-dioleoylphosphatidylcholine) with an addition of 5 mol % DOPE-PEG₂₀₀₀ (1,2-diacyl-sn-glycero-3-phosphatidylethanolamine-N-[poly(ethyleneglycol) 2000]). The “fuzzy” membrane mimics the cellular plasma membrane including the glycocalyx. We found adhesion and subsequent receptor migration into the contact zone. Using membrane tension jumps to probe the equation of state of the two-dimensional “gas” of bound receptor pairs within the contact zone, we found strong, attractive lateral interactions. Received 16 February 2001     

Bilayers of neutral lipids bear a small but significant charge

Many experiments done on neutral lipid bilayers in pure water show weak repulsions. These weak forces prevent vesicles from adhering and are generally overcome by adding some salt in the aqueous medium. They also appear as stray repulsions in surface forces measurements made on lipid bilayers. Using a surface forces apparatus in pure water and in salt solution, we have measured the forces between two stearoyl-oleoyl-phosphatidyl-choline (SOPC) bilayers and between two dimiristoyl-phosphatidyl-ethanolamine (DMPE) bilayers. The results show that the repulsions are due to a small amount of negative charges coming from impurities in SOPC. This was quantitatively confirmed by electrophoretic measurements. There are 3 times less charges in the case of DMPE layers. The effect of these charges which is negligible at high salt concentration may significantly affect the adhesion energy and behaviour of neutral lipid bilayers between 0 and salt. Received 18 December 1998     

脂质体包裹荧光受体方法研究a-突触核蛋白在磷脂膜上的结构和动态特征

α-突触核蛋白(α-synuclein,α-syn)在帕金森病的发病机理中起着关键的作用,因而近年来受到了越来越广泛的关注.α-syn在膜上的动力学过程对理解其功能至关重要.本文使用基于脂质体的单分子荧光衰减方法——LipoFRET,首次对较高浓度下α-syn与磷脂膜的相互作用的动态过程进行了单分子层面上的研究.研究发现,在溶液中α-syn浓度升高时,其中央NAC区域可离开磷脂膜表面进入水相中;而N端部分位于膜表面内的位置变浅,并有更高的概率脱离膜表面进入溶液中.利用单分子荧光成像对α-syn解离的观察则发现,随着溶液中的α-syn浓度升高,脂质体上的α-syn解离速率加快.因此高浓度下,α-syn在膜上各区域垂直位置变化促进了蛋白从膜上的解离.结合LipoFRET的实验结果可以推断,α-syn的解离可能是由于不同的α-syn分子膜作用位点互相竞争而导致的解离.这样的特征,可能是体内环境中影响α-syn控制其聚集的重要性质.     

N-body study of anisotropic membrane inclusions: Membrane mediated interactions and ordered aggregation

We study the collective behavior of inclusions inducing local anisotropic curvatures in a flexible fluid membrane. The N-body interaction energy for general anisotropic inclusions is calculated explicitly, including multi-body interactions. Long-range attractive interactions between inclusions are found to be sufficiently strong to induce aggregation. Monte Carlo simulations show a transition from compact clusters to aggregation on lines or circles. These results might be relevant to proteins in biological membranes or colloidal particles bound to surfactant membranes. Received 30 July 1999 and Received in final form 8 September 1999     

Modeling of recognition sites of nucleic acid bases aaand amide side chains of amino acids. Combination of experimental and theoretical approaches

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as - ΔH (kJ mole^-1) decreases as: m⁹Gua (- 59.5) > m ¹Cyt (- 57.0) > m ⁹Ade (- 52.0) ≫m ¹Ura (- 40.6). We have determined that in the double stranded DNA only purine bases can be recognized. Received 5 February 2002 and Received in final form 14 March 2002 Published online 13 September 2002     

Protein–membrane interactions investigated with surface-induced fluorescence attenuation

Research on protein–membrane interactions has been undeveloped due to the lack of proper techniques to detect the position of proteins at membranes because membranes are usually only about 4-nm thick. We have recently developed a new method named surface-induced fluorescence attenuation(SIFA) to track both vertical and lateral kinetics of a single labelling dye in supported lipid bilayers. It takes advantage of strong interaction between a light-emitting dye and a partially reflecting surface. By applying the technique to membrane proteins being fluorescently labelled at different residues, here we show that SIFA can measure not only the insertion depth of a dye inside a lipid bilayer, but also the position of a dye in solution near the surface. SIFA can therefore be used to study membrane proteins of various types.