Metal-mediated peptide assembly: use of metal coordination to change the oligomerization state of an alpha-helical coiled-coil

Metal coordination is used to alter the oligomerization state of a designed peptide structure. The 30-residue polypeptide AQ-Pal14Pal21contains two metal-binding 4-pyridylalanine (Pal) residues on its solvent-exposed surface and exists as a very stable two-stranded alpha-helical coiled-coil. Upon the addition of Pt(en)(NO3)2, a significant conformational change to a metal-bridged, four-helix bundle is seen.     

Construction of a pH-responsive artificial membrane fusion system by using designed coiled-coil polypeptides

In many viruses, pH-responsive coiled-coil domains in the specific fusion proteins play important roles in membrane fusion and the infection of viruses into host cells. To investigate the relationship between the conformational change of the coiled coil and the fusion process, we have introduced a de novo designed polypeptide as a model system of the coiled-coil domain. This system enables the systematic study of the dynamics of pH-responsive coiled-coil polypeptide-membrane interactions. First, we designed and synthesized pH-responsive isoleucine-zipper triple-stranded coiled-coil polypeptides. Then the relationship between the pH-induced conformational change of the polypeptide and the membrane's interactive properties was studied by physicochemical methods. Structural changes in the designed polypeptides were examined by means of circular dichroism measurements. And finally, the behavior of the membrane fusion was investigated by leakage of liposomal contents, turbidity analysis, dynamic light scattering, and lipid mixing experiments. Our data show that coiled-coil formation under acidic pH conditions enhances polypeptide-induced membrane fusion. The results in this study demonstrate that an artificial membrane fusion system can be constructed on a molecular level by the use of a pH-responsive isoleucine-zipper triple-stranded coiled-coil polypeptide.     

Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.     

Temperature profiling of polypeptides in reversed-phase liquid chromatography. II. Monitoring of folding and stability of two-stranded alpha-helical coiled-coils

The present study extends the utility of reversed-phase high-performance liquid chromatography (RP-HPLC) to monitor folding and stability of de novo designed synthetic two-stranded alpha-helical coiled-coils. Thus, we have compared the effect of temperature on the RP-HPLC retention behaviour of both oxidized (two identical five-heptad alpha-helical peptides linked by a disulfide bridge) and reduced coiled-coil analogues with various amino acids substituted into the hydrophobic core of the coiled-coil. We were able to correlate the RP-HPLC retention behaviour of the oxidized analogues over the temperature range of 10 to 80 degrees C with the stability of the analogues as determined by conventional thermal and chemical denaturation approaches. In addition, the contribution of a disulfide bridge to coiled-coil stability was highlighted by comparing the elution behaviour of the oxidized and reduced analogues. Overall, we demonstrate the excellent potential of "temperature profiling" by RP-HPLC to monitor differences in oligomerization state and protein stability.     

Time-dependent wave packet study on trans-cis isomerization of HONO driven by an external field

The present paper is devoted to a full quantum mechanical study of the cis-->trans isomerization of HONO. In contrast to our previous study [Richter et al., J. Chem. Phys. 120, 6072 (2004)], the dynamics is now performed in the presence of an external time-dependent field in order to be closer to experimental conditions. A six-dimensional dipole surface is computed. Using a previously developed potential energy surface [Richter et al., J. Chem. Phys. 120, 1306 (2004)], all eigenstates up to 4000 cm(-1) are calculated. We simulate the dynamics during and after excitation by an electromagnetic pulse whose parameters are chosen to efficiently trigger the isomerization. Our investigations show that there is a selective isomerization pathway.     

The role of exchange-correlation functionals in the potential energy surface and dynamics of N(2) dissociation on W surfaces

We study the dissociative adsorption of N(2) on W(100) and W(110) by means of density functional theory and classical dynamics. Working with a full six-dimensional adiabatic potential energy surface (PES), we find that the theoretical results of the dynamical problem strongly depend on the choice of approximate exchange-correlation functional for the determination of the PES. We consider the Perdew-Wang-91 [Perdew et al., Phys. Rev. B 46, 6671 (1992)] and Perdew-Burke-Ernzerhof (RPBE) [Hammer et al., Phys. Rev. B 59, 7413 (1999)] functionals and carry out a systematic comparison between the dynamics determined by the respective PESs. Even though it has been shown in earlier works that the RPBE may provide better values for the chemisorption energies, our study brings evidence that it gives rise to a PES with excessive repulsion far from the surface.     

A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks

The rotation and translation block (RTB) method of Durand et al. [Biopolymers 34, 759 (1994)] and Tama et al. [Proteins 41, 1 (2000)] provides an appealing way to calculate low-frequency normal modes of large biomolecules by restricting the space of motions to exclude internal motions of preselected rigid fragments within the molecule. These fragments are modeled essentially as rigid bodies and the need to calculate high-frequency relative motions of the atoms that form them is obviated in a natural way. Here we extend the RTB approach into a method for computing the classical (Newtonian) dynamics of a biomolecule, or any large molecule, with effective rigid-body constraints applied to a prechosen set of internal molecular fragments. This method, to be termed RTB dynamics, is easy to implement, conserves the total energy of the system, does not require the construction of the matrix of second spatial derivatives of the potential-energy function (Hessian matrix), and can be used to compute the classical dynamics of a system moving in an arbitrary anharmonic force field. An elementary numerical application to signal propagation in the small membrane-bound polypeptide gramicidin-A is presented for illustration purposes.     

A numerical study of the effect of insoluble surfactants on the stability of a viscous drop translating in a Hele-Shaw cell

A circular drop is a linearly stable solution for the buoyancy-driven motion of drops in a Hele-Shaw cell [Gupta et al. J. Colloid Interface Sci.218(1), 338 (1999)]. In the absence of surface-active agents, an initially prolate drop always goes to a steady circular shape while initially oblate drops exhibit complex dynamics [Gupta et al. J. Colloid Interface Sci.222, 107 (2000)]. In this study, the effect of insoluble surfactant impurities on the critical conditions for drop breakup is explored by using the Langmuir adsorption framework in conjunction with a physically based expression for the depth-averaged tangential stress exerted on a two-phase interface in a Hele-Shaw cell. It is shown that the presence of surfactants can have both a stabilizing and a destabilizing effect on the shape of the drop, depending on the Bond number, the magnitude of the initial perturbation, and the strength of surface convection. Similar to the clean drop dynamics, two marginally stable branches are found. Increasing the surface Peclet number results in the stabilization of the main branch while the secondary branch shifts to higher Bond numbers. The mode of breakup is also found to be strongly influenced by the strength of surface convection.     

On the probability of nucleation at the surface of freezing drops

Recent publications have proposed that nucleation in the freezing of supercooled drops occurs at the drop surface, an idea supported by statistical thermodynamic arguments by Cahn [J. Chem. Phys. 1977, 66, 3667] coupled with thermodynamic arguments by Tabazadeh et al. [Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15873]. Whether this phenomenon is general is examined by molecular dynamics simulations of the freezing of deeply supercooled liquid clusters of SeF6. It is found for this model system that while nucleation occurs not infrequently at the surface, it more often takes place in the interior. The probability for surface nucleation increases with the depth of supercooling. How this relates to theories of Cahn and Tabazadeh et al. is discussed briefly.     

Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: molecular mechanics and correlated ab initio study

Potential energy surfaces of monohydrated and dihydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs were examined by the molecular dynamics/quenching technique using the Cornell et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of molecular dynamics/quenching calculations allowed us to evaluate the free energy surface. The most stable and populated structures found were fully reoptimized at the correlated ab initio level employing the resolution of identity M?ller-Plesset method. A systematic study of the base pairs' microhydration using both the empirical and the high-level correlated ab initio approaches is presented for the first time. We show that the occurrence of water molecules and their gradually increasing number as well as the methylation of the bases favor stacked structures over the planar hydrogen-bonded ones. These results based on the correlated ab initio calculations are in the excellent agreement with data obtained from our previous empirical potential molecular dynamics study (Kabelác et al. Chem.-Eur. J. 2001, 7, 2067).     

Dynamic surface tension of polyelectrolyte/surfactant systems with opposite charges: two states for the surfactant at the interface

The molecular reorientation model of Fainerman et al. is conceptually adapted to explain the dynamic surface tension behavior in polyelectrolyte/surfactant systems with opposite charges. The equilibrium surface tension curves and the adsorption dynamics may be explained by assuming that there are two different states for surfactant molecules at the interface. One of these states corresponds to the adsorption of the surfactant as monomers, and the other to the formation of a mixed complex at the surface. The model also explains the plateaus that appear in the dynamic surface tension curves and gives a picture of the adsorption process.     

Crystallization of alkane melts induced by carbon nanotubes and graphene nanosheets: a molecular dynamics simulation study

The crystallization of alkane melts on carbon nanotubes (CNT) and the surface of graphene nanosheets (GNS) is investigated using molecular dynamics (MD) simulations. The crystallization process of the alkane melts is analyzed in terms of the bond-orientational order parameter, atomic radial distribution for the CNT/alkane, atomic longitudinal distribution for the GNS/alkane, and diffusion properties. The dimensional effects of the different carbon-based nanostructures on the crystallization of alkane melts are shown. It is found that one-dimensional CNT has a stronger ability to induce the crystallization of the polymer than that of two-dimensional GNS, which provides a support at molecular level for the experimental observation [Li et al., J. Am. Chem. Soc., 2006, 128, 1692 and Xu et al., Macromolecules, 2010, 43, 5000]. From the MD simulations, we also find that the crystallization of alkane molecules has been completed with the highly cooperative processes of adsorption and orientation.     

Tension-induced morphological transition in mixed lipid bilayers

Recently, Rozovsky et al. reported on the morphology and dynamics of superstructures in three-component lipid bilayers containing saturated lipid, unsaturated lipid, and cholesterol (Rozovsky, S.; Kaizuka, Y.; Groves, J. T. J. Am. Chem. Soc. 2005, 127, 36). We suggest that the observed sequence of the striped-to-hexagonal morphological transition in mixed bilayers can be attributed to an enhanced membrane surface tension that is induced by the vesicle adhesion onto the solid surface.     

Large-amplitude quantum mechanics in polyatomic hydrides. II. A particle-on-a-sphere model for XH(n) (n=4,5)

This paper describes the application of a relatively simple, but computationally tractable, "particle-on-a-sphere" (POS) model for quantum-mechanical calculation of large-amplitude, H atom dynamics in polyatomic hydrides (XH(n)), based on radially relaxed, two-dimensional angular motion of H atoms on the surface of a sphere. This work focuses on systems with many degrees of freedom, i.e., XH(4) (eight dimensional) and XH(5) (ten dimensional), with corresponding molecular analogs of CH(4) and CH(5) (+) and is applicable to rovibrationally excited states with J> or =0. A pairwise-additive potential fit for CH(5) (+), which yields remarkable agreement with geometries, energies, and barrier heights on the full-dimensional surface of Brown et al. [J. Chem. Phys. 121, 4105 (2004)] is presented. Comparisons with experimental data and diffusion quantum Monte Carlo (DMC) methods test convergence for the POS model and provide insight into multidimensional quantum rovibrational dynamics. In particular, POS energy-level patterns for a series of scaled CH(5) (+) potentials indicate an absence of strong tunneling behavior, consistent with the highly delocalized wave functions, large zero-point energies, and small interconversion barriers noted in previous DMC studies of Brown et al.     

Quasiclassical trajectory calculations comparing the reactivity and dynamics of symmetric and asymmetric stretch and the role of the bending mode excitations of methane in the Cl + CH4 reaction

To analyze the effects of the symmetric (nu(1)) and asymmetric (nu(3)) stretch mode excitations and the role played by the "umbrella" bending (nu(4)) mode excitation in the reactivity and the dynamics of the gas-phase Cl+CH(4) reaction, an exhaustive dynamics study was performed. Quasiclassical trajectory (QCT) calculations, including corrections to avoid zero-point energy leakage along the trajectories, were used in this work on an analytical potential energy surface previously developed by Espinosa-Garcia et al. [J. Chem. Phys. (to be published)]. First, with respect to the reactivity, we found that the nu(1) mode excitation is more reactive than the nu(3) mode by a factor of 1.20, in agreement with the experimental tendency between these modes. The inclusion of the nu(4) bending mode practically does not affect this relative reactivity, (nu(1+)nu(4))(nu(3+)nu(4)) = 1.16. Second, with respect to the dynamics (rotovibrational and angular distributions of the products), the two stretch modes, nu(1) and nu(3), give very similar pictures, reproducing the experimental behavior, and the nu(4) "umbrella" mode does not affect the dynamics. The satisfactory reproduction (always qualitatively acceptable and sometimes even quantitatively) of a great variety of experimental data by the QCT study presented here lends confidence to the potential energy surface constructed by Espinosa-Garcia et al. [J. Chem. Phys. (to be published)].     

Adsorption configuration effects on the surface diffusion of large organic molecules: the case of Violet Lander

Violet Lander (C(108)H(104)) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology.     

State-to-state reaction probabilities for the H+O2(v,j)-->O+OH(v',j') reaction on three potential energy surfaces

We report state-to-state and total reaction probabilities for J=0 and total reaction probabilities for J=2 and 4 for the title reaction, both for ground-state and initially rovibrationally excited reactants. The results for three different potential energy surfaces are compared and contrasted. The potential energy surfaces employed are the DMBE IV surface by Pastrana et al. [J. Phys. Chem. 94, 8073 (1990)], the surface by Troe and Ushakov (TU) [J. Chem. Phys. 115, 3621 (2001)], and the new XXZLG ab initio surface by Xu et al. [J. Chem. Phys. 122, 244305 (2005)]. Our results show that the total reaction probabilities from both the TU and XXZLG surfaces are much smaller in magnitude for collision energies above 1.2 eV compared to the DMBE IV surface. The three surfaces also show different behavior with regards to the effect of initial state excitation. The reactivity is increased on the XXZLG and the TU surfaces and decreased on the DMBE IV surface. Vibrational and rotational product state distributions for the XXZLG and the DMBE IV surface show different behaviors for both types of distributions. Our results show that for energies above 1.25 eV the dynamics on the DMBE IV surface are not statistical. However, there is also evidence that the dynamics on the XXZLG surface are not purely statistical for energies above the onset of the first excited product vibrational state v'=1. The magnitude of the total reaction probability is decreased for J>0 for the DMBE IV and the XXZLG surfaces for ground-state reactants. However, for initially rovibrationally excited reactants, the total reaction probability does not decrease as expected for both surfaces. As a result the total cross section averaged over all Boltzmann accessible rotational states may well be larger than the cross section reported in the literature for j=1.     

Sliding friction between polymer surfaces: a molecular interpretation

For two contacting rigid bodies, the friction force F is proportional to the normal load and independent of the macroscopic contact area and relative velocity V (Amonton's law). With two mutually sliding polymer samples, the surface irregularities transmit deformation to the underlying material. Energy loss along the deformation cycles is responsible for the friction force, which now appears to depend strongly on V [see, e.g., N. Maeda et al., Science 297, 379 (2002)]. We base our theoretical interpretation on the assumption that polymer chains are mainly subjected to oscillatory "reptation" along their "tubes." At high deformation frequencies-i.e., with a large sliding velocity V-the internal viscosity due to the rotational energy barriers around chain bonds hinders intramolecular mobility. As a result, energy dissipation and the correlated friction force strongly diminish at large V. Derived from a linear differential equation for chain dynamics, our results are basically consistent with the experimental data by Maeda et al. [Science 297, 379 (2002)] on modified polystyrene. Although the bulk polymer is below T(g), we regard the first few chain layers below the surface to be in the liquid state. In particular, the observed maximum of F vs V is consistent with physically reasonable values of the molecular parameters. As a general result, the ratio FV is a steadily decreasing function of V, tending to V(-2) for large velocities. We evaluate a much smaller friction for a cross-linked polymer under the assumption that the junctions are effectively immobile, also in agreement with the experimental results of Maeda et al. [Science 297, 379 (2002)].