Connecting cluster dynamics and protein folding

The relaxation dynamics of clusters can be interpreted in terms of the topographies of their potential surfaces. Systems with short-range potentials have sawtooth-like potential surfaces with small drops in energy from one local minimum to the next and few-body motions as the clusters move from one minimum to another; such systems readily take on amorphous structures. These are called “glass-formers". Systems with long-range forces have potentials whose topographies are like rough staircases, with some large drops in energy from one minimum to the next; their well-to-well passages involve very collective motions and such systems are excellent structure-seekers. They find their way to well-ordered, highly selective structures under almost all circumstances. These characteristics generalize to describe the potential surfaces and folding behavior of polypeptides and proteins. The forces are effective long-range forces due to the polymer chain. Staircase topographies emerge both from direct sampling of potential surfaces and from the inversion of the kinetics generated by a much more aaabstract topological model, from which folding pathways can be inferred. Received 4 December 2000     

Chain conformations and photoluminescence of poly(di-n-octylfluorene)

The diverse steady-state spectroscopic properties of poly(di-n-octylfluorene) are addressed from a molecular-level perspective. Modeling of representative oligomers support the experimental observation of at least three distinguishable classes of conformational isomers with differing chain torsion angles. One class appears to be populated by a single compact structural isomer, and this conforms to the so-called beta phase. A rigorous Franck-Condon analysis of the photoluminescence in conjunction with Frenkel-type exciton band structure calculations is performed. These results accurately reproduce all major spectral features of the photoabsorption and those of singlet exciton emission.     

基于氨基酸位置特异性的蛋白质Loop区结构预测改进方法

蛋白质loop区的结构预测是理解蛋白质功能的重要一环,而长loop区的结构预测至今还是生物信息学中的难题.目前己经出现了多种loop结构的算法,其中LEAP是预测精度最高的算法之一,但它在长loop区初始主链构象采样上仍有较大的改进余地.本文中我们将蛋白质二级结构预测算法SPINE X与LEAP算法结合起来,构建了新的主链扭转角分布图(拉氏图),在主链初始构象采样中引入氨基酸在蛋白序列中的位置特异性信息,使得初始构象的采样更具针对性,对取自CASP10单链蛋白的loop测试集的分析表明,对长度为10,11,12个氨基酸的长loop区,改进后算法都比原始LEAP算法的预测精度有显著提升.这种引入氨基酸位置特异性从而提高预测精度的思路有望进一步推广至loop结构预测的其他算法.     

Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings

A simple and robust method for determining the relative orientations of covalently linked protein domains using conjoined rigid body/torsion angle dynamics simulated annealing on the basis of residual dipolar couplings is presented. In this approach each domain is treated as a rigid body and the relevant degrees of conformational freedom are restricted to the backbone torsion angles (phi, psi) of the linker between the domains. By this means translational information afforded by the presence of an intact linker is preserved. We illustrate this approach using the domain-swapped dimer of the HIV-inactivating protein cyanovirin-N as an example.     

Optimized angle selection for radial sampled NMR experiments

Sparse sampling offers tremendous potential for overcoming the time limitations imposed by traditional Cartesian sampling of indirectly detected dimensions of multidimensional NMR data. Unfortunately, several otherwise appealing implementations are accompanied by spectral artifacts that have the potential to contaminate the spectrum with false peak intensity. In radial sampling of linked time evolution periods, the artifacts are easily identified and removed from the spectrum if a sufficient set of radial sampling angles is employed. Robust implementation of the radial sampling approach therefore requires optimization of the set of radial sampling angles collected. Here we describe several methods for such optimization. The approaches described take advantage of various aspects of the general simultaneous multidimensional Fourier transform in the analysis of multidimensional NMR data. Radially sampled data are primarily contaminated by ridges extending from authentic peaks. Numerical methods are described that definitively identify artifactual intensity and the optimal set of sampling angles necessary to eliminate it under a variety of scenarios. The algorithms are tested with both simulated and experimentally obtained triple resonance data.     

Ab initio computational studies on molecular conformation of N-methyl-glyphosate

Conformational analysis of N-methyl-glyphosate has been carried out using an ab initio molecular orbital (MO) method at the HF/3-21G* levels of theory and the results are compared with the results of a previously studied compound, namely glyphosate. The potential energy surface of the molecule obtained by varying the central torsion angles (Φ, ψ) was investigated in detail. Fourteen conformers with 5 kcal mol^?1 energy cut-off have been selected from the potential energy surface for geometry optimization to locate the true minimum on the conformational space. The minimum has been found to be at (—62°, 110°.) for the central torsion angles. This conformation is stabilized by hydrogen bond interactions (O-H…O and C-H…O) and the interactions due to protons nearer to each other. This cationic field leads to the formation of a hydrophobic patch in this structure, as well as in the structures closer to the global minimum. This patch may destabilize the favourable interaction of N-methyl-glyphosate with the surrounding amino acid residues in the binding cavity as they form the cationic field throughout the glyphosate binding region.     

A double-minimum skeletal torsion in 1-silabicyclo[2.2.2]octane by microwave spectroscopy

The 1-silabicyclo[2.2.2]octane molecule HSi(CH₂CH₂)₃CH was investigated by microwave spectroscopy. The observed spectra followed the symmetric-rotor pattern with the unresolved K structures, but were accompanied by many strong vibrational satellites. A series of the prominent satellites was assigned to the excited states of the skeletal torsion. The transition frequencies and the relative intensities which were measured for the satellites were used to determine the double-minimum potential function to the skeletal torsion. The height of the potential hump and the equilibrium torsional angle, which was defined as the SiCCC dihedral angle, were determined to be 606 ± 40 cal/mole and 21.3° ± 1.0°, respectively. The results that the double-minimum nature of the potential function is more pronounced in 1-silabicyclo[2.2.2]octane than in other bicyclo[2.2.2]octane derivatives studied previously are discussed in detail in terms of the internal-rotation potential around the CC and CSi bonds and the strains in the valence angles of the C and Si atoms.     

On wide-band mirrors for soft X-ray range

The properties of smooth curved surfaces which can deflect the soft X-ray beams to large angles and reflect them effectively are considered. The wave sliding along the curved cylindrical surface has been analysed and the structure of the electromagnetic field has been found both in the medium and in vacuum. Large reflectivity has been predicted in wavelength regions 50 Å < λ < 150 Å and λ < 20 Å for several elements with known optical constants. In contrast to the multilayer structures which are widely used now, the curved mirrors provide a large reflectivity in a broad X-ray wavelength region.     

Isosteres of peptides: boron analogs as dipolar forms of α‐amino acids – a theoretical study

Modification of peptides to produce peptidomimetics is of great interest, with the aim of designing potent, selective, and metabolically stable analogs having certain conformational properties. Organoboranes have been reported in the literature with a wide range of therapeutic applications. One of the therapeutically important class of molecules is amine‐carboxyboranes derived from amino acids by replacement of the Cα atom of an amino acid/peptide by boron. The conformational preferences of these peptides, with respect to backbone ω, ?, and ψ torsion angles, have been investigated by theoretical calculations. The amide bond in these molecules has the same geometry in the ground and transition states as the natural peptides. However, the boron isosteres of glycine and alanine peptides are less structured than their natural derivatives, but are distinguished by structures with a positive value for the ? angle, which is normally disfavored for natural peptides. This property could be used to build peptides with a geometry not usually seen in natural peptides. Copyright © 2007 John Wiley & Sons, Ltd.     

Densities of states in the unoccupied bands of palladium in the region of ΓL

Features in the angle-resolved secondary electron emission from a Pd(111) surface are compared with regions of high one-dimensional densities of states in calculated band structures. Earlier measurements at normal exit are confirmed and extended over a range of angles away from ΓL and a new feature which disperses rapidly with angle is detected; very good agreement with an RAPW band structure is found.     

A practical cross-section for scattering from rough surfaces at very low grazing angles in both the forward and backward directions

In this paper we develop an extension of the small slope approximation (SSA) for scattering from randomly rough Dirichlet surfaces, which includes some multiple scattering. This extension is designated by SSA+. We focus on scattering at very low grazing angles where multiple scattering of both the incident and scattered fields is of importance. Numerical results for the SSA+ bistatic scattering cross-section for very low forward grazing angles are presented using the Gaussian roughness spectrum and for both very low forward and very low backward grazing angles using the Pierson–Moskowitz and modified power law spectra. The results are restricted to an angle of incidence of 80°. It is shown that when the lowest-order SSA gives reasonably accurate results, the SSA+ increases the accuracy up to at least the final 0.2° of grazing in the forward direction. In the backward direction, the SSA+ gives good results for the Pierson–Moskowitz spectrum, but the results are less dramatic.     

Sub-wavelength surface structuring of NiTi alloy by femtosecond laser pulses

Generation of self-organized sub-wavelength surface structures on a nickel–titanium alloy plate by femtosecond laser pulses is investigated experimentally through line-scribing experiments in air. It is found that Bragg-like relief gratings, with the orientation perpendicular to the laser polarization, are formed over the entire laser-scribed regions. The average period is measured as 630±30 nm. Distinctive features of these novel surface structures include nanoparticle-covered grating ridges and the maintainable spatial period regardless of incidence angles. With different laser parameters and sample scan speeds, sub-wavelength grating structures can evolve into cellular-like nanotextures. Optimal conditions for forming these surface structures are determined in terms of laser energy and scan speed. Elementary analyses of the structured surfaces by X-ray diffraction and photoelectron spectroscopy reveal that both the crystal structures and the chemical elements can remain in their original states, but the surface grains are refined and the atomic percentages are varied after femtosecond laser treatments.     

Determination of molecular geometry by high-order multiple-quantum evolution in solid-state NMR

The principles of molecular geometry determination by high-quantum heteronuclear local field spectroscopy in solid-state NMR are discussed. The extreme multiple-quantum coherences in a cluster of nuclear spins are allowed to evolve in the presence of heteronuclear through-space couplings to two spins of a different type. The multiple-quantum dephasing curve is independent of the homonuclear spin-spin couplings and may be described in terms of geometric parameters. The triple-quantum version of the experiment is demonstrated by determining the psi torsion angle in a [(15)N(2), (13)C(3)]-labeled sample of the peptide ala-ala-gly. Two regions of torsion angle space fit the experimental data, one in the neighborhood of -152 degrees and one in the neighborhood of +161 degrees. The latter determination is in excellent agreement with the X-ray estimate of +160.5 degrees.     

Calculation of 13C chemical shifts in rna nucleosides: structure-13C chemical shift relationships.

Isotropic 13C chemical shifts of the ribose sugar in model RNA nucleosides are calculated using SCF and DFT-GIAO ab initio methods for different combinations of ribose sugar pucker, exocyclic torsion angle, and glycosidic torsion angle. Idealized conformations were obtained using structures that were fully optimized by ab initio DFT methods starting with averaged parameters from a collection of crystallographic data. Solid-state coordinates of accurate crystal or neutron diffraction structures were also examined directly without optimization. The resulting 13C chemical shifts for the two sets of calculations are then compared. The GIAO-DFT method overestimates the shifts by an average of 5 ppm while the GIAO-SCF underestimates the shifts by the same amount. However, in the majority of cases the errors appear to be systematic, as the slope of a plot of calculated vs experimental shifts is very close to unity, with minimal scatter. The values of the 13C NMR shifts of the ribose sugar are therefore sufficiently precise to allow for statistical separation of sugar puckering modes and exocyclic torsion angle conformers, based on the canonical equation model formulated in a previous paper.     

Bistatic scattering and depolarization by randomly rough surfaces: application to the natural rough surfaces in X-band

Abstract

The scattering of waves by random rough surfaces has important applications in the remote sensing of oceans and land. The problem of developing a model for rough surfaces is very difficult since, at best, the scattering coefficient σ⁰ is dependent upon (at least) the radar frequency, geometrical and physical parameters, incident and observation angles, and polarization. The problem of electromagnetic scattering from a randomly rough surface is analysed using the Kirchhoff approximation (stationary phase, scalar approximation), the small-perturbation model and the two-scale models. A first major new consideration in this paper is the polarimetric signature calculations as a function of the transmitter location and receiver location for a bistatic radio-link. We calculate the like- and cross-polarized received power directly using the scattering coefficients, without calculating the Mueller matrix. Next, a study of the regions of validity of the Kirchhoff and small-perturbation rough surface scattering models (in the bistatic case) is presented. Comparisons between the numerical calculations and the models are made for various surface rms heights and correlation lengths both normalized to the incident wavenumber (denoted by σ and L, respectively). By using these two parameters to form a two-dimensional space, the approximate regions of validity are then established. The second major new consideration is the development of a theoretical two-scale model describing bistatic reflectivity as well as the numerical results computed for the bistatic radar cross section from rough surfaces especially from the sea and snow-covered surfaces. The results are used to show the Brewster angle effect on near-grazing angle scattering.     

Bistatic scattering and depolarization by randomly rough surfaces: application to the natural rough surfaces in X-band

The scattering of waves by random rough surfaces has important applications in the remote sensing of oceans and land. The problem of developing a model for rough surfaces is very difficult since, at best, the scattering coefficient σ⁰ is dependent upon (at least) the radar frequency, geometrical and physical parameters, incident and observation angles, and polarization. The problem of electromagnetic scattering from a randomly rough surface is analysed using the Kirchhoff approximation (stationary phase, scalar approximation), the small-perturbation model and the two-scale models. A first major new consideration in this paper is the polarimetric signature calculations as a function of the transmitter location and receiver location for a bistatic radio-link. We calculate the like- and cross-polarized received power directly using the scattering coefficients, without calculating the Mueller matrix. Next, a study of the regions of validity of the Kirchhoff and small-perturbation rough surface scattering models (in the bistatic case) is presented. Comparisons between the numerical calculations and the models are made for various surface rms heights and correlation lengths both normalized to the incident wavenumber (denoted by σ and L, respectively). By using these two parameters to form a two-dimensional space, the approximate regions of validity are then established. The second major new consideration is the development of a theoretical two-scale model describing bistatic reflectivity as well as the numerical results computed for the bistatic radar cross section from rough surfaces especially from the sea and snow-covered surfaces. The results are used to show the Brewster angle effect on near-grazing angle scattering.     

Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants

We apply Bayesian inference to analyze three-bond scalar coupling constants in an objective and consistent way. The Karplus curve and a Gaussian error law are used to model scalar coupling measurements. By applying Bayes' theorem, we obtain a probability distribution for all unknowns, i.e., the torsion angles, the Karplus parameters, and the standard deviation of the Gaussian. We infer all these unknowns from scalar coupling data using Markov chain Monte Carlo sampling and analytically derive a probability distribution that only involves the torsion angles.     

A simple fabrication method for mechanically robust superhydrophobic surface by hierarchical aluminum hydroxide structures

Superhydrophobic surfaces with uniformly superhydrophobic surface where nano-scale structures were fabricated by alkali surface modification method and self-assembled monolayer coating. To enhance mechanical durability of the superhydrophobicity, we propose the fabrication process for dual-scale hierarchical structures combining both microstructure via sandblasting techniques and the nanostructured aluminum hydroxide layer. The superhydrophobic surfaces fabricated by both methods exhibited a high water contact angle and very low contact angle hysteresis. By forming the hierarchical structure, the mechanical durability of superhydrophobic aluminum hydroxide surface was improved. The resulting hierarchical structures are suitable for diverse applications of aluminum in various industrial areas, including self-cleaning, anti-frosting, and microfluidic devices for rigorous environments.     

Determination of the backbone torsion psi angle by tensor correlation of chemical shift anisotropy and heteronuclear dipole-dipole interaction

We demonstrate that the backbone torsion psi angle of a uniformly labeled residue can be determined accurately by correlating the chemical shift anisotropy of the carbonyl carbon and the 13C-1H heteronuclear dipole-dipole interaction of the alpha carbon. To obtain the highest sensitivity for the psi angle determination, the following conditions are desired: (i) the recoupling pulse sequences for the CSA and the heteronuclear dipolar interactions are gamma encoded, in which the spatial parts of m=2 are selected; (ii) the homonuclear polarization transfer is based on the scalar spin-spin coupling. Experimental data were obtained for [U-13C, 15N]-alanine and N-acetyl-[U-13C, 15N]-d,l-valine under magic-angle spinning at 25kHz. Only three data points are required for the measurements and the dihedral angles determined are in excellent agreement with the diffraction data.