Effective protein conformational sampling based on predicted torsion angles

Protein structure prediction is a long‐standing problem in molecular biology. Due to lack of an accurate energy function, it is often difficult to know whether the sampling algorithm or the energy function is the most important factor for failure of locating near‐native conformations of proteins. This article examines the size dependence of sampling effectiveness by using a perfect “energy function”: the root‐mean‐squared distance from the target native structure. Using protein targets up to 460 residues from critical assessment of structure prediction techniques (CASP11, 2014), we show that the accuracy of near native structures sampled is relatively independent of protein sizes but strongly depends on the errors of predicted torsion angles. Even with 40% out‐of‐range angle prediction, 2 Å or less near‐native conformation can be sampled. The result supports that the poor energy function is one of the bottlenecks of structure prediction and predicted torsion angles are useful for overcoming the bottleneck by restricting the sampling space in the absence of a perfect energy function. © 2015 Wiley Periodicals, Inc.     

Characterizations of some homogeneous Hopf real hypersurfaces in a nonflat complex space form by extrinsic shapes of trajectories

We characterize some homogeneous Hopf real hypersurfaces in a nonflat complex space form by studying trajectories for Sasakian magnetic fields whose extrinsic shapes are tangentially of order 2.     

Evidence for a transition in deformation mechanism in nanocrystalline pure titanium processed by high-pressure torsion

Nanocrystalline titanium with an average grain size of about 60–70 nm was prepared by high-pressure torsion. The results of hardness and structural evolutions indicate that a strain-induced hardening–softening–hardening–softening behaviour occurs. For coarse-grained titanium, 〈a〉-type dislocation multiplication, twinning and a high pressure-induced α-to-ω phase transformation play major roles to accommodate deformation, leading to a significant strain hardening. As deformation proceeds, dynamic recrystallisation leads to a decrease in dislocation density, especially for 〈a〉-type dislocations, leading to a slight strain softening. The 〈c〉-component dislocation multiplication dominates the deformation when the grain size decreases to 100 nm and 〈c〉-component dislocation multiplication, grain refinement and the α-to-ω phase transformation contribute to the second strain hardening. The following strain softening is attributed to dynamic recovery.     

On the degree of Hilbert polynomials associated to the torsion functor

Let be a local, Noetherian ring and an ideal. A question of Kodiyalam asks whether for fixed , the polynomial giving the th Betti number of has degree equal to the analytic spread of minus one. Under mild conditions on , we show that the answer is positive in a number of cases, including when is divisible by or is an integrally closed -primary ideal.

     

The solution of integral equations with strongly singular kernels applied to the torsion of cracked circular cylinder

In this paper,the functions of warping displacement interruption defined on the crack lines are taken for the fundamental unknown functions.The torsion problem of cracked circular cylinder is reduced to solving a system of integral equations with strongly singular kernels.Using the numerical method of these equations,the torsional rigidities and the stress intensity factors are calculated to solve the torsion problem of circular cylinder with star-type and other different types of cracks.The numerical results are satisfactory.     

Application of an improved boundary element method on the problem of elastic torsion

An improved boundary clement method has been used in analyzing and calculating the problems of the torsion of a prismatic bar with elliptical cross-section. In this paper the calculated results correspond with the values of boundary element method. However, the quantity of data required by the improved boundary element method is much less than that required by boundary element method, and the calculating time will be greatly reduced. Therefore, the procedure of this paper is an economical and efficient numerical computational way for solving Poisson equation problem.     

S-系的扭类

假设S是有0,1的半群,τ是S-系的遗传扭论,对任意的右S-系M,Tτ（M）是M的τ-扭根。x∈Tτ（M）当且仅当存在某个τ-稠密右同余ρ,使得对任意的（S1,S2）∈ρ均有xs1=xs2,同时,当右S-系M是τ-扭自由时,M的τ-稠密同余是M的本质同余,特别,对忠实的遗传扭论τ,S的τ-稠密右同余是S     

一种改进边界元法在弹性扭转问题中的应用

本文用一种改进边界元法分析与计算了椭圆截面等直杆的扭转问题.并与边界元法的解进行比较,其结果极为符合.然而,改进边界元法较边界元法所需要的数据量少得多,计算时间也将大大减少了.因此,本文方法对求解Poisson方程问题是一种经济而行之有效的数值计算方法.     

Determination of Multiple φ-Torsion Angles in Proteins by Selective and Extensive C Labeling and Two-Dimensional Solid-State NMR

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive ¹³C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective ¹³C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-¹³C]glucose preferentially labels the ends of the side chains, while [2-¹³C]glycerol labels the C^α of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles φ simultaneously, using an isotropic–anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively ¹³C labeled protein were performed using ¹⁵N–¹³C 2D correlation spectroscopy. From the time dependence of the ¹⁵N–¹³C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective ¹³C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.