On the relationship between catalytic residues and their protein contact number

Due to advances in structural biology, an increasing number of protein structures of unknown function have been deposited in Protein Data Bank (PDB). These proteins are usually characterized by novel structures and sequences. Conventional comparative methodology (such as sequence alignment, structure comparison, or template search) is unable to determine their function. Thus, it is important to identify protein's function directly from its structure, but this is not an easy task. One of the strategies used is to analyze whether there are distinctive structure-derived features associated with functional residues. If so, one may be able to identify the functional residues directly from a single structure. Recently, we have shown that protein weighted contact number is related to atomic thermal fluctuations and can be used to derive motional correlations in proteins. In this report, we analyze the weighted contact-number profiles of both catalytic residues and non-catalytic residues for a dataset of 760 structures. We found that catalytic residues have distinct distributions of weighted contact numbers from those of non-catalytic residues. Using this feature, we are able to effectively differentiate catalytic residues from other residues with a single optimized threshold value. Our method is simple to implement and compares favourably with other more sophisticated methods. In addition, we discuss the physics behind the relationship between catalytic residues and their contact numbers as well as other features (such as residue centrality or B-factors) associated with catalytic residues.     

Preparation and Characterization of Epoxy/Inorganic Anti‐electrostatic Nanocomposites Using Submicrometer Al(OH)3 and Colloid Al2O3

New organic‐inorganic hybrid materials and their anti‐electrostatic hybrid membranes are prepared via sol‐gel process. The polycondensation of epoxy oligomers and AEAPS/Al₂O₃ complexes which are organically surface modified submicrometer aluminum trihydroxide inorganic fillers with an active aminoterminal silane coupling agent, N‐(2‐aminoethyl)‐3‐aminopropyltrimethoxysilane (AEAPS), are performed. AEAPS enhances the interfacial interactions between the inorganic fillers and epoxy polymers. Meanwhile, this coupling agent maintains well dispersion of fillers in these composites. To improve the mechanical strength and thermal stability, pyromellitic dianhydride (PMDA) is used as curing agent. These hybrid films prepared from this method have excellent physical properties, such as UV‐shielding, high transmission in visible resign (> 85%), high hardness (7～8H) , high adhesive force (7～8) and low relative surface resistance (9.71 × 10¹¹～1.26 × 10¹⁰ Ω/cm²) with anti‐electrostatic characters. For thermal resistance, the best Td value of epoxy/PMDA/AEAPS/Al₂O₃ is 378.6 °C which is 85.4 °C higher than that of neat epoxy resin. Physical properties of these materials are almost the same as those of the nanocomposites prepared from expensive colloid Al₂O₃. Evidences from TEM micrograph show that the inorganic additives are dispersed evenly in organic matrix with nanometer scale.     

Viscosity solutions of a class of degenerate quasilinear parabolic equations with Dirichlet boundary condition

This paper is concerned with viscosity solutions for a class of degenerate quasilinear parabolic equations in a bounded domain with homogeneous Dirichlet boundary condition. The equation under consideration arises from a number of practical model problems including reaction–diffusion processes in a porous medium. The degeneracy of the problem appears on the boundary and possibly in the interior of the domain. The goal of this paper is to establish some comparison properties between viscosity upper and lower solutions and to show the existence of a continuous viscosity solution between them. An application of the above results is given to a porous-medium type of reaction–diffusion model which demonstrates some distinctive properties of the solution when compared with the corresponding semilinear problem.     

三角帆蚌钩介幼虫体外培养及变态稚贝的形态变化

以超纯水为对照,利用普通温控培养箱,在(24.0±1.0)℃条件下对三角帆蚌钩介幼虫进行了15d的体外培养实验.结果显示:钩介幼虫排出体外24h内存活率显著下降为50.7%(p=0.006);A组(MEM高糖)、B组(RPMI1640)、C组(MEM 199)幼虫变态率分别为(7.5±3.9)%、(13.3±12.0)%、(42.1±10.0)%;D组(L-15)的幼虫变态率最高,为(66.1±3.8)%,极显著高于C组(p=0.007).相关分析表明,培养液中葡萄糖含量与钩介幼虫变态率存在显著负相关(r=-0.886).利用光镜和扫描电镜对体外培养变态发育的稚贝形态观察发现:稚贝双壳表面圆形凹陷数量和深度比幼虫显著减少,双壳边缘外套膜增厚,在外套膜、斧足表面分布有大量乳状突起,但形态不同.体外培养稚贝的外部形态和内部器官均发生了显著改变,完成了变态发育过程.     

Numerical simulation of three-dimensional unsteady viscous flow past finite cylinders in an unbounded fluid at low intermediate reynolds numbers

The flow past finite circular cylinders for Reynolds numbers 40 and 70 were simulated by numerical solutions of the incompressible Navier-Stokes equations. A nonuniform cartesian grid was used for the computation. The numerical scheme used was the QUICK scheme. Comparisons with experimental measurements of Jayaweera and Mason show that the results of the simulation are satisfactory. Features of three-dimensional unsteady viscous flow past finite cylinders, such as the pyramidal wake and the three-dimensional von Karmen vortex street, are successfully simulated.This work was supported by U.S. NSF Division of Atmospheric Science, Physical Meteorology Program, Grant ATM-9002299. All correspondence must be addressed to P.K. Wang.     

Block monotone iterative methods for numerical solutions of nonlinear elliptic equations

Summary. Two block monotone iterative schemes for a nonlinear algebraic system, which is a finite difference approximation of a nonlinear elliptic boundary-value problem, are presented and are shown to converge monotonically either from above or from below to a solution of the system. This monotone convergence result yields a computational algorithm for numerical solutions as well as an existence-comparison theorem of the system, including a sufficient condition for the uniqueness of the solution. An advantage of the block iterative schemes is that the Thomas algorithm can be used to compute numerical solutions of the sequence of iterations in the same fashion as for one-dimensional problems. The block iterative schemes are compared with the point monotone iterative schemes of Picard, Jacobi and Gauss-Seidel, and various theoretical comparison results among these monotone iterative schemes are given. These comparison results demonstrate that the sequence of iterations from the block iterative schemes converges faster than the corresponding sequence given by the point iterative schemes. Application of the iterative schemes is given to a logistic model problem in ecology and numerical ressults for a test problem with known analytical solution are given. Received August 1, 1993 / Revised version received November 7, 1994     

Monotone iterative methods for finite difference system of reaction-diffusion equations

Summary This paper presents an existence-comparison theorem and an iterative method for a nonlinear finite difference system which corresponds to a class of semilinear parabolic and elliptic boundary-value problems. The basic idea of the iterative method for the computation of numerical solutions is the monotone approach which involves the notion of upper and lower solutions and the construction of monotone sequences from a suitable linear discrete system. Using upper and lower solutions as two distinct initial iterations, two monotone sequences from a suitable linear system are constructed. It is shown that these two sequences converge monotonically from above and below, respectively, to a unique solution of the nonlinear discrete equations. This formulation leads to a well-posed problem for the nonlinear discrete system. Applications are given to several models arising from physical, chemical and biological systems. Numerical results are given to some of these models including a discussion on the rate of convergence of the monotone sequences.     

Asymptotic behavior of a reaction-diffusion system in bacteriology

This paper is concerned with the asymptotic behavior of the solution for a coupled system of reaction-diffusion equations which describes the bacteria growth and the diffusion of histidine and buffer concentrations. Under the basic boundary condition of Neumann type or mixed type the coupled system can have infinitely many steady-state solutions. The present paper gives some explicit information on the asymptotic limit of the time-dependent solution in relation to these steady states. This information exhibits some rather distinct properties of the solutions between the Neumann boundary problem and the Dirichlet or mixed boundary problem.     

Acid-Base Properties of the Ground and Excited States of Ruthenium(II) Tris(4′-methyl-2,2′-bipyridine-4-carboxylic Acid)

The acid dissociation constant, pK_a, for the ground and excited states of ruthenium tris(4′-methyl-2,2′-bipyridine-4-carboxylic acid) complex have been measured. The ground state pK_a obtained from the pH titration curve of the complex absorption at 454 nm was 2.5. The lifetimes of the excited-state for deprotonated and protonated ruthenium complexes are 595 and 150 ns, respectively. The excited-state pK_a* is obtained from the emission titration curve at 630 nm and corrected for the excited-state lifetime to be 4.2. The increase of 1.7 pH units in the acid dissociation constant in the excited-state indicates that the ligand is much more basic in the excited-state. This result confirms the MLCT assignment for the lowest electronic transition of [Ru(mbpyCOOH)₃]²⁺.