A Facile Method for the Separation of Methionine Sulfoxide Diastereomers,Structural Assignment,and DFT Analysis

Methionine (Met) oxidation is an important biological redox node, with hundreds if not thousands of protein targets. The process yields methionine oxide (MetO). It renders the sulfur chiral, producing two distinct, diastereomerically related products. Despite the biological significance of Met oxidation, a reliable protocol to separate the resultant MetO diastereomers is currently lacking. This hampers our ability to make peptides and proteins that contain stereochemically defined MetO to then study their structural and functional properties. We have developed a facile method that uses supercritical CO₂ chromatography and allows obtaining both diastereomers in purities exceeding 99 %. ¹H NMR spectra were correlated with X-ray structural information. The stereochemical interconversion barrier at sulfur was calculated as 45.2 kcal mol⁻¹, highlighting the remarkable stereochemical stability of MetO sulfur chirality. Our protocol should open the road to synthesis and study of a wide variety of stereochemically defined MetO-containing proteins and peptides.     

Asymptotic analysis for multi-objective sequential stochastic assignment problems

ABSTRACT

We provide an asymptotic analysis of multi-objective sequential stochastic assignment problems (MOSSAP). In MOSSAP, a fixed number of tasks arrive sequentially, with an n-dimensional value vector revealed upon arrival. Each task is assigned to one of a group of known workers immediately upon arrival, with the reward given by an n-dimensional product-form vector. The objective is to maximize each component of the expected reward vector. We provide expressions for the asymptotic expected reward per task for each component of the reward vector and compare the convergence rates for three classes of Pareto optimal policies.     

On weighting two criteria with a parameter in combinatorial optimization problems

Two criteria in a combinatorial problem are often combined in a weighted sum objective using a weighting parameter between 0 and 1. For special problem types, e.g., when one of the criteria is a bottleneck value, efficient algorithms are known that solve for a given value of the weighting parameter.     

Application of THz Vibrational Spectroscopy to Molecular Characterization and the Theoretical Fundamentals: An Illustration Using Saccharide Molecules

This work illustrates several theoretical fundamentals for the application of THz vibrational spectroscopy to molecular characterization in the solid state using two different types of saccharide systems as examples. Four subjects have been specifically addressed: (1) the qualitative differences in the molecular vibrational signatures monitored by THz and mid‐IR vibrational spectroscopy; (2) the selection rules for THz vibrational spectroscopy as applied to crystalline and amorphous systems; (3) a normal mode simulation, using α‐l ‐xylose as an example; and (4) a rigorous mode analysis to quantify the percentage contributions of the intermolecular and intramolecular vibrations to the normal mode of interest.     

Efficient algorithms for three‐dimensional axial and planar random assignment problems

Beautiful formulas are known for the expected cost of random two‐dimensional assignment problems, but in higher dimensions even the scaling is not known. In three dimensions and above, the problem has natural “Axial” and “Planar” versions, both of which are NP‐hard. For 3‐dimensional Axial random assignment instances of size n, the cost scales as Ω(1/ n), and a main result of the present paper is a linear‐time algorithm that, with high probability, finds a solution of cost O(n^–1+o(1)). For 3‐dimensional Planar assignment, the lower bound is Ω(n), and we give a new efficient matching‐based algorithm that with high probability returns a solution with cost O(n log n). © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 46, 160–196, 2015     

A new framework for implicit restarting of the Krylov–Schur algorithm

This paper introduces a new framework for implicit restarting of the Krylov–Schur algorithm. It is shown that restarting with arbitrary polynomial filter is possible by reassigning some of the eigenvalues of the Rayleigh quotient through a rank‐one correction, implemented using only the elementary transformations (translation and similarity) of the Krylov decomposition. This framework includes the implicitly restarted Arnoldi (IRA) algorithm and the Krylov–Schur algorithm with implicit harmonic restart as special cases. Further, it reveals that the IRA algorithm can be turned into an eigenvalue assignment method. Copyright © 2014 John Wiley & Sons, Ltd.     

Forwarding and optical indices of 4-regular circulant networks

An all-to-all routing in a graph G is a set of oriented paths of G, with exactly one path for each ordered pair of vertices. The load of an edge under an all-to-all routing R is the number of times it is used (in either direction) by paths of R, and the maximum load of an edge is denoted by $\pi (G,R)$. The edge-forwarding index $\pi (G)$ is the minimum of $\pi (G,R)$ over all possible all-to-all routings R, and the arc-forwarding index $\overrightarrow{\pi }(G)$ is defined similarly by taking direction into consideration, where an arc is an ordered pair of adjacent vertices. Denote by $w(G,R)$ the minimum number of colours required to colour the paths of R such that any two paths having an edge in common receive distinct colours. The optical index $w(G)$ is defined to be the minimum of $w(G,R)$ over all possible R, and the directed optical index $\overrightarrow{w}(G)$ is defined similarly by requiring that any two paths having an arc in common receive distinct colours. In this paper we obtain lower and upper bounds on these four invariants for 4-regular circulant graphs with connection set $\{\pm 1,\pm s\}$, $1<s<n/2$. We give approximation algorithms with performance ratio a small constant for the corresponding forwarding index and routing and wavelength assignment problems for some families of 4-regular circulant graphs.     

Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment

An automated NMR chemical shift assignment algorithm was developed using multi-objective optimization techniques. The problem is modeled as a combinatorial optimization problem and its objective parameters are defined separately in different score functions. Some of the heuristic approaches of evolutionary optimization are employed in this problem model. Both, a conventional genetic algorithm and multi-objective methods, i.e., the non-dominated sorting genetic algorithms II and III (NSGA2 and NSGA3), are applied to the problem. The multi-objective approaches consider each objective parameter separately, whereas the genetic algorithm followed a conventional way, where all objectives are combined in one score function. Several improvement steps and repetitions on these algorithms are performed and their combinations are also created as a hyper-heuristic approach to the problem. Additionally, a hill-climbing algorithm is also applied after the evolutionary algorithm steps. The algorithms are tested on several different datasets with a set of 11 commonly used spectra. The test results showed that our algorithm could assign both sidechain and backbone atoms fully automatically without any manual interactions. Our approaches could provide around a 65% success rate and could assign some of the atoms that could not be assigned by other methods.     

A method for C(alpha) direct-detection in protonless NMR

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.     

一种新的六氢喹啉衍生物的NMR研究

应用¹H NMR,¹³C NMR,DEPT,¹H-¹H COSY,HSQC,HMBC等多种NMR实验测试分析方法,确证了一种新的六氢喹啉衍生物2,7,7-三甲基-4-(4-羟基-3-甲氧基）苯基-5-氧代-1,4,5,6,7,8-六氢喹啉-3-羧酸甲酯的结构,并对它的¹H、¹³C信号进行了归属.