Very efficient search for protein alignment--VESPA

A novel approach to the problem of protein alignments is described, which in comparison with existing approaches is visibly more efficient. This approach is based on superposition of amino acid adjacency matrices of a pair of proteins, which have been modified to record the sequential order of amino acids. As a result, one obtains simultaneously all segments of the two proteins which are shifted relative to one another by one or more positions in either directions, without need of a prior exhaustive search for an alignment that included unproductive directions and unknown displacement steps.     

icoshift: An effective tool for the alignment of chromatographic data

The Interval Correlation Optimised Shifting algorithm (icoshift) has recently been introduced for the alignment of nuclear magnetic resonance spectra. The method is based on an insertion/deletion model to shift intervals of spectra/chromatograms and relies on an efficient Fast Fourier Transform based computation core that allows the alignment of large data sets in a few seconds on a standard personal computer. The potential of this programme for the alignment of chromatographic data is outlined with focus on the model used for the correction function. The efficacy of the algorithm is demonstrated on a chromatographic data set with 45 chromatograms of 64,000 data points. Computation time is significantly reduced compared to the Correlation Optimised Warping (COW) algorithm, which is widely used for the alignment of chromatographic signals. Moreover, icoshift proved to perform better than COW in terms of quality of the alignment (viz. of simplicity and peak factor), but without the need for computationally expensive optimisations of the warping meta-parameters required by COW. Principal component analysis (PCA) is used to show how a significant reduction on data complexity was achieved, improving the ability to highlight chemical differences amongst the samples.     

基于非天然氨基酸的蛋白质生物正交标记

生物正交化学反应正日益成为在活体内对生物大分子进行特异标记的一种有效方法. 最近涌现出的一个突出的例子是将金属钯催化的碳碳偶联反应这一在有机合成领域具有里程碑意义的反应拓展到生物大分子的标记上. 在活细胞上进行生物正交反应的一个先决条件是需要将参与这类反应的正交官能团特异地引入到目标生物大分子当中. 遗传密码子拓展技术是将多种生物正交活性基团引入到蛋白质当中的一种先进的手段; 最近发展出的基于吡咯赖氨酸氨酰合成酶和tRNA的体系能够将携带有生物正交官能团的非天然氨基酸有效地引入到原核生物、真核生物, 甚至是动物体内的蛋白质上. 在这一展望中, 我们首先介绍在生物正交反应和遗传密码子拓展这两个领域内的研究前沿与进展. 接着我们将讨论将这些新发展的研究工具, 尤其是基于钯催化的生物正交反应和基于吡咯赖氨酸氨酰合成酶的遗传密码子拓展技术, 应用于标记和修饰哺乳动物细胞蛋白质上的优势和诱人前景. 生物相兼容性更好的正交反应和更为灵活的非天然氨基酸引入技术必将有力地增强和拓宽人们在活细胞环境下特异操纵蛋白质的能力.     

Protein posttranslational modifications: the chemistry of proteome diversifications

The diversity of distinct covalent forms of proteins (the proteome) greatly exceeds the number of proteins predicted by DNA coding capacities owing to directed posttranslational modifications. Enzymes dedicated to such protein modifications include 500 human protein kinases, 150 protein phosphatases, and 500 proteases. The major types of protein covalent modifications, such as phosphorylation, acetylation, glycosylation, methylation, and ubiquitylation, can be classified according to the type of amino acid side chain modified, the category of the modifying enzyme, and the extent of reversibility. Chemical events such as protein splicing, green fluorescent protein maturation, and proteasome autoactivations also represent posttranslational modifications. An understanding of the scope and pattern of the many posttranslational modifications in eukaryotic cells provides insight into the function and dynamics of proteome compositions.     

GCALIGNER 1.0: An alignment program to compute a multiple sample comparison data matrix from large eco‐chemical datasets obtained by GC

GCALIGNER 1.0 is a computer program designed to perform a preliminary data comparison matrix of chemical data obtained by GC without MS information. The alignment algorithm is based on the comparison between the retention times of each detected compound in a sample. In this paper, we test the GCALIGNER efficiency on three datasets of the chemical secretions of bumble bees. The algorithm performs the alignment with a low error rate (<3%). GCALIGNER 1.0 is a useful, simple and free program based on an algorithm that enables the alignment of table‐type data from GC.     

An Amperometric Glucose Sensor Based on Isoporous Crystalline Protein Membranes as Immobilization Matrix

Abstract

S-layer ultrafiltration membranes (SUMs) with an active filtration layer composed of coherent two-dimensional, isoporous protein crystals (S-layers) have been used as matrix for immobilizing monolayers of enzymes. Since S-layers are formed by periodic repetition of identical protein subunits, functional groups are present on the crystalline array in an identical position and orientation. As a consequence monolayers of enzymes can bind in a geometrically well defined way. For the covalent immobilization of enzymes carboxyl groups from the S-layer protein were activated with carbodiimide and allowed to react with amino groups of the enzyme. SUMs were employed as a new type of immobilization matrix for the developement of an amperometric glucose sensor using glucose oxidase (GOD) as the biologically active component. Glucose oxidase covalently bound to the surface of the S-layer protein retained approximately 40% of its activity. The enzyme loaded SUMs were covered with a layer of gold or platinum to function as working electrodes. These sensors yielded high signals (150nA/mm²/mmol glucose), fast response times (10–30s) and a linearity range up to 12 mM glucose. The stability under working conditions was more than 48 hours. There was no loss in activity after a storage period of 6 month.     

CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs

For biological applications, sequence alignment is an important strategy to analyze DNA and protein sequences. Multiple sequence alignment is an essential methodology to study biological data, such as homology modeling, phylogenetic reconstruction and etc. However, multiple sequence alignment is a NP-hard problem. In the past decades, progressive approach has been proposed to successfully align multiple sequences by adopting iterative pairwise alignments. Due to rapid growth of the next generation sequencing technologies, a large number of sequences can be produced in a short period of time. When the problem instance is large, progressive alignment will be time consuming. Parallel computing is a suitable solution for such applications, and GPU is one of the important architectures for contemporary parallel computing researches. Therefore, we proposed a GPU version of ClustalW v2.0.11, called CUDA ClustalW v1.0, in this work. From the experiment results, it can be seen that the CUDA ClustalW v1.0 can achieve more than 33× speedups for overall execution time by comparing to ClustalW v2.0.11.     

植物白头翁毒蛋白的分离、纯化及其组分测定

植物白头翁（ａｍｅｎｏｎｅ）茎的抽提液经ＣＭ－ＳＦＦ柱和ＳｅｐｈａｃｒｙｌＳ－２００柱分离纯化,得到一种毒蛋白,用高效凝胶蛋白柱和反相高效液相色谱法结合光电二极管阵列检测器确认分离峰的纯度,在高效凝胶蛋白柱上制备了少量毒蛋白纯样,测定了蛋白分子量和氨基酸组成。     

A New Hybrid Model of Amino Acid Substitution for Protein Functional Classification

In recent years, methods of protein sequences analysis have been gradually evolved into two directions: One is based on the models of probability and statistics1-4; the other is based on the digital signal processing technologies 5-8. The latter mainly converts the protein character sequences into digital signals and uses some signal processing methods to analyze them, i.e., fast Fourier transform (FFT). However, it is still unsolved how to characterize the protein sequences accurately with …     

Time-dependent density-functional and reduced density-matrix methods for few electrons: Exact versus adiabatic approximations

To address the impact of electron correlations in the linear and non-linear response regimes of interacting many-electron systems exposed to time-dependent external fields, we study one-dimensional (1D) systems where the interacting problem is solved exactly by exploiting the mapping of the 1D N-electron problem onto an N-dimensional single electron problem. We analyze the performance of the recently derived 1D local density approximation as well as the exact-exchange orbital functional for those systems. We show that the interaction with an external resonant laser field shows Rabi oscillations which are detuned due to the lack of memory in adiabatic approximations. To investigate situations where static correlations play a role, we consider the time-evolution of the natural occupation numbers associated to the reduced one-body density matrix. Those studies shed light on the non-locality and time-dependence of the exchange and correlation functionals in time-dependent density and density-matrix functional theories.     

基于Diels-Alder生物正交反应的蛋白质快速位点特异性标记方法

蛋白质的位点特异性修饰近年来取得了重要进展. 本文对该领域新近发展的利用高张力烯烃或炔烃与四嗪类化合物的Diels-Alder生物正交反应, 通过基因编码的方式在蛋白质中位点特异性地插入其中一个组分, 从而实现蛋白质的快速荧光标记进行了介绍.     

Characterization of Peanut Protein Hydrolysate and Structural Identification of Umami-Enhancing Peptides

Umami peptides are naturally found in various foods and have been proven to be essential components contributing to food taste. Defatted peanut powder hydrolysate produced by a multiprotease (Flavorzyme, Alcalase, and Protamex) was found to elicit an umami taste and umami-enhancing effect. The taste profiles, hydrolysis efficiency, amino acids, molecular weight distribution, Fourier transform infrared spectroscopy (FT-IR), and separation fractions obtained by ultrafiltration were evaluated. The results showed that peanut protein was extensively hydrolyzed to give mainly (up to 96.84%) free amino acids and peptides with low molecular weights (<1000 Da). Furthermore, β-sheets were the major secondary structure. Fractions of 1–3000 Da and <1000 Da prominently contributed to the umami taste and umami enhancement. To obtain umami-enhancing peptides, these two fractions were further purified by gel filtration chromatography, followed by sensory evaluation. These peptides were identified as ADSYRLP, DPLKY, EAFRVL, EFHNR, and SDLYVR by ultra-performance liquid chromatography (UPLC), and had estimated thresholds of 0.107, 0.164, 0.134, 0.148, and 0.132 mmol/L, respectively. According to the results of this work, defatted peanut powder hydrolysate had an umami taste and umami-enhancing effect, and is a potential excellent umami peptide precursor material for the food industry.     

Rational Heme Protein Design: All Roads Lead to Rome

Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C? H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme‐binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure–property–reactivity–function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.     

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.     

Influence of Enzymatic Hydrolysis and Molecular Weight Fractionation on the Antioxidant and Lipase / α-Amylase Inhibitory Activities In Vitro of Watermelon Seed Protein Hydrolysates

This study aims to evaluate the potential in vitro antioxidant and anti-obesity activities of watermelon seed protein hydrolysates (WSPH) obtained using different combinations of enzymes alcalase–proteinase K (ALC-PK) and alcalase–actinidin (ALC-ACT). There was a direct relationship between the degree of hydrolysis (DH) and the biological activities of the WSPH, with the highest DPPH (approximately 85%) and lipase inhibitory activities (≈59%) appreciated at DH of 36–37% and 33–35% when using ALC-PK and ALC-ACT, respectively. Following molecular weight fractionation, the ALC-PK WSPH < 3 kDa (F1) assayed at 1 mg.mL⁻¹ had the highest DPPH-radical scavenging (89.22%), ferrous chelating (FC) (79.83%), reducing power (RP) (A 0.51), lipase inhibitory (71.36%), and α-amylase inhibitory (62.08%) activities. The amino acid analysis of ALC-PK WSPH and its fractions revealed a relationship between the biological activity of the extracts and their composition. High contents of hydrophobic amino acids, arginine, and aromatic amino acids were related to high antioxidant, lipase inhibitory, and α-amylase inhibitory activities in the extracts, respectively. Overall, this study revealed that underutilized protein sources such as WSPH, using the appropriate combination of enzymes, could result in the generation of new ingredients and compounds with powerful antioxidant and anti-obesity activities with promising applications as nutraceuticals or functional foods.     

Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies

Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set of sequence segments in 1D, a set of amino acid contact pairs in 2D, and a set of traces in 3D at the secondary structure level. A test of fourteen cases shows that the accuracy of predicted secondary structures is critical for deriving topologies. The use of significant long-range contact pairs is most effective at enriching the rank of the maximum-match topology for proteins with a large number of secondary structures, if the secondary structure prediction is fairly accurate. It was observed that the enrichment depends on the quality of initial topology candidates in this approach. We provide detailed analysis in various cases to show the potential and challenge when combining three sources of information.     

Effect of Acetylation on Physicochemical and Functional Properties of Commercial Pumpkin Protein Concentrate

The purpose of the present study was to determine the effects of acetylation with different doses of acetic anhydride on the chemical composition and chosen functional properties of commercial pumpkin protein concentrate (PPC). The total protein content decreased as compared to unmodified samples. Electrophoretic analysis revealed that in the acetylated pumpkin protein, the content of the heaviest protein (35 kDa) decreased in line with increasing concentrations of modifying reagent. Acetylation of PPC caused a significant increase in water-binding and oil-absorption capacity and for emulsifying properties even at the dose of 0.4 mL/g. Additionally, an increase in foaming capacity was demonstrated for preparations obtained with 2.0 mL/g of acetic anhydride, whereas acetylation with 0.4 and 1.0 mL/g caused a decrease in protein solubility as compared to native PPC.