Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure

A three-dimensional structure of the NAD-dependent D -lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge-based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D -LDH subunit shows, as for the formate dehydrogenase, an α/β structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His-296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg-235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe-299, a candidate for stabilizing the methyl group of the substrate. © 1995 Wiley-Liss, Inc.     

Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: Construction of models and comparison with experiment

Homology modeling methods have been used to construct models of two proteins—the histidine-containing phosphocarrier protein (HPr) from Mycoplasma capricolum and human eosinophil-derived neurotoxin (EDN). Comparison of the models with the subsequently determined X-ray crystal structures indicates that the core regions of both proteins are reasonably well reproduced, although the template structures are closer to the X-ray structures in these regions—possible enhancements are discussed. The conformations of most of the side chains in the core of HPr are well reproduced in the modeled structure. As expected, the conformations of surface side chains in this protein differ significantly from the X-ray structure. The loop regions of EDN were incorrectly modeled—reasons for this and possible enhancements are discussed. © 1995 Wiley-Liss, Inc.     

光钳操纵生物活体的动态监测技术的研究

采用摄像、录像和视屏监控系统及显色偏振装置与光钳系统耦合,从空间分辨、色分辨和时间分辨多方面改善系统品质,实现了光钳捕获与操纵生物活体的动态监测、实时记录、资料保存和屏幕再现的功能,并能测量光钳操纵细胞的位移量和由此计算操纵速度,提高了光钳的自我调整和光钳操纵细胞的精细度。本研究为激光光钳技术在细胞工程等方面的应用研究提供了行之有效的技术手段。     

Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.

An algorithm is presented for the accurate and rapid generation of multiple protein sequence alignments from tertiary structure comparisons. A preliminary multiple sequence alignment is performed using sequence information, which then determines an initial superposition of the structures. A structure comparison algorithm is applied to all pairs of proteins in the superimposed set and a similarity tree calculated. Multiple sequence alignments are then generated by following the tree from the branches to the root. At each branchpoint of the tree, a structure-based sequence alignment and coordinate transformations are output, with the multiple alignment of all structures output at the root. The algorithm encoded in STAMP (STructural Alignment of Multiple Proteins) is shown to give alignments in good agreement with published structural accounts within the dehydrogenase fold domains, globins, and serine proteinases. In order to reduce the need for visual verification, two similarity indices are introduced to determine the quality of each generated structural alignment. Sc quantifies the global structural similarity between pairs or groups of proteins, whereas Pij' provides a normalized measure of the confidence in the alignment of each residue. STAMP alignments have the quality of each alignment characterized by Sc and Pij' values and thus provide a reproducible resource for studies of residue conservation within structural motifs.     

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

基于深度最大输出网络的抗体种型特异性B细胞表位预测

B细胞表位研究有助于肽段疫苗研制,抗体研制以及疾病诊断和治疗研究.不同的B细胞表位诱导免疫系统产生不同的抗体种型,探索研究能够诱导特异性抗体产生的B细胞表位具有重要意义.基于二肽组成特征,利用深度最大输出网络算法训练构建三个二类分类器,分别对应诱导三种不同特异性抗体的B细胞表位,即IgA表位,IgE表位以及IgG表位.通过五折交叉验证训练和测试这三个分类器,获得AUC的值分别为0.78,0.93以及0.78.IgA表位和IgE表位分类器的预测能力优于其它IgA表位和IgE表位分类器,IgG表位分类器和其它IgG表位分类器的预测能力相当.     

Cloning,expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus

The aim of this study was to clone, express, and characterize a β-xylosidase (Tlxyn1) from the thermophilic fungus Thermomyces lanuginosus SSBP in Pichia pastoris GS115 as well as analyze optimal activity and stability using computational and experimental methods. The enzyme was constitutively expressed using the GAP promoter and secreted into the medium due to the alpha-mating factor secretion signal present on the expression vector pBGPI. The 1276 bp gene consists of an open reading frame that does not contain introns. A 12% SDS–PAGE gel revealed a major protein band at an estimated molecular mass of 50 kDa which corresponded to zymogram analysis. The three-dimensional structure of β-xylosidase was predicted, and molecular dynamics simulations at different ranges of temperature and pH were performed in order to predict optimal activity and folding energy. The results suggested a strong conformational temperature and pH dependence. The recombinant enzyme exhibited optimal activity at pH 7 and 50°C and retained 80% activity at 50°C, pH 7 for about 45 min. This is the first report of the cloning, functional expression, and simulations study of a β-xylosidase from Thermomyces species in a fungal host.     

竞争和景观格局相互作用对外来入侵物种传播影响的动态模拟

通过中性景观模型和元胞自动机模型模拟了不同景观格局、不同竞争力和关键种群特征的外来入侵物种的传播动态,模拟结果表明:(1)竞争力强的外来入侵物种,可利用生境面积越大,集聚度越高,越有利于其入侵和传播,而对竞争力弱的外来入侵物种来说,可利用生境面积越小,越分散,越有利于其生存。竞争力强可以有效利用整块的高集聚度的资源,而弱竞争力的外来入侵物种为了逃避土著种的竞争往往趋向于分布在分散的小生境中;(2)可利用生境面积大于50%时,景观格局集聚度越小,竞争力弱的外来入侵物种适应环境的弛豫时间越长;(3)外来入侵物种的传播与种子产量呈正相关关系,与繁殖年龄呈负相关关系,拟合关系因景观格局和竞争而异;(4)平均迁移距离对外来入侵物种传播的影响最大,在管理过程中应根据不同的目标,不同的景观格局、竞争力和种群特征选择合适的管理措施。     

1982-2012年中亚地区植被时空变化特征及其与气候变化的相关分析

干旱区植被生态系统对气候变化极为敏感,并且干旱区的植被变化研究对全球碳循环具有重要意义。然而近几十年来,中亚干旱区植被对气候变化的响应机制尚不甚明朗。利用归一化植被指数NDVI数据集和MERRA（Modern-Era Retrospective Analysis for Research and Applications）气象数据,采用经验正交函数（EOF,Empirical Orthogonal Function）和最小二乘法等方法系统分析了31a（1982-2012年）来中亚地区NDVI在不同时间尺度的时空变化特征。进一步分析和研究NDVI与气温和降水的相关性,结果表明：1982-2012年,中亚地区年NDVI总体呈现缓慢增长趋势,而1994年以后年NDVI呈现明显下降趋势,尤其在哈萨克斯坦北部草原地区下降趋势尤为突出。这可能是由于过去30年间,中亚地区降水累计量的持续减少造成的。NDVI的季节变化表明春季NDVI增长最为明显,冬季则显著下降。与平原区相比,中亚山区的NDVI值增长幅度最大,并且山区年NDVI与季节NDVI呈现显著增加趋势（P < 0.05）。中亚地区年NDVI与年降水量正相关,而年NDVI与气温变化存在弱负相关。年NDVI和气温的正相关中心在中亚南部地区,负相关中心则出现在哈萨克斯坦的西部和北部地区;NDVI和降水的相关性中心刚好与气温相反。此外,在近30年间的每年6月至9月,中亚地区NDVI与气温存在近一个月的时间延迟现象。本研究为中亚干旱区生态系统变化和中亚地区碳循环的估算提供科学依据。     

人类最大可持续海洋足迹的模拟

在William Rees ＆ Mathis Wackernagel最初提出的生态足迹模型理论所划分的六类基本生态生产性土地面积中,海洋以其能为人类提供鱼类等海产品而被单独列为水域一项。海洋生物资源是一种典型的可再生资源,人类只有采取合理的开发策略方可保证海洋生物资源最大的可持续生产量。借用生态足迹、生物承载力概念的内涵,提出海洋足迹、海洋承载力两个新概念;运用非线性科学理论在海洋足迹与海洋承载力呈二次非线性关系的假设下,建立海洋承载力二次非线性开发的动力模式,并运用稳定性分析理论对其求解、分析。结果表明：（1）海洋承载力与其增长率呈正相关关系,与海洋足迹增长率呈负相关关系;（2）为保证海洋生物资源的可持续利用,人类必须控制最大海洋足迹增长率为r/xm（r为海洋承载力增长率,xm为最大海洋承载力）,方可获得可持续的最大海洋足迹为rxm/4,此时海洋承载力可以维持在稳定的平衡态（为其最大承载力的一半）。