基于HNP三态模型及相对熵方法的蛋白质折叠研究

把20种氨基酸简化为3类:疏水氨基酸(hydrophobic,H)、亲水氨基酸(hydrophilic,P)及中性氨基酸(neutral,N),每个氨基酸简化为一个点,用其C!原子来代替.采用非格点模型,以相对熵作为优化函数,进行蛋白质三维结构预测.为了与基于相对熵方法的蛋白质设计工作进行统一,采用了新的接触强度函数.选用蛋白质数据库中的天然蛋白质作为测试靶蛋白,结果表明,采用该模型和方法取得了较好的结果,预测结构相对于天然结构的均方根偏差在0.30～0.70nm之间.该工作为基于相对熵及HNP模型的蛋白质设计研究打下了基础.     

四种结构类型的蛋白质设计方法

给出了以疏水一亲水模型为基础的蛋白质设计方法,该方法以物理学原理为基础,以相对熵作为优化的目标函数。对四种不同结构类型的天然结构的真实蛋白质进行了检测,分析了影响检测成功率的主要因素,结果表明,该方法是普适的,可用于对不同结构类型的蛋白质设计序列。     

基于格子模型的蛋白质设计方法

提出一个简单有效的蛋白质设计方法,这一方法完全基于物理学原理. 与同类工作相比,该方法在很大程度上可节省对序列空间进行的搜索,是对同类工作的简化与发展. 对三个平面格子模型进行的检验表明该方法是成功的. 该方法可进一步用于真实蛋白质的三维非格子模型.     

蛋白质二级结构预测: 基于词条的最大熵马尔科夫方法

提出了一种新的蛋白质二级结构预测方法. 该方法从氨基酸序列中提取出和自然语言中的“词”类似的与物种相关的蛋白质二级结构词条, 这些词条形成了蛋白质二级结构词典, 该词典描述了氨基酸序列和蛋白质二级结构之间的关系. 预测蛋白质二级结构的过程和自然语言中的分词和词性标注一体化的过程类似. 该方法把词条序列看成是马尔科夫链, 通过Viterbi算法搜索每个词条被标注为某种二级结构类型的最大概率, 其中使用词网格描述分词的结果, 使用最大熵马尔科夫模型计算词条的二级结构概率. 蛋白质二级结构预测的结果是最优的分词所对应的二级结构类型. 在4个物种的蛋白质序列上对这种方法进行测试, 并和PHD方法进行比较. 试验结果显示, 这种方法的Q3准确率比PHD方法高3.9%, SOV准确率比PHD方法高4.6%. 结合BLAST搜索的局部相似的序列可以进一步提高预测的准确率. 在50个CASP5目标蛋白质序列上进行测试的结果是: Q3准确率为78.9%, SOV准确率为77.1%. 基于这种方法建立了一个蛋白质二级结构预测的服务器, 可以通过http://www.insun.hit.edu.cn:81/demos/biology/index.html来访问.     

一种新的蛋白质结构类预测方法

基于氨基酸的16种分类模型,给出蛋白质序列的派生序列,进而结合加权拟熵和LZ复杂度构造出34维特征向量来表示蛋白质序列。借助于贝叶斯分类器对同源性不超过25%的640数据集进行蛋白质结构类预测,准确度达到71.28%。     

基于深度学习的蛋白质建模与设计

随着蛋白质序列及结构数据的大量累积,在获得了大量描述性信息之后如何有效利用海量数据,从已有数据中高效提取信息并且应用到下游任务当中就成为了研究者亟待解决的问题。蛋白质的设计可使新蛋白的研发不再受限于实验条件,这对药物靶点预测、新药研发和材料设计等领域具有重要意义。深度学习作为一种高效的数据特征提取方法,可以通过它对蛋白质数据进行建模,进而加入先验信息对蛋白质进行设计。故此基于深度学习的蛋白质设计就成为一个具有广阔前景的研究领域。文中主要阐述基于深度学习的蛋白质序列与结构数据的建模和设计方法。详述该方法的策略、原理、适用范围、应用实例。讨论了深度学习方法在本领域的应用前景及局限性,以期为相关研究提供参考。     

非线性模型在蛋白质薄膜厚度测定中的应用

分子通过测定蛋白质薄膜厚度变化而定量地研究生物分子间的相互作用,探讨了基于光学干涉光的薄膜厚度的测量方法,借助于在玻璃基底表面沉积的聚苯乙烯薄膜对噪声的抑制,使用非线性回归模型对生物传感器的检测信号进行了分析。通过反射干涉光谱光测定到乙型肝炎表面抗原在聚苯乙烯－玻璃表面的吸附使薄膜厚度增加了３．３ｎｍ。随着５μｇ／ｍｌ,１０μｇ／ｍｌ,２０μｇ／ｍｌ,３０μｇ／ｍｌ和５０μｇ／ｍｌ浓度的乙型肝炎表     

神经网络在蛋白质二级结构预测中的应用

介绍了蛋白质二级结构预测的研究意义,讨论了用在蛋白质二级结构预测方面的神经网络设计问题,并且较详尽地评述了近些年来用神经网络方法在蛋白质二级结构预测中的主要工作进展情况,展望了蛋白质结构预测的前景。     

遗传算法在蛋白质结构预测中的应用

遗传算法(geneticalgorithm,GA)作为一种自适应启发式概率性迭代式全局搜索算法,具有不依赖于问题模型的特性、全局最优性、隐含并行性、高效性、解决不同非线性问题的鲁棒性特点,目前已经广泛应用于自动控制、机器人学、计算机科学、模式识别、模糊人工神经和工程优化等设计领域。本文首先介绍了GA的基本原理,即搜索的基本过程;随后总结了GA与传统算法相比所具有的优点;第三部分则分别综述了GA在蛋白质结构预测中主要使用的模型、设计和执行策略,以及使用GA与其他算法相互结合预测蛋白质结构的研究进展;最后提出了作者对GA研究中存在问题的认识和研究展望。     

计算方法在蛋白质相互作用研究中的应用

计算方法在蛋白质相互作用研究的各个阶段扮演了一个重要的角色。对此,作者将从以下几个方面对计算方法在蛋白质相互作用及相互作用网络研究中的应用做一个概述：蛋白质相互作用数据库及其发展;数据挖掘方法在蛋白质相互作用数据收集和整合中的应用;高通量方法实验结果的验证;根据蛋白质相互作用网络预测和推断未知蛋白质的功能;蛋白质相互作用的预测。     

氮素对不同类型玉米籽粒氨基酸、蛋白质含量及其组分变化的影响

以普通玉米掖单22和高油玉米高油115为材料,研究了不同供氮条件下玉米籽粒中蛋白质及其组分的含量、清蛋白和球蛋白含量、醇溶蛋白和谷蛋白含量、籽粒氨基酸总鼍以及氨基酸组分含量的品种差异。结果表明。氮素供应水平对两种类型玉米灌浆期间籽粒蛋白质含量变化作用相同,前期逐渐下降,至成熟期略有升高;籽粒清蛋白和球蛋白、醇溶蛋白和符蛋白含量变化动态各处理基本一致,两种类型玉米籽粒清蛋白含量随时间的推移逐渐降低。球蛋门含量的变化动态旱单峰曲线,峰值出现在授粉后30d。醇溶蛋白含量均呈“V”型变化,以授粉30d后最低。谷蛋白的含量则均呈上升趋势。氮素供应水平对两种类型玉米籽粒中各蛋白质组分禽量的变化的影响作用有所不同。对高油115籽粒中球蛋白含量的影响较小;施氮水平并不改变两种类型玉米籽粒氨基酸总量的变化趋势。但两种类型玉米籽粒中氨基酸组分的含量变化较大。     

A Novel Method for Prediction of Protein Domain Using Distance-Based Maximal Entropy

Detecting the boundaries of protein domains is an important and challenging task in both experimental and computational structural biology. In this paper, a promising method for detecting the domain structure of a protein from sequence information alone is presented. The method is based on analyzing multiple sequence alignments derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence. Then they are combined into a single predictor using support vector machine. What is more important, the domain detection is first taken as an imbal- anced data learning problem. A novel undersampling method is proposed on distance-based maximal entropy in the feature space of Support Vector Machine （SVM）. The overall precision is about 80%. Simulation results demonstrate that the method can help not only in predicting the complete 3D structure of a protein but also in the machine learning system on general im- balanced datasets.     

Dietary CP and amino acid restriction has a different impact on the dynamics of protein,amino acid and fat deposition in entire male,castrated and female pigs

Breeding efforts over the last decades altered markedly empty body (EB) composition of pigs. This study aimed to re-evaluate the dynamics of changes in the composition and deposition rate of fat, protein and amino acids (AA) in the EB from birth to 140 kg BW depending on the dietary CP and AA supply in a current pig genotype. In the experiment 66 entire male, 58 castrated and 66 female Swiss Large White pigs were used. From 20 kg BW onwards, they had either ad libitum access to a control (C) diet or a diet (LP) compared to diet C only 80% of CP, lysine, methione+cystine, threonine and tryptophan. The EB composition was determined at birth on eight boars and eight females, at 10 and 20 kg BW on two boars, two castrates and two females, and at 20 kg intervals from 40 to 140 kg BW, on four pigs per gender and dietary treatment. Each EB fraction was weighed and analysed for protein, fat and AA profile. The AA-to-lysine ratio was calculated and the different chemical component contents were fitted to allometric regressions. Overall, C-boars had the greatest EB protein and AA content and deposition rates, and lowest fat content and deposition rates. At the beginning of the grower period, LP-castrates and females displayed the lowest protein and AA and the highest fat deposition rates. However, compared with their counterparts in the C-group, in LP-castrates and females protein and AA deposition rates were greater above 64 and 40 kg EB weight, respectively, whereas fat deposition rates was lower above 80 kg EB weight. Thus, there seems a great potential to optimise protein and AA efficiency especially in the finisher period in castrates and females. Important individual variations were found in the essential AA-to-lysine ratio of the EB. Phenylalanine and threonine-to-lysine ratios decreased with increasing EB weight. Valine- and threonine-to-lysine ratios in C-castrates and C-females were 5% and 4% greater than recently reported by the National Research Council (NRC) whereas cysteine-, methionine- and tyrosine-to-lysine ratios were lower by 34%, 25% and 10%, respectively. The clear differences found between the EB AA-to-lysine ratios in the present study and the NRC might partly be explained by the genotype and the temporal changes in the relative weight of each EB fraction or changes in the AA profile. Nevertheless, these findings on changes in the essential AA profile of tissue protein warrant further studies.     

由铬革屑制备可溶性蛋白及氨基酸的研究

成品铬革屑中蛋白质含量在 70 %以上 ,处理成小颗粒后与水、Ca(OH) 2 按 1∶4 0∶0 .4的比例混合 ,90℃反应 5h ,可溶性蛋白转化率近 6 0 % ,且在升温后加入Ca(OH) 2 有利于退鞣。以 6mol/L盐酸水解皮革蛋白粉制备复合氨基酸 ,水解 14h ,水解液以HD -I树脂脱色 ,氨基酸损失较少 ,且动态脱色效率明显高于静态脱色 ,采用 717树脂脱酸可获得pH4 .5 - 5的复合氨基酸溶液 ,总得率为 6 0 .1%。     

虫草不同部位氨基酸和蛋白质的分布研究

本文对云南丽江地区出产虫草不同部位的蛋白质、氨基酸的组成进行定量分析,从中找出虫草中蛋白质及水解氨基酸的组成和分布的定量规律。     

核酸、氨基酸分类和蛋白质二级结构关系的分析与分子设计

核酸序列中包含一定的蛋白质结构信息。根据通常情况下遗传密码表中密码子中间位的碱基配对时产生的氢键数目,尝试将20种氨基酸划分为两类,并用自编的计算机软件对蛋白质二级结构数据库中两类氨基酸的类聚现象进行了统计分析。结果表明,使用这种方法对氨基酸进行划分后,氨基酸残基具有较大概率与划入同一类的氨基酸残基相邻出现,并且这种聚集体对二级结构具有一定的偏好性。最后按照该方法设计了一段氨基酸序列并给出了预测服务器预测得到的结构。     

核酸、氨基酸分类和蛋白质二级结构关系的分析与分子设计

核酸序列中包含一定的蛋白质结构信息。根据通常情况下遗传密码表中密码子中间位的碱基配对时产生的氢键数目,尝试将20种氨基酸划分为两类,并用自编的计算机软件对蛋白质二级结构数据库中两类氨基酸的类聚现象进行了统计分析。结果表明,使用这种方法对氨基酸进行划分后,氨基酸残基具有较大概率与划入同一类的氨基酸残基相邻出现,并且这种聚集体对二级结构具有一定的偏好性。最后按照该方法设计了一段氨基酸序列并给出了预测服务器预测得到的结构。     

Analyses of Soluble Protein,Total and Free Amino Acids in Leaves of Different Ecotypes of Phragmites communis Growing in the Hexi Corridor

The difference of total and free amino acids and protein extracted from the leaves of four different reed ecotypes growing in Hexi corridor of Gansu Province were investigated. In all of the different reed ecotypes, the content of Asp, Glu, Gly, Leu and Ala in total amino acids were high, while the contents of Ala, Phe, Met and Thr, Pro in total amino acids varied among different reed ecotypes. Albeit Ala, Glu, Asp, Gly and Ser were the chief composition of free amino acids in leaves of all reed ecotypes, but temarkble difference was found in the content of each free amino acid from different reed ecotypes. The content of free Pro in leaves of salt meadow and salt meadow-sand dune transitional zone reed were 3.5 and 1.6 times respectively as much as in leaves of swamp reed. Swamp reed had 11 soluble proteins whereas other three reed ecotypes show that each has 13 soluble proteins. Three “salt adaptation proteins” (66 kD, 40.3 kD, 16.5 kD) were found in leaves of three reed ecotypes with varying degree of salt stress, however, the contents of 3 “salt adaptation protens” showed a negative correlation with the degree of salt stress. There was a large amount of “special protein” (11.7 kD) in leaves of sand dune reeds. These results suggest that the difference in cytogene expression takes a priority basis of adaptation of reed plants to different habitats, while a closer relationship of reeds tolerance to salt or drought stress with Pro accumulation in cells is seen than with the of accumulation stress adaptation protein.