基于LightGBM的蛋白质类泛素化修饰位点预测

蛋白质类泛素化修饰位点的准确识别对基础研究和药物开发都具有重要意义.该文提出了一种基于蛋白质序列特征的类泛素化修饰位点预测模型.该模型结合氨基酸的物理化学属性统计特征和氨基酸序列二元语法模式特征,训练一种轻量型梯度提升机(Light gradient boosting machine,LightGBM)分类器预测某个蛋...     

手性铜(I)/SaBOX配合物催化cis-1,2-二取代烯烃与α-硝基重氮乙酸酯的高非对映选择性以及高对映选择性环丙烷化反应（英文）

利用手性金属铜(I)与边臂修饰的双噁唑啉的配合物作为催化剂,发展了一种催化cis-1,2-二取代烯烃与α-硝基重氮乙酸酯发生高立体选择性环丙烷化反应的新方法.该反应可以获得高达97%的收率、99/1 dr和98%的对映选择性,得到多取代的手性环丙烷.这一方法为合成具有光学活性的环丙烷α-氨基酸以及非天然α-氨基酸衍生物提供了有效途径.     

后合成修饰的锆基MOFs在药物传递中的研究

以金属有机框架材料UiO-66-NH₂为载体对恩诺沙星(Enr)进行装载，考察其药物装载能力及其药物的释放效果.用一锅法制备装载Enr的UiO-66-NH₂(Enr@UiO-66-NH₂)的纳米粒子，利用不同的蛋白质或氨基酸对Enr@UiO-66-NH₂进行了活化和修饰，对制得的蛋白质或氨基酸修饰的纳米粒子样品通过X射线粉末衍射(XRD)和红外光谱法(IR)对其进行结构确证及表征，发现氨基化修饰UiO-66产生的一系列产物是成功的.在PBS溶液中对其进行药物释放实验，并进行荧光检测记录实验结果.     

不同方法修饰玻璃表面制备蛋白质芯片的对比

分别采用3-氨基丙基-三甲氧基硅烷、戊二醛、多聚赖氨酸、聚丙烯酰胺、琼脂糖、硝化纤维修饰玻璃表面,对6种不同修饰表面制备的蛋白质芯片进行对比研究,探讨制备蛋白质芯片的合适玻璃表面修饰方法.利用原子力学显微镜对其表面进行表征,通过点样蛋白于修饰后的玻片表面制备蛋白质芯片,比较不同修饰表面对蛋白质的固定效率和固定效果.结果发现:氨基、醛基、聚赖氨酸修饰玻片为二维平面结构,琼脂糖、聚丙烯酰胺、硝化纤维修饰玻片其表面不仅有多孔结构,而且有一定厚度;琼脂糖修饰玻片所得的荧光强度最高,背景较低,是一种理想的制备蛋白质芯片的表面修饰方法.     

用毛发合成胱胺酸

动物的羽毛、人类的头发及指甲即是由一种叫角质蛋白(Keratin)的蛋白质所构成.同时蛋白质为构成生物体的细胞膜所必须,水解天然蛋白质生产氨基酸流程,应用酸水解天然蛋白质技术,将无机酸水解毛发中的角质蛋白质,提取其中胱胺酸,同时解决了家禽养殖业产生的羽毛废弃物问题.     

不同嗜盐机制微生物蛋白质组特性及其识别

选取两种不同嗜盐机制微生物蛋白质组,并将其同非嗜盐微生物蛋白质组进行比较.研究结果发现:积累无机盐的蛋白质氨基酸组成与非嗜盐相差明显,而积累细胞相容性物质的嗜盐蛋白则差异较小,后者分子中His和分子量较小的氨基酸均显著多于非嗜盐蛋白,而Ala则相反;两种类型蛋白质中酸性氨基酸和碱性氨基酸的差值均显著高于非嗜盐蛋白.基于此,使用一种新型Person通用核函数的支持向量机对3种类型蛋白进行识别,其精度可达84.1%,优于其他核函数的支持向量机及其他机器学习算法.     

决策树算法预测人类病毒的蛋白质磷酸化位点

本文基于决策树分类算法构建人类病毒蛋白质磷酸化修饰位点的预测模型。采用氨基酸物理化学性质对蛋白质序列进行特征提取,并分析丝氨酸、苏氨酸和酪氨酸磷酸化位点邻近序列的氨基酸性质。同时考察了不同分类算法对预测结果的影响。通过10倍交叉验证,利用决策树算法预测丝氨酸、苏氨酸和酪氨酸磷酸化位点的MCC分别达到77.31%、75.91%和71.94%,表明本文提出的方法能有效地预测人类病毒的磷酸化修饰位点。     

非蛋白氨基酸的应用和功能研究进展

自然界中从细菌到人类的所有蛋白质主要都是由20种氨基酸组成的,这20种氨基酸称为蛋白氨基酸,也称为基本氨基酸或标准氨基酸.非蛋白氨基酸是指除组成蛋白质的20种常见氨基酸以外的含有氨基和羧基的化合物.非蛋白氨基酸多为蛋白氨基酸的类似物或取代衍生物,如甲基化、磷酸化、羟化、糖苷化、交联等等.除此之外,还包括β、γ、δ氨基酸及D-氨基酸.非蛋白氨基酸多以游离或小肽的形式存在于生物的各种细胞或组织中.     

不同类氨基酸的使用度对蛋白质折叠速率的影响

根据氨基酸约化分类,定义描述氨基酸序列信息的参量—相对氨基酸使用度(RAAU),在现有数据库和相关文献的基础上,建立了包含相对氨基酸使用度和蛋白质折叠信息的蛋白质折叠数据库.在此基础上,分析了相对氨基酸使用度对蛋白质折叠速率的影响.结果表明,强亲水类氨基酸和强疏水类氨基酸的使用对蛋白质的折叠速率的影响截然相反.对不同类蛋白质,其相对氨基酸使用度对蛋白质折叠速率的影响有明显差异.     

畜禽产品加工过程中有害物质的形成机制及抑制措施--以杂环胺为例

畜禽产品加工过程中容易形成致癌性、致突变性的杂环胺.IQ型杂环胺通过非酶褐变形成,即包含肌酸、氨基酸、糖的美拉德反应;氨基咔啉主要是通过氨基酸和蛋白质在高于300℃的温度下热解产生.研究表明,随着加工温度的升高和加工时间的延长,杂环胺含量显著上升.一些天然植物提取物以及抗氧化剂对杂环胺的形成有一定抑制作用.介绍了杂环胺的结构、分类、含量、影响因素等,重点对杂环胺的形成机制及抑制措施进行了分析.     

Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code.

One serious limitation facing protein engineers is the availability of only 20 'proteinogenic' amino acids encoded by natural messenger RNA. The lack of structural diversity among these amino acids restricts the mechanistic and structural issues that can be addressed by site-directed mutagenesis. Here we describe a new technology for incorporating non-standard amino acids into polypeptides by ribosome-based translation. In this technology, the genetic code is expanded through the creation of a 65th codon-anticodon pair from unnatural nucleoside bases having non-standard hydrogen-bonding patterns. This new codon-anticodon pair efficiently supports translation in vitro to yield peptides containing a non-standard amino acid. The versatility of the ribosome as a synthetic tool offers new possibilities for protein engineering, and compares favourably with another recently described approach in which the genetic code is simply rearranged to recruit stop codons to play a coding role.     

Role of arginine-tRNA in protein degradation by the ubiquitin pathway

Degradation of intracellular proteins through the ubiquitin and ATP-dependent proteolysis pathway involves several steps. Initially, ubiquitin is covalently linked to the proteolytic substrate in an ATP-requiring reaction. Proteins marked by ubiquitin may then be selectively lysed in a reaction that also requires ATP (for reviews see refs 1-3). A major question concerns the structural features of a protein that make it a specific substrate for ubiquitin-mediated degradation. It was shown that a free alpha-NH2 group is one important feature of the protein structure recognized by the ubiquitin ligation system, and that the half-life in vivo of a protein with an exposed amino terminus depends on its amino terminal residue. We have previously demonstrated that transfer RNA (tRNA) is essential for conjugation of ubiquitin and for the subsequent degradation of proteins with acidic amino termini (aspartate or glutamate). We now show that tRNA is required for post-translational conjugation of arginine to acidic amino termini of proteins, a modification that is essential for their degradation by the ubiquitin pathway.     

Chemical remodelling of cell surfaces in living animals

Cell surfaces are endowed with biological functionality designed to mediate extracellular communication. The cell-surface repertoire can be expanded to include abiotic functionality through the biosynthetic introduction of unnatural sugars into cellular glycans, a process termed metabolic oligosaccharide engineering. This technique has been exploited in fundamental studies of glycan-dependent cell-cell and virus-cell interactions and also provides an avenue for the chemical remodelling of living cells. Unique chemical functional groups can be delivered to cell-surface glycans by metabolism of the corresponding unnatural precursor sugars. These functional groups can then undergo covalent reaction with exogenous agents bearing complementary functionality. The exquisite chemical selectivity required of this process is supplied by the Staudinger ligation of azides and phosphines, a reaction that has been performed on cultured cells without detriment to their physiology. Here we demonstrate that the Staudinger ligation can be executed in living animals, enabling the chemical modification of cells within their native environment. The ability to tag cell-surface glycans in vivo may enable therapeutic targeting and non-invasive imaging of changes in glycosylation during disease progression.     

Peptide segment ligation: A new method for synthesis of peptide and protein

The protein structure-function relationships are al-ways highlighted in the field of life science. Protein syn-thesis from genomic sequence data is gaining significance in the post-genomic era of biomedical research by pro-viding direct access to functional proteins. The manually or automatically stepwise solid phase peptide synthesis (SPPS) allows peptide of up to 60 residues to be routinely constructed in good yield and high purity[1,2]. The assem-bly of longer proteins via the gene engine…     

修饰作用导致大豆蛋白氨基酸低效化问题的研究进展

大豆蛋白是广泛应用的食品加工原料,是人体可摄入的优质氨基酸来源,工业生产中为提高大豆蛋白的加工功能特性,常对其进行修饰改性。然而修饰改性有时会导致氨基酸消化吸收低效化。综述了大豆蛋白的功能特性及营养价值、主要修饰作用及其对氨基酸有效性影响,并对现阶段国内外研究的动态进行了分析,并提出今后的研究方向和展望,较全面地呈现修饰导致的大豆蛋白氨基酸低效化问题的研究进展,进一步解释蛋白聚合体与氨基酸消化性的关系,为提高大豆蛋白利用率,创新加工生产提供参考。     

Cloning and characterization of a new actin gene from Oryza sativa L.

Using Rho family member osRACD as bait, a new member of actin gene family -Act was isolated from Oryza sativa by yeast two-hybrid system. The full-length cDNA was cloned with 5' RACE technology, which contains an open reading frame of 1134 bp with a predicted protein of 377 amino acids. Sequence alignment revealed 96% to 81.8% identities with some known actin proteins in plants. The method of bioinformatics was used to analyze the protein modification sites, structure and evolution of the gene. Southern blot analysis showed that Act is a single-copy gene in the genome. The result of RT-PCR showed it is ubiquitously expressed in root, shoot, callus and panicle in a temporal fashion. The relationship between Rho family and actin family in evolution and function was also studied.     

扫描隧道显微镜诱导吸附有甘氨酸的Cu(111)表面铜台阶的产生和运动

氨基酸是蛋白质的构成单元,它在金属表面的吸附为研究蛋白质同金属相互作用奠定了基础。吸附了氨基酸的金属表面会发生诸如重构改变或小面化等形貌的变化,但这些变化在吸附了氨基酸的全部金属表面都能够发生。在较大负偏压(|V_b|＞2.5V)的条件下使用扫描隧道显微镜(STM)扫描吸附有甘氨酸的Cu(111)表面,在扫描区域内原有铜台阶的形状发生了变化并产生了新的铜台阶。本文对甘氨酸在铜表面形貌变化中所起的作用进行了讨论。     

新型冠状病毒膜蛋白的生物信息学分析

为了研究新型冠状病毒膜蛋白(SARS-CoV-2 M蛋白)结构及性质.基于生物信息学分析M蛋白质基因结构、二级结构和三级结构、翻译后的修饰和进化历程.结果表明,M蛋白为疏水性蛋白,其基因编码区长度为669bp,编码222个氨基酸;M蛋白启动子区内不存在甲基化位点,存在17潜在的转录因子结合位点;其二级结构以无规则卷曲和β折叠为主,不含外分泌信号肽,存在3个跨膜结构域、2对二硫键、37个磷酸化位点、1个N连接的糖基化位点和6个B细胞抗原结合位点;进化树分析表明,SARS-CoV-2 M蛋白与蝙蝠冠状病毒的M蛋白具有同源性.此结果为深入研究其结构与功能提供了理论数据,也为疫情防治提供了参考依据.     

Counting integral numbers of amino acid residues per polypeptide chain

Proteins have integral numbers of each of the 20 amino acids. However, all the currently accepted methods of determining this number measure the ratio of moles of amino acid residue per mole of protein. This value is rarely close to an integer, due to experimental errors in determination of the molar amounts of both amino acid residues and polypeptide chain. A simple method which gives integral values of amino acid residues per polypeptide chain, independent of any other properties of the protein, would be useful in characterising proteins. We describe here one method; it is illustrated for the case of Cys residues, although the approach should be useful for many of the other 19 usual amino acids.