抗原肽与MHC分子相互作用的QSAR模型研究

分别采用氨基酸序列及氨基酸结构描述符方法定量研究了短肽-MHC(major histocompatibility complex)分子结合亲合力的定量构效关系(QSAR)模型, 用这两个模型对短肽与HLA-A*0201分子结合的805个预测样本进行了预测, 预测准确度分别达到66.8%和65.5%. 采用了去除“劣点”方法检验模型的鲁棒性, 结果证明两个模型都具有良好的鲁棒性. 通过改变两个模型的参数, 对氨基酸残基个数为8或10的CTL(cytotoxicy T lymphocyte)表位进行预测.     

抗原肽与MHC分子相互作用QM/MM分子动力学模拟研究

在MHC I类(major histocompatibility complex class I)分子抗原加工提呈过程中抗原蛋白在抗原提呈细胞(antigen-presenting cells, APC)的胞浆中被蛋白酶体(proteasome)裂解成短肽peptide, 由转运相关蛋白(transporter associated with antigen processing, TAP)将蛋白酶体裂解产生的短肽片段从胞浆转运至内质网腔. 短肽peptide在内质网中与新生成的MHC I类分子结合, 形成peptide-MHC复合体被提呈到APC细胞表面, 与T细胞表面抗原受体(T cell receptor, TCR)特异性识别结合, 使得CTL细胞开始活化、增殖、分化, 进而对肿瘤细胞进行特异性杀伤. 目前对CTL细胞如何识别抗原肽-MHC复合物分子及抗原短肽peptide如何与主要组织相容性复合体MHC分子的相互作用识别结合的机理还不是很清楚. 传统的预测CTL细胞表位的方法没有考虑受体与配体结合过程中电子结构的变化, 电子结构的变化需要用量子力学方法来处理. 本文采用QM/MM多尺度生物大分子的分子动力学模拟方法, 以天然抗原肽TAX (LLFGYPVYVYU)与HLA-A*0201分子结合的晶体结构为模板, 替换抗原肽“锚点”氨基酸, 将口袋氨基酸残基的原子极化电荷在空间形成的静电势用电多极矩分量表示. 用箱线图分析每个口袋氨基酸分子静电势变化和功能, 确定Pocket B的Glu63和Lys66的功能是精细识别氨基酸和一级结合氨基酸, Pocket F的Asp77, Tyr84的功能是精细识别氨基酸, 而Asp77, Lys146是一级结合氨基酸, 表明QM/MM方法在提取抗原肽与MHC I类分子识别结合特异性信息是可行的, 这对了解免疫识别机理和指导肿瘤疫苗的开发都具有指导意义.     

HLA-A*0201限制性CTL表位定量结构与活性研究

采用VHSE氨基酸结构描述子表征HLA-A*0201限制性表位结构, 以遗传算法和偏最小二乘相结合(GA-PLS)对102个训练集进行定量构效关系建模. 剔除3个异常样本后, 据候选模型交互检验及50个外部测试集预测结果, 筛选得到最优偏最小二乘模型(A＝2), 其R², Q²和 分别为0.755, 0.621和0.680. 构效研究显示: CTL表位活性主要与1, 2, 7, 8, 9位氨基酸残基疏水、1, 2位立体及6位残基电性等性质密切相关.     

含有28个氨基酸的复杂多肽的串级质谱全序列分析研究

利用MALDI-TOF/TOF MS和ESI-MS/MS对一种含有多达28个氨基酸的复杂合成多肽成功进行了全序列测定. 通过调节激光强度、碰撞诱导解离(CID)能量等质谱参数以及依据不同序列分析软件, 获得了涵盖所有b型和y型碎片离子的串级质谱图. 结果显示这种方法可以有效地解决de novo测序方法遇到的谱峰过于复杂导致运算死机等问题. 通过讨论如何对含有超过20个氨基酸片断的多肽进行合格串级质谱实验, 为蛋白质组学肽段序列测定提供了新的方法和思路.     

分子模拟用于尤文肉瘤EWS-FLI1蛋白HLA-A2.1限制性CTL表位的筛选

为获得尤文肉瘤EWS-FLI1融合蛋白有效的HLA-A2.1限制性CTL表位, 综合运用BIMAS, SYFPEITHI, Predep和IEDB方案对EWS-FLI1进行CTL表位的预测, 得出8个CTL表位9肽序列; 应用多项式方案、量化基序方案对8个表位9肽进一步进行筛选, 获得其中4个9肽序列, 并进一步运用分子模拟方法初步模拟了4个表位肽与HLA-A2.1分子间的相互结合作用; 应用标准Fmoc方案合成CTL表位肽, RP-HPLC与MS分别鉴定合成肽的纯度与分子量; 通过亲和力实验验证了表位肽QIQLWQFLL_{(EWS-FLI1 304)}与HLA-A2.1有较强的结合力, 从而为表位肽的后继免疫学特性研究提供了基础. 本研究提供了一个合理高效的表位筛选方法.     

HLA-A*0201限制性CTL表位肽的三维定量构效关系的研究

运用比较分子力场(CoMFA)和比较分子相似性指数分析(CoMFA)方法研究了50个HLA-A^*0201限制性CTL表位九肽结构与亲和性间的关系,另外15个表位九肽作为预测集用于检验模型的预测能力.结果表明采用CoMSIA得到的构效关系模型(q^2=0.628,r^2=0.997,F=840.419)要明显优于采用CoMFA得到的构效关系模型.在CoMSIA计算中,当引入疏水场时,三维构效关系模型得到明显改善,通过该三维构效关系模型,可较精确地估算预测集中15个CTL表位肽与HLA-A^*0201间的亲和力(r^2pred=0.743).通过分析分子场等值面图在空间的分布,可以观察到表位肽分子周围的立体及疏水特征对表位肽与HLA-A^*0201间结合亲和力的影响,从而为进一步对CTL表位肽进行结构改造并基于此进行治疗性疫苗分子设计提供理论基础.     

朊病毒蛋白113-120序列多肽的反相液相色谱保留行为与构象稳定性的关系

朊病毒（Prion)蛋白是人和动物慢性中枢神经系统退化病的传染源,该蛋白的113－120序列被认为在其致病和传染机理中起着重要作用。以反相高效液相色谱为分析手段,研究了Prion蛋白113－120序列多肽的色谱保留行为。通过比较不同温度、不同流动相条件下该多肽色谱保留行为的变化,发现在乙腈溶液为上时,1nKw随温度的变化关系和Van′t Hoff曲线均比简单,说明该多肽在乙腈溶液中所采取的构象均较稳定,不易受温度的影响。以甲醇溶液为流动相时,具有游离末端的多肽的1nKw随温度变化关系和Van′t Hoff曲线比末端羧基和氨基分别被酰胺封闭的多肽要复杂,说明具有游离末端的多肽在甲醇溶液中所采取的构象相对较不稳定,易受环境的影响。这些结果进一步证明,113－120序列在Prion蛋白构象变化中可能起着重要作用。     

纳升电喷雾串联质谱"序列对接法"确定多肽的加钠位点

用QuattroM icro三级四极串联质谱分析常见的20种氨基酸的加钠效果。结果表明,绝大多数氨基酸与钠离子的非共价键结合力很弱甚至没有,但脯氨酸和苯丙氨酸很容易形成加钠离子峰。采用“序列对接法”测出重组人酸性纤维细胞生长因子(rh-a FGF)C-端肽段的全序列,并确定钠离子的加成位点为该肽段的第6位脯氨酸(6Pro)。通过酸化样品溶液获得无加钠、无序列间隙的该肽全序列,与加钠肽段的序列一致。     

溶剂诱导黑色素瘤抗原基因-2特定表位多肽异构的LC/MS研究

 研究乙醇、甲醇两种常用溶剂系统对固相合成的黑色素瘤抗原基因 2 (MAGE 2 )的特定表位多肽 (171 179)异构的影响。分别运用乙醇、甲醇溶剂体系以及极性溶剂二甲基亚砜 (DMSO)作对照预处理固相合成的黑色素瘤抗原特异性MAGE 2表位多肽 (171～ 179) ,然后用反相高效液相色谱 /质谱联用技术 (RP HPLC/MS)对合成的表位多肽的m/z进行Q1正离子监测扫描分析 ,观察其在不同溶剂系统预处理下的异构情况 ,以选择合理的预处理条件。结果发现采用乙醇及甲醇溶样时MAGE 2表位多肽有异构体产生 ,极性溶剂DMSO溶样的表位多肽未有异构现象发生。     

基于序列特征筛选与支持向量回归预测蛋白质折叠速率

折叠速率预测对阐明蛋白质折叠机理意义重大.本文收集了115条目前已知折叠速率的蛋白质样本(包括二态、多态和混态蛋白),为了较全面地表征蛋白质分子的一级结构信息,提取序列长度、氨基酸残基多尺度组分、成对残基k-space特征与基于残基物理化学性质的地统计学关联总共9357维特征.经改进的二元矩阵重排过滤器和多轮末尾淘汰非线性筛选,获得23个物理化学意义明确的保留特征,建立的非线性支持向量回归模型Jackknife交叉验证的相关系数R=0.95,优于文献报道及其他参比特征选择方法.支持向量回归解释体系表明折叠速率与保留描述符的非线性回归极显著,分析了各保留描述符对折叠速率的影响,结果表明蛋白质折叠速率与序列长度、中短程关联特征、三联体残基组份特征等密切相关.     

Sequence Analysis of Polypeptide by Mass Spectrometry

The method described in this work provides a sensitive and fast technique for investigating the primary structure of peptides with molecular weight up to 3340 amu. Usually, the metastable ion kinetic energy spectra (MIKES) and collisional activated decomposition (CAD) spectra provide complementary information for the FAB mass spectra, the MIKES and CAD spectra generally contain high-mass sequence ions.     

多肽一级结构表征与抗菌肽QSAM建模

从整体上考虑多肽一级结构, 提出了3种仅基于多肽氨基酸序列、 计算简便、 适于不等长肽和可捕获多肽上下文关联特征的多肽新描述子, 即地统计学关联(GS-AA531)描述子、多尺度组分与关联(MSCC)描述子和地统计学关联与多尺度组分(GS-AA531-MSC)描述子. 将其应用于2个抗菌肽体系(等长肽与不等长肽)的结构表征, 并以支持向量回归建立QSAM模型. 模型的拟合、 留一法及独立测试结果表明, 结合特征筛选的新描述子GS-AA531与GS-AA531-MSC的预测精度明显稳定且优于其它参比描述子, 在多肽QSAM研究中具有广泛应用前景.     

Sequence comparison and environmental adaptation of a bacterial endonuclease

The periplasmic/extracellular bacterial enzyme endonuclease I was chosen as a model system to identify features that might be responsible for temperature- and salt adaptation. A statistical study of amino acid sequence properties belonging to endonuclease I enzymes from three mesophilic habitats (non-marine, brackish water and marine), and three marine temperature groups (psychrophile, intermediate and mesophile) has been conducted. Ten new endonuclease I genes have been sequenced in order to increase the sample size. A bioinformatical method of property dependent statistical analysis of alignments has been applied. To our knowledge this is the first time these methods have been used in order to investigate environmental adaptation of enzymes. Adaptation to low temperature seems to involve increased surface isoelectric point and hydrophobicity in contrast to salt adaptation in which the isoelectric point and hydrophobicity at the surface decreases. Redistribution of charge and hydrophobicity might be the most important signature for cold adaptation and salt adaptation of this enzyme class. The results indicate that general trends of adaptation are possible to elucidate from the amino acid sequences. Also in this paper a new scale of stratified B-factors, derived from the Protein Data Bank, is presented.     

Restriction Endonuclease Analysis of Mitochondrial DNA of Muntjacs and Related Deer

Twelve restriction endonucleases were employed to analyze the mitochondrial DNA of four species of muntjacs and two related species of deer: red muntjac (M. muntjak), Gongshan muntjac (M. gongshanensis ), black muntjac (M. crinifrons), Chinese muntjac (M. reevesi), tufted deer (Elaphodus cephalophus), and forest musk deer (Moschus berezovskii). A total of 170 restriction fragments were detected among the samples. Fragments data were used to calculate the genetic distance (i. e. percent sequence divergency) among species, which in turn were used to construct a phylogenetic tree and to estimate divergency times. Our analysis indicates that the black muntjac and the Gongshan muntjac are most closely related, and that they are closely realted to the red muntjac and the Chinese muntjac. Additionally, the tufted deer is genetically closer to muntjacs than the musk deer is.     

SVM and SVR-based MHC-binding prediction using a mathematical presentation of peptide sequences

At present, there are a number of methods for the prediction of T-cell epitopes and major histocompatibility complex (MHC)-binding peptides. Despite numerous methods for predicting T-cell epitopes, there still exist limitations that affect the reliability of prevailing methods. For this reason, the development of models with high accuracy are crucial. An accurate prediction of the peptides that bind to specific major histocompatibility complex class I and II (MHC-I and MHC-II) molecules is important for an understanding of the functioning of the immune system and the development of peptide-based vaccines. Peptide binding is the most selective step in identifying T-cell epitopes. In this paper, we present a new approach to predicting MHC-binding ligands that takes into account new weighting schemes for position-based amino acid frequencies, BLOSUM and VOGG substitution of amino acids, and the physicochemical and molecular properties of amino acids. We have made models for quantitatively and qualitatively predicting MHC-binding ligands. Our models are based on two machine learning methods support vector machine (SVM) and support vector regression (SVR), where our models have used for feature selection, several different encoding and weighting schemes for peptides. The resulting models showed comparable, and in some cases better, performance than the best existing predictors. The obtained results indicate that the physicochemical and molecular properties of amino acids (AA) contribute significantly to the peptide-binding affinity.     

Sequence identification,structure prediction and validation of tannase from Aspergillusniger N5-5

Tannases produced by filamentous fungi are in a family of important hydrolases of gallotannins and have broad industry applications. But until now, the 3-D structures of fungi tannases have not been reported. The protein sequence deduced from the cDNA sequence obtained using RT-PCR amplification was identified as tannase through sequence alignment and phylogenetic analysis. Structure models based on the tannase sequence were collected using I-TASSER, and the model with the best match to the surface charge density-pH titration profile was selected as the final structure for tannase from Aspergillusniger N5-5. This work provides an effective method for protein structure research. The structure constructed in this work should be very important to understand the enzyme bioactivities and further developments of fungi tannases.     

信息拓扑指数与烷烃分子热力学性质的关系

Two topological information indices were constructed based on Randic and Wiener indices, and the values of topological information indices for 85 alkanes were calculated. The thermodynamic properties such as the standard enthalpies of formation, the standard entropies and the standard free energies of formation for these alkanes were also correlated with these topological and information indices. It is found that the thermodynamic properties calculated for both gaseous and liquid states of the 85 alkanes are in excellent agreement with the experimental values through the regression analysis.     

脱铝丝光沸石的制备和结构特征

用高温水蒸气结合酸洗的方法制备了SiO_2/Al_2O_3为16～186的脱铝丝光沸石。用X光衍射和红外光谱法研究了它们的结构持征。随丝光沸石脱铝,晶格参数呈非线性和各向不同步收缩。由于α方向发生明显收缩,使椭园形主孔道的长轴方向缩小。其骨架振动频率自600～1300cm~(-1)随着脱铝明显向高频方向漂移。当Al/u.c.自4脱至3时,丝光沸石的结构特征发生了明显的变化,可能与骨架上2位铝的脱除有关。当Al/u.c.≤3时,有新的Si—O—Si骨架生成,同时晶体重排为均匀有序的结构。     

二维泡沫稳定性与拓扑学性质的关系研究

研究了二维泡沫形成、进化及其拓扑学性质随时间的变化关系以及影响其稳定性的因素.探索了二维泡沫初始有序化的气泡进化和完全无序化的气泡进化的两种过程,并分析在无序化气泡的进化过程中,平均气泡面积随时间的变化呈现出α=1.5的幂指数关系,以及该指数大于VonNeumann定律的时间指数的可能原因.讨论了气泡的边数分布及其二阶矩.