抑癌基因p53密码子偏好性分析及其突变致癌预测

p53是人类恶性肿瘤中最常见的突变基因,与人类肿瘤的发生相关性最高,也是基因研究中热度最高的基因之一。为深入研究人类p53基因突变机理,选取了6条人类p53基因mRNA序列。首先,利用基于RSCU方法下的多重变量分析软件CodonW对影响密码子使用的各项参数进行计算和统计分析,分析可得,密码子适应指数(CAI)与最优密码子使用频率(FOP)、密码子偏爱指数(CBI)均呈极显著正相关(p<0.01);有效密码子数(ENC)与密码子偏爱指数(CBI)、GC含量、GC3s、最优密码子使用频率(FOP)、第三位碱基G3s、密码子适应指数(CAI)均呈极显著负相关(p<0.01)。然后,再利用QRSCU编码方法,对p53密码子偏好性间距进行了分析设计,得出了基于拟氨基酸编码的方法能充分体现p53密码子对同义密码子的一致偏好性的结论,且p53基因更偏好使用以c或g结尾的同义密码子。以上各项参数也充分验证了拟氨基酸编码方法与p53密码子偏好性研究结果的紧密关联性。最后,结合前人对抑癌基因p53突变致癌的研究,对该6条基因序列作了病变预测,从而为人类恶性肿瘤的预防和预测提供重要的理论依据。     

基于QRSCU方法的RHD基因的偏好性研究及其应用

Rh血型系统作为人类最复杂的血型系统之一,其临床意义仅次于ABO血型系统.研究人类Rh血型系统中RHD基因对同义密码子的使用偏好性有助于从生物信息学角度了解RHD基因的编码特征.本文基于拟氨基酸编码方法,计算了人类Rh血型系统中RHD基因的同义密码子的相对使用度(quasi relative synonymous codonusage,QRSCU)及4种碱基分别出现在密码子3'端的相对频率(quasi relative frequency of nucleotide to codon3',QRFN3').通过分析计算结果中RHD基因的QRSCU值,得出RHD基因偏好使用以C或G结尾的同义密码子,也说明RHD基因偏好使用密码子-反密码子结合作用强的同义密码子,且避免使用结合作用中度的同义密码子.另外,通过分析计算结果中RHD基因的ORFN3'值,得出RHD基因的同义密码子对后面所接的第一个碱基的使用也有很强的使用偏好性.     

磷化蛋白phospho—p5315的电化学免疫传感器

p53蛋白是调控人体内细胞生长和监控细胞分裂时DNA的复制最重要的分子．它是一种重要的肿瘤抑制基因,能防止癌变．还能帮助细胞基因修复缺陷。但当人体受到紫外光照射或化学致癌物的作用时,p53不能执行上述功能时,对细胞的增殖失去控制,往往就会导致细胞发生癌变。据报道超过一半的人体癌细胞中．     

CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes

Codon usage bias reveals the silent molecular evolution pattern. Previous research showed the codon usage bias was associated with many biological processes, such as protein expression level, genetic coding error minimization, mRNA stability, codon context, tRNA richness, CpG suppression, DNA methylation, and tissue or organ specificity. In this paper we reviewed major methods of codon usage bias measurement. Since most of existing methods are only suitable for the comparison of codon usage bias within a single genome, we introduced a new informatics index, referred to as synonymous codon usage order (SCUO), to measure synonymous codon usage bias within and across genomes. In this method, Shannon informational theory was applied to describe the SCUO of each gene using a value ranging from 0 to 1, with larger values associated with greater codon usage bias. We compared our method with the codon adaptation index (CAI) method for measuring codon bias in Escherichia coli and Sacharomyces cerevisiae. We also studied the correlation between SCUO and CAI, and the relation of SCUO with gene length, gene function, and GC composition. In addition, we explored the correlation between SCUO and mRNA abundance in S. cerevisiae using SAGE expression data. The software package codonO is freely available at http://digbio.missouri.edu/～wanx/cu/codonO/.     

p53抑癌基因电化学阻抗传感器研究

基于电化学阻抗技术构建了一种检测p53抑癌基因的电化学传感器.首先利用自组装作用将末端带巯基的探针p53抑癌基因(p53-DNA)固定于金电极表面,根据传感器结合前后电子转移阻抗值的变化,对目标p53-DNA进行了测定.以pH =7.4的5mmol/L K3[Fe(CN)6]-5mmol/L K4[Fe(CN)6]平衡电对溶液作为检测液,检测目标p53-DNA的线性浓度范围为1.0×10-8～ 1.0×10-6 mol/L,其检出限为3.0×10-9 mol/L(S/N =3).对5.0×10-8 mol/L的目标p53-DNA进行11次平行测定,其RSD为3.4％.该传感器制作简单、灵敏高、选择性好,且无需标记,易于操作.     

Computational screening and design of S100B ligand to block S100B–p53 interaction

The binding of S100B to p53 disables the biological function of p53 as a tumor suppressor and thus causes cancer. It is very important to explore the interaction between S100B and p53 and to develop inhibitors to block the interaction in anti-cancer development. In this work, the interaction of S100B to p53 was studied using molecular dynamics (MD) at the atomic level and organic molecules have been identified as potential inhibitors to block the S100B–p53 interaction. It was indicated in the simulations that S100B residues around GLU45 and GLU46 play an important role in the binding of S100B to p53. The three dimensional structure of S100B obtained from S100B–p53 complex (PDB ID: 1DT7) was used as the target protein receptor. Multiple LUDI screenings for S100B ligands were performed using different searching radii 6.23 Å, 7.23 Å, 8.23 Å, 9.23 Å and 10.23 Å with a searching center which was defined as the geometrical center of S100B residues that are within 5 Å from the p53 C-terminal peptide in the complex. Potential organic compounds were screened from the ZINC database using LUDI program implemented in Cerius2 package and evaluated as potential S100B ligands to block the S100B–p53 interaction. The top-scored compounds were selected for binding affinity calculation. The results show that these top-scored ZINC compounds bind in the location where p53 binds and interact with S100B in a similar fashion as p53, and therefore it is expected that they have the potential to block S100B from binding to p53. The ADME and toxicity properties of the potential S100B ligands were also evaluated.     

Preparation of an electrochemical PNA biosensor for detection of target DNA sequence and single nucleotide mutation on p53 tumor suppressor gene corresponding oligonucleotide

Development of an electrochemical biosensor based on peptide nucleic acid (PNA) probe for detection of target DNA sequence and single nucleotide mutation in p53 tumor suppressor gene corresponding oligonucleotide using methylene blue (MB) as an electrochemical indicator is described. The interaction between MB and short sequence of p53, one of the most important tumor suppressor genes due to its dysfunction in the majority of human cancers, was studied by differential pulse voltammety (DPV). Probe modified electrode was prepared by self-assembled monolayer (SAM) formation of thiolated PNA molecules on the surface of gold electrode (GE). The hybridization of PNA probe with target DNA was performed in solution to form PNA-DNA hybrid on the surface of the GE. A significant increase in the reduction signal of MB was observed upon hybridization of the probe with the complementary DNA. The selectivity of the biosensor was studied using noncomplementary oligonucleotides. Furthermore, our results confirmed the ability of the sensor to detect single base mismatch in the sample oligonucleotide. The influence of probe concentration on the effective discrimination against noncomplementary sequence and point mutation was also investigated. Diagnostic performance of the biosensor is described and the detection limit is found 6.82 × 10⁻¹⁰ M. The electrochemical impedance spectroscopy was also employed to further investigate the sensor function.     

Prediction of dual agents as an activator of mutant p53 and inhibitor of Hsp90 by docking,molecular dynamic simulation and virtual screening

Heat shock protein90s (Hsp90s) play a crucial role in the development of cancer, and their inhibitors are a main target for tumor suppression. P53 also is a tumor suppressor, but in cancer cells, mutations in the p53 gene lead to the inactivation and accumulation of protein. For instance, the ninth p53 cancer mutation, Y220C, destabilizes the p53 core domain. Small molecules have been assumed to bind to Y220C DNA-binding domain and reactivate cellular mutant p53 functions. In this study, one of the mutant p53 activators is suggested as an Hsp90 inhibitor according to a pyrazole scaffold. To confirm a new ligand as a dual agent, molecular docking and molecular dynamic simulations were performed on both proteins (p53 and Hsp90). Molecular dynamic simulations were also conducted to evaluate the obtained results on the other two pyrazole structures, one known as Hsp90 inhibitor and the other as the reported mutant p53 activator. The findings indicate that the new ligand was stable in the active site of both proteins. Finally, a virtual screening was performed on ZINC database, and a set of new dual agents was proposed according to the new ligand scaffold.     

基于本体的空管人为差错分析研究与应用

为实现空管人为差错致因及危险等级语义分析,开发人为差错本体分析软件。通过空管运行人为差错(HeraJanus)及人为差错预测(Hera-Predict)手册中获取的领域知识构建领域本体;结合事故调查报告知识创建存储本体,建立Hera-Janus本体知识库,根据类与个体之间的关系定义Jena推理规则。通过Eclipse平台中的Jena应用调用Pellet推理机分析实际案例,在人机交互界面给出差错类型及危险程度,其结果表明了空管事故智能化分析的有效性和可行性。     

蛋白质二级结构预测中的HMM及I／O HMM方法研究

文章主要介绍了在蛋白质结构预测中两种被有效使用的模型--隐马尔可夫模型和输入隐马尔可夫模型，分别阐述了其原理、算法及应用实例。数值实验表明，这两种方法对小样本的预测实用具有较强的适应性。     

缠论和相似灰色模型的预测方法在股价拐点预测中的研究应用

针对股价拐点预测研究中拐点序列重构和振荡序列预测问题,提出一种缠论和相似灰色模型结合的预测方法。首先,在缠论基础上系统地给出序列重构的基本理论,再针对灰色理论在振荡序列中预测的不足,提出纵向残差和横向偏差相关系数与灰色理论相结合的相似灰色预测模型;然后利用纵向偏差—横向残差相关系数对历史数据进行匹配计算,得到预测误差最小的灰色模型参数,以加权求和的方式实现具有振荡特性的股价拐点预测。最后两组股价拐点预测实验表明,所归纳的序列重构理论是有效的,与其他常用灰色模型对比表明,相似灰色模型可有效提高振荡序列的预测精度。