DNA损伤致p53-Mdm2相互作用的动力学模型

最新实验结果表明，在受到各种辐射而引起DNA损伤后，在单体细胞和群体细胞情况下，细胞中的p53蛋白浓度表现为非衰减振荡和衰减振荡两种不同的动力学行为.通过研究p53-Mdm2负反馈回路的非线性动力学行为，分析了各种(特别是DNA损伤、p53和 Mdm2蛋白浓度三者之间)动力学关系，提出了一个能同时描述这两种不同动力学行为的非线性模型. 关键词： p53-Mdm2负反馈回路 非衰减振荡和衰减振荡 非线性动力学模型     

Mdm2生成速率调控的p53-Mdm2振子的全局动力学和稳定性

肿瘤抑制蛋白p53的动力学在一定程度上可以决定DNA损伤后的细胞命运.p53的动力学行为与p53信号通路中p53-Mdm2振子模块密切相关.然而,p53的负调控子Mdm2的生成速率的增加使其在一些癌细胞中过表达.因此探讨Mdm2生成速率对p53动力学的影响有重要意义.同时,PDCD5作为p53的激活子也调控p53的表达.因此,本文针对PDCD5调控的p53-Mdm2振子模型,通过分岔分析获得了Mdm2生成速率所调控的p53的单稳态、振荡以及单稳态与振荡共存的动力学行为,且稳定性通过能量面进行了分析.此外,噪声强度对p53动力学的稳定性有重要的影响.因此,针对p53的振荡行为,探讨了噪声强度对势垒高度和周期的影响.本文所获得的结果对理解DNA损伤后的p53信号通路调控起到一定的指导作用.     

Biophysical characterization of DNA binding from single molecule force measurements

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.     

The birhythmicity increases the diversity of p53 oscillation induced by DNA damage

The tumor suppressor p53 mediates the cellular response to various stresses. It was experimentally shown that the concentration of p53 can show oscillations with short or long periods upon DNA damage. The underlying mechanism for this phenomenon is still not fully understood. Here, we construct a network model comprising the ATM-p53-Wip1 and p53-Mdm2 negative feedback loops and ATM autoactivation. We recapitulate the typical features of p53 oscillations including p53 birhythmicity. We show the dependence of p53 birhythmicity on various factors such as the phosphorylation status of ATM. We also perform stochastic simulation and find the noise-induced transitions between two modes of p53 oscillation,which increases the p53 variability in both the amplitude and period. These results suggest that p53 birhythmicity enhances the responsiveness of p53 network, which may facilitate its tumor suppressive function.     

DNA损伤致p53-Mdm2相互作用的非线性动力学模型(英文)

p53-Mdm2相互作用在DNA损伤的细胞响应方面起着非常重要的作用。最新实验结果表明,在受到各种辐射损伤而引起DNA损伤后,细胞中的p53蛋白浓度在单体细胞和群体细胞情况下,表现为非衰减振荡和衰减振荡两种不同的动力学行为。通过研究p53 -Mdm2负反馈回路的非线性动力学,分析了各种（特别是DNA损伤,p53和Mdm2浓度三者之间的）动力学关系,提出了一个能同时描述这两种不同动力学行为的非线性模型。 Exploring the nonlinear dynamics of the negative feedback loop composed of p53 and Mdm2 proteins, we propose a signal-response model to study the dynamical mechanism of the different oscillatory behaviors for the activities of p53 and Mdm2 proteins both in individual and population of cells. It is shown that the sustained and damped oscillatory dynamics could be described in a unified way when the dynamics of damage-derived signal is properly introduced.     

A unified model for studying DNA damage-induced p53–Mdm2 interaction

Exploring the nonlinear dynamics of the negative feedback loop composed of p53 and Mdm2 proteins, we propose a signal–response model to study the dynamical mechanism of the different oscillatory behaviors for the activities of p53 and Mdm2 proteins both in individual and populations of cells. It will be shown that the sustained and damped oscillatory dynamics could be described in a unified way when the dynamics of the damage-derived signal is properly introduced.     

Insight into binding modes of p53 and inhibitors to MDM2 based on molecular dynamic simulations and principal component analysis

Inhibition of the p53–MDM2 interaction is a new therapeutic strategy to activate the wild-type function of p53 in tumors. Molecular dynamics (MD) simulations and calculations of binding free energies were performed to investigate the binding mechanisms of p53 and two inhibitors PMI and VZV to MDM2. The results show that van der Waals interaction is the main force to control the bindings of ligands to the hydrophobic cleft of MDM2, which basically agrees with the previous calculated and experimental studies. The results from the RMSF calculation, cross-correlation analysis and principal component (PC) analysis prove that the ligand bindings produce a significant effect on the conformation of the binding cleft of MDM2. In addition, the calculations of residue-based free energy decomposition suggest that the CH–CH, CH–π, and π–π interactions dominate the bindings of p53 and inhibitors to MDM2. This study can provide significant help for the design of potent inhibitors targeting the p53–MDM2 interaction.     

Mathematical Modeling of Linear Docking. I. Determination of Regions of Binding of Protein Molecules

We report on the results of mathematical simulation of the interaction of various sequences of proteins Mdm2, P53, and Nap1 in accordance with the developed algorithms that were used for identifying the region of binding of various proteins during the formation of biological complexes P53–Mdm2, Mdm2–Mdm2, and Nap1–Nap1. The approach developed in this work will make it possible to determine active regions of binding of polypeptide chains of various proteins and to choose and synthesize highly selective peptides that will be bound in the active center of a protein and will lead to its activation or inhibition and blocking of its biological functions.     

基于分子动力学和自由能计算研究小分子对HIF-VHL相互作用的抑制机理

蛋白-蛋白相互作用涉及多种生理过程. 其中HIF-VHL作为局部缺血性心脏病的重要靶标得到了学术界和工业界的广泛关注. 本文使用分子动力学模拟和结合自由能计算研究pro-like的小分子抑制剂对VHL-HIF的抑制机理. Pro-like抑制剂能够与HIF竞争性地结合在VHL蛋白上,从而破坏VHL-HIF相互作用. 基于抑制机理给出了pro-like抑制剂的优化策略.     

细胞周期依赖性激酶2与其抑制剂的残基特异性结合的计算分析

细胞周期依赖性激酶2(CDK2)是细胞周期调控中的关键大分子.在癌细胞中,CDK2常被过度表达,因此抑制CDK2的表达是治疗乳腺癌、白血病和淋巴瘤等多种癌症有效的方法,在分子水平上定量表征CDK2与其抑制剂之间的相互作用,可为药物开发提供更深入的蛋白质与抑制剂的相互作用机制和线索,本文采用计算丙氨酸扫描和相互作用熵方法,研究CDK2与13种抑制剂结合的微观机制,该方法得到的结合自由能与实验值之间的相关系数为0.76～0.83.计算结果揭示了这13种抑制剂中的两种结合模式,即范德华占优势和静电占优势.通过将总能量分解为每个残基的贡献,确定了结合过程中五个疏水残基为热点残基,同时发现了能够决定CDK2与抑制剂结合强度的残基.     

First-principles study of the formation mechanisms of nitrogen molecule in annealed ZnO

Recently, N₂ molecule was reported to induce localized states in the band gap and trap two holes in ZnO. In this Letter, the detailed mechanism for the formation of N₂ molecule in high temperature annealing process in ZnO was investigated based on density-functional theory. By analyzing the interactions between N-related defects, we found that the nitrogen molecule would form by the binding of two interstitial nitrogen atoms. Interstitial oxygen facilitated the formation of N₂ by kicking out N_O to interstitial site. The formation of nitrogen molecule in ZnO would cause low doping efficiency and degeneration of the p-type in annealing process. Our results could explain the recently reported formation of N₂ molecule in high temperature annealing process in N-doped ZnO. Appropriate annealing conditions were suggested in order to get p-type ZnO.     

Studying Complexes Between PPI Dendrimers and Mant-ATP

The aim of this study was to investigate the interactions between poly(propylene imine) (PPI) dendrimers and 2′-/3′-O-(N′-methylanthraniloyl)-ATP (Mant-ATP). Mant-ATP was used as a model molecule. Purine and pyrimidine nucleoside analogues are antimetabolites commonly used in therapy for cancer. Drug molecules can complex with dendrimers in two ways: therapeutic agents may be attached in dendrimer interior or bind to functional groups on the surface. Drugs attached to nanoparticles are characterized by improved solubility, pharmacokinetics and stability. Here, we have used poly(propylene imine) dendrimers of the 4th and 5th generations (PPI G4 and PPI G5) with primary amino surface groups partially modified with maltose (PPI-m) or without modification (PPI). We assessed the efficiency of complex formation in relation to dendrimer generation, pH of solution and the type of dendrimer used. A double fluorimetric titration method was used to estimate the binding constant (K _b ) and the number of binding centers per molecule of the binding agent (n).     

单分子动力学研究大肠杆菌单链结合蛋白与单链DNA的结合过程

大肠杆菌单链结合蛋白(E.coli SSB)具有与单链DNA(single-stranded DNA,ssDNA)结合的性质,起着保护ssDNA及引导相关蛋白质反应的重要作用,然而,它与ssDNA的结合过程及其细节尚未得到确定的研究结果.本文采用单分子磁镊对E.coli SSB/ssDNA复合体进行拉力测试,并采用单分子化学反应动力学方法对测试结果进行分析.研究发现:E.coli SSB在ssDNA上的结合过程分为两个不同的阶段,一个是在临界力下快速的结合缠绕阶段,一个是随着力的进一步减小逐步缠绕的阶段.从中得到了E.coli SSB与ssDNA的化学反应系数,并得到了相应的自由能参数.采用自由能校准的方法,得到了SSB与ssDNA结合的完整自由能曲线,从而揭示了E.coli SSB与ssDNA的结合特征.本文的分析方法也可以应用于相似的化学反应的研究中.     

癌基因MDM2阻断剂的分子结构的NMR研究

根据P53-MDM2复合物晶体结构,设计合成了非肽类小分子作为MDM2的阻断剂.利用超导核磁共振波谱仪,测定了化合物的¹H谱、¹³C谱、¹H-¹H COSY谱、HMQC和HMBC谱,确定了化合物的结构,归属了化合物的¹H、¹³C化学位移,为筛选抗癌活性化合物提供了理论依据.     

塞来昔布的密度泛函理论计算及光谱分析

塞来昔布(Celecoxib, CXB)是COX-2的高选择性抑制剂,经过20年的发展已经成为世界范围内使用最为广泛的一类处方药.本文基于密度泛函理论,使用B3LYP泛函,6-311++G(d, p)基组进行结构优化.在此工作上对该药物分子的结构、红外光谱、拉曼光谱、分子前线轨道、静电势和激发态性质做了一系列的研究.结果表明：CXB分子是一个稳定的非平面扭曲结构,此结构使得该药物分子在COX-2上的疏水通道中可以迅速通过,从而形成了一个可与苯磺酰胺片段结合的结合腔.对化合物进行频率计算,分别得到红外光谱和拉曼光谱,与实验采集的数据进行对比,呈现出较好的一致性.对分子的基态进行前线轨道和静电势的分析,磺酰胺基与COX-2易形成氢键作用.在CXB分子的激发态研究中发现,CXB分子的激发态性质主要由第1激发态、第3激发态和第6激发态共同决定.这为理解CXB的作用机理提供了重要的信息,也为后期扩展CXB衍生物提供了理论基础.     

Structural insights of dipeptidyl peptidase-IV inhibitors through molecular dynamics-guided receptor-dependent 4D-QSAR studies

Dipeptidyl peptidase-IV (DPP-IV) inhibitors are promising antidiabetic agents. Currently, several DPP-IV inhibitors have been approved for therapeutic use in diabetes mellitus. Receptor-dependent 4D-QSAR is comparatively a new approach which uses molecular dynamics simulations to generate conformational ensemble profiles of compounds representing a dynamic state of compounds at a target’s binding site. This work describes a receptor-dependent 4D-QSAR study on triazolopiperazine derivatives. QSARINS multiple linear regression method was adopted to generate 4D-QSAR models. A model with 9 variables was found to have better predictive accuracy with \({R}^{2}=0.692\), \({Q}^{2}\) (leave-one-out) = 0.592 and \({R}^{2}\) predicted = 0.597. The location of these 9 variables at the binding site of DPP-IV revealed the importance of the residues Val711, Tyr662, Tyr666, Val202, Asp200 and Thr199 in making critical interactions with DPP-IV inhibitors. The study of these critical interactions revealed the structural features required in DPP-IV inhibitors. Thus, in this study the importance of a halogen substituent on a phenyl ring, the extent of substitution on the triazolopiperazine ring, the presence of an ionizable amino group and the presence of a hydrophobic substituent that can bind deeper in binding pocket of DPP-IV were revealed.     

VPRBP 蛋白与Abl 激酶诱发、抑制前列腺癌的 一种物理机制

在本文基于Hill动力学与Michaelis-Menten方程,建立理论模型研究VPRBP蛋白与Abl激酶诱发、抑制前列腺癌的一种物理机制.研究发现,DNA损伤使得ATM(共济失调毛细血管扩张症突变)很快激活,并激活上调p53蛋白表达,DNA损伤的后续破坏会在很大程度上通过p53表达上调而被抑制. VPRBP通过上调MDM2蛋白的激活水平,使得p53表达水平异常,进而无法正常抑制前列腺癌的发生发展.通过考察Abl在前列腺癌进程中的作用发现,Abl使得AKT的表达水平下调,由于Abl对AKT的抑制作用,致使在AKT信号通路中MDM2表达水平受到抑制,进而稳定p53表达.由此表明了,过少的Abl对AKT的抑制程度减弱,不仅使得细胞代谢出现紊乱,而且还会促使p53正常的周期表达水平异常,对DNA损伤诱发的肿瘤抑制性减弱,进而促进前列腺癌的发生发展.基于本文模型,可以预测VPRBP与Abl作为诱发、抑制前列腺癌的调节剂对现有和潜在的抗癌治疗较为敏感. VPRBP与Abl在诱发、抑制前列腺癌过程中的时滞效应,导致信号通路中p53与PTEN蓄积量增多、AKT蓄积量减少,以及Plk1周期振荡相位转移...     

光谱法研究3H-吲哚探针分子与Triton X-100胶束间的相互作用

用光谱法研究了荧光分子2－（对－己基胺基）苯基－3,3－二甲基－5－乙酯基－3H吲哚基－甲基二辛基磺化铵（A）与Triton X-100胶束间的相互作用,测定了A在不同浓度的Trtiton X-100溶液中的吸收光谱,荧光光谱和荧光寿命,实验得到了A与胶束的结合常数Ks,A在胶束中所处环境的极性及其在胶束中发生的pH效应,结果表明,A与胶束间存在较强的相互作用,A在胶束中所处环境的极性及其在胶束中发生的pH效应,结果表明：A与胶束间存在较强的相互作用;A在胶束中所处环境的极性接近于甲醇的极性,并推测出了A的不同基团在胶束中所处的不同位置,同时发现：在Triton X-100胶束中A可探测到两个位置,但当Triton X-100的浓度过大时,A只能探测到一个位置。