靶标诱导的核酸适配体链构象转变的计算机模拟研究

Aptamers are short, single stranded oligonucleotides that bind potently and selectively to their targets by adopting distinct secondary and tertiary structures. The ligand-induced conformational transition of aptamer is the key to understanding the molecular recognition mechanism. Although many experimental and computational research have been performed, how the sequence and chemical composition of the nucleic acid and the solution environment including ions type and salt concentration alter the conformational transition of nucleic acid are still far from fully understood. In our previous research, we proposed a computational approach SELEX in silico to search the sequence space for potent aptamers. We successfully applied SELEX in silico on theophylline-binding RNA aptamer and L-argininamide-binding DNA aptamer, identified several novel aptamers with better ligand-binding affinity, which were published at J. Chem. Theory Comput (2015) and J. Phys. Chem. Lett (2017), respectively. In this proposal, we are attempting to study the conformational transition of nucleic acid aptamer from two directions: chemical information of nucleic acid aptamer and solution environment including ions type and salt concentration. By combining the molecular simulation approaches such as all-atom/coarse-grained molecular dynamics simulation, Markov State Models, molecular docking, we will construct the aptamer folding-ligand binding free energy landscape. By the integration with previous experimental results, we will probably reveal the molecular mechanism though which the mutation/ions affect the conformational transition of nucleic acid. The experimental technologies like CD/ITC/NMR/ will be used to verify our findings. Based on these research, we will optimize aptamer towards high affinity or specificity and greatly broaden the application of aptamer in real life. Our study will not only shed lights on the molecular recognition mechanism of aptamer, but also deepen the understanding of the physical nature of the ligand-induced conformational transition of nucleic acid.

核酸适配体是一类能高亲和、强特异地识别靶标的短链DNA或RNA。作为一种特殊的高分子链，核酸适配体在靶标诱导下发生的链构象转变是其靶标识别的核心部分，是其化学生物学传感器构建的基础，但相关研究较少，其物理本质不明确。申请人关注核酸适配体的分子识别机制，前期采用分子模拟研究适配体的序列-结构-功能关系，相关成果发表在JPCL和JCTC等。本申请拟以链构象转变为核心，从核酸适配体的碱基序列、溶液离子及其浓度两个方向研究靶标诱导的核酸链构象转变过程中各类化学基团和各类相互作用的贡献。通过分子动力学、马尔科夫状态模型、分子对接等建立核酸适配体的折叠-结合自由能面，理解碱基突变、金属离子影响其链构象转变的作用机制，进行核酸适配体序列优化设计并使用CD/ITC/NMR等实验验证。本研究中阐明的核酸适配体链构象变化过程及其影响因素将有助于理解核酸适配体的分子识别机制，加深核酸链构象变化的物理本质理解。

核酸适配体是一类能高亲和、强特异地识别靶标的短链DNA或RNA，靶标诱导的核酸适配体链构象转变是其靶标识别的核心。本项目围绕链构象转变，从核酸适配体的靶标识别及其影响因素和精确描述链构象变化的计算工具开发两个方向展开研究。我们采用分子动力学、马尔科夫状态模型、分子对接和残基作用网络等工具实现了对以核酸适配体为代表的生物大分子构象变化的精准描述，揭示靶标结合、金属离子、突变等调控核酸适配体链构象变化的机制，实现了计算驱动的核酸适配体新靶标发现，丰富了人们对核酸适配体靶标特异性的认识。我们提出残基接触打分以精确描述残基间的接触强度，从而实现对微观构象变化的精细表征，并将其成功应用在核酸适配体、G蛋白偶联受体等生物大分子，阐述了这些生物大分子的构象受配体结合或突变调控而影响其功能的具体机制，为深入理解生物大分子的构象变化及其功能关联机制和药物设计提供了重要的研究基础。本研究按照申报书原定计划开展并顺利实施，取得了预期研究成果。项目在执行期间共合作培养博士2名，硕士1名，博士后1名。发表标注本基金资助的学术论文8篇，其中项目负责人以第一作者或共同第一作者在Elife、Cell Research、Nature Communication、Journal of Medicinal Chemistry、Signal Transduction and Targeted Therapy等知名期刊发表论文6篇。