分子模拟技术在植物体系的前沿应用与进展

doi:10.13560/j.cnki.biotech.bull.1985.2025-0676

生物技术通报 ›› 2026, Vol. 42 ›› Issue (2): 136-148.doi: 10.13560/j.cnki.biotech.bull.1985.2025-0676

分子模拟技术在植物体系的前沿应用与进展

曲航¹^,²^,³(), 张准¹^,²^,³, 张叶卓¹^,²^,³, 刘锡霖⁴, 李晔¹^,²^,³()

^1.北京林业大学生物科学与技术学院林木遗传育种全国重点实验室，北京 100083
^2.北京林业大学生物科学与技术学院林木育种与生态修复国家工程研究中心，北京 100083
^3.北京林业大学生物科学与技术学院林木、花卉遗传育种教育部重点实验室，北京 100083
^4.北京林业大学草业与草原学院，北京 100083

收稿日期:2025-06-27 出版日期:2026-02-26 发布日期:2026-03-17
通讯作者: 李晔，女，博士，副教授，研究方向：基于分子模拟研究植物体系中蛋白互作、物质跨膜转运的机理；E-mail: liye0223@bjfu.edu.cn
作者简介:曲航，男，研究方向：基于分子模拟研究植物蛋白互作的分子机制；E-mail: quhang@bjfu.edu.cn
基金资助:
林木遗传育种全国重点实验室（北京林业大学）基本科研业务费项目(TGBFRF202507);国家重点研发计划(2022YFF0712500);高等学校学科创新引智计划(B13007);北京林业大学“5·5工程”科研创新团队项目(BLRC2023A01)

Cutting-edge Applications and Advancements of Molecular Simulation in Plant Systems

QU Hang¹^,²^,³(), ZHANG Zhun¹^,²^,³, ZHANG Ye-zhuo¹^,²^,³, LIU Xi-lin⁴, LI Ye¹^,²^,³()

^1.State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083
^2.National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083
^3.Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083
^4.College of Grassland Science, Beijing Forestry University, Beijing 100083

Received:2025-06-27 Published:2026-02-26 Online:2026-03-17

摘要/Abstract

摘要：

随着计算机技术的飞速发展，分子模拟技术（molecular simulation）在探究植物蛋白互作、物质跨膜转运及细胞壁形成等方面展现出显著优势。针对近年来分子模拟技术在植物体系中的前沿应用，本文综述其最新研究进展，重点阐述分子动力学、分子对接、量子力学/分子力学结合方法及蒙特卡洛模拟技术在植物细胞壁、细胞膜、蛋白质互作及药用植物开发中的应用，并分析对比各方法的优缺点；最后针对分子模拟在植物体系的研究中面临的挑战进行展望，随着机器学习、新型算法及力场开发等相关领域的发展，有望进一步推动分子模拟技术在植物领域的应用。本文通过系统总结分子模拟技术在植物体系中的应用，旨在为植物体系的相关研究提供新的技术和新思路。

关键词: 分子模拟, 植物, 细胞壁, 蛋白互作, 药用植物, 技术应用

Abstract:

With the rapid advancement of computer technology, molecular simulation has demonstrated significant advantages in studying protein interaction mechanisms, transmembrane transport processes, and cell wall formation in plants. Focusing on the cutting-edge application of molecular simulation technology in plant systems in recent years, this review systematically summarizes the cutting-edge research progress of molecular simulation in plant systems. It focuses on the application of molecular dynamics, molecular docking, combined quantum mechanics/molecular mechanics methods and Monte Carlo simulation technology in plant cell walls, cell membranes, protein interactions and medicinal plant development, as well as analyzing and comparing the advantages and disadvantages of each method. Finally, the challenges are prospected while using molecular simulation in the study of plant systems. With the development of related fields such as machine learning, new algorithms and force field development, it is expected to further promote the application of molecular simulation technology in the plant field. This review systematically summarizes molecular simulation technologies in plant system research, aiming to offer innovative methodologies and perspectives for related studies in this field.

Key words: molecular simulation, plants, cell wall, protein interaction, medicinal plant, technical applications

曲航, 张准, 张叶卓, 刘锡霖, 李晔. 分子模拟技术在植物体系的前沿应用与进展[J]. 生物技术通报, 2026, 42(2): 136-148.

QU Hang, ZHANG Zhun, ZHANG Ye-zhuo, LIU Xi-lin, LI Ye. Cutting-edge Applications and Advancements of Molecular Simulation in Plant Systems[J]. Biotechnology Bulletin, 2026, 42(2): 136-148.

图/表 3

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技术 Technology	原理 Principle	优势 Advantage	劣势 Disadvantage	应用 Application	参考文献 Reference
分子动力学模拟 Molecular dynamics simulation	将分子体系中的每个原子或分子视为具有一定质量和相互作用的质点，通过求解这些质点的牛顿运动方程，得到它们在时间上的运动轨迹和状态	拥有原子级分辨率，捕捉瞬时构象态；可精确控制生物环境变量；可凭借空间分解算法实现高效并行计算	时间步长受限；计算资源消耗大；模拟长时间尺度事件时需借助额外技术支持	植物细胞壁结构与力学性质；新材料与仿生应用；植物-病原体相互作用	［13，16-23］
分子对接 Molecular docking	在受体活性位点区域通过空间结构互补和能量最小化原则来搜寻配体与受体是否能产生相互作用以及它们之间的最佳结合模式	高通量虚拟筛选，可降低实验成本；支持多种配体类型，适用场景多样；可进行多种结合模式预测	准确性受靶标结构分辨率限制；溶剂效应和评分函数参数简化可能导致偏差；构象采样不充分，易遗漏全局最优构象	植物激素与受体互作；次生代谢产物与酶活性；植物-病原体互作与抗病机制；植物源农药/药物开发	［17，24-29］
量子力学/分子力学组合方法 QM/MM	将整个体系分为QM与MM部分，QM部分用量子力学方法处理，而MM部分用分子力学方法处理，以最大程度同时保证计算精度与速度	原子级分辨率揭示反应过渡态和短寿命中间体；可突破实验技术对超快反应的时间分辨限制；结合了QM区的高精度与MM区的高效性	高精度计算导致时间尺度受限；计算复杂度高，资源消耗大；QM区与MM区边界拟合需保持力场一致性	酶催化机制解析；光合作用中的光驱动过程；逆境响应中的自由基反应	［30-41］
蒙特卡洛模拟 Monte Carlo simulation	通过随机扰动分子体系的微观状态，并根据能量判据接受或拒绝新状态，从而实现对体系平衡态性质的高效采样	无需计算能量梯度，降低计算复杂度；可高效获取热力学平衡态的结构统计特征；能通过扰动规则适配多系综，有较高灵活性	缺乏时间维度信息，无法直接表征动力学参数；计算效率受采样策略和算法优化水平影响	酶-底物反应路径解析；光合膜的超分子组织解析；植物激素与受体的结合自由能计算	［42-50］

技术 Technology	原理 Principle	优势 Advantage	劣势 Disadvantage	应用 Application	参考文献 Reference
分子动力学模拟 Molecular dynamics simulation	将分子体系中的每个原子或分子视为具有一定质量和相互作用的质点，通过求解这些质点的牛顿运动方程，得到它们在时间上的运动轨迹和状态	拥有原子级分辨率，捕捉瞬时构象态；可精确控制生物环境变量；可凭借空间分解算法实现高效并行计算	时间步长受限；计算资源消耗大；模拟长时间尺度事件时需借助额外技术支持	植物细胞壁结构与力学性质；新材料与仿生应用；植物-病原体相互作用	［13，16-23］
分子对接 Molecular docking	在受体活性位点区域通过空间结构互补和能量最小化原则来搜寻配体与受体是否能产生相互作用以及它们之间的最佳结合模式	高通量虚拟筛选，可降低实验成本；支持多种配体类型，适用场景多样；可进行多种结合模式预测	准确性受靶标结构分辨率限制；溶剂效应和评分函数参数简化可能导致偏差；构象采样不充分，易遗漏全局最优构象	植物激素与受体互作；次生代谢产物与酶活性；植物-病原体互作与抗病机制；植物源农药/药物开发	［17，24-29］
量子力学/分子力学组合方法 QM/MM	将整个体系分为QM与MM部分，QM部分用量子力学方法处理，而MM部分用分子力学方法处理，以最大程度同时保证计算精度与速度	原子级分辨率揭示反应过渡态和短寿命中间体；可突破实验技术对超快反应的时间分辨限制；结合了QM区的高精度与MM区的高效性	高精度计算导致时间尺度受限；计算复杂度高，资源消耗大；QM区与MM区边界拟合需保持力场一致性	酶催化机制解析；光合作用中的光驱动过程；逆境响应中的自由基反应	［30-41］
蒙特卡洛模拟 Monte Carlo simulation	通过随机扰动分子体系的微观状态，并根据能量判据接受或拒绝新状态，从而实现对体系平衡态性质的高效采样	无需计算能量梯度，降低计算复杂度；可高效获取热力学平衡态的结构统计特征；能通过扰动规则适配多系综，有较高灵活性	缺乏时间维度信息，无法直接表征动力学参数；计算效率受采样策略和算法优化水平影响	酶-底物反应路径解析；光合膜的超分子组织解析；植物激素与受体的结合自由能计算	［42-50］

分子模拟技术在植物体系的前沿应用与进展

Cutting-edge Applications and Advancements of Molecular Simulation in Plant Systems

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