AI 中文总结
研究膜变形蛋白晶格模拟难题，提出耦合Helfrich膜的柔性蛋白质晶格模型，以网格蛋白晶格为例，量化材料属性，比较弯曲刚度解释，验证模型，还展示新代码并应用于HIV-1未成熟Gag晶格。
AI 中文摘要
膜变形蛋白晶格在包括内吞作用和病毒出芽等重要及致病生物学过程中起关键作用。对于此类大规模膜重塑事件，在模拟中实现必要的长度和时间尺度可能困难。本文提出一个在过阻尼状态下，耦合到傅里叶空间中传播的Helfrich膜的柔性蛋白质晶格模型，主要关注内吞机制重要部分的膜结合网格蛋白晶格。通过屈曲方法量化其材料属性以测量弯曲刚度随粗粒化势能函数力常数的变化。通过与用类似Helfrich弯曲能项模拟球形网格蛋白包被弯曲能时观察到的有效刚度比较，展示弯曲刚度的解释如何随蛋白包被结构变化。验证模型时发现模拟膜的张力导致网格蛋白包被几何形状变化符合理论预期。最后展示了将通过刚体反应扩散组装的结构（使用NERDSS模拟包）转换到柔性膜耦合动力学框架的新代码，并应用于膜结合的HIV-1未成熟Gag晶格。
英文摘要
Membrane-deforming protein lattices play a central role in essential and pathogenic remodeling processes, including clathrin-mediated endocytosis and viral budding. Simulating these systems at biologically relevant length and time scales requires mesoscale approaches that preserve structural detail while avoiding the computational cost of atomistic resolution. Here, we present a hybrid simulation framework that couples a particle-based flexible protein lattice to a continuum membrane model, enabling systematic investigation of how lattice geometry and rigidity influence dynamic membrane remodeling. We validate the coupled model by comparing simulation results with theoretical predictions for membranes under increasing tension. Using buckling-based deformations of pre-assembled clathrin lattices, we quantify the lattice flexural rigidity and establish a direct relationship between the force constants in the coarse-grained energy and the emergent mechanical properties of the lattice. We then compare this flexural rigidity to an effective rigidity commonly used in continuum descriptions of sphere-forming protein assemblies. Although the flexural rigidity is set solely by the energy function, the effective rigidity depends on lattice size and connectivity, with the two measures converging only for weakly connected lattices. As a result, the effective rigidity relevant for spherical bud formation increases as the lattice grows. This size-dependent stiffening highlights the importance of structural details in interpreting lattice mechanics and cautions against assuming a single constant stiffness throughout assembly. We demonstrate the generality of the method by applying it to pre-assembled viral lattices generated with NERDSS. This work provides a validated framework for simulating how deformable, stable protein assemblies of diverse geometry couple to membrane dynamics and remodeling.
CommentsManuscript: 12 pages, 7 figures. SI: 4 pages, 4 figures
