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基于集成的KRAS与靶向不同结合位点的DARPin蛋白相互作用的结合自由能分析及网络分析:揭示调控热点和变构结合的分子决定因素及通用结构

Ensemble-Based Binding Free Energy Profiling and Network Analysis of the KRAS Interactions with DARPin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants and Universal Architecture of Regulatory Hotspots and Allosteric Binding.

作者信息

Alshahrani Mohammed, Parikh Vedant, Foley Brandon, Verkhivker Gennady

机构信息

Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.

Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.

出版信息

Biomolecules. 2025 Jun 5;15(6):819. doi: 10.3390/biom15060819.

Abstract

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conformational restriction and allosteric modulation. Mutational scanning across all four DARPin systems identifies a core set of evolutionarily constrained residues that function as universal hotspots in KRAS recognition. KRAS residues I36, Y40, M67, and H95 consistently emerge as critical contributors to binding stability. Binding free energy computations show that, despite similar binding modes, K27 relies heavily on electrostatic contributions from major binding hotspots while K55 exploits a dense hydrophobic cluster enhancing its effector-mimetic signature. The allosteric binders K13 and K19, by contrast, stabilize a KRAS-specific pocket in the α3-loop-α4 motif, introducing new hinges and bottlenecks that rewire the communication architecture of KRAS without full immobilization. Network-based analysis reveals a strikingly consistent theme: despite their distinct mechanisms of recognition, all systems engage a unifying allosteric architecture that spans multiple functional motifs. This architecture is not only preserved across complexes but also mirrors the intrinsic communication framework of KRAS itself, where specific residues function as central hubs transmitting conformational changes across the protein. By integrating dynamic profiling, energetic mapping, and network modeling, our study provides a multi-scale mechanistic roadmap for targeting KRAS, revealing how engineered proteins can exploit both conserved motifs and isoform-specific features to enable precision modulation of KRAS signaling in oncogenic contexts.

摘要

KRAS是一种关键的癌蛋白,它通过与RAF1等下游效应器相互作用来调节细胞增殖和存活。尽管在理解KRAS生物学方面取得了重大进展,但KRAS变构的结构和动力学机制仍知之甚少。在本研究中,我们采用微秒级分子动力学模拟、突变扫描、结合自由能计算以及动态网络建模,来剖析工程化的DARPin蛋白K27、K55、K13和K19如何通过从效应器模拟到构象限制和变构调节等多种分子机制与KRAS结合。对所有四个DARPin系统进行突变扫描,确定了一组进化上保守的核心残基,这些残基在KRAS识别中起通用热点的作用。KRAS残基I36、Y40、M67和H95始终是结合稳定性的关键贡献者。结合自由能计算表明,尽管结合模式相似,但K27严重依赖主要结合热点的静电贡献,而K55利用密集的疏水簇增强其效应器模拟特征。相比之下,变构结合剂K13和K19稳定了α3-环-α4基序中的KRAS特异性口袋,引入了新的铰链和瓶颈,在不完全固定的情况下重新连接了KRAS的通信架构。基于网络的分析揭示了一个惊人一致的主题:尽管它们的识别机制不同,但所有系统都采用了跨越多个功能基序的统一变构架构。这种架构不仅在复合物中得以保留,还反映了KRAS自身的内在通信框架, 其中特定残基作为中心枢纽传递蛋白质内的构象变化。通过整合动态分析、能量图谱和网络建模,我们的研究为靶向KRAS提供了一个多尺度的机制路线图,揭示了工程化蛋白如何利用保守基序和异构体特异性特征来实现致癌环境中KRAS信号的精确调节。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/52d6/12190860/436222d49cb6/biomolecules-15-00819-g001.jpg

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