Supplementary Material for the manuscript entitled "Proteomics Analysis Identifies the Ribosome Associated Coiled-Coil Domain-Containing Protein-124 as a Novel Interaction Partner of Nucleophosmin-1"

Suppl. Figure MD_3. Molecular Dynamics (MD) Simulation Metrics for Ccdc124-Npm1 Protein Interactions. (A) Root Mean Square Deviation (RMSD) and Radius of Gyration (Rg) profiles over 100ns of MD simulations showcasing Ccdc124 pentamers derived from both wt and mutA heterodecamer configurations. (B) RMSD and Rg trajectories over 100ns of MD simulations for Npm1 pentamers originating from both wt and mutA heterodecamer models. (C) Energy trends throughout the 100ns simulation. The energy dynamics for both Ccdc124 and Npm1 from the wt and mutA heterodecamer formations are delineated, underscoring the energy oscillations. Notably, lower values in this context indicate a conformation of enhanced stability. Suppl. Data 3. Interaction map for the Ccdc124-Npm1(wt) heterodecameric structure details residue-specific interaction types, including hydrogen bonds, salt bridges, Pi stacking, disulfides, and van der Waals interactions. The map also provides information on surface compatibility and buried solvent-accessible surface area (SASA) for interacting residue pairs. Suppl. Data 4. Interaction map for the Ccdc124-Npm1(mutA) heterodecameric structure details residue-specific interaction types, including hydrogen bonds, salt bridges, Pi stacking, disulfides, and van der Waals interactions. The map also provides information on surface compatibility and buried SASA for interacting residue pairs. Suppl. Video S1. Molecular docking structure of the monomeric Ccdc124-Npm1(wt) interaction, with an in-depth depiction of potential interaction interfaces and residues. Ccdc124 is illustrated by red ribbons, Npm1(wt) by orange ribbons, while blue and pink surfaces represent electropositive and electronegative regions, respectively. Suppl. Video S2. Superimposed heterodecameric structure depicting the Ccdc124-Npm1(wt) interaction. Ccdc124 is represented by red ribbons, Npm1(wt) by orange ribbons. Electropositive and electronegative regions are shown in blue and pink surfaces, respectively. Suppl. Video S3. Molecular Dynamics simulation of Ccdc124-Npm1(wt) heterodecamer structure. Ccdc124 is depicted in red ribbons and Npm1(mutA) in orange ribbons. Suppl. Video S4. Molecular docking structure of the monomeric Ccdc124-Npm1(mutA) interaction, with an in-depth depiction of potential interaction interfaces and residues. Ccdc124 is illustrated by red ribbons, Npm1(mutA) by orange ribbons, while blue and pink surfaces represent electropositive and electronegative regions, respectively. Suppl. Video S5. Superimposed heterodecameric structure depicting the Ccdc124-Npm1(mutA) interaction. Ccdc124 is represented by red ribbons, Npm1(mutA) by orange ribbons. Electropositive and electronegative regions are shown in blue and pink surfaces, respectively. Suppl. Video S6. Molecular Dynamics simulation of Ccdc124-Npm1(mutA) heterodecamer structure. Ccdc124 is depicted in red ribbons and Npm1(mutA) in orange ribbons.

补充图MD_3：Ccdc124-Npm1蛋白相互作用的分子动力学(MD)模拟指标。(A) 100纳秒(ns)分子动力学模拟过程中的均方根偏差(Root Mean Square Deviation, RMSD)与回转半径(Radius of Gyration, Rg)曲线，展示了源自野生型(wild type, wt)与突变体A(mutant A, mutA)异十聚体构象的Ccdc124五聚体。(B) 100ns分子动力学模拟过程中，针对源自野生型与突变体A异十聚体模型的Npm1五聚体的均方根偏差与回转半径轨迹。(C) 100ns模拟全程的能量变化趋势：清晰描绘了野生型与突变体A异十聚体构象中Ccdc124与Npm1的能量动态变化，并突出了能量振荡现象。值得注意的是，本研究语境下数值越低，代表对应构象的稳定性越强。

补充数据3：Ccdc124-Npm1(野生型,wt)异十聚体结构的相互作用图谱，详细列出了残基水平的相互作用类型，包括氢键、盐桥、π堆积、二硫键与范德华相互作用。该图谱还提供了相互作用残基对的表面兼容性与溶剂可及表面积(Solvent-accessible surface area, SASA)掩埋量相关信息。

补充数据4：Ccdc124-Npm1(mutA)异十聚体结构的相互作用图谱，详细列出了残基水平的相互作用类型，包括氢键、盐桥、π堆积、二硫键与范德华相互作用。该图谱还提供了相互作用残基对的表面兼容性与溶剂可及表面积(SASA)掩埋量相关信息。

补充视频S1：单体Ccdc124-Npm1(野生型,wt)相互作用的分子对接结构，深入展示了潜在相互作用界面与残基。其中Ccdc124以红色丝带(ribbon)模型呈现，Npm1(野生型)以橙色丝带模型呈现，蓝色与粉色表面分别代表电正性区域与电负性区域。

补充视频S2：展示Ccdc124-Npm1(野生型,wt)相互作用的叠加异十聚体结构。Ccdc124以红色丝带模型呈现，Npm1(野生型)以橙色丝带模型呈现，电正性区域与电负性区域分别以蓝色与粉色表面展示。

补充视频S3：Ccdc124-Npm1(野生型,wt)异十聚体结构的分子动力学模拟。Ccdc124以红色丝带模型呈现，Npm1(mutA)以橙色丝带模型呈现。

补充视频S4：单体Ccdc124-Npm1(mutA)相互作用的分子对接结构，深入展示了潜在相互作用界面与残基。其中Ccdc124以红色丝带模型呈现，Npm1(mutA)以橙色丝带模型呈现，蓝色与粉色表面分别代表电正性区域与电负性区域。

补充视频S5：展示Ccdc124-Npm1(mutA)相互作用的叠加异十聚体结构。Ccdc124以红色丝带模型呈现，Npm1(mutA)以橙色丝带模型呈现，电正性区域与电负性区域分别以蓝色与粉色表面展示。

补充视频S6：Ccdc124-Npm1(mutA)异十聚体结构的分子动力学模拟。Ccdc124以红色丝带模型呈现，Npm1(mutA)以橙色丝带模型呈现。