一种用于单分子荧光共振能量转移技术推测无规蛋白结构的新方法
详细信息 查看官网全文
- 英文论文题名：An Adequate Account of Excluded Volume Is Necessary To Infer Compactness and Asphericity of Disordered Proteins by F?rster Resonance Energy Transfer
- 论文作者：宋建晖 ; Gregory-Neal Gomes ; Claudiu C.Gradinaru ; Hue Sun Chan
- 英文论文作者：Jianhui Song ; Gregory-Neal Gomes ; Claudiu C.Gradinaru ; Hue Sun Chan ; School of Polymer Science & Engineering ; Qingdao University of Science & Technology ; Department of Biochemistry ; University of Toronto ; Department of Chemical & Physical Sciences ; University of Toronto Mississauga
- 年：2016
- 作者机构：青岛科技大学高分子科学与工程学院;Department of Biochemistry,University of Toronto;Department of Chemical & Physical Sciences,University of Toronto Mississauga;
- 论文关键词：排斥体积作用 ; 无规蛋白 ; 荧光共振能量转移 ; 计算机模拟
- 会议召开时间：2016-08-25
- 会议录名称：中国化学会2016年软物质理论计算与模拟会议论文摘要集
- 语种：中文
- 分类号：O629.73;O657.3
- 学会代码：ZGHY
- 会议名称：中国化学会2016年软物质理论计算与模拟会议
- 会议地点：中国天津
- 主办单位：中国化学会
- 学会名称：中国化学会
- 页数：2
- 文件大小：1794k
- 原文格式：D
- 会议级别：全国
摘要
单分子荧光共振能量转移技术是研究无规蛋白结构的重要工具之一,通过搜索与实验测得的平均能量转移效率相匹配的末端距分布来推测相应构象系综的结构性质。由于末端距分布依赖于所采用的高分子链模型,因此选择恰当的高分子链模型对于蛋白分子结构推测的准确性起着至关重要的作用。为了更清楚地描述荧光效率-分子构象之间转换的物理基础,我们采用粗粒化链模型通过计算模拟进行大量的构象抽样,并在此基础上构建基于给定分子回转半径和非球形程度的条件化构象子系综,通过寻找与实验测量值具有最佳拟合的构象子系综,可以推测所测量的蛋白分子在无序状态的"最可几"回转半径和非球形程度。为了验证新方法的可行性,我们考察了具有90个残基长度的的天然无规蛋白Sic1(细胞周期激活酶抑制剂),相对于依赖于高斯链模型或Sanchez模型等传统方法,运用新方法获得的分子尺寸更加塌缩,推测的分子回转半径和流体力学半径结果分别与小角X射线散射的核磁共振结果一致。传统方法推测分子尺寸偏差较大的原因主要是由于所依赖的模型忽视或者不能恰当处理排斥体积相互作用,过高估计了具有较小分子末端距的分子链分布几率,造成在较高变性剂浓度条件下推测的分子尺寸偏大。因此,我们可以推论,对于Sic1这样的天然无规蛋白,其构象特征不再适合用均一的的伸展或塌缩构象系综来描述,以一定方式将构象子系综组合而成的非均一构象系综可能更加适用。
Single-molecule F?rster resonance energytransfer(smF RET) is an important tool for studying disordered proteins.It is commonly utilized to infer structural properties of conformational ensembles by matching experimental average energy transfer_(exp) with simulated ?E?sim computed from the distribution of end-to-end distances in polymer models.Toward delineating the physical basis of such interpretative approaches,we conduct extensive sampling of coarse-grained protein chains with excluded volume to determine the distribution of end-to-end distances conditioned upon given values of radius of gyration Rg and asphericity A.Accordingly,we infer the most probable Rg and A of a protein disordered state by seeking the best fit between _(exp) and _(sim) among various(Rg,A) subensembles.Application of our method to residues 1-90 of the intrinsically disordered cyclin-dependent kinase(Cdk) inhibitor Sic1 results in inferred ensembles with more compact conformations than those inferred by conventional procedures that presume either a Gaussian chain model or the mean-field Sanchez polymer theory.The Sic1 compactness we infer is in good agreement with small-angle X-ray scattering data for Rg and NMR measurement of hydrodynamic radius Rh.In contrast,owing to neglect or underappreciation of excluded volume,conventional procedures can significantly overestimate the probabilities of short end-to-end distances,leading to unphysically large smF RET-inferred Rg at high [GdmCl].It follows that smF RETSic1 data are incompatible with the presumed homogeneously expanded or contracted conformational ensembles in conventional procedures but are consistent with heterogeneous ensembles allowed by our subensemble method of inference..
Single-molecule F?rster resonance energytransfer(smF RET) is an important tool for studying disordered proteins.It is commonly utilized to infer structural properties of conformational ensembles by matching experimental average energy transfer
引文
[1]Song,J.;Gomes,G-N.;Gradinaru,C.C.;Chan,H.S.J.Chem.Phys.B 2015,119:15191-15202.
[2]Mazouchi A.,Zhang Z.,Bahram A.,Gomes G-N.,Lin H.,Song J.,Chan H.S.,Forman-Kay J.D.,Gradinaru C.C.Biophys.J.,2016,110:1510-1522.
[2]Mazouchi A.,Zhang Z.,Bahram A.,Gomes G-N.,Lin H.,Song J.,Chan H.S.,Forman-Kay J.D.,Gradinaru C.C.Biophys.J.,2016,110:1510-1522.