色氨酸笼的环形排列：添加疏水钉后的折叠拯救。
Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple.
作者信息
Byrne Aimee, Kier Brandon L, Williams D V, Scian Michele, Andersen Niels H
机构信息
Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
出版信息
RSC Adv. 2013 Nov 21;2013(43). doi: 10.1039/C3RA43674H.
Abstract
The Trp-cage, at 20 residues in length, is generally acknowledged as the smallest fully protein-like folding motif. Linking the termini by a two-residue unit and excising one residue affords circularly permuted sequences that adopt the same structure. This represents the first successful circular permutation of any fold of less than 50-residue length. As was observed for the original topology, a hydrophobic staple near the chain termini is required for enhanced fold stability.
摘要
由20个残基组成的色氨酸笼通常被认为是最小的完全类似蛋白质的折叠基序。通过一个双残基单元连接末端并切除一个残基可得到采用相同结构的环形排列序列。这代表了长度小于50个残基的任何折叠的首次成功环形排列。正如在原始拓扑结构中所观察到的，链末端附近的疏水钉对于增强折叠稳定性是必需的。
相似文献
1
Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple.色氨酸笼的环形排列：添加疏水钉后的折叠拯救。
RSC Adv. 2013 Nov 21;2013(43). doi: 10.1039/C3RA43674H.
2
Optimizing the fold stability of the circularly permuted Trp-cage motif.优化环化 Trp-cage 基序的折叠稳定性。
Biopolymers. 2019 Dec;110(12):e23327. doi: 10.1002/bip.23327. Epub 2019 Sep 3.
3
Circular permutation of granulocyte colony-stimulating factor.粒细胞集落刺激因子的环状排列
Biochemistry. 1999 Apr 6;38(14):4553-63. doi: 10.1021/bi982224o.
4
Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.通过分子动力学模拟研究色氨酸侧链动力学对Trp笼微型蛋白质折叠的作用。
PLoS One. 2014 Feb 7;9(2):e88383. doi: 10.1371/journal.pone.0088383. eCollection 2014.
5
Circular permutation of T4 lysozyme.T4溶菌酶的环形排列
Biochemistry. 1993 Nov 23;32(46):12311-8. doi: 10.1021/bi00097a006.
6
Random circular permutation of DsbA reveals segments that are essential for protein folding and stability.DsbA的随机环形排列揭示了蛋白质折叠和稳定性所必需的片段。
J Mol Biol. 1999 Mar 5;286(4):1197-215. doi: 10.1006/jmbi.1998.2531.
7
Ab initio folding of a trefoil-fold motif reveals structural similarity with a β-propeller blade motif.从头折叠三叶型结构基序揭示了与β-发夹叶状结构基序的结构相似性。
Protein Sci. 2020 May;29(5):1172-1185. doi: 10.1002/pro.3850. Epub 2020 Mar 25.
8
Diversification of Protein Cage Structure Using Circularly Permuted Subunits.利用环状排列的亚基实现蛋白质笼结构的多样化。
J Am Chem Soc. 2018 Jan 17;140(2):558-561. doi: 10.1021/jacs.7b10513. Epub 2018 Jan 2.
9
Folding of circular and permuted chymotrypsin inhibitor 2: retention of the folding nucleus.环状和置换型胰凝乳蛋白酶抑制剂2的折叠：折叠核心的保留
Biochemistry. 1998 Jun 2;37(22):8139-46. doi: 10.1021/bi980250g.
10
Reversing the typical pH stability profile of the Trp-cage.逆转色氨酸笼的典型pH稳定性曲线。
Biopolymers. 2019 Mar;110(3):e23260. doi: 10.1002/bip.23260. Epub 2019 Feb 19.
引用本文的文献
1
Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1].用于蛋白质模拟力场基准测试的基于结构的实验数据集 [文章 v0.1]
ArXiv. 2025 Mar 25:arXiv:2303.11056v2.
2
Interplay between C Methylation and C Stereochemistry in the Folding Energetics of a Helix-Rich Miniprotein.富含螺旋的微型蛋白质折叠能量学中C甲基化与C立体化学之间的相互作用。
Chembiochem. 2025 Mar 15;26(6):e202401022. doi: 10.1002/cbic.202401022. Epub 2025 Jan 24.
3
Design and Engineering of Miniproteins.微型蛋白质的设计与工程
ACS Bio Med Chem Au. 2022 Apr 28;2(4):316-327. doi: 10.1021/acsbiomedchemau.2c00008. eCollection 2022 Aug 17.
4
Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein.色氨酸笼状小蛋白嗜温与嗜热突变体的热力学计算模型
ACS Omega. 2022 Apr 12;7(16):13448-13454. doi: 10.1021/acsomega.1c06206. eCollection 2022 Apr 26.
5
Stapled Peptides Inhibitors: A New Window for Target Drug Discovery.钉肽抑制剂：靶向药物发现的新窗口。
Comput Struct Biotechnol J. 2019 Feb 19;17:263-281. doi: 10.1016/j.csbj.2019.01.012. eCollection 2019.
6
Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization.设计肽折叠中的芳基-芳基相互作用：光谱特征及结构稳定的最佳位置
Biopolymers. 2016 Jun;105(6):337-356. doi: 10.1002/bip.22821.
7
Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage.通过过渡态刚性化调整蛋白质折叠动力学的尝试频率：应用于色氨酸笼。
J Phys Chem Lett. 2015 Feb 5;6(3):521-6. doi: 10.1021/jz502654q.
8
Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function.强化结构，照亮途径：应用分子限制和光来操控蛋白质折叠、自组装及功能。
Sci China Chem. 2014 Dec;57(12):1615-1624. doi: 10.1007/s11426-014-5225-5.
9
Folding dynamics and pathways of the trp-cage miniproteins.色氨酸笼状小蛋白的折叠动力学与途径
Biochemistry. 2014 Sep 30;53(38):6011-21. doi: 10.1021/bi501021r. Epub 2014 Sep 16.
10
Circular permutation of a WW domain: folding still occurs after excising the turn of the folding-nucleating hairpin.WW 结构域的环状排列：在切除折叠成核发夹的转角后仍会发生折叠。
J Am Chem Soc. 2014 Jan 15;136(2):741-9. doi: 10.1021/ja410824x. Epub 2014 Jan 3.
本文引用的文献
1
Chemical Synthesis of a Circular Protein Domain: Evidence for Folding-Assisted Cyclization.环状蛋白质结构域的化学合成：折叠辅助环化的证据。
Angew Chem Int Ed Engl. 1998 Feb 16;37(3):347-349. doi: 10.1002/(SICI)1521-3773(19980216)37:3<347::AID-ANIE347>3.0.CO;2-5.
2
Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage.利用D-氨基酸阐明蛋白质折叠机制：应用于色氨酸笼。
Chem Phys. 2013 Aug 30;422. doi: 10.1016/j.chemphys.2013.01.021.
3
Structural insights into the Trp-cage folding intermediate formation.结构洞察色氨酸笼折叠中间态的形成。
Chemistry. 2013 Feb 18;19(8):2628-40. doi: 10.1002/chem.201203764. Epub 2013 Jan 14.
4
Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.色氨酸笼（Trp-cage）迷你蛋白结构的晶体和 NMR 结构，可作为计算折叠预测的基准。
Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12521-5. doi: 10.1073/pnas.1121421109. Epub 2012 Jul 16.
5
Computational design of thermostabilizing D-amino acid substitutions.热稳定性 D-氨基酸取代的计算设计。
J Am Chem Soc. 2011 Nov 23;133(46):18750-9. doi: 10.1021/ja205609c. Epub 2011 Oct 27.
6
Achieving secondary structural resolution in kinetic measurements of protein folding: a case study of the folding mechanism of Trp-cage.在蛋白质折叠动力学测量中实现二级结构解析：色氨酸笼折叠机制的案例研究
Angew Chem Int Ed Engl. 2011 Nov 11;50(46):10884-7. doi: 10.1002/anie.201104085. Epub 2011 Sep 29.
7
Cooperativity network of Trp-cage miniproteins: probing salt-bridges.色氨酸笼状微蛋白的协同网络：探测盐桥。
J Pept Sci. 2011 Sep;17(9):610-9. doi: 10.1002/psc.1377. Epub 2011 Jun 6.
8
Four small puzzles that Rosetta doesn't solve.四个罗塞塔石碑无法解答的小谜题。
PLoS One. 2011;6(5):e20044. doi: 10.1371/journal.pone.0020044. Epub 2011 May 20.
9
Amino acids with hydrogen-bonding side chains have an intrinsic tendency to sample various turn conformations in aqueous solution.具有氢键侧链的氨基酸在水溶液中具有固有倾向来采样各种环构象。
Chemistry. 2011 Jun 6;17(24):6789-97. doi: 10.1002/chem.201100016. Epub 2011 May 5.
10
Optimal salt bridge for Trp-cage stabilization.最佳盐桥稳定 Trp-cage。
Biochemistry. 2011 Feb 22;50(7):1143-52. doi: 10.1021/bi101555y. Epub 2011 Feb 1.
Zotero 插件