蛋白质中的标度与自组织临界性 I.
Scaling and self-organized criticality in proteins I.
作者信息
Phillips J C
机构信息
Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA.
出版信息
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3107-12. doi: 10.1073/pnas.0811262106. Epub 2009 Feb 13.
Abstract
The complexity of proteins is substantially simplified by regarding them as archetypical examples of self-organized criticality (SOC). To test this idea and elaborate on it, this article applies the Moret-Zebende SOC hydrophobicity scale to the large-scale scaffold repeat protein of the HEAT superfamily, PR65/A. Hydrophobic plasticity is defined and used to identify docking platforms and hinges from repeat sequences alone. The difference between the MZ scale and conventional hydrophobicity scales reflects long-range conformational forces that are central to protein functionality.
摘要
将蛋白质视为自组织临界性（SOC）的典型例子，可大大简化其复杂性。为了验证并详细阐述这一观点，本文将莫雷特 - 泽本德（Moret-Zebende）SOC疏水性标度应用于HEAT超家族的大规模支架重复蛋白PR65/A。定义了疏水性可塑性，并仅从重复序列中识别对接平台和铰链。MZ标度与传统疏水性标度之间的差异反映了对蛋白质功能至关重要的长程构象力。
相似文献
1
Scaling and self-organized criticality in proteins I.蛋白质中的标度与自组织临界性 I.
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3107-12. doi: 10.1073/pnas.0811262106. Epub 2009 Feb 13.
2
Scaling and self-organized criticality in proteins II.蛋白质中的标度与自组织临界性 II。
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3113-8. doi: 10.1073/pnas.0811308105. Epub 2009 Jan 5.
3
Scaling and self-organized criticality in proteins: Lysozyme c.蛋白质中的标度与自组织临界性：溶菌酶c
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Nov;80(5 Pt 1):051916. doi: 10.1103/PhysRevE.80.051916. Epub 2009 Nov 20.
4
A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function.疏水性量表的严格测试：两种序列同一性为88%但结构和功能不同的蛋白质。
Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9233-7. doi: 10.1073/pnas.0803264105. Epub 2008 Jun 30.
5
PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis.PR65，磷酸酶 PP2A 的 HEAT 重复支架，是一个连接力和催化的弹性接头。
Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2467-72. doi: 10.1073/pnas.0914073107. Epub 2010 Jan 25.
6
Predicting Protein Surface Property with its Surface Hydrophobicity.用蛋白表面疏水性预测蛋白表面性质。
Protein Pept Lett. 2021;28(8):938-944. doi: 10.2174/0929866528666210222160603.
7
Hydropathic self-organized criticality: a magic wand for protein physics.
Protein Pept Lett. 2012 Oct;19(10):1089-93. doi: 10.2174/092986612802762741.
8
A simple atomic-level hydrophobicity scale reveals protein interfacial structure.简单的原子级疏水性尺度揭示蛋白质界面结构。
J Mol Biol. 2014 Jan 23;426(2):484-98. doi: 10.1016/j.jmb.2013.09.039. Epub 2013 Oct 10.
9
Self-organized criticality and pattern emergence through the lens of tropical geometry.自组织临界性与热带几何视角下的模式涌现。
Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8135-E8142. doi: 10.1073/pnas.1805847115. Epub 2018 Aug 15.
10
Quantitative theory of hydrophobic effect as a driving force of protein structure.作为蛋白质结构驱动力的疏水作用定量理论。
Protein Sci. 2014 Apr;23(4):387-99. doi: 10.1002/pro.2420. Epub 2014 Feb 19.
引用本文的文献
1
Folding-unfolding asymmetry and a computational algorithm.折叠-展开不对称性与一种计算算法。
R Soc Open Sci. 2023 May 3;10(5):221594. doi: 10.1098/rsos.221594. eCollection 2023 May.
2
Topological bio-scaling analysis as a universal measure of protein folding.拓扑生物尺度分析作为蛋白质折叠的通用度量方法。
R Soc Open Sci. 2022 Jul 13;9(7):220160. doi: 10.1098/rsos.220160. eCollection 2022 Jul.
3
Relating SARS-CoV-2 variants using cellular automata imaging.利用元胞自动机成像技术关联 SARS-CoV-2 变体。
Sci Rep. 2022 Jun 18;12(1):10297. doi: 10.1038/s41598-022-14404-6.
4
Hydropathicity-based prediction of pain-causing NaV1.7 variants.基于疏水性的疼痛相关 NaV1.7 变体预测。
BMC Bioinformatics. 2021 Apr 23;22(1):212. doi: 10.1186/s12859-021-04119-2.
5
Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel's pore: a modeling study.围绕电压门控钠离子通道孔的原子水力亲疏性的非敏感性和非关键性：一项建模研究。
J Biol Phys. 2021 Mar;47(1):61-77. doi: 10.1007/s10867-021-09565-w. Epub 2021 Mar 18.
6
Survival of Virus Particles in Water Droplets: Hydrophobic Forces and Landauer's Principle.病毒颗粒在水滴中的存活：疏水力与兰道尔原理
Entropy (Basel). 2021 Jan 30;23(2):181. doi: 10.3390/e23020181.
7
A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme.一种基于氨基酸残基贡献的蛋白质相互作用自由能模型：T4溶菌酶点突变稳定性评估
Technology (Singap World Sci). 2019 Mar-Jun;7(1-2):12-39. doi: 10.1142/s233954781950002x. Epub 2019 Apr 26.
8
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis.蛋白质动力学中的长程相关性：结构数据和模态分析的证实。
PLoS Comput Biol. 2020 Feb 13;16(2):e1007670. doi: 10.1371/journal.pcbi.1007670. eCollection 2020 Feb.
9
From superhydrophobicity to icephobicity: forces and interaction analysis.从超疏水性到憎冰性：力与相互作用分析
Sci Rep. 2013;3:2194. doi: 10.1038/srep02194.
10
Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions.重新审视蛋白质内部的误区：使用质量分形疏水性-分形和极化率-分形维数研究蛋白质。
PLoS One. 2009 Oct 16;4(10):e7361. doi: 10.1371/journal.pone.0007361.
本文引用的文献
1
Thermoreversible lysozyme hydrogels: properties and an insight into the gelation pathway.热可逆溶菌酶水凝胶：性质及对凝胶化途径的深入了解。
Soft Matter. 2008 May 14;4(6):1313-1325. doi: 10.1039/b716966c.
2
Abrupt boundaries of intermediate phases and space filling in oxide glasses.
J Phys Condens Matter. 2008 May 21;20(20):202101. doi: 10.1088/0953-8984/20/20/202101. Epub 2008 Apr 15.
3
Ageing, fragility and the reversibility window in bulk alloy glasses.
J Phys Condens Matter. 2005 Jan 12;17(1):L1-7. doi: 10.1088/0953-8984/17/1/L01. Epub 2004 Dec 10.
4
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.细胞遗传学正常的急性髓系白血病基因组的DNA测序
Nature. 2008 Nov 6;456(7218):66-72. doi: 10.1038/nature07485.
5
Determination of ligand-binding sites on proteins using long-range hydrophobic potential.利用长程疏水势确定蛋白质上的配体结合位点。
Biol Pharm Bull. 2008 Aug;31(8):1552-8. doi: 10.1248/bpb.31.1552.
6
Competing interactions create functionality through frustration.相互竞争的相互作用通过受挫产生功能。
Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10635-6. doi: 10.1073/pnas.0805716105. Epub 2008 Jul 31.
7
Maximum entropy approach for deducing amino Acid interactions in proteins.
Phys Rev Lett. 2008 Feb 22;100(7):078102. doi: 10.1103/PhysRevLett.100.078102. Epub 2008 Feb 20.
8
Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core.将犰狳重复蛋白设计为通用的肽结合支架：疏水核心的一致性设计与计算优化
J Mol Biol. 2008 Mar 7;376(5):1282-304. doi: 10.1016/j.jmb.2007.12.014. Epub 2007 Dec 14.
9
PP2A: unveiling a reluctant tumor suppressor.蛋白磷酸酶2A：揭示一种“不情愿”的肿瘤抑制因子
Cell. 2007 Jul 13;130(1):21-4. doi: 10.1016/j.cell.2007.06.034.
10
Amino acid hydrophobicity and accessible surface area.氨基酸疏水性与可及表面积。
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jan;75(1 Pt 1):011920. doi: 10.1103/PhysRevE.75.011920. Epub 2007 Jan 19.
Zotero 插件