酶活性部位柔性的分形分析

doi:10.3969/j.issn.0438-1157.2013.02.035

化工学报 ›› 2013, Vol. 64 ›› Issue (2): 671-675.DOI: 10.3969/j.issn.0438-1157.2013.02.035

酶活性部位柔性的分形分析

彭鑫¹, 张雨薇¹, 王梦凡¹, 齐崴^1,2, 苏荣欣^1,2, 何志敏^1,2

1. 天津大学化工学院,天津 300072;
2. 化学工程联合国家重点实验室,天津 300072

收稿日期:2012-08-13 修回日期:2012-09-30 出版日期:2013-02-05 发布日期:2013-02-05
通讯作者: 何志敏
作者简介:彭鑫(1986—),男,博士研究生。
基金资助:
国家自然科学基金项目(20976125,31071509);天津市应用基础研究计划面上项目(10JCYBJC05100)。

Fractal analysis of flexibility of enzyme active sites

PENG Xin¹, ZHANG Yuwei¹, WANG Mengfan¹, QI Wei^1,2, SU Rongxin^1,2, HE Zhimin^1,2

1. School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China;
2. State of Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China

Received:2012-08-13 Revised:2012-09-30 Online:2013-02-05 Published:2013-02-05
Supported by:
supported by the National Natural Science Foundation of China(20976125, 31071509) and the Science and Technology Commission Program of Tianjin(10JCYBJC05100).

摘要/Abstract

关键词: 分形维数, 蛋白质, 盒维数, 活性部位, 结构

Abstract: Fractal geometry provides a mathematical formalism for describing complex spatial and dynamical structures.Therefore the enzyme molecules with irregular and self-similar structure can be studied thoroughly based on the fractal theory.In this paper the principle of box-counting dimension was used to investigate the impact of temperature and inhibitor on the structural changes of global enzymes and active sites of enzymes.The results suggested that the fractal dimension of enzyme molecule was greater than the fractal dimension of its active site.With increasing temperature, the calculated box-counting dimensions of global enzymes and their active sites all increased, especially for active sites.When enzyme was combined to the inhibitor, the dimensions of global enzymes did not change obviously, while the dimensions of active sites all decreased, indicating the decline of complexity for active sites.

Key words: fractal dimensions, protein, box-counting dimension, active site, structure

中图分类号:

Q617
Q811.4

彭鑫, 张雨薇, 王梦凡, 齐崴, 苏荣欣, 何志敏. 酶活性部位柔性的分形分析[J]. 化工学报, 2013, 64(2): 671-675.

PENG Xin, ZHANG Yuwei, WANG Mengfan, QI Wei, SU Rongxin, HE Zhimin. Fractal analysis of flexibility of enzyme active sites[J]. CIESC Journal, 2013, 64(2): 671-675.

参考文献 23

[1]	Mandelbrot B B.Fractal:Form, Chance and Dimension[M].San Francisco:Freeman, 1977:1-365
[2]	Goldberger M A, West B J.Fractals in physiology and medicine[J].Yale J.Biol.Med., 1987, 60(5):421-435
[3]	Bak P, Chen K.The physics of fractal[J].Physica D, 1989, 38(1):5-12
[4]	Perfect E, Kay B D.Applications of fractals in soil and tillage research:a review[J].Soil Till.Res., 1995, 36(1):1-20
[5]	Lewis M, Rees D C.Fractal surfaces of protein[J].Science, 1985, 230(4730):1163-1165
[6]	Peng X, Qi W, Su R X, He Z M.Describing some characters of serine proteinase using fractal analysis[J].Chaos Soliton.Fract., 2012, 45(7):1017-1023
[7]	Agnieszka A K, Ramon G G, Pau C, Cristian O P, Manuel P, Jana S.Fractal dimension as a measure of surface roughness of G protein-coupled receptors:implications for structure and function[J].J.Mol.Model., 2012, 18(9):4465-4475
[8]	Banerji A, Ghosh I.Fractal symmetry of protein interior:what have we learned?[J].Cell.Mol.Life Sci., 2011, 68(16):2711-2737
[9]	Yu Z G, Vo A, Gong Z M, Long S C.Fractals in DNA sequence analysis[J].Chin.Phys.B, 2002, 11(12):1313-1318
[10]	Stapleton H J, Allen J P, Flynn C P, Stinson D G, Kurtz S R.Fractal form of proteins[J].Phys.Rev.Lett., 1980, 45(17):1456-1459
[11]	Moret M A, Miranda J G V, Nogueira Jr E, Santana M C, Zebende G F.Self-similarity and protein chains[J].Phys.Rev.E, 2005, 71(012901):1-3
[12]	Moret M A, Santana M C, Zebende G F, Pascutti P G.Self-similarity and protein compactness[J].Phys.Rev.E, 2009, 80(041908):1-4
[13]	Enright M B, Leitner D M.Mass fractal dimension and the compactness of proteins[J].Phys.Rev.E, 2005, 71(011912):1-9
[14]	Enright M B, Yu X, Leitner D M.Hydration dependence of the mass fractal dimension and anomalous diffusion of vibrational energy in proteins[J].Phys.Rev.E, 2006, 73(051905):1-9
[15]	Isvoran A, Licz A, Unipan L, Morariu V V.Determination of the fractal dimension of the lysozyme backbone for three different organisms[J].Chaos Soliton.Fract., 2001, 12(4):757-760
[16]	Koshland Jr D E.The key-lock theory and the induced fit theory[J].Angew.Chew.Int.Edit., 1995, 33(23):2375-2378
[17]	Berman H M, Westbrook J, Feng Z K, Gilliland G, Bhat T N, Weissig H, Shindyalov L N, Bourne P E.The protein data bank[J].Nucleic Acids Res., 2000, 28(1):235-242
[18]	Zou Chenglu(邹承鲁), Zhou Junmei(周筠梅), Zhou Haimeng(周海梦).Flexibility of Enzyme Active Sites(酶活性部位的柔性)[M].Shandong:Shandong Science and Technology Press, 2005:178-198
[19]	Mandelbrot B B.The Fractal Geometry of Nature[M].New York:Freeman, 1982:1-458
[20]	Peng Xin(彭鑫), Zhang Yuwei(张雨薇), Qi Wei(齐崴), Su Rongxin(苏荣欣), Wu Shaomin(吴少敏), He Zhimin(何志敏).Fractal analysis of proteins based on box dimension[J].Acta Chim.Sinica(化学学报), 2010, 68(11):1143-1147
[21]	Farin D,Avnir D,Unger K K, Behrens D, Kral H.Characterization of Porous Solids[M].Amsterdam:Elsevier, 1988:1-645
[22]	Tsou C L.Active site flexibility in enzyme catalysis[J].Ann.NY.Acad.Sci., 1998, 864(14):1-8
[23]	Mattos C, Giammona D A, Petsko G A, Ringe D. Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors[J].Biochemistry, 1995, 34(10):3193-3203

酶活性部位柔性的分形分析

Fractal analysis of flexibility of enzyme active sites

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献 23

相关文章 15

编辑推荐

Metrics

本文评价

[1]	程成, 段钟弟, 孙浩然, 胡海涛, 薛鸿祥. 表面微结构对析晶沉积特性影响的格子Boltzmann模拟[J]. 化工学报, 2023, 74(S1): 74-86.
[2]	叶展羽, 山訸, 徐震原. 用于太阳能蒸发的折纸式蒸发器性能仿真[J]. 化工学报, 2023, 74(S1): 132-140.
[3]	陈天华, 刘兆轩, 韩群, 张程宾, 李文明. 喷雾冷却换热强化研究进展及影响因素[J]. 化工学报, 2023, 74(8): 3149-3170.
[4]	邢雷, 苗春雨, 蒋明虎, 赵立新, 李新亚. 井下微型气液旋流分离器优化设计与性能分析[J]. 化工学报, 2023, 74(8): 3394-3406.
[5]	胡兴枝, 张皓焱, 庄境坤, 范雨晴, 张开银, 向军. 嵌有超小CeO₂纳米粒子的碳纳米纤维的制备及其吸波性能[J]. 化工学报, 2023, 74(8): 3584-3596.
[6]	王海, 林宏, 王晨, 许浩洁, 左磊, 王军锋. 高压静电场强化多孔介质表面沸腾传热特性研究[J]. 化工学报, 2023, 74(7): 2869-2879.
[7]	陈雅鑫, 袁航, 刘冠章, 毛磊, 杨纯, 张瑞芳, 张光亚. 蛋白质纳米笼介导的酶自固定化研究进展[J]. 化工学报, 2023, 74(7): 2773-2782.
[8]	刘春雨, 周桓宇, 马跃, 岳长涛. CaO调质含油污泥干燥特性及数学模型[J]. 化工学报, 2023, 74(7): 3018-3027.
[9]	李勇, 高佳琦, 杜超, 赵亚丽, 李伯琼, 申倩倩, 贾虎生, 薛晋波. Ni@C@TiO₂核壳双重异质结的构筑及光热催化分解水产氢[J]. 化工学报, 2023, 74(6): 2458-2467.
[10]	龙臻, 王谨航, 任俊杰, 何勇, 周雪冰, 梁德青. 离子液体协同PVCap抑制天然气水合物生成实验研究[J]. 化工学报, 2023, 74(6): 2639-2646.
[11]	刘道银, 陈柄岐, 张祖扬, 吴琰. 颗粒聚团结构对曳力特性影响的数值模拟[J]. 化工学报, 2023, 74(6): 2351-2362.
[12]	陈韶云, 徐东, 陈龙, 张禹, 张远方, 尤庆亮, 胡成龙, 陈建. 单层聚苯胺微球阵列结构的制备及其吸附性能[J]. 化工学报, 2023, 74(5): 2228-2238.
[13]	张建华, 陈萌萌, 孙雅雯, 彭永臻. 部分短程硝化同步除磷耦合Anammox实现生活污水高效脱氮除磷[J]. 化工学报, 2023, 74(5): 2147-2156.
[14]	侯文起, 孙彦, 董晓燕. 碱化修饰甲状腺素运载蛋白显著增强对淀粉样β蛋白聚集的抑制作用[J]. 化工学报, 2023, 74(5): 2100-2110.
[15]	刘尚豪, 贾胜坤, 罗祎青, 袁希钢. 基于梯度提升决策树的三组元精馏流程结构最优化[J]. 化工学报, 2023, 74(5): 2075-2087.