晶体中蛋白质的动力学：实验与简单模型的比较
Dynamics of proteins in crystals: comparison of experiment with simple models.
作者信息
Kundu Sibsankar, Melton Julia S, Sorensen Dan C, Phillips George N
机构信息
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
出版信息
Biophys J. 2002 Aug;83(2):723-32. doi: 10.1016/S0006-3495(02)75203-X.
Abstract
The dynamic behavior of proteins in crystals is examined by comparing theory and experiments. The Gaussian network model (GNM) and a simplified version of the crystallographic translation libration screw (TLS) model are used to calculate mean square fluctuations of C(alpha) atoms for a set of 113 proteins whose structures have been determined by x-ray crystallography. Correlation coefficients between the theoretical estimations and experiment are calculated and compared. The GNM method gives better correlation with experimental data than the rigid-body libration model and has the added benefit of being able to calculate correlations between the fluctuations of pairs of atoms. By incorporating the effect of neighboring molecules in the crystal the correlation is further improved.
摘要
通过比较理论与实验来研究晶体中蛋白质的动态行为。使用高斯网络模型（GNM）和晶体学平移振动螺旋（TLS）模型的简化版本，来计算113种蛋白质的α碳原子的均方波动，这些蛋白质的结构已通过X射线晶体学确定。计算并比较理论估计值与实验之间的相关系数。与刚体振动模型相比，GNM方法与实验数据的相关性更好，并且具有能够计算原子对波动之间相关性的额外优势。通过纳入晶体中相邻分子的影响，相关性进一步提高。
相似文献
1
Dynamics of proteins in crystals: comparison of experiment with simple models.晶体中蛋白质的动力学：实验与简单模型的比较
Biophys J. 2002 Aug;83(2):723-32. doi: 10.1016/S0006-3495(02)75203-X.
2
vGNM: a better model for understanding the dynamics of proteins in crystals.虚拟全局网络模型：理解晶体中蛋白质动力学的更好模型。
J Mol Biol. 2007 Jun 8;369(3):880-93. doi: 10.1016/j.jmb.2007.03.059. Epub 2007 Mar 28.
3
Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors.蛋白质动力学简单网络模型的批判性评估及其与晶体学B因子的比较。
Phys Biol. 2008 Jun 24;5(2):026008. doi: 10.1088/1478-3975/5/2/026008.
4
Crystal nucleation for a model of globular proteins.球状蛋白质模型的晶体成核
J Chem Phys. 2004 May 1;120(17):8318-26. doi: 10.1063/1.1695321.
5
Protein dynamics derived from clusters of crystal structures.源自晶体结构簇的蛋白质动力学。
Biophys J. 1997 Dec;73(6):2891-6. doi: 10.1016/S0006-3495(97)78317-6.
6
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease.结晶蛋白动力学中的涨落与关联：葡萄球菌核酸酶的模拟分析
Biophys J. 2005 Apr;88(4):2554-63. doi: 10.1529/biophysj.104.056101. Epub 2005 Jan 28.
7
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.蛋白质结构中氨基酸的各向异性波动：来自X射线晶体学和弹性网络模型的见解。
Bioinformatics. 2007 Jul 1;23(13):i175-84. doi: 10.1093/bioinformatics/btm186.
8
Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.从平移-振动-螺旋结构系综预测X射线漫散射。
Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1657-67. doi: 10.1107/S1399004715007415. Epub 2015 Jul 28.
9
Comparison of crystal structure and theory for 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine.2-氨基-1-甲基-6-苯基咪唑并[4,5-b]吡啶的晶体结构与理论比较
Chem Res Toxicol. 1996 Apr-May;9(3):574-9. doi: 10.1021/tx950168b.
10
Convective instability in protein crystal growth.蛋白质晶体生长中的对流不稳定性。
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Aug;70(2 Pt 1):021603. doi: 10.1103/PhysRevE.70.021603. Epub 2004 Aug 17.
引用本文的文献
1
Using graphlet degree vectors to predict atomic displacement parameters in protein structures.利用图元度数向量预测蛋白质结构中的原子位移参数。
Acta Crystallogr D Struct Biol. 2023 Dec 1;79(Pt 12):1109-1119. doi: 10.1107/S2059798323009142. Epub 2023 Nov 21.
2
Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions.必需位点扫描分析：一种检测调节蛋白质整体运动分散性位点的新方法。
Comput Struct Biotechnol J. 2020 Jun 18;18:1577-1586. doi: 10.1016/j.csbj.2020.06.020. eCollection 2020.
3
Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.分析具有序列特异性和距离相关性相互作用的蛋白质弹性网络中的涨落特性。
Biomolecules. 2019 Sep 30;9(10):549. doi: 10.3390/biom9100549.
4
Normal Mode Analysis as a Routine Part of a Structural Investigation.正常模式分析作为结构研究的常规部分。
Molecules. 2019 Sep 10;24(18):3293. doi: 10.3390/molecules24183293.
5
Sequence-specific dynamic information in proteins.蛋白质中的序列特异性动态信息。
Proteins. 2019 Oct;87(10):799-804. doi: 10.1002/prot.25747. Epub 2019 Jun 11.
6
Computational protein structure refinement: Almost there, yet still so far to go.计算蛋白质结构优化：已近完成，却仍任重道远。
Wiley Interdiscip Rev Comput Mol Sci. 2017 May-Jun;7(3). doi: 10.1002/wcms.1307. Epub 2017 Mar 28.
7
Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs.共进化残基可提供 nSNVs 的蛋白质动力学特征和疾病易感性信息。
PLoS Comput Biol. 2018 Nov 29;14(11):e1006626. doi: 10.1371/journal.pcbi.1006626. eCollection 2018 Nov.
8
Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method.基于机器学习方法预测单克隆抗体中的蛋氨酸氧化风险。
MAbs. 2018 Nov-Dec;10(8):1281-1290. doi: 10.1080/19420862.2018.1518887. Epub 2018 Sep 25.
9
Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics.从弹性网络模型得出的蛋白质动态社区与通过分子动力学定义的社区非常吻合。
PLoS One. 2018 Jun 20;13(6):e0199225. doi: 10.1371/journal.pone.0199225. eCollection 2018.
10
Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.布拉格和漫散射X射线散射分子动力学模拟中的内部蛋白质运动
IUCrJ. 2018 Jan 25;5(Pt 2):172-181. doi: 10.1107/S2052252518000519. eCollection 2018 Mar 1.
本文引用的文献
1
Anisotropy of fluctuation dynamics of proteins with an elastic network model.基于弹性网络模型的蛋白质涨落动力学各向异性
Biophys J. 2001 Jan;80(1):505-15. doi: 10.1016/S0006-3495(01)76033-X.
2
3
Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data.基于结构的蛋白质动力学分析：溶菌酶理论结果与X射线衍射和核磁共振弛豫数据的比较。
Proteins. 1999 Dec 1;37(4):654-67. doi: 10.1002/(sici)1097-0134(19991201)37:4<654::aid-prot15>3.0.co;2-j.
4
Crystallographic evaluation of internal motion of human alpha-lactalbumin refined by full-matrix least-squares method.用全矩阵最小二乘法精修的人α-乳白蛋白内部运动的晶体学评估。
J Mol Biol. 1999 Mar 26;287(2):347-58. doi: 10.1006/jmbi.1999.2598.
5
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.基于单参数原子分析的蛋白质中的大幅度弹性运动
Phys Rev Lett. 1996 Aug 26;77(9):1905-1908. doi: 10.1103/PhysRevLett.77.1905.
6
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.可视化和量化分子拟合优度：带有显式氢原子的小探针接触点
J Mol Biol. 1999 Jan 29;285(4):1711-33. doi: 10.1006/jmbi.1998.2400.
7
Crystallography & NMR system: A new software suite for macromolecular structure determination.晶体学与核磁共振系统：用于大分子结构测定的新软件套件。
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. doi: 10.1107/s0907444998003254.
8
Hierarchical protein structure superposition using both secondary structure and atomic representations.使用二级结构和原子表示的分层蛋白质结构叠加
Proc Int Conf Intell Syst Mol Biol. 1997;5:284-93.
9
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.使用单参数谐振子势直接评估蛋白质中的热涨落。
Fold Des. 1997;2(3):173-81. doi: 10.1016/S1359-0278(97)00024-2.
10
Protein dynamics determined by backbone conformation and atom packing.由主链构象和原子堆积决定的蛋白质动力学。
Protein Eng. 1997 Apr;10(4):373-80. doi: 10.1093/protein/10.4.373.
Zotero 插件