根据高分辨率X射线晶体学或核磁共振数据构建流体动力学珠子模型。
Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.
作者信息
Byron O
机构信息
Department of Biochemistry, University of Leicester, United Kingdom.
出版信息
Biophys J. 1997 Jan;72(1):408-15. doi: 10.1016/S0006-3495(97)78681-8.
Abstract
Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed.
摘要
诸如HYDRO之类的计算机软件，基于大量的理论工作，能够对溶液中的大分子进行流体动力学建模，这些大分子在计算机界面上被表示为球体的集合。通过将珠子模型必须符合的尽可能多的标准纳入建模过程，可优化任何令人满意的最终模型的独特性。现在已经制定并测试了一种算法（从原子到珠子的AtoB算法），该算法允许根据高分辨率X射线晶体学或核磁共振数据直接构建珠子模型。如此生成的模型随后作为后续迭代建模过程的明智初始估计，从而加速收敛到溶液构象的合理表示。该算法在几种蛋白质上的成功应用表明，包括那些与溶剂化有关的流体动力学参数的预测可以得到证实。
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本文引用的文献
1
Modelling of the serine-proteinase fold by X-ray and neutron scattering and sedimentation analyses: occurrence of the fold in factor D of the complement system.通过X射线、中子散射和沉降分析对丝氨酸蛋白酶折叠结构进行建模：补体系统因子D中折叠结构的存在情况。
Biochem J. 1993 Oct 1;295 ( Pt 1)(Pt 1):87-99. doi: 10.1042/bj2950087.
2
Molecular modelling of the domain structure of factor I of human complement by X-ray and neutron solution scattering.通过X射线和中子溶液散射对人补体I因子结构域结构进行分子建模。
Biochem J. 1993 Oct 1;295 ( Pt 1)(Pt 1):101-8. doi: 10.1042/bj2950101.
3
HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules.HYDRO：一个用于预测大分子流体动力学性质的计算机程序。
Biophys J. 1994 Aug;67(2):530-1. doi: 10.1016/S0006-3495(94)80512-0.
4
Hydrodynamic studies of a complex between the Fc fragment of human IgE and a soluble fragment of the Fc epsilon RI alpha chain.人IgE的Fc片段与FcεRIα链可溶性片段之间复合物的流体动力学研究
Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1841-5. doi: 10.1073/pnas.92.6.1841.
5
Protein and nucleic acid hydration and cosolvent interactions: establishment of reliable baseline values at high cosolvent concentrations.蛋白质和核酸的水合作用及共溶剂相互作用：在高共溶剂浓度下建立可靠的基线值。
Biophys Chem. 1994 Dec;53(1-2):57-68. doi: 10.1016/0301-4622(94)00076-x.
6
Hydrodynamics of segmentally flexible macromolecules.分段柔性大分子的流体动力学
Eur Biophys J. 1994;23(5):307-22. doi: 10.1007/BF00188655.
7
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8
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Protein Sci. 1993 Dec;2(12):2154-66. doi: 10.1002/pro.5560021215.
9
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Q Rev Biophys. 1981 Feb;14(1):81-139. doi: 10.1017/s0033583500002080.
10
Conformation of myosin in dilute solution as estimated from hydrodynamic properties.根据流体动力学性质估算的稀溶液中肌球蛋白的构象。
Biochemistry. 1980 Oct 28;19(22):5118-23. doi: 10.1021/bi00563a028.
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