Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data

Hur O; Karplus K

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Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data

机译：用有限的实验数据将NMR质子距离转换为相应的重原子距离以预测蛋白质结构的方法

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This paper proposes a strategy to translate experimental H-1 NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, alpha-protons, beta-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, alpha-protons, beta-protons in alpha-helices, anti-parallel beta-sheets and parallel beta-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.

机译：本文提出了一种将H-1 NMR质子距离实验约束转换为相应的重原子距离约束的策略，以预测蛋白质的结构。质子间距离与相应的重原子距离之间的关系是通过研究良好解析的X射线蛋白质结构来确定的。将酰胺质子，α-质子，β-质子和侧链甲基质子的质子间距离数据与散点图中的相应重原子作图，然后对下限，上限和最佳拟合拟合线性方程。我们还将散布图转换为二维热图和三维直方图，以识别数据点集中的区域。还列出了酰胺质子，α-质子，α-螺旋中的β-质子，反平行β-折叠片和平行β-折叠片之间的常见质子间距。从重原子对及其对应的质子对之间的距离关系中我们发现了几种模式。将我们所有将质子间距离转换成其相应的重原子距离的上限，下限和最佳拟合结果列于表中。

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《Protein engineering design & selection: PEDS》 |2005年第12期|共9页
作者
Hur O; Karplus K;
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正文语种 eng
中图分类蛋白质（朊）化学加工工业;
关键词
heavy atom distance; NMR; proton distance;

机译：重原子距离NMR质子距离;

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专利

1. Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data [J] . Hur O, Karplus K Protein engineering design & selection: PEDS . 2005,第12期

机译：用有限的实验数据将NMR质子距离转换为相应的重原子距离以预测蛋白质结构的方法
2. Determination of three‐dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms Circumventing problems associated with folding [J] . Clore G.Marius, Gronenborn Angela M., Nilges Michael FEBS Letters . 1988,第1期

机译：通过原子随机阵列的动态模拟退火从质子间距离数据确定蛋白质的三维结构
3. A simple method for delineating well‐defined and variable regions in protein structures determined from interproton distance data [J] . Clore G.Marius, Gronenborn Angela M., Nilges Michael FEBS Letters . 1987,第1期

机译：在质子间距离数据确定的蛋白质结构中定义轮廓分明的可变区的简单方法
4. Comparison of distance geometry and molecular dynamics for calculation of Peptide structures from experimental NMR data [C] . Alexander G.Milbradt, Marc Fuhrmans, Christian Renner International Peptide Symposium;European Peptide Symposium . 2005

机译：实验性NMR数据计算距离几何和分子动力学的比较
5. New protein structure prediction method using inter-residue distances and a theoretical investigation of the isomerization of azobenzene and disubstituted azobenzenes. [D] . Crecca, Christina R. 2008

机译：一种新的利用残基间距离预测蛋白质结构的方法以及对偶氮苯和二取代的偶氮苯异构化的理论研究。
6. Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction [O] . Yuangen Yao, Rong Gui, Quan Liu, 2017

机译：距离截止和残基间隔对蛋白质结构预测中距离相关原子对电位性能的影响
7. Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data [O] . Oscar Hur, Kevin Karplus 2005

机译：用有限的实验数据将NMR质子距离转化为蛋白质结构预测的相应重原子距离的方法

Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data

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