Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.
Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.
复制标题
分子动力学模拟中肽 13C 羰基化学屏蔽各向异性的参数化。
DOI：
10.1002/cphc.200700003
复制
发表时间：
2007
期刊：
影响因子：
--
通讯作者：
Zuiderweg,ErikRP
中科院分区：
文献类型：
--
作者：
Jordan,DanielM;Mills,KMaria;Andricioaei,Ioan;Bhattacharya,Akash;Palmo,Kim;Zuiderweg,ErikRP
核磁共振化学屏蔽各向异性弛豫是研究蛋白质和核酸在溶液中动力学过程的重要工具。在此，我们研究了局域几何的动态变化如何影响羰基碳核的化学屏蔽各向异性弛豫，使用以下方案：1）使用密度泛函理论，计算了103个模型肽基N-甲基乙酰胺（NMA）构象的羰基13 C ′ CSA. 2)计算出的13 C 'CSA参数的变化与变量之间包含交叉项的二次超曲面进行拟合。3)通过比较20个分子动力学快照的13 C ′ CSA的预测值和从头计算值，验证了CSA超曲面的预测质量。4)基于化学哈佛分子力学（CHARMM）分子动力学轨道，利用量子力学修正力场，对钙调素和GB 3的超曲面进行了预测，并对NMA三聚体进行了分子动力学模拟，得到了由键长和键角畸变引起的CSA涨落及其自相关和互相关函数.我们发现，波动可以表示为0.93的CSA张量的缩放因子为两个R1和R2松弛的螺旋，线圈和片的残基一样。这一结果很重要，因为它确定了13 C ′弛豫是测量蛋白质中有趣的动力学事件的有效工具。
NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl13C′ CSA is computed for 103 conformations of the model peptide groupN‐methylacetamide (NMA). 2) The variations in computed13C′ CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated13C′ CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond‐length and bond‐angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca2+‐saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for bothR1andR2relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that13C′ relaxation is a valid tool for measurement of interesting dynamical events in proteins.