Krishnan Marimuthu, Smith Jeremy C
UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
J Am Chem Soc. 2009 Jul 29;131(29):10083-91. doi: 10.1021/ja901276n.
Changes in the free energy barrier (DeltaE), entropy, and motional parameters associated with the rotation of methyl groups in a protein (calmodulin (CaM)) on binding a ligand (the calmodulin-binding domain of smooth-muscle myosin (smMLCKp)) are investigated using molecular dynamics simulation. In both the bound and uncomplexed forms of CaM, the methyl rotational free energy barriers follow skewed-Gaussian distributions that are not altered significantly upon ligand binding. However, site-specific perturbations are found. Around 11% of the methyl groups in CaM exhibit changes in DeltaE greater than 0.7 kcal/mol on binding. The rotational entropies of the methyl groups exhibit a nonlinear dependence on DeltaE. The relations are examined between motional parameters (the methyl rotational NMR order parameter and the relaxation time) and DeltaE. Low-barrier methyl group rotational order parameters deviate from ideal tetrahedrality by up to approximately 20%. There is a correlation between rotational barrier changes and proximity to the protein-peptide binding interface. Methyl groups that exhibit large changes in DeltaE are found to report on elements in the protein undergoing structural change on binding.
利用分子动力学模拟研究了蛋白质（钙调蛋白（CaM））结合配体（平滑肌肌球蛋白的钙调蛋白结合结构域（smMLCKp））时甲基基团旋转相关的自由能势垒（ΔE）、熵和运动参数的变化。在CaM的结合态和非复合态中，甲基旋转自由能势垒均遵循偏态高斯分布，配体结合后无显著变化。然而，发现了位点特异性扰动。CaM中约11%的甲基基团在结合时ΔE变化大于0.7 kcal/mol。甲基基团的旋转熵对ΔE呈现非线性依赖。研究了运动参数（甲基旋转核磁共振序参数和弛豫时间）与ΔE之间的关系。低势垒甲基基团旋转序参数与理想四面体的偏差高达约20%。旋转势垒变化与靠近蛋白质 - 肽结合界面之间存在相关性。发现ΔE变化大的甲基基团反映了结合时蛋白质中发生结构变化的元素。
