Diehl Carl, Genheden Samuel, Modig Kristofer, Ryde Ulf, Akke Mikael
Center for Molecular Protein Science, Biophysical Chemistry, Lund University, Lund, Sweden.
J Biomol NMR. 2009 Sep;45(1-2):157-69. doi: 10.1007/s10858-009-9356-5. Epub 2009 Jul 30.
The conformational entropy of proteins can make significant contributions to the free energy of ligand binding. NMR spin relaxation enables site-specific investigation of conformational entropy, via order parameters that parameterize local reorientational fluctuations of rank-2 tensors. Here we have probed the conformational entropy of lactose binding to the carbohydrate recognition domain of galectin-3 (Gal3), a protein that plays an important role in cell growth, cell differentiation, cell cycle regulation, and apoptosis, making it a potential target for therapeutic intervention in inflammation and cancer. We used (15)N spin relaxation experiments and molecular dynamics simulations to monitor the backbone amides and secondary amines of the tryptophan and arginine side chains in the ligand-free and lactose-bound states of Gal3. Overall, we observe good agreement between the experimental and computed order parameters of the ligand-free and lactose-bound states. Thus, the (15)N spin relaxation data indicate that the molecular dynamics simulations provide reliable information on the conformational entropy of the binding process. The molecular dynamics simulations reveal a correlation between the simulated order parameters and residue-specific backbone entropy, re-emphasizing that order parameters provide useful estimates of local conformational entropy. The present results show that the protein backbone exhibits an increase in conformational entropy upon binding lactose, without any accompanying structural changes.
蛋白质的构象熵对配体结合自由能有显著贡献。核磁共振自旋弛豫能够通过参数化二阶张量局部重排涨落的序参量，对构象熵进行位点特异性研究。在此，我们探究了乳糖与半乳糖凝集素-3（Gal3）的碳水化合物识别结构域结合时的构象熵，Gal3在细胞生长、细胞分化、细胞周期调控和细胞凋亡中发挥重要作用，使其成为炎症和癌症治疗干预的潜在靶点。我们使用（15）N自旋弛豫实验和分子动力学模拟来监测Gal3在无配体和乳糖结合状态下色氨酸和精氨酸侧链的主链酰胺和仲胺。总体而言，我们观察到无配体和乳糖结合状态下实验和计算得到的序参量之间有良好的一致性。因此，（15）N自旋弛豫数据表明分子动力学模拟为结合过程的构象熵提供了可靠信息。分子动力学模拟揭示了模拟序参量与残基特异性主链熵之间存在相关性，再次强调序参量为局部构象熵提供了有用的估计。目前的结果表明，蛋白质主链在结合乳糖时构象熵增加，且无任何伴随的结构变化。
