|
|
Biophysics 2024
基于弹性网络模型和微扰响应扫描的PKC-θ的动力学和关键残基研究
|
Abstract:
PKC-θ (protein kinase C-theta)激酶能够对底物蛋白中的丝氨酸/苏氨酸进行磷酸化修饰，并参与T细胞活化、信号转导及免疫应答等重要生理过程，与许多免疫疾病相关，因此研究PKC-θ的结构动力学及其关键位点具有重要意义。在本工作中，我们对PKC-θ构建了弹性网络模型，并在慢运动模式下识别出了结构中重要的功能区域。通过残基的运动相关性分析发现：N端小叶和C端大叶的运动是负相关的，这一致于两叶间的“开合运动”，有助于结合配体的稳定；此外，催化相关残基与DFG基序的运动呈正相关，这有利于催化功能的发挥。接着，利用微扰响应扫描方法来识别变构关键残基，结果发现，高敏感性残基对配体结合及酶的催化活性很重要。这项工作有助于加强对PKC-θ结构动力学的理解，并为设计激酶抑制剂提供重要信息。
PKC-θ (Protein Kinase C-theta) can phosphorylate the serine/threonine of substrate protein, participating in important physiological processes such as T cell activation, signal transduction and immune response, and related to many immune diseases. Thus, it is of great significance to study its structural dynamics and key residues. In this work, we construct PKC-θ’s elastic network model, and the important functional areas are identified based on GNM’s slow motion modes. According to interresiduemotion correlations, it is found that there exists a negative motion correlation between N-lobe and C-lobe, consistent with their open-closed motion, which helps for the bound ligand’s stability; in addition, there is a positive motion correlation between DFG motif and catalysis related residues, which is conducive to the catalytic function exertion. Then, the perturbation response scanning method is used to identify the key residues for allostery, and the results suggest that the key residues of high sensitivity are important for ligand binding and enzyme’s catalytic activity. This work helps to strengthen the understanding of structural dynamics of PKC-θ and provides important information for kinase inhibitor design.
| [1] | Isakov, N. (2018) Protein Kinase C (PKC) Isoforms in Cancer, Tumor Promotion and Tumor Suppression. Seminars in Cancer Biology, 48, 36-52. https://doi.org/10.1016/j.semcancer.2017.04.012 |
| [2] | Zeng, L., Webster, S.V. and Newton, P.M. (2012) The Biology of Protein Kinase C. In: Islam, M., Ed., Calcium Signaling. Advances in Experimental Medicine and Biology, Vol. 740, Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2888-2_28 |
| [3] | Ohno, S., Akita, Y., Hata, A., et al. (1991) Structural and Functional Diversities of a Family of Signal Transducing Protein Kinases, Protein Kinase C Family; Two Distinct Classes of PKC, Conventional cPKC and Novel nPKC. Advances in Enzyme Regulation, 31, 287-303. https://doi.org/10.1016/0065-2571(91)90018-H |
| [4] | Chand, S., Mehta, N., Bahia, M.S., et al. (2012) Protein Kinase C-Theta Inhibitors: A Novel Therapy for Inflammatory Disorders. Current Pharmaceutical Design, 18, 4725-4276. https://doi.org/10.2174/138161212802651625 |
| [5] | Brezar, V., Tu, W.J. and Seddiki, N. (2015) PKC-Theta in Regulatory and Effector T-Cell Functions. Frontiers in Immunology, 6, Article 530. https://doi.org/10.3389/fimmu.2015.00530 |
| [6] | Seco, J., Ferrer-Costa, C., Campanera, J.M., et al. (2012) Allosteric Regulation of PKCθ: Understanding Multistep Phosphorylation and Priming by Ligands in AGC Kinases. Proteins: Structure, Function, and Bioinformatics, 80, 269-280. https://doi.org/10.1002/prot.23205 |
| [7] | Keranen, L.M., Dutil, E.M. and Newton, A.C. (1995) Protein Kinase C Is Regulated in vivo by Three Functionally Distinct Phosphorylations. Current Biology, 5, 1394-1403. https://doi.org/10.1016/S0960-9822(95)00277-6 |
| [8] | Kornev, A.P. and Taylor, S.S. (2015) Dynamics-Driven Allostery in Protein Kinases. Trends in Biochemical Sciences, 40, 628-647. https://doi.org/10.1016/j.tibs.2015.09.002 |
| [9] | Kannan, N., Haste, N., Taylor, S.S., et al. (2007) The Hallmark of AGC Kinase Functional Divergence Is Its C-Terminal Tail, a Cis-Acting Regulatory Module. Proceedings of the National Academy of Sciences of the United States of America, 104, 1272-1277. https://doi.org/10.1073/pnas.0610251104 |
| [10] | Torkamani, A., Kannan, N., Taylor, S.S., et al. (2008) Congenital Disease SNPs Target Lineage Specific Structural Elements in Protein Kinases. Proceedings of the National Academy of Sciences, 105, 9011-9016. https://doi.org/10.1073/pnas.0802403105 |
| [11] | Hemmer, W., Mcglone, M., Tsigelny, I., et al. (1997) Role of the Glycine Triad in the ATP-Binding Site of cAMP-Dependent Protein Kinase. The Journal of Biological Chemistry, 272, 16946-16954. https://doi.org/10.1074/jbc.272.27.16946 |
| [12] | Liu, Y., Graham, C., Li, A., et al. (2002) Phosphorylation of the Protein Kinase C-Theta Activation Loop and Hydrophobic Motif Regulates Its Kinase Activity, But Only Activation Loop Phosphorylation Is Critical to in vivo Nuclear-Factor-κB Induction. Biochemical Journal, 361, 255-265. https://doi.org/10.1042/bj3610255 |
| [13] | Hatmal, M.M. and Taha, M.O. (2017) Simulated Annealing Molecular Dynamics and Ligand-Receptor Contacts Analysis for Pharmacophore Modeling. Future Medicinal Chemistry, 9, 1141-1159. https://doi.org/10.4155/fmc-2017-0061 |
| [14] | Iqbal, S., Anantha, K.D. and Gunasekaran, K. (2017) Identification of Potential PKC Inhibitors through Pharmacophore Designing, 3D-QSAR and Molecular Dynamics Simulations Targeting Alzheimer’s Disease. Journal of Biomolecular Structure & Dynamics, 36, Article ID: 1406824. https://doi.org/10.1080/07391102.2017.1406824 |
| [15] | Tirion, M.M. (1996) Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Physical Review Letters, 77, 1905-1908. https://doi.org/10.1103/PhysRevLett.77.1905 |
| [16] | Bahar, I., Atilgan, A.R. and Erman, B. (1997) Direct Evaluation of Thermal Fluctuations in Proteins Using a Single-Parameter Harmonic Potential. Folding & Design, 2, 173-181. https://doi.org/10.1016/S1359-0278(97)00024-2 |
| [17] | Atilgan, A.R., Durell, S.R., Jernigan, R.L., et al. (2001) Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model. Biophysical Journal, 80, 505-515. https://doi.org/10.1016/S0006-3495(01)76033-X |
| [18] | Atilgan, C. and Atilgan, A.R. (2009) Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein. PLOS Computational Biology, 5, e1000544. https://doi.org/10.1371/journal.pcbi.1000544 |
| [19] | Liang, Z., Zhu, Y., Liu, X., et al. (2020) Role of Protein-Protein Interactions in Allosteric Drug Design for Dnamethyltransferases. Advances in Protein Chemistry and Structural Biology, 121, 49-84. https://doi.org/10.1016/bs.apcsb.2019.12.005 |
| [20] | Omori, S., Fuchigami, S., Ikeguchi, M., et al. (2009) Linear Response Theory in Dihedral Angle Space for Protein Structural Change upon Ligand Binding. Journal of Computational Chemistry, 30, 2602-2608. https://doi.org/10.1002/jcc.21269 |
| [21] | Dutta, A., Krieger, J., Lee, J.Y., et al. (2015) Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences. Structure, 23, 1692-1704. https://doi.org/10.1016/j.str.2015.07.002 |
| [22] | Bahar, I., Atilgan, A.R., Demirel, M.C., et al. (1998) Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability. Physical Review Letters, 80, 2733-2736. https://doi.org/10.1103/PhysRevLett.80.2733 |
| [23] | George, D.M., Breinlinger, E.C., Friedman, M., et al. (2015) Discovery of Selective and Orally Bioavailable Protein Kinase Cθ(PKCθ) Inhibitors from a Fragment Hit. Journal of Medicinal Chemistry, 58, 222-236. https://doi.org/10.1021/jm500669m |
| [24] | 徐锋. 蛋白激酶催化域分子内共进化网络分析[D]: [博士学位论文]. 上海: 复旦大学, 2008. |
| [25] | Komander, D., Kular, G., Deak, M., et al. (2005) Role of T-Loop Phosphorylation in PDK1 Activation, Stability, and Substrate Binding. Journal of Biological Chemistry, 280, 18797-18802. https://doi.org/10.1074/jbc.M500977200 |
| [26] | Yeung, W., Ruan, Z. and Kannan, N. (2020) Emerging Roles of the αC-β4 Loop in Protein Kinase Structure, Function, Evolution, and Disease. IUBMB Life, 72, 1189-1202. https://doi.org/10.1002/iub.2253 |
| [27] | Pearce, L.R., Komander, D. and Alessi, D.R. (2010) The Nuts and Bolts of AGC Protein Kinases. Nature Reviews Molecular Cell Biology, 11, 9-22. https://doi.org/10.1038/nrm2822 |
