Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases.
Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases.
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DOI：
10.7554/elife.83368
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发表时间：
2022-12-23
期刊：
影响因子：
7.7
通讯作者：
Levy RM
中科院分区：
文献类型：
--
作者：
Gizzio J;Thakur A;Haldane A;Levy RM
蛋白激酶催化结构域的非活性构象（其中DFG基序具有“DFG-out”取向并且激活环折叠）呈现可药用结合口袋，其在癌症治疗中被FDA批准的“II型抑制剂”靶向。酪氨酸激酶（TK）通常显示与广谱II型抑制剂的强结合亲和力，而丝氨酸/苏氨酸激酶（STKs）通常结合更弱，我们在此认为这是由于TK与STKs之间的激活环的折叠至延伸构象平衡的差异。为了研究这一点，我们使用序列协变分析与波茨哈密顿统计能量模型，以指导绝对结合自由能分子动力学模拟74蛋白质配体复合物。使用计算的结合自由能与实验值一起，我们通过间接方法估计了激活环的大规模（~17-20 μ m）构象变化的自由能成本，绕过了直接模拟构象变化的非常具有挑战性的问题。我们还使用了Potts统计势来将大序列集合穿过活性和非活性激酶状态。基于结构和基于序列的分析是一致的;它们一起表明TK进化为具有相对于活性构象的经典“折叠活化环”DFG-出构象的自由能罚分，即平均比STK的相应值小4-6 kcal/mol。Potts统计能量分析表明了这种观察的分子基础，其中TK的活化环在活性构象中对催化环基序更弱地“锚定”，并在非活性构象中形成更稳定的底物模拟相互作用。这些结果为TK和STKs的不同功能特性提供了分子基础，并对II型抑制剂的靶向选择性具有药理学意义。
Inactive conformations of protein kinase catalytic domains where the DFG motif has a “DFG-out” orientation and the activation loop is folded present a druggable binding pocket that is targeted by FDA-approved ‘type-II inhibitors’ in the treatment of cancers. Tyrosine kinases (TKs) typically show strong binding affinity with a wide spectrum of type-II inhibitors while serine/threonine kinases (STKs) usually bind more weakly which we suggest here is due to differences in the folded to extended conformational equilibrium of the activation loop between TKs vs. STKs. To investigate this, we use sequence covariation analysis with a Potts Hamiltonian statistical energy model to guide absolute binding free-energy molecular dynamics simulations of 74 protein-ligand complexes. Using the calculated binding free energies together with experimental values, we estimated free-energy costs for the large-scale (~17–20 Å) conformational change of the activation loop by an indirect approach, circumventing the very challenging problem of simulating the conformational change directly. We also used the Potts statistical potential to thread large sequence ensembles over active and inactive kinase states. The structure-based and sequence-based analyses are consistent; together they suggest TKs evolved to have free-energy penalties for the classical ‘folded activation loop’ DFG-out conformation relative to the active conformation, that is, on average, 4–6 kcal/mol smaller than the corresponding values for STKs. Potts statistical energy analysis suggests a molecular basis for this observation, wherein the activation loops of TKs are more weakly ‘anchored’ against the catalytic loop motif in the active conformation and form more stable substrate-mimicking interactions in the inactive conformation. These results provide insights into the molecular basis for the divergent functional properties of TKs and STKs, and have pharmacological implications for the target selectivity of type-II inhibitors.
影响因子：
3.5
作者：
Sun Q;Biswas A;Vijayan RSK;Craveur P;Forli S;Olson AJ;Castaner AE;Kirby KA;Sarafianos SG;Deng N;Levy R
通讯作者：
Levy R