Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins.
Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins.
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DOI：
10.1021/acs.jpcb.1c01269
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发表时间：
2021-06-24
期刊：
影响因子：
--
通讯作者：
Kekenes-Huskey PM
中科院分区：
文献类型：
--
作者：
Immadisetty K;Sun B;Kekenes-Huskey PM
钙（Ca 2+）结合蛋白（CBP）的小清蛋白（PV）家族的成员具有相对高水平的序列相似性。然而，它们对竞争离子如镁（Mg 2+）的Ca 2+亲和力和选择性可以广泛变化。我们对几种具有微摩尔至纳摩尔Ca 2+亲和力的α-小清蛋白（αPV）构建体进行了分子动力学模拟，以确定有助于其离子结合的结构和动力学特征。具体来说，我们检查了D94 S/G98 E构建体，其Ca 2+亲和力（Δ-18 kcal/mol）相对于WT（Δ-22 kcal/mol）和S55 D/E59 D变体具有增强的亲和力（Δ-24 kcal/mol）。此外，我们还研究了Mg 2+与这些亚型的结合，其比Ca 2+弱得多。我们使用平均球近似（MSA）理论来评估蛋白质EF-手域内的离子结合热力学，以解释离子的有限尺寸和周围电解质组成的影响。虽然MSA评分区分了Mg 2+和Ca 2+，但它们并不表明PV亚型之间结合环处的Ca 2+结合不同。相反，分子力学广义玻恩近似（MM/GBSA）能量量化了蛋白质在结合离子时的结构重排，表明S55 D/E59 D αPV相对于WT有利于钙结合−20 kcal/mol，而D94 S/G98 E αPV有利于钙结合30 kcal/mol。与此同时，S55 D/E59 D αPV和D94 S/G98 E αPV变体的Mg 2+结合分别为−18.32和−1.65 kcal/mol。这些能量暗示了除了氧配位之外对离子结合的重要贡献，这源于α-螺旋度，β-折叠特征和氢键的变化。因此，Ca 2+亲和力和对Mg 2+的选择性是源于蛋白质离子结合位点内的局部效应以及其他地方的非局部贡献的新兴特性。我们的研究结果拓宽了我们对α-小清蛋白（αPV）离子结合的分子基础的理解，这些分子基础可能由广泛的Ca 2+结合蛋白家族成员共享。
Members of the parvalbumin (PV) family of calcium (Ca2+) binding proteins (CBPs) share a relatively high level of sequence similarity. However, their Ca2+ affinities and selectivities against competing ions like magnesium (Mg2+) can widely vary. We conducted molecular dynamics simulations of several α-parvalbumin (αPV) constructs with micromolar to nanomolar Ca2+ affinities, to identify structural and dynamic features that contribute to their binding of ions. Specifically, we examined a D94S/G98E construct with a reported lower Ca2+ affinity (≈ −18 kcal/mol) relative to the WT (≈ −22 kcal/mol) and an S55D/E59D variant with enhanced affinity (≈ −24 kcal/mol). Additionally, we also examined the binding of Mg2+ to these isoforms, which is much weaker than Ca2+. We used mean spherical approximation (MSA) theory to evaluate ion binding thermodynamics within the proteins’ EF-hand domains to account for impact of ions’ finite sizes and the surrounding electrolyte composition. While the MSA scores differentiated Mg2+ from Ca2+, they did not indicate that Ca2+ binding at the binding loop differed between the PV isoforms. Instead, molecular mechanics generalized Born approximation (MM/GBSA) energies that quantify the structural rearrangement of the proteins upon binding ions indicate that S55D/E59D αPV favors Ca2+ binding by −20 kcal/mol relative to WT versus 30 kcal/mol for D94S/G98E αPV. Meanwhile, Mg2+ binding was favored for the S55D/E59D αPV and D94S/G98E αPV variants by −18.32 and −1.65 kcal/mol, respectively. These energies implicate significant contributions to ion binding beyond oxygen coordination, which stemmed from changes in α-helicity, β-sheet character and hydrogen bonding. Hence, Ca2+ affinity and selectivity against Mg2+ are emergent properties stemming from both local effects within the proteins’ ion binding sites as well as non-local contributions elsewhere. Our findings broaden our understanding of the molecular bases governing α-parvalbumin (αPV) ion binding that are likely shared by members of the broad family of Ca2+ binding proteins.
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