Toward assessing the position-dependent contributions of backbone hydrogen bonding to β-sheet folding thermodynamics employing amide-to-ester perturbations
Toward assessing the position-dependent contributions of backbone hydrogen bonding to β-sheet folding thermodynamics employing amide-to-ester perturbations
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DOI：
10.1021/ja045934s
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发表时间：
2004-12-29
影响因子：
15
通讯作者：
Kelly, JW
中科院分区：
文献类型：
--
作者：
Deechongkit, S;Dawson, PE;Kelly, JW
蛋白质中的酰胺至酯主链取代通过用相应的α-羟基酸替换α-氨基酸残基、保留主链的立体化学和构象以及侧链的结构来实现。该取代用酯0（其不是氢键供体）取代酰胺NH（氢键供体），并用酯羰基（较弱的氢键受体）取代酰胺羰基（强氢键受体），从而扰乱折叠能量学。酰胺-酯扰动用于评估PIN WW结构域（一种三链β折叠蛋白）中每个氢键的热力学贡献。我们的研究结果表明，去除氢键供体不稳定的天然状态比削弱氢键受体和不稳定的程度是强烈依赖于取代的酰胺键的位置。在转角附近或在β链末端的氢键比在疏水核心内被保护的氢键影响更小。由于酰胺和酯的溶剂化和静电相互作用的差异，由酰胺-酯取代引起的β-折叠不稳定不能与氢键强度直接相关。我们提出了这些差异的修正，以获得近似的氢键强度不稳定的能量。然而，这些校正并不改变上述趋势，表明酰胺-酯突变的不稳定能是骨架酰胺氢键形成的自由能的良好一级近似。
An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding a-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester 0 (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. beta-Sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.