High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.
High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.
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DOI：
10.1371/journal.pone.0123146
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Marshall GR
中科院分区：
文献类型：
--
作者：
Kuster DJ;Liu C;Fang Z;Ponder JW;Marshall GR
蛋白质螺旋中非线性氢键的理论和实验证据无处不在。特别是，酰胺三中心氢键是蛋白质高分辨率晶体结构中螺旋的共同特征。这些高分辨率结构（1.0 至 1.5 Å 标称晶体分辨率）可定位主链原子，不受建模约束的显着偏差，并将 Φ = -62°、ψ = -43 确定为蛋白质螺旋的一致主链扭转角。这些扭转角保留了经典鲍林 α 螺旋的 α-β 碳的原子位置，同时允许酰胺羰基形成分叉氢键，正如 Némethy 等人首先提出的那样。 1967 年。使用 AMOEBA（生物分子应用原子多极优化能量学）对水中的封端 12 残基寡丙氨酸进行分子动力学模拟，AMOEBA 是一种包括多极静电和极化性的第二代力场，再现了实验观察到的高分辨率螺旋构象，并正确地将酰胺键羰基重新定向为分叉氢键。这种对主链扭转角的简单修改协调了实验和理论观点，提供了酰胺三中心氢键作为蛋白质螺旋关键组成部分的统一观点。它们被结构生物学家忽视的原因取决于酰胺键方向上类似曲轴的小变化，这种变化可以维持整体螺旋参数（螺旋螺距 (p) 和每转残基 (n)）。鲍林 3.613 α-螺旋符合高分辨率实验数据，但酰胺-羰基电子密度略有例外，但之前相关的主链扭转角 (Φ, Ψ) 需要稍作修改才能与三原子中心氢键和多极静电相协调。因此，提出了一种新的标准螺旋，即 3.613/10-、Némethy- 或 N-螺旋。由于使用单极力场的约束以及用于蛋白质电子密度的低分辨率细化的假设二级结构，PDB 中的此类结构通常表现出线性氢键。
Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.
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影响因子：
14.9
作者：
Felder CE;Prilusky J;Silman I;Sussman JL
通讯作者：
Sussman JL
DOI：
10.1107/s0907444902003359
发表时间：
2002-05-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Hovmöller, S;Zhou, T;Ohlson, T
通讯作者：
Ohlson, T
影响因子：
3.4
作者：
Best, Robert B.;Buchete, Nicolae-Viorel;Hummer, Gerhard
通讯作者：
Hummer, Gerhard
影响因子：
5.6
作者：
ARNOTT, S;WONACOTT, AJ
通讯作者：
WONACOTT, AJ
影响因子：
2.9
作者：
HODGKIN, EE;CLARK, JD;MARSHALL, GR
通讯作者：
MARSHALL, GR