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High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR - PLoS ONE (2015)

Bottom Line: 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 3.6(13) 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 3.6(13/10)-, Némethy- or N-helix, is proposed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Washington University, St. Louis, MO, United States of America.

ABSTRACT
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 3.6(13) 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 3.6(13/10)-, 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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Related in: MedlinePlus

The appearance of electron density as a function of the nominal resolution of the experimental crystallographic data, (adapted from similar figure for the N-terminal fragment (Lys1—Val2—Phe3) of triclinic lysozyme (PDB: 2vb1) from Wlodawer et al. [33] for which permission to reproduce by the journal was not granted).
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pone.0123146.g004: The appearance of electron density as a function of the nominal resolution of the experimental crystallographic data, (adapted from similar figure for the N-terminal fragment (Lys1—Val2—Phe3) of triclinic lysozyme (PDB: 2vb1) from Wlodawer et al. [33] for which permission to reproduce by the journal was not granted).

Mentions: Fortunately, the quality of protein crystal structures has improved dramatically over the past several decades. Early protein crystals diffracted poorly, and data collection was generally limited to a 2.5 Å resolution, or greater. Wlodower et al. illustrated the impact of nominal resolution on the electron density map from which structural models are derived [33] (Fig 4shows a similar comparison based on crambin 3NIR). Whereas the highest resolution of 0.65 Å in the lysozyme structure employed data from 184,676 reflections for the electron-density map calculation, only 415 reflections were included at 5 Å resolution. Note that while higher-resolution maps provide enough geometric detail to unambiguously determine the amide plane and C = O vectors, there are multiple ways one could build a molecular model into density maps of poorer resolution [33]. X-ray crystallography is capable of localizing heavy atoms with astounding accuracy, so how is it possible for errors in helical populations to go undetected in so many crystallographic experiments? Interestingly, there is a straightforward two-part explanation: (i) hydrogens are less visible to X-ray diffraction due to their very small electronic cross-section; and (ii) the crystallographically determined positions of the heavy atoms, Cα-C-N-Cα, of the peptide backbone specify a unique helical configuration, i.e. helical parameters, the number of residues per turn and number of atoms in a hydrogen-bonding ring that was originally determined by fiber diffraction. The backbone torsional parameters (Φ, ψ) for helical models having the same helical parameters, however, are determined by the orientation of the carbonyl C = O vector which have limited, but significant, degrees of freedom for the same helical parameters based on the insight of Némethy et al. [9].


High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR - PLoS ONE (2015)

The appearance of electron density as a function of the nominal resolution of the experimental crystallographic data, (adapted from similar figure for the N-terminal fragment (Lys1—Val2—Phe3) of triclinic lysozyme (PDB: 2vb1) from Wlodawer et al. [33] for which permission to reproduce by the journal was not granted).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403875&req=5

pone.0123146.g004: The appearance of electron density as a function of the nominal resolution of the experimental crystallographic data, (adapted from similar figure for the N-terminal fragment (Lys1—Val2—Phe3) of triclinic lysozyme (PDB: 2vb1) from Wlodawer et al. [33] for which permission to reproduce by the journal was not granted).
Mentions: Fortunately, the quality of protein crystal structures has improved dramatically over the past several decades. Early protein crystals diffracted poorly, and data collection was generally limited to a 2.5 Å resolution, or greater. Wlodower et al. illustrated the impact of nominal resolution on the electron density map from which structural models are derived [33] (Fig 4shows a similar comparison based on crambin 3NIR). Whereas the highest resolution of 0.65 Å in the lysozyme structure employed data from 184,676 reflections for the electron-density map calculation, only 415 reflections were included at 5 Å resolution. Note that while higher-resolution maps provide enough geometric detail to unambiguously determine the amide plane and C = O vectors, there are multiple ways one could build a molecular model into density maps of poorer resolution [33]. X-ray crystallography is capable of localizing heavy atoms with astounding accuracy, so how is it possible for errors in helical populations to go undetected in so many crystallographic experiments? Interestingly, there is a straightforward two-part explanation: (i) hydrogens are less visible to X-ray diffraction due to their very small electronic cross-section; and (ii) the crystallographically determined positions of the heavy atoms, Cα-C-N-Cα, of the peptide backbone specify a unique helical configuration, i.e. helical parameters, the number of residues per turn and number of atoms in a hydrogen-bonding ring that was originally determined by fiber diffraction. The backbone torsional parameters (Φ, ψ) for helical models having the same helical parameters, however, are determined by the orientation of the carbonyl C = O vector which have limited, but significant, degrees of freedom for the same helical parameters based on the insight of Némethy et al. [9].

Bottom Line: 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 3.6(13) 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 3.6(13/10)-, Némethy- or N-helix, is proposed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Washington University, St. Louis, MO, United States of America.

ABSTRACT
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 3.6(13) 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 3.6(13/10)-, 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.

Show MeSH
Related in: MedlinePlus