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On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures.

ABSTRACT: Protein structures are stabilized by a variety of noncovalent interactions (NCIs), including the hydrophobic effect, hydrogen bonds, electrostatic forces and van der Waals' interactions. Our knowledge of the contributions of NCIs, and the interplay between them remains incomplete. This has implications for computational modeling of NCIs, and our ability to understand and predict protein structure, stability, and function. One consideration is the satisfaction of the full potential for NCIs made by backbone atoms. Most commonly, backbone-carbonyl oxygen atoms located within ?-helices and ?-sheets are depicted as making a single hydrogen bond. However, there are two lone pairs of electrons to be satisfied for each of these atoms. To explore this, we used operational geometric definitions to generate an inventory of NCIs for backbone-carbonyl oxygen atoms from a set of high-resolution protein structures and associated molecular-dynamics simulations in water. We included more-recently appreciated, but weaker NCIs in our analysis, such as n??* interactions, C?-H bonds and methyl-H bonds. The data demonstrate balanced, dynamic systems for all proteins, with most backbone-carbonyl oxygen atoms being satisfied by two NCIs most of the time. Combinations of NCIs made may correlate with secondary structure type, though in subtly different ways from traditional models of ?- and ?-structure. In addition, we find examples of under- and over-satisfied carbonyl-oxygen atoms, and we identify both sequence-dependent and sequence-independent secondary-structural motifs in which these reside. Our analysis provides a more-detailed understanding of these contributors to protein structure and stability, which will be of use in protein modeling, engineering and design.

SUBMITTER: Bartlett GJ

PROVIDER: S-EPMC4941217 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures.

Bartlett Gail J GJ Woolfson Derek N DN

Protein science : a publication of the Protein Society 20160225 4

Protein structures are stabilized by a variety of noncovalent interactions (NCIs), including the hydrophobic effect, hydrogen bonds, electrostatic forces and van der Waals' interactions. Our knowledge of the contributions of NCIs, and the interplay between them remains incomplete. This has implications for computational modeling of NCIs, and our ability to understand and predict protein structure, stability, and function. One consideration is the satisfaction of the full potential for NCIs made ...[more]

PMID: 26833776

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Project description:Stereoactive electron lone pairs derived from filled 5/6s2 states of p-block cations are an intriguing electronic and geometric structure motif that have been exploited for diverse applications such as thermoelectrics, thermochromics, photocatalysis, and nonlinear optics. Layered trivanadates are dynamic intercalation hosts, where the insertion of cations can be used to tune electron correlation, charge localization, and magnetic ordering. However, the interaction of 5/6s2 stereoactive electron lone pairs with layered trivanadates remains unexplored. In this study, we contrast s- and p-block trivanadates and map off-centering in the coordination environment and reduction in symmetry arising from the stereochemical activity of lone pair cations to the emergence of filled antibonding lone-pair 6s2-O 2p hybridized states. The former is studied by high-resolution single-crystal X-ray diffraction studies of TlV3O8 and isostructural RbV3O8 to probe distinct differences in Tl and Rb coordination environments and the resulting modulation of V-V interactions in V3O8 slabs. The latter has been probed by variable-energy hard X-ray photoelectron spectroscopy (HAXPES) measurements, which manifest orbital-specific contributions from bonding and antibonding interactions of stereoactive Tl 6s2 electron lone pairs in TlV3O8. The spectroscopic assignment of valence band states to stereoactive lone pairs is further corroborated by first-principles electronic structure calculations, crystal orbital Hamilton population analyses, and electron localization function maps. The presence of the Tl 6s2 electron lone pair in TlV3O8 brings about the off-centering of Tl+ cations, which leads to anisotropy in Tl-O bonds. The off-centering of Tl ions weakens V-O bonds in one direction, which subsequently strengthens directional V-V coupling. Magnetic measurements reveal ferromagnetic signatures for both RbV3O8 and TlV3O8. However, the differences in V···V interactions significantly affect the energy balance of the superexchange interactions, resulting in an ordering temperature of 140 K for TlV3O8 as compared to 125 K for RbV3O8. The results demonstrate the distinctive effects of stereochemically active lone pairs in modifying electronic structure near the Fermi level and for mediating superexchange interactions.

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On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures.

Publications

On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures.

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