Newly identified C–H⋯O hydrogen bond in histidine

Steinert, Ryan M.; Kasireddy, Chandana; Heikes, Micah E.; Mitchell-Koch, Katie R.

doi:10.1039/d2cp02048c

Cited by 4 publications

(5 citation statements)

References 81 publications

(104 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For histidine, the CH or NH of the imidazole ring can generally have a strong pi-interaction when facing the center of the benzene ring 70 , 71 . However, in the UBR4 UBR structure, the benzene rings of phenylalanine are perpendicular to the imidazole ring, indicating a relatively lower affinity than the others.…”

Section: Resultsmentioning

confidence: 99%

Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates

Jeong,

Lee,

et al. 2023

Commun Biol

View full text Add to dashboard Cite

The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.

show abstract

Section: Resultsmentioning

confidence: 99%

Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates

Jeong,

Lee,

et al. 2023

Commun Biol

View full text Add to dashboard Cite

show abstract

“…A survey of the structures obtained from both neutron and X-ray diffraction reveals a multitude of C-H. . .O interactions involving the imidazole ring [127,128] (e.g., Figure 5). Their strength suggests functional implications.…”

Section: Bonds Involving C-h Methine Groups In Hismentioning

confidence: 99%

“…A range of enzymes contains histidines within their active sites, and the C-H groups of imidazole are involved in various interactions. For example, in carbonic anhydrase, three histidines bind Zn 2+ , and the conformation of one is stabilized by a Cε-H acting as a donor to carboxyl of Glu106 [128]. No comprehensive survey of thefunctional roles of C-H…O bonds in enzymatic reactions has been published to date.…”

Section: Bonds Involving C-h Methine Groups In Hismentioning

confidence: 99%

C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids

Derewenda

2023

IJMS

View full text Add to dashboard Cite

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.

show abstract

“…For GH/Zn, we observed the greater broadening of 1623 cm -1 peak at 70 % RH, while AH/Zn spectra did not show appreciable change. [53][54][55] The signal at 1455 cm -1 due to carboxylate symmetric stretching also intensified with high RH. This finding led us to further explore the effects of RH on GH/Zn and AH/Zn nanofiber assemblies in the solid state.…”

mentioning

confidence: 95%

“…AFM also revealed that GH/Zn reorganized into spherical structures upon hydration, where directional hydrogen bonding is displaced by interactions with water-vapor in line with FT-IR data (Figure S20). 53,55 Using DFT calculations, we optimized water complexes featuring both GH/Zn and AH/Zn dimers, incorporating two water molecules inserted between the dimers which disrupt the intermolecular C=O•••H−N hydrogen bonds (Figure S35 in SI). The energy of formation (ΔEw) for these complexes and their corresponding enthalpy change (ΔHw) are as follows: ΔEw values are -17.7 and -17.0 kcal/mol, while ΔHw values are -13.9 and -12.9 kcal/mol (details in SI, Table S5), respectively.…”

mentioning

confidence: 99%

Water-Vapor Responsive and Erasable Metallo-Peptide Nanofibers

Dey,

Ulijn,

Chen

et al. 2024

Preprint

View full text Add to dashboard Cite

Short peptides are versatile molecules for the construction of supramolecular materials. Most reported peptide materials are hydrophobic, stiff, and show limited response to environmental conditions in the solid-state. Herein, we describe a design strategy for minimalistic supramolecular metallo-peptide nanofibers that, depending on their sequence, change stiffness, or reversibly assemble in the solid-state, in response to changes in relative humidity (RH). We tested a series of histidine (H) containing dipeptides with varying hydrophobicity, XH, where X is G, A, L, Y (glycine, alanine, leucine, and tyrosine). The one-dimensional fiber formation is supported by metal coordination and dynamic H-bonds. Solvent conditions were identified where GH/Zn and AH/Zn formed gels that upon air-drying gave rise to nanofibers. Upon exposure of the nanofiber networks to increasing RH, a reduction in stiffness was observed with GH/Zn fibers reversibly (dis-)assembled at 60-70 % RH driven by a rebalancing of H-bonding interactions between peptides and water. When these metallo-peptide nanofibers were deposited on the surface of polyimide films and exposed to varying RH, peptide/water-vapor interactions in the solid-state mechanically transferred to the polymer film, leading to the rapid and reversible folding-unfolding of the films, thus demonstrating RH-responsive actuation.

show abstract

Newly identified C–H⋯O hydrogen bond in histidine

Abstract: Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).

Cited by 4 publications

References 81 publications

Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates

Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates

C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids

Water-Vapor Responsive and Erasable Metallo-Peptide Nanofibers

Contact Info

Product

Resources

About