Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

Wilson, Katie A.; Wetmore, Stacey D.

doi:10.1007/s11224-017-0954-7

Cited by 13 publications

(15 citation statements)

References 107 publications

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“…In summary, we can conclude that calorimetry analysis confirmed the affinity sequence of CH–π stacking residues to be: Trp>Tyr≈Phe>Val>Ala. The same trend was obtained by the analysis of QM calculations and is also in agreement with a recent study on CH–π interactions with carbohydrates in nucleic acids …”

Section: Resultssupporting

confidence: 92%

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Houser

Kozmon²,

Mishra

et al. 2020

Chemistry A European J

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The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell–cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal‐ion‐mediated interaction, and non‐polar dispersion interactions. The role of dispersion‐driven CH–π interactions (stacking) in protein–carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non‐polar interactions are equally important. In this study, we analyzed the CH–π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X‐ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH–π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol−1. All the results show that the stacking CH–π interactions in protein–carbohydrate complexes can be considered to be a driving force of the binding in such complexes.

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Section: Resultssupporting

confidence: 92%

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Houser

Kozmon²,

Mishra

et al. 2020

Chemistry A European J

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“…As the oligonucleotide chain remained close to the GO, the CSA value increased up to 2 nm 2 at t ≈ 2.50 ns, corresponding to the formation of three hydrogen bonds and a T-shaped π-π stacking in which the rings adopt a perpendicular geometry [30], as shown in Figure 4. This type of π-stacking has been previously observed in DNA-protein interactions [31]. Despite respecting our π-π stacking criteria, the GO region involved was heavily oxidised, and this oxidation could shield and significantly weaken the π-stacking energy.…”

Section: Single-stranded Dna Adsorption On Go In the Presence Of Mg 2supporting

confidence: 63%

Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

et al. 2020

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Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.

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“…These select examples illustrate the structural diversity and potential importance of ribose–amino acid contacts in nature. Furthermore, sugar–π interactions have been reported to be common in DNA–protein complexes ( 33 , 34 , 37 ) and folded RNA structures ( 38 ), while similar interactions between carbohydrates and amino acids have long been accepted to play indispensable roles in glycobiology ( 39–44 ). By analogy, sugar–π interactions could likely modulate RNA–protein binding.…”

Section: Introductionmentioning

confidence: 99%

Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes

Wilson

Kung

D’souza

et al. 2021

Nucleic Acids Research

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A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.

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Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

Cited by 13 publications

References 107 publications

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes

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