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

Derewenda, Zygmunt Stanislaw

doi:10.3390/ijms241713165

Cited by 19 publications

(3 citation statements)

References 179 publications

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“…Some recent papers − have suggested that a direct nonclassical hydrogen bond between Ade:C2 and Thy:O2 may account for part of the stability of Watson–Crick and Hoogsteen A·T pairs. This suggestion was based on the experimental vibrational frequency measurement of the O2-containing carbonyl group in Thy and its solvatochromatic shift in duplex DNA as well as theoretical calculations of vibrational signatures of A·T pairs in vacuum. − While vibrational shifts suggest that the O2 carbonyl may be involved directly in the A·T pair, they may also arise from interaction with weakly bound water molecules in the minor groove .…”

Section: Results and Discussionmentioning

confidence: 99%

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair

Mak

2024

ACS Phys. Chem Au

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Base pairing complementarity is central to DNA function. G•C and A•T pair specificity is thought to originate from the different number of hydrogen bonds the pairs make. Quantifying how many hydrogen bonds exist can be difficult because water molecules in the surrounding can make up for or disrupt direct hydrogen bonds, and the hydration structures around A•T and G•C pairs on duplex DNA are distinct. Large-scale computer simulations have been used here to create a detailed map for the hydration structure on A•T and G•C base pairs in water. The contributions of specific hydration waters to the free energy of each of the hydrogen bonds in the A•T and G•C pairs were computed. Using the equilibrium fractions of hydrated versus unhydrated states from the hydration profiles, the impact of specific bound waters on each hydrogen bond can be uniquely quantified using a thermodynamic construction. The findings suggest that hydration water in the minor groove of an A•T pair can provide up to about 2 kcal/mol of free energy advantage, effectively making up for the missing third hydrogen bond in the A•T pair compared to G•C, rendering the intrinsic thermodynamic stability of the A•T pair almost synonymous with G•C.

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Section: Results and Discussionmentioning

confidence: 99%

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair

Mak

2024

ACS Phys. Chem Au

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“…CH•••O H-bonding has been debatable; however, quantum studies have characterized them as weaker and with minute directionality than the conventional H-bonds [83]. In structural biology, these bonds were only appreciated about 40 years ago, with immense contributions to the structural integrity of biomolecules, recognition and binding, and catalysis [84,85]. In conclusion, Pandit and colleagues found that two types of complexes exist in each mixture of dilauroylphosphatidylcholine (DLPC): cholesterol and (DPPC): cholesterol, exhibiting stoichiometries of 1:1 and 2:1; however, the DLPC: cholesterol was more populated with species of a 1:1 ratio and vice versa for the DDPC: cholesterol.…”

Section: Computational Tools In the Design Of Liposome-based Drug Del...mentioning

confidence: 99%

Structure-function relationships in the modification of liposomes for targeted drug delivery in infectious diseases

Pamela Seele

2024

Liposomes - A Modern Approach in Research [Working Title]

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The introduction of liposomes has caused a paradigm shift in medicine, offering novel solutions to problems that are ancient to the drug discovery and development for HIV, TB, and malaria. These are the three deadliest infectious diseases that are endowed with complex pathophysiological and biological mechanisms that allow them to thrive in their hosts through escaping the immune system and capturing key pathways. Disease heterogeneity and lack of suitable models to replicate the disease states make compounds the poor pharmacokinetic issues associated with these diseases. Liposomes are lipid-based nanocarriers that are employed for drug formulations, preservation, and storage. Importantly, they can be tailored for targeted and controlled release. Structure–function relationships are crucial to consider in liposome design as they affect key interactions between the carrier drug and the target cell, which impact on drug release, cellular uptake, bioavailability, biodistribution, and toxicity. Herein, lipid composition, size, lamellarity, zeta potential/charge as well as surface modification with cholesterol, PEG, peptides, and antibodies are discussed with respect to selectivity in targeting diseased cells. The role of computational tools in expediting the liposome technology is reviewed, highlighting the impact of forces of interaction between biomolecules and the conditions of the environment.

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“…Evolution can also change the hydrogen bond donor to a weaker variant to attain the same effect, for example replacing O–H with S–H or even acetylenic C–H or other C–H groups (e.g. 109 ). Pharmaceutical chemistry cannot engineer the protein to which the drug has to bind, so modification of proteins by introducing weaker H-bonds is a path open to evolution but not to technology, which is why human industry prefers the use of fluorine as a weak H-bond acceptor.…”

Section: Potential Interdictors Of Fluorine As a Major Component Of B...mentioning

confidence: 99%

Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth

Petkowski,

Seager,

Bains

2024

Sci Rep

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Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C–F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C–F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C–F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth’s biochemistry. C–F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.

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

Cited by 19 publications

References 179 publications

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair

Structure-function relationships in the modification of liposomes for targeted drug delivery in infectious diseases

Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth

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