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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2O, N, C and sp 3C Unified Atoms with Naphthalene sp 2C Atoms in Water. Biochemistry 2023; 62:2841-2853. [PMID: 37695675 DOI: 10.1021/acs.biochem.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably C═O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. Sp3C-sp3C (hydrophobic), sp3C-sp2C (hydrophobic, CH-π), sp2C-sp2C (hydrophobic, π-π), and sp3C-sp2N interactions are favorable, sp2C-sp2N interactions are neutral, while sp2O-sp2O and sp2N-sp2N self-interactions and sp2O-sp3C interactions are unfavorable. Here, from determinations of favorable effects of 14 amides on naphthalene solubility at 10, 25, and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp2O, sp2N, sp2C, and sp3C unified atoms with aromatic sp2C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp2O-aromatic sp2C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g., lone pair-π), while amide sp3C- and sp2C-aromatic sp2C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes.
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xian Cheng
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally-determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2 O, N, C and sp 3 C Unified Atoms with Naphthalene sp 2 C Atoms in Water. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548600. [PMID: 37503153 PMCID: PMC10370101 DOI: 10.1101/2023.07.12.548600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp 2 atoms of amides, aromatics and other groups occur in protein self-assembly processes including folding, oligomerization and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp 2 O with amide sp 2 N unified atoms (presumably C=O···H-N hydrogen bonds) and amide/aromatic sp 2 C (lone pair-π, n-π * ) are particularly favorable. Sp 3 C-sp 3 C (hydrophobic), sp 3 C-sp 2 C (hydrophobic, CH-π), sp 2 C-sp 2 C (hydrophobic, π-π) and sp 3 C-sp 2 N interactions are favorable, sp 2 C-sp 2 N interactions are neutral, while sp 2 O-sp 2 O and sp 2 N-sp 2 N self-interactions and sp 2 O-sp 3 C interactions are unfavorable. Here, from determinations of favorable effects of fourteen amides on naphthalene solubility at 10, 25 and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp 2 O, sp 2 N, sp 2 C and sp 3 C unified atoms with aromatic sp 2 C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp 2 O-aromatic sp 2 C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g. lone pair-π) while amide sp 3 C- and sp 2 C-aromatic sp 2 C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp 2 atoms in protein processes. Table of Contents Graphic
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Irina A. Shkel
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Xian Cheng
- Biophysics Program, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - M. Thomas Record
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
- Biophysics Program, University of Wisconsin – Madison, Madison, Wisconsin 53706
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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Sieg JP, McKinley LN, Huot MJ, Yennawar NH, Bevilacqua PC. The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability. Biochemistry 2022; 61:2579-2591. [PMID: 36306436 PMCID: PMC9669196 DOI: 10.1021/acs.biochem.2c00488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the complex network of interactions among RNA, the metabolome, and divalent Mg2+ under conditions that mimic the Escherichia coli cytoplasm. We determined Mg2+ binding constants for the top 15 E. coli metabolites, comprising 80% of the metabolome by concentration at physiological pH and monovalent ion concentrations. These data were used to inform the development of an artificial cytoplasm that mimics in vivo E. coli conditions, which we term "Eco80". We empirically determined that the mixture of E. coli metabolites in Eco80 approximated single-site binding behavior toward Mg2+ in the biologically relevant free Mg2+ range of ∼0.5 to 3 mM Mg2+, using a Mg2+-sensitive fluorescent dye. Effects of Eco80 conditions on the thermodynamic stability, chemical stability, structure, and catalysis of RNA were examined. We found that Eco80 conditions lead to opposing effects on the thermodynamic and chemical stabilities of RNA. In particular, the thermodynamic stability of RNA helices was weakened by 0.69 ± 0.12 kcal/mol, while the chemical stability was enhanced ∼2-fold, which can be understood using the speciation of Mg2+ between weak and strong Mg2+-metabolite complexes in Eco80. Overall, the use of Eco80 reflects RNA function in vivo and enhances the biological relevance of mechanistic studies of RNA.
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Affiliation(s)
- Jacob P. Sieg
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Lauren N. McKinley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Melanie J. Huot
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - Neela H. Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
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Cheng X, Shkel IA, O'Connor K, Record MT. Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water. Proc Natl Acad Sci U S A 2020; 117:27339-27345. [PMID: 33087561 PMCID: PMC7959557 DOI: 10.1073/pnas.2012481117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Folding and other protein self-assembly processes are driven by favorable interactions between O, N, and C unified atoms of the polypeptide backbone and side chains. These processes are perturbed by solutes that interact with these atoms differently than water does. Amide NH···O=C hydrogen bonding and various π-system interactions have been better characterized structurally or by simulations than experimentally in water, and unfavorable interactions are relatively uncharacterized. To address this situation, we previously quantified interactions of alkyl ureas with amide and aromatic compounds, relative to interactions with water. Analysis yielded strengths of interaction of each alkylurea with unit areas of different hybridization states of unified O, N, and C atoms of amide and aromatic compounds. Here, by osmometry, we quantify interactions of 10 pairs of amides selected to complete this dataset. An analysis yields intrinsic strengths of six favorable and four unfavorable atom-atom interactions, expressed per unit area of each atom and relative to interactions with water. The most favorable interactions are sp2O-sp2C (lone pair-π, presumably n-π*), sp2C-sp2C (π-π and/or hydrophobic), sp2O-sp2N (hydrogen bonding) and sp3C-sp2C (CH-π and/or hydrophobic). Interactions of sp3C with itself (hydrophobic) and with sp2N are modestly favorable, while sp2N interactions with sp2N and with amide/aromatic sp2C are modestly unfavorable. Amide sp2O-sp2O interactions and sp2O-sp3C interactions are more unfavorable, indicating the preference of amide sp2O to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, N-ethylpyrrolidone [NEP], and polyvinylpyrrolidone [PVP]) on protein stability.
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Affiliation(s)
- Xian Cheng
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Kevin O'Connor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - M Thomas Record
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706;
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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Hadži S, Lah J. Origin of heat capacity increment in DNA folding: The hydration effect. Biochim Biophys Acta Gen Subj 2020; 1865:129774. [PMID: 33164852 DOI: 10.1016/j.bbagen.2020.129774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Understanding DNA folding thermodynamics is crucial for prediction of DNA thermal stability. It is now well established that DNA folding is accompanied by a decrease of the heat capacity ∆cp, F, however its molecular origin is not understood. In analogy to protein folding it has been assumed that this is due to dehydration of DNA constituents, however no evidence exists to support this conclusion. METHODS Here we analyze partial molar heat capacity of nucleic bases and nucleosides in aqueous solutions obtained from calorimetric experiments and calculate the hydration heat capacity contribution ∆cphyd. RESULTS We present hydration heat capacity contributions of DNA constituents and show that they correlate with the solvent accessible surface area. The average contribution for nucleic base dehydration is +0.56 J mol-1 K-1 Å-2 and can be used to estimate the ∆cp, F contribution for DNA folding. CONCLUSIONS We show that dehydration is one of the major sources contributing to the observed ∆cp, F increment in DNA folding. Other possible sources contributing to the overall ∆cp, F should be significant but appear to compensate each other to high degree. The calculated ∆cphyd for duplexes and noncanonical DNA structures agree excellently with the overall experimental ∆cp, F values. By contrast, empirical parametrizations developed for proteins result in poor ∆cphyd predictions and should not be applied to DNA folding. GENERAL SIGNIFICANCE Heat capacity is one of the main thermodynamic quantities that strongly affects thermal stability of macromolecules. At the molecular level the heat capacity in DNA folding stems from removal of water from nucleobases.
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Affiliation(s)
- S Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - J Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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