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Kelemen ÁA, Perczel A, Horváth D, Jákli I. Amide isomerization pathways: Electronic and structural background of protonation- and deprotonation-mediated cis-trans interconversions. J Chem Phys 2023; 159:154301. [PMID: 37843061 DOI: 10.1063/5.0165772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
The cis-trans isomerization of amide bonds leads to wide range of structural and functional changes in proteins and can easily be the rate-limiting step in folding. The trans isomer is thermodynamically more stable than the cis, nevertheless the cis form can play a role in biopolymers' function. The molecular system of N-methylacetamide · 2H2O is complex enough to reveal energetics of the cis-trans isomerization at coupled cluster single-double and coupled cluster single-double and perturbative triple [CCSD(T)] levels of theory. The cis-trans isomerization cannot be oversimplified by a rotation along ω, since this rotation is coupled with the N-atom pyramidal inversion, requesting the introduction of a second dihedral angle "α." Full f(ω,α) potential energy surfaces of the different amide protonation states, critical points and isomerization reaction paths were determined, and the barriers of the neutral, O-protonated and N-deprotonated amides were found too high to allow cis-trans interconversion at room temperature: ∼85, ∼140, and ∼110 kJ mol-1, respectively. For the N-protonated amide bond, the cis form (ω = 0°) is a maximum rather than a minimum, and each ω state is accessible for less than ∼10 kJ mol-1. Here we outline a cis-trans isomerization pathway with a previously undescribed low energy transition state, which suggests that the proton is transferred from the more favorable O- to the N-protonation site with the aid of nearby water molecules, allowing the trans → cis transition to occur at an energy cost of ≤11.6 kJ mol-1. Our results help to explain why isomerase enzymes operate via protonated amide bonds and how N-protonation of the peptide bond occurs via O-protonation.
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Affiliation(s)
- Ádám A Kelemen
- HUN-REN-ELTE Protein Modelling Research Group, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- Hevesy György PhD School of Chemistry, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - András Perczel
- HUN-REN-ELTE Protein Modelling Research Group, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Dániel Horváth
- HUN-REN-ELTE Protein Modelling Research Group, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Imre Jákli
- HUN-REN-ELTE Protein Modelling Research Group, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
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Khan AH, Hussmann KR, Powalla D, Hoerner S, Kruusmaa M, Tuhtan JA. An open 3D CFD model for the investigation of flow environments experienced by freshwater fish. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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