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Xiong R, Xu L, Tang Y, Cao M, Li H. Identifying the protonation site and the scope of non-proline cis-peptide bond conformations: a first-principles study on protonated oligopeptides. Phys Chem Chem Phys 2023; 25:13989-13998. [PMID: 37194311 DOI: 10.1039/d3cp00690e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The existence of non-proline cis-peptide bond conformations of protonated triglycine proposed by us has been verified through a recent IR-IR double resonance experiment. However, the scope of such unique structures in protonated oligopeptides and whether protonation at amide oxygen is more stable than that at traditional amino nitrogen remain unsolved. In this study, the most stable conformers of a series of protonated oligopeptides were fully searched. Our findings reveal that the special cis-peptide bond structure appears with high energies for diglycine and is energetically less favored for tetra- and pentapeptides, while it acts as the global minimum only for tripeptides. To explore the formation mechanism of the cis-peptide bond, electrostatic potential analysis, and intramolecular interactions were analyzed. Advanced theoretical calculations confirmed that amino nitrogen is still preferred as the protonated site in most cases except glycylalanylglycine(GAG). The energy difference between the two protonated isomers of GAG is only 0.03 kcal mol-1, indicating that the tripeptide is most likely to be protonated on the amide oxygen first. We also conducted chemical (infrared (IR)) and electronic (X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS)) structure calculations of these peptides to identify their notable differences unambiguously. This study thus provides valuable information for exploring the scope of cis-peptide bond conformation and the competition between two different protonated ways.
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Affiliation(s)
- Rui Xiong
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Li Xu
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Yong Tang
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Mengge Cao
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
| | - Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education, Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui, 230601, China.
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Li H, Hua W, Wang Z, Liu A, Jiang J, Luo Y. Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine. J Phys Chem A 2020; 124:2215-2224. [PMID: 32091898 DOI: 10.1021/acs.jpca.9b10756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.
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Affiliation(s)
- Hongbao Li
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weijie Hua
- Department of Applied Physics, School of Science, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Zhiqiang Wang
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China
| | - Axue Liu
- Institutes of Physical Science and Information Technology, Key Laboratory of Structure and Functional Regulation of Hybrid Materials, Ministry of Education. Anhui Graphene Engineering Laboratory, Anhui University, Hefei, Anhui 230601, China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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