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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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Villar JJS, Valdez ARL, Setiadi DH, Csizmadia IG, Viskolcz B, Rágyanszki A. An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.
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Affiliation(s)
- John Justine S. Villar
- Scientific Computing Laboratory, Department of Computer Science, University of the Philippines, Diliman, 1101 Quezon City, Philippines
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | - Adrian Roy L. Valdez
- Scientific Computing Laboratory, Department of Computer Science, University of the Philippines, Diliman, 1101 Quezon City, Philippines
| | - David H. Setiadi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Imre G. Csizmadia
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | - Anita Rágyanszki
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
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Le Donne A, Bodo E. Isomerization patterns and proton transfer in ionic liquids constituents as probed by ab-initio computation. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.11.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Li H, Jiang J, Luo Y. Identification of the protonation site of gaseous triglycine: the cis-peptide bond conformation as the global minimum. Phys Chem Chem Phys 2017; 19:15030-15038. [DOI: 10.1039/c7cp01997a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive ab initio investigations have been performed to characterize stable conformers of protonated triglycine (GGGH) in the gas phase.
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Affiliation(s)
- Hongbao Li
- Hefei National Laboratory for Physical Sciences at the Microscale
- School of Chemistry and Materials Science
- University of Science and Technology of China
- Hefei
- 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
- 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
- China
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Yuan Y, Mills MJL, Popelier PLA, Jensen F. Comprehensive analysis of energy minima of the 20 natural amino acids. J Phys Chem A 2014; 118:7876-91. [PMID: 25084473 DOI: 10.1021/jp503460m] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(═O)-N(H)-(H)Cα(R)-C(═O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of βL, γL, δL, and αL of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-Cα-C(═O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-Cα(HαCβ)-C'(═O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.
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Affiliation(s)
- Yongna Yuan
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester M1 7DN, Great Britain and
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