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Dong HC, Hsu PJ, Kuo JL. Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials. Phys Chem Chem Phys 2024; 26:11126-11139. [PMID: 38530660 DOI: 10.1039/d3cp05659g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.
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Affiliation(s)
- Hieu Cao Dong
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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Otaki H, Ishiuchi SI, Fujii M, Sugita Y, Yagi K. Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Phys Chem Chem Phys 2024; 26:9906-9914. [PMID: 38477212 DOI: 10.1039/d4cp00064a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Vibrational spectroscopy combined with theoretical calculations is a powerful tool for analyzing the interaction and conformation of peptides at the atomistic level. Nonetheless, identifying the structure becomes increasingly difficult as the peptide size grows large. One example is acetyl-SIVSF-N-methylamide, a capped pentapeptide, whose atomistic structure has remained unknown since its first observation [T. Sekiguchi, M. Tamura, H. Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, S. Ishiuchi and M. Fujii, Angew. Chem., Int. Ed., 2018, 57, 5626-5629]. Here, we propose a novel conformational search method, which exploits the structure-spectrum correlation using a similarity score that measures the agreement of theoretical and experimental spectra. Surprisingly, the two conformers have distinctly different energy and geometry. The second conformer is 25 kJ mol-1 higher in energy than the other, lowest-energy conformer. The result implies that there are multiple pathways in the early stage of the folding process: one to the global minimum and the other to a different basin. Once such a structure is established, the second conformer is unlikely to overcome the barrier to produce the most stable structure due to a vastly different hydrogen bond network of the backbone. Our proposed method can characterize the lowest-energy conformer and kinetically trapped, high-energy conformers of complex biomolecules.
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Affiliation(s)
- Hiroki Otaki
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo, Nagasaki, Nagasaki 852-8521, Japan
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Fujii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Ma Z, Chen L, Xu C, Fournier JA. Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions. J Phys Chem Lett 2023; 14:9683-9689. [PMID: 37871134 DOI: 10.1021/acs.jpclett.3c02661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.
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Affiliation(s)
- Zifan Ma
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Liangyi Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Chuzhi Xu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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Vogt E, Langeland J, Kjær C, Lindkvist TT, Kjaergaard HG, Nielsen SB. Effect of Freezing out Vibrational Modes on Gas-Phase Fluorescence Spectra of Small Ionic Dyes. J Phys Chem Lett 2021; 12:11346-11352. [PMID: 34780698 DOI: 10.1021/acs.jpclett.1c03259] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
While action spectroscopy of cold molecular ions is a well-established technique to provide vibrationally resolved absorption features, fluorescence experiments are still challenging. Here we report the fluorescence spectra of pyronin-Y and resorufin ions at 100 K using a newly constructed setup. Spectra narrow upon cooling, and the emission maxima blueshift. Temperature effects are attributed to the population of vibrational excited levels in S1, and that frequencies are lower in S1 than in S0. This picture is supported by calculated spectra based on a Franck-Condon model that not only predicts the observed change in maximum, but also assigns Franck-Condon active vibrations. In-plane vibrational modes that preserve the mirror plane present in both S0 and S1 of resorufin and pyronin Y account for most of the observed vibrational bands. Finally, at low temperatures, it is important to pick an excitation wavelength as far to the red as possible to not reheat the ions.
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Affiliation(s)
- Emil Vogt
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark
| | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus, Denmark
| | | | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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