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Nishikawa K, Tanaka H, Kuwahata K, Tachikawa M, Udagawa T. Nuclear quantum effects on the intramolecular hydrogen bonds in biuret and biguanide. Phys Chem Chem Phys 2024; 26:24364-24369. [PMID: 39258336 DOI: 10.1039/d4cp02047b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
We focus on the unique aspects of biuret and biguanide, which form six-membered ring structures via intramolecular hydrogen bonds. The proton donor and acceptor atoms differ between biuret and biguanide, leading to varying energy barrier heights for proton transfer. We performed path integral molecular dynamics (PIMD) simulations for biuret and biguanide to investigate the correlation between proton transfer and the degree of the delocalization of π-electrons in the six-membered ring framework structure. The results indicate that the π-electrons in the framework structure are delocalized regardless of the ease of intramolecular proton transfer.
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Affiliation(s)
- Kotomi Nishikawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
| | - Hikaru Tanaka
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
| | - Kazuaki Kuwahata
- Tokyo Tech Academy for Convergence of Materials and Informatics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masanori Tachikawa
- Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
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Kumar P, Agarwal PK, Cuneo MJ. On the Case of the Misplaced Hydrogens. Chembiochem 2021; 22:288-297. [PMID: 32706524 PMCID: PMC7952024 DOI: 10.1002/cbic.202000376] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Indexed: 12/30/2022]
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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Thomson B, Both J, Wu Y, Parrish RM, Martínez TJ, Boxer SG. Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. J Phys Chem B 2019; 123:4844-4849. [PMID: 31117606 PMCID: PMC7061054 DOI: 10.1021/acs.jpcb.9b01571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.
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Affiliation(s)
| | | | | | - Robert M. Parrish
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Shibazaki C, Arai S, Shimizu R, Saeki M, Kinoshita T, Ostermann A, Schrader TE, Kurosaki Y, Sunami T, Kuroki R, Adachi M. Hydration Structures of the Human Protein Kinase CK2α Clarified by Joint Neutron and X-ray Crystallography. J Mol Biol 2018; 430:5094-5104. [DOI: 10.1016/j.jmb.2018.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
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Yonezawa K, Shimizu N, Kurihara K, Yamazaki Y, Kamikubo H, Kataoka M. Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal. Sci Rep 2017; 7:9361. [PMID: 28839266 PMCID: PMC5570954 DOI: 10.1038/s41598-017-09718-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/28/2017] [Indexed: 11/09/2022] Open
Abstract
Because of its high pKa, arginine (Arg) is believed to be protonated even in the hydrophobic environment of the protein interior. However, our neutron crystallographic structure of photoactive yellow protein, a light sensor, demonstrated that Arg52 adopts an electrically neutral form. We also showed that the hydrogen bond between the chromophore and Glu46 is a so-called low barrier hydrogen bond (LBHB). Because both the neutral Arg and LBHB are unusual in proteins, these observations remain controversial. To validate our findings, we carried out neutron crystallographic analysis of the E46Q mutant of PYP. The resultant structure revealed that the proportion of the cationic form is higher in E46Q than in WT, although the cationic and neutral forms of Arg52 coexist in E46Q. These observations were confirmed by the occupancy of the deuterium atom bound to the N η1 atom combined with an alternative conformation of the N(η2)D2 group comprising sp2 hybridisation. Based on these results, we propose that the formation of the LBHB decreases the proton affinity of Arg52, stabilizing the neutral form in the crystal.
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Affiliation(s)
- Kento Yonezawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Kazuo Kurihara
- National Institutes for Quantum and Radiological Science and Technology (QST), 2-4 Oaza- Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Yoichi Yamazaki
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan. .,Comprehensive Research Organization for Science and Society, Research Center for Neutron Science and Technology, 162-1 Shirakata, Tokai, Ibaraki, 319-1106, Japan.
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Hirano K, Nakano H, Nakao Y, Sato H, Sakaki S. Photo absorption of
p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach. J Comput Chem 2017; 38:1567-1573. [DOI: 10.1002/jcc.24784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/01/2017] [Accepted: 02/22/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Kenji Hirano
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Yoshihide Nakao
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Hirofumi Sato
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering; Kyoto University; Kyoto 615-8510 Japan
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Graen T, Inhester L, Clemens M, Grubmüller H, Groenhof G. The Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution. J Am Chem Soc 2016; 138:16620-16631. [PMID: 27966904 DOI: 10.1021/jacs.6b05609] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There has been considerable debate on the existence of a low-barrier hydrogen bond (LBHB) in the photoactive yellow protein (PYP). The debate was initially triggered by the neutron diffraction study of Yamaguchi et al. ( Proc. Natl. Acad. Sci., U. S. A. , 2009 , 106 , 440 - 444 ) who suggested a model in which a neutral Arg52 residue triggers the formation of the LBHB in PYP. Here, we present an alternative model that is consistent within the error margins of the Yamaguchi structure factors. The model explains an increased hydrogen bond length without nuclear quantum effects and for a protonated Arg52. We tested both models by calculations under crystal, solution, and vacuum conditions. Contrary to the common assumption in the field, we found that a single PYP in vacuum does not provide an accurate description of the crystal conditions but instead introduces strong artifacts, which favor a LBHB and a large 1H NMR chemical shift. Our model of the crystal environment was found to stabilize the two Arg52 hydrogen bonds and crystal water positions for the protonated Arg52 residue in free MD simulations and predicted an Arg52 pKa upshift with respect to PYP in solution. The crystal and solution environments resulted in almost identical 1H chemical shifts that agree with NMR solution data. We also calculated the effect of the Arg52 protonation state on the LBHB in 3D nuclear equilibrium density calculations. Only the charged crystal structure in vacuum supports a LBHB if Arg52 is neutral in PYP at the previously reported level of theory ( J. Am. Chem. Soc. , 2014 , 136 , 3542 - 3552 ). We attribute the anomalies in the interpretation of the neutron data to a shift of the potential minimum, which does not involve nuclear quantum effects and is transferable beyond the Yamaguchi structure.
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Affiliation(s)
- Timo Graen
- Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
| | - Ludger Inhester
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
| | - Maike Clemens
- Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
| | - Gerrit Groenhof
- Department of Chemistry and Nanoscience Center, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylän Yliopisto, Finland
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