51
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Zuehlsdorff TJ, Napoli JA, Milanese JM, Markland TE, Isborn CM. Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. J Chem Phys 2018; 149:024107. [PMID: 30007372 DOI: 10.1063/1.5025517] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joel M Milanese
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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52
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Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta Crystallogr D Struct Biol 2018; 74:800-813. [PMID: 30082516 PMCID: PMC6079631 DOI: 10.1107/s2059798318004588] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/19/2018] [Indexed: 11/10/2022] Open
Abstract
The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability. In this study, the deposited data, models and model-to-data fit for all PDB entries that used neutron diffraction as the source of experimental data have been analysed. In many cases, the reported Rwork and Rfree values were not reproducible. In such cases, the model and data files were analysed to identify the reasons for this mismatch. The issues responsible for the discrepancies are summarized and explained. The analysis unveiled limitations to the annotation, deposition and validation of models and data, and a lack of community-wide accepted standards for the description of neutron models and data, as well as deficiencies in current model refinement tools. Most of the issues identified concern the handling of H atoms. Since the primary use of neutron macromolecular crystallography is to locate and directly visualize H atoms, it is important to address these issues, so that the deposited neutron models allow the retrieval of the maximum amount of information with the smallest effort of manual intervention. A path forward to improving the annotation, validation and deposition of neutron models and hybrid X-ray and neutron models is suggested.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul Langan
- Neutron Science Directorate, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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53
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Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, Herschlag D. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. J Am Chem Soc 2018; 140:9827-9843. [DOI: 10.1021/jacs.8b01596] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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54
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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55
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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56
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KOMOTO N, YOSHIKAWA T, ONO J, NAKAI H. Development of the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method for Photoreceptor Protein. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2018. [DOI: 10.2477/jccj.2018-0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nana KOMOTO
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University,3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
| | - Takeshi YOSHIKAWA
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University,3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
| | - Junichi ONO
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
| | - Hiromi NAKAI
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University,3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
- ESICB Kyoto University, Kyotodaigaku-Katsura, Nishigyo-ku, Kyoto, Kyoto 615-8520, JAPAN
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57
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Ito S, Iwaki M, Sugita S, Abe-Yoshizumi R, Iwata T, Inoue K, Kandori H. Unique Hydrogen Bonds in Membrane Protein Monitored by Whole Mid-IR ATR Spectroscopy in Aqueous Solution. J Phys Chem B 2017; 122:165-170. [PMID: 29215887 DOI: 10.1021/acs.jpcb.7b11064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein function is coupled to its structural changes, for which stimulus-induced difference Fourier-transform infrared (FTIR) spectroscopy is a powerful method. By optimizing the attenuated total reflection (ATR)-FTIR analysis on sodium-pumping rhodopsin KR2 in aqueous solution, we first measured the accurate difference spectra upon sodium binding in the whole IR region (4000-1000 cm-1). The new spectral window allows the analysis of not only the fingerprint region (1800-1000 cm-1) but also the hydrogen-bonding donor region (4000-1800 cm-1), revealing an unusually strong hydrogen bond of Tyr located in the sodium binding site of KR2. Progress in ATR-FTIR difference spectroscopy provides an approach to investigating stimulus-induced structural changes of membrane proteins under physiological aqueous conditions.
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Affiliation(s)
| | | | | | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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58
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Mizutani Y. Time-Resolved Resonance Raman Spectroscopy and Application to Studies on Ultrafast Protein Dynamics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043
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59
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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60
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Wang L, Fried SD, Markland TE. Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. J Phys Chem B 2017; 121:9807-9815. [DOI: 10.1021/acs.jpcb.7b06985] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lu Wang
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Stephen D. Fried
- Medical Research
Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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61
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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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62
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Nakano M, Yoshikawa T, Hirata S, Seino J, Nakai H. Computerized implementation of higher-order electron-correlation methods and their linear-scaling divide-and-conquer extensions. J Comput Chem 2017; 38:2520-2527. [PMID: 28795766 DOI: 10.1002/jcc.24912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/28/2017] [Accepted: 07/25/2017] [Indexed: 11/11/2022]
Abstract
We have implemented a linear-scaling divide-and-conquer (DC)-based higher-order coupled-cluster (CC) and Møller-Plesset perturbation theories (MPPT) as well as their combinations automatically by means of the tensor contraction engine, which is a computerized symbolic algebra system. The DC-based energy expressions of the standard CC and MPPT methods and the CC methods augmented with a perturbation correction were proposed for up to high excitation orders [e.g., CCSDTQ, MP4, and CCSD(2)TQ ]. The numerical assessment for hydrogen halide chains, polyene chains, and first coordination sphere (C1) model of photoactive yellow protein has revealed that the DC-based correlation methods provide reliable correlation energies with significantly less computational cost than that of the conventional implementations. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Masahiko Nakano
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Takeshi Yoshikawa
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801.,CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Junji Seino
- Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.,CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.,Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.,ESICB, Kyoto University, Kyoto, 615-8520, Japan
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63
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Oktaviani NA, Pool TJ, Yoshimura Y, Kamikubo H, Scheek RM, Kataoka M, Mulder FAA. Active-Site pKa Determination for Photoactive Yellow Protein Rationalizes Slow Ground-State Recovery. Biophys J 2017; 112:2109-2116. [PMID: 28538148 DOI: 10.1016/j.bpj.2017.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 11/16/2022] Open
Abstract
The ability to avoid blue-light radiation is crucial for bacteria to survive. In Halorhodospira halophila, the putative receptor for this response is known as photoactive yellow protein (PYP). Its response to blue light is mediated by changes in the optical properties of the chromophore para-coumaric acid (pCA) in the protein active site. PYP displays photocycle kinetics with a strong pH dependence for ground-state recovery, which has remained enigmatic. To resolve this problem, a comprehensive pKa determination of the active-site residues of PYP is required. Herein, we show that Glu-46 stays protonated from pH 3.4 to pH 11.4 in the ground (pG) state. This conclusion is supported by the observed hydrogen-bonded protons between Glu-46 and pCA and Tyr-42 and pCA, which are persistent over the entire pH range. Our experimental results show that none of the active-site residues of PYP undergo pH-induced changes in the pG state. Ineluctably, the pH dependence of pG recovery is linked to conformational change that is dependent upon the population of the relevant protonation state of Glu-46 and the pCA chromophore in the excited state, collaterally explaining why pG recovery is slow.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Trijntje J Pool
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Ruud M Scheek
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Frans A A Mulder
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, the Netherlands; Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark.
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64
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Hiromoto T, Meilleur F, Shimizu R, Shibazaki C, Adachi M, Tamada T, Kuroki R. Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type. Protein Sci 2017; 26:1953-1963. [PMID: 28707339 PMCID: PMC5606550 DOI: 10.1002/pro.3230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 11/23/2022]
Abstract
T4 phage lysozyme is an inverting glycoside hydrolase that degrades the murein of bacterial cell walls by cleaving the β‐1,4‐glycosidic bond. The substitution of the catalytic Thr26 residue to a histidine converts the wild type from an inverting to a retaining enzyme, which implies that the original general acid Glu11 can also act as an acid/base catalyst in the hydrolysis. Here, we have determined the neutron structure of the perdeuterated T26H mutant to clarify the protonation states of Glu11 and the substituted His26, which are key in the retaining reaction. The 2.09‐Å resolution structure shows that the imidazole group of His26 is in its singly protonated form in the active site, suggesting that the deprotonated Nɛ2 atom of His26 can attack the anomeric carbon of bound substrate as a nucleophile. The carboxyl group of Glu11 is partially protonated and interacts with the unusual neutral state of the guanidine moiety of Arg145, as well as two heavy water molecules. Considering that one of the water‐binding sites has the potential to be occupied by a hydronium ion, the bulk solvent could be the source for the protonation of Glu11. The respective protonation states of Glu11 and His26 are consistent with the bond lengths determined by an unrestrained refinement of the high‐resolution X‐ray structure of T26H at 1.04‐Å resolution. The detail structural information, including the coordinates of the deuterium atoms in the active site, provides insight into the distinctively different catalytic activities of the mutant and wild type enzymes. PDB Code(s): 5XPE; 5XPF
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Affiliation(s)
- Takeshi Hiromoto
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Rumi Shimizu
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Chie Shibazaki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Taro Tamada
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Ryota Kuroki
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan
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65
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Oksanen E, Chen JCH, Fisher SZ. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules. Molecules 2017; 22:molecules22040596. [PMID: 28387738 PMCID: PMC6154725 DOI: 10.3390/molecules22040596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/21/2022] Open
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
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Affiliation(s)
- Esko Oksanen
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39, 22362 Lund, Sweden.
| | - Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Suzanne Zoë Fisher
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
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66
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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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67
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Probing the early stages of photoreception in photoactive yellow protein with ultrafast time-domain Raman spectroscopy. Nat Chem 2017. [PMID: 28644485 DOI: 10.1038/nchem.2717] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Unveiling the nuclear motions of photoreceptor proteins in action is a crucial goal in protein science in order to understand their elaborate mechanisms and how they achieve optimal selectivity and efficiency. Previous studies have provided detailed information on the structures of intermediates that appear during the later stages (>ns) of such photoreception cycles, yet the initial events immediately after photoabsorption remain unclear because of experimental challenges in monitoring nuclear rearrangements on ultrafast timescales, including protein-specific low-frequency motions. Using time-domain Raman probing with sub-7-fs pulses, we obtain snapshot vibrational spectra of photoactive yellow protein and a mutant with high sensitivity, providing insights into the key responses that drive photoreception. Our data show a drastic intensity drop of the excited-state marker band at 135 cm-1 within a few hundred femtoseconds, suggesting a rapid weakening of the hydrogen bond that anchors the chromophore. We also track formation of the first ground-state intermediate over the first few picoseconds and fully characterize its vibrational structure, revealing a substantially-twisted cis conformation.
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68
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Yang C, Kim SO, Kim Y, Yun SR, Choi J, Ihee H. Photocycle of Photoactive Yellow Protein in Cell-Mimetic Environments: Molecular Volume Changes and Kinetics. J Phys Chem B 2017; 121:769-779. [PMID: 28058827 DOI: 10.1021/acs.jpcb.6b13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using various spectroscopic techniques such as UV-visible spectroscopy, circular dichroism spectroscopy, NMR spectroscopy, small-angle X-ray scattering, transient grating, and transient absorption techniques, we investigated how cell-mimetic environments made by crowding influence the photocycle of photoactive yellow protein (PYP) in terms of the molecular volume change and kinetics. Upon addition of molecular crowding agents, the ratio of the diffusion coefficient of the blue-shifted intermediate (pB) to that of the ground species (pG) significantly changes from 0.92 and approaches 1.0. This result indicates that the molecular volume change accompanied by the photocycle of PYP in molecularly crowded environments is much smaller than that which occurs in vitro and that the pB intermediate under crowded environments favors a compact conformation due to the excluded volume effect. The kinetics of the photocycle of PYP in cell-mimetic environments is greatly decelerated by the dehydration, owing to the interaction between the protein and small crowding agents, but is barely affected by the excluded volume effect. The results lead to the inference that the signaling transducer of PYP may not necessarily utilize the conformational change of PYP to sense the signaling state.
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Affiliation(s)
- Cheolhee Yang
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Seong Ok Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Yonggwan Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - So Ri Yun
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Jungkweon Choi
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science , Daejeon 305-701, Republic of Korea.,Department of Chemistry, KAIST , Daejeon 305-701, Republic of Korea
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69
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An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase. Sci Rep 2017; 7:40517. [PMID: 28098177 PMCID: PMC5241826 DOI: 10.1038/srep40517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023] Open
Abstract
The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.
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70
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Lin J, Pozharski E, Wilson MA. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry 2017; 56:391-402. [PMID: 27989121 PMCID: PMC5805389 DOI: 10.1021/acs.biochem.6b00906] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.
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Affiliation(s)
- Jiusheng Lin
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, 21201,Institute for Bioscience and Biotechnology Research, Rockville, MD 20850,To whom correspondence can be addressed: Edwin Pozharski: or Mark A. Wilson:
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588,To whom correspondence can be addressed: Edwin Pozharski: or Mark A. Wilson:
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71
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Yoshimura Y, Oktaviani NA, Yonezawa K, Kamikubo H, Mulder FAA. Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
| | - Kento Yonezawa
- Graduate School of Materials Science Nara Institute of Science and Technology, Ikoma, Nara Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science Nara Institute of Science and Technology, Ikoma, Nara Japan
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
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72
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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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73
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Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. Biophys J 2016; 110:1346-54. [PMID: 27028644 DOI: 10.1016/j.bpj.2016.01.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 11/21/2022] Open
Abstract
Bacterial pathogens or cancer cells can acquire multidrug resistance, which causes serious clinical problems. In cells with multidrug resistance, various drugs or antibiotics are extruded across the cell membrane by multidrug transporters. The multidrug and toxic compound extrusion (MATE) transporter is one of the five families of multidrug transporters. MATE from Pyrococcus furiosus uses H(+) to transport a substrate from the cytoplasm to the outside of a cell. Crystal structures of MATE from P. furiosus provide essential information on the relevant H(+)-binding sites (D41 and D184). Hybrid quantum mechanical/molecular mechanical simulations and continuum electrostatic calculations on the crystal structures predict that D41 is protonated in one structure (Straight) and, both D41 and D184 protonated in another (Bent). All-atom molecular dynamics simulations suggest a dynamic equilibrium between the protonation states of the two aspartic acids and that the protonation state affects hydration in the substrate binding cavity and lipid intrusion in the cleft between the N- and C-lobes. This hypothesis is examined in more detail by quantum mechanical/molecular mechanical calculations on snapshots taken from the molecular dynamics trajectories. We find the possibility of two proton transfer (PT) reactions in Straight: the 1st PT takes place between side-chains D41 and D184 through a transient formation of low-barrier hydrogen bonds and the 2nd through another H(+) from the headgroup of a lipid that intrudes into the cleft resulting in a doubly protonated (both D41 and D184) state. The 1st PT affects the local hydrogen bond network and hydration in the N-lobe cavity, which would impinge on the substrate-binding affinity. The 2nd PT would drive the conformational change from Straight to Bent. This model may be applicable to several prokaryotic H(+)-coupled MATE multidrug transporters with the relevant aspartic acids.
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74
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Yoshimura Y, Oktaviani NA, Yonezawa K, Kamikubo H, Mulder FAA. Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 56:239-242. [PMID: 27897362 DOI: 10.1002/anie.201609605] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/09/2022]
Abstract
Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a 13 C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the 15 Nη and 15 Nϵ chemical shifts of an arginine head group are correlated with that of the directly attached 13 Cζ . In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the 15 N-1 H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila. Although only three Hη atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.
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Affiliation(s)
- Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Kento Yonezawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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75
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Mix LT, Kirpich J, Kumauchi M, Ren J, Vengris M, Hoff WD, Larsen DS. Bifurcation in the Ultrafast Dynamics of the Photoactive Yellow Proteins from Leptospira biflexa and Halorhodospira halophila. Biochemistry 2016; 55:6138-6149. [DOI: 10.1021/acs.biochem.6b00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- L. Tyler Mix
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Julia Kirpich
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jie Ren
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Mikas Vengris
- Faculty
of Physics, Laser Research Centre, Vilnius University, Sauletekio
10, LT-10233 Vilnius, Lithuania
| | - Wouter D. Hoff
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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76
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Synthesis, Structure, and Magnetic Properties of New Spin Crossover Fe(II) Complexes Forming Short Hydrogen Bonds with Substituted Dicarboxylic Acids. CRYSTALS 2016. [DOI: 10.3390/cryst6100131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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77
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Taenzler PJ, Sadeghian K, Ochsenfeld C. A Dynamic Equilibrium of Three Hydrogen-Bond Conformers Explains the NMR Spectrum of the Active Site of Photoactive Yellow Protein. J Chem Theory Comput 2016; 12:5170-5178. [DOI: 10.1021/acs.jctc.6b00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Phillip Johannes Taenzler
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
| | - Keyarash Sadeghian
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
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78
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Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. Transient low-barrier hydrogen bond in the photoactive state of green fluorescent protein. Phys Chem Chem Phys 2016; 17:30876-88. [PMID: 25953497 DOI: 10.1039/c5cp01067e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we have analyzed the feasibility of spontaneous proton transfer in GFP at the Franck-Condon region directly after photoexcitation. Computation of a sizeable portion of the potential energy surface at the Franck-Condon region of A the structure shows the process of proton transfer to be unfavorable by 3 kcal mol(-1) in S1 if no further structural relaxation is permitted. The ground vibrational state is found to lie above the potential energy barrier of the proton transfer in both S0 and S1. Expectation values of the geometry reveal that the proton shared between the chromophore and W22, and the proton shared between Ser205 and Glu222 are very close to the center of the respective hydrogen bonds, giving support to the claim that the first transient intermediate detected after photoexcitation (I0*) has characteristics similar to those of a low-barrier hydrogen bond [Di Donato et al., Phys. Chem. Chem. Phys., 2012, 13, 16295]. A quantum dynamical calculation of the evolution in the excited state shows an even larger probability of finding those two protons close to the center compared to in the ground state, but no formation of the proton-transferred product is observed. A QM/MM photoactive state geometry optimization, initiated using a configuration obtained by taking the A minimum and moving the protons to the product side, yields a minimum energy structure with the protons transferred and in which the His148 residue is substantially closer to the now anionic chromophore. These results indicate that: (1) proton transfer is not possible if structural relaxation of the surroundings of the chromophore is prevented; (2) protons H1 and H3 especially are found very close to the point halfway between the donor and acceptor after photoexcitation when the zero-point energy is considered; (3) a geometrical parameter exists (the His148-Cro distance) under which the structure with the protons transferred is not a minimum, and that, if included, should lead to the fluorescing I* structure. The existence of an oscillating stationary state between the reactants and products of the triple proton transfer reaction can explain the dual emission reported for the I0* intermediate of wtGFP.
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Affiliation(s)
- Marc Nadal-Ferret
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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79
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Yang D, Zheng R, Lv J. Hydrogen bonding and excited state properties of the photoexcited hydrogen-bonded (E
)-S
-(2-aminopropyl) 3-(4-hydroxyphenyl)prop-2-enethioate complexes. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Dapeng Yang
- College of Mathematics and Information Science; North China University of Water Resources and Electric Power; Zhengzhou 450045 China
| | - Rui Zheng
- College of Mathematics and Information Science; North China University of Water Resources and Electric Power; Zhengzhou 450045 China
| | - Jian Lv
- College of Mathematics and Information Science; North China University of Water Resources and Electric Power; Zhengzhou 450045 China
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80
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Kanematsu Y, Tachikawa M, Takano Y. Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile. J Comput Chem 2016; 37:2140-5. [PMID: 27349328 DOI: 10.1002/jcc.24438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/20/2016] [Accepted: 05/25/2016] [Indexed: 11/06/2022]
Abstract
The short hydrogen bond between tyrosine Yz and D1-His190 of photosystem II (PSII) was investigated using multicomponent quantum mechanics, where the quantum fluctuation of a hydrogen nucleus was incorporated into electronic structure calculation. Our computation demonstrated that the deuteration for hydrogen in the short hydrogen bond of PSII led to the reduction of the O…N distance. It indicated an inverse Ubbelohde effect typically recognized in strong and symmetric hydrogen-bonding clusters such as FHF(-) and H3O2-. We confirmed that the relation between the geometric isotope effect and the symmetry of the potential energy profile of FHF(-) was reasonably agreed with that of PSII. According to this agreement, the short hydrogen bond in PSII can be regarded as a short strong hydrogen bond. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yusuke Kanematsu
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-Ku, Yokohama, 236-0027, Japan.,Department of biomedical information sciences, Graduate School of Information Sciences, Hiroshima City University, Ozuka-Higashi 3-4-1, Asa-Minami-Ku, Hiroshima, 731-3194, Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-Ku, Yokohama, 236-0027, Japan
| | - Yu Takano
- Department of biomedical information sciences, Graduate School of Information Sciences, Hiroshima City University, Ozuka-Higashi 3-4-1, Asa-Minami-Ku, Hiroshima, 731-3194, Japan
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81
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The use of neutron scattering to determine the functional structure of glycoside hydrolase. Curr Opin Struct Biol 2016; 40:54-61. [PMID: 27494120 DOI: 10.1016/j.sbi.2016.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 11/21/2022]
Abstract
Neutron diffraction provides different information from X-ray diffraction, because neutrons are scattered by atomic nuclei, whereas X-rays are scattered by electrons. One of the key advantages of neutron crystallography is the ability to visualize hydrogen and deuterium atoms, making it possible to observe the protonation state of amino acid residues, hydrogen bonds, networks of water molecules and proton relay pathways in enzymes. But, because of technical difficulties, less than 100 enzyme structures have been evaluated by neutron crystallography to date. In this review, we discuss the advantages and disadvantages of neutron crystallography as a tool to investigate the functional structure of glycoside hydrolases, with some examples.
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82
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Can low-barrier hydrogen bond exist in systems with second row elements? An ab initio path integral molecular dynamics study for deprotonated hydrogen sulfide dimer. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1958-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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83
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O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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84
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Pande K, Hutchison CDM, Groenhof G, Aquila A, Robinson JS, Tenboer J, Basu S, Boutet S, DePonte DP, Liang M, White TA, Zatsepin NA, Yefanov O, Morozov D, Oberthuer D, Gati C, Subramanian G, James D, Zhao Y, Koralek J, Brayshaw J, Kupitz C, Conrad C, Roy-Chowdhury S, Coe JD, Metz M, Xavier PL, Grant TD, Koglin JE, Ketawala G, Fromme R, Šrajer V, Henning R, Spence JCH, Ourmazd A, Schwander P, Weierstall U, Frank M, Fromme P, Barty A, Chapman HN, Moffat K, van Thor JJ, Schmidt M. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 2016; 352:725-9. [PMID: 27151871 DOI: 10.1126/science.aad5081] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 04/05/2016] [Indexed: 11/02/2022]
Abstract
A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
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Affiliation(s)
- Kanupriya Pande
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Andy Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Josef S Robinson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason Tenboer
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Shibom Basu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jennifer Brayshaw
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Chelsie Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse D Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Markus Metz
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Paulraj Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. IMPRS-UFAST, Max Planck Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas D Grant
- Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gihan Ketawala
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Keith Moffat
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Jasper J van Thor
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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85
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Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew Chem Int Ed Engl 2016; 55:4924-7. [PMID: 26958828 DOI: 10.1002/anie.201509989] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/27/2016] [Indexed: 11/11/2022]
Abstract
Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.
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Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Troy Wymore
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Amit Das
- Solid State Physics Division, BARC, Trombay, Mumbai, 400085, India
| | - Chen-Hsiang Shen
- Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin, 71 avenue des Martyrs - CS 20156, 38042, Grenoble Cedex 9, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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86
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Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Troy Wymore
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Amit Das
- Solid State Physics Division; BARC; Trombay Mumbai 400085 India
| | - Chen-Hsiang Shen
- Departments of Chemistry and Biology; Georgia State University; Atlanta GA 30302 USA
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - David A. Keen
- ISIS Facility; Rutherford Appleton Laboratory; Harwell Oxford Didcot OX11 0QX UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group; Institut Laue Langevin; 71 avenue des Martyrs - CS 20156 38042 Grenoble Cedex 9 France
| | - John M. Louis
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health, DHHS; Bethesda MD 20892-0520 USA
| | - Paul Langan
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Irene T. Weber
- Departments of Chemistry and Biology; Georgia State University; Atlanta GA 30302 USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
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87
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Gamiz-Hernandez AP, Kaila VRI. Conversion of light-energy into molecular strain in the photocycle of the photoactive yellow protein. Phys Chem Chem Phys 2016; 18:2802-9. [DOI: 10.1039/c5cp05244k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Photoactive Yellow Protein (PYP) converts light energy into molecular strain, stored in the early pR0-photocycle intermediate.
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Affiliation(s)
| | - Ville R. I. Kaila
- Department Chemie
- Technische Universität München (TUM)
- D-85747 Garching
- Germany
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88
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KAWASHIMA Y, SAWADA K, NAKAJIMA T, TACHIKAWA M. Nuclear Quantum Effect on the Intermolecular Hydrogen Bond of Acetic Acid − phosphorous Acid Anion Cluster: an ab initio Path Integral Molecular Dynamics Study. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yukio KAWASHIMA
- RIKEN Advanced Institute for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe,650-0047 Japan
| | - Keisuke SAWADA
- RIKEN Advanced Institute for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe,650-0047 Japan
| | - Takahito NAKAJIMA
- RIKEN Advanced Institute for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe,650-0047 Japan
| | - Masanori TACHIKAWA
- Graduate School of Nanobioscience, Yokohama City University Seto 22-2, Kanazawa-ku, Yokohama, Japan
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89
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Tamura K, Hayashi S. Role of Bulk Water Environment in Regulation of Functional Hydrogen-Bond Network in Photoactive Yellow Protein. J Phys Chem B 2015; 119:15537-49. [DOI: 10.1021/acs.jpcb.5b07555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Tamura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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90
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Kanematsu Y, Kamikubo H, Kataoka M, Tachikawa M. Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein. Comput Struct Biotechnol J 2015; 14:16-9. [PMID: 27274362 PMCID: PMC4687478 DOI: 10.1016/j.csbj.2015.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 11/16/2022] Open
Abstract
Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21 Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440-4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07 Å. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with O…O distance of 2.47 Å on the equilibrium structure, and that with O…O distance of 2.56 Å on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.
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Affiliation(s)
- Yusuke Kanematsu
- Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan; Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Hironari Kamikubo
- Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mikio Kataoka
- Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
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91
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Kanematsu Y, Tachikawa M. Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme. J Chem Phys 2015; 141:185101. [PMID: 25399161 DOI: 10.1063/1.4900987] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.
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Affiliation(s)
- Yusuke Kanematsu
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
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92
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Hamada N, Tan Z, Kanematsu Y, Inazumi N, Nakamura R. Influence of a chromophore analogue in the protein cage of a photoactive yellow protein. Photochem Photobiol Sci 2015; 14:1722-8. [PMID: 26178816 DOI: 10.1039/c5pp00176e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved spectra of a photoactive yellow protein (PYP) containing cyano-p-coumaric acid (CHCA) were recorded. To understand the mechanism of photo-isomerization, an electron-withdrawing CN group was introduced into the PYP to alter the C[double bond, length as m-dash]C double bond character. Free CHCA chromophores in aqueous solution underwent photo-isomerization whereas PYP with a bound CHCA (PYP-CN) exhibited no photocycle at acidic or alkaline pH or in urea and other solutions. Furthermore, no photocycle was observed with PYP mutants after illumination. This phenomenon cannot be fully explained by the electron-withdrawing properties of the CN group. We conclude that the CHCA chromophore in PYP was locked in the protein cage and that the CN group interacted with the protein residues.
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Affiliation(s)
- Norio Hamada
- Science & Technology Entrepreneurship Laboratory (e-square), Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan.
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93
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White PB, Hong M. (15)N and (1)H Solid-State NMR Investigation of a Canonical Low-Barrier Hydrogen-Bond Compound: 1,8-Bis(dimethylamino)naphthalene. J Phys Chem B 2015; 119:11581-9. [PMID: 26244754 DOI: 10.1021/acs.jpcb.5b06171] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Strong or low-barrier hydrogen bonds have often been proposed in proteins to explain enzyme catalysis and proton-transfer reactions. So far (1)H chemical shifts and scalar couplings have been used as the main NMR spectroscopic signatures for strong H-bonds. In this work, we report simultaneous measurements of (15)N and (1)H chemical shifts and N-H bond lengths by solid-state NMR in (15)N-labeled 1,8-bis(dimethylamino)naphthalene (DMAN), which contains a well-known strong NHN H-bond. We complexed DMAN with three different counteranions to examine the effects of the chemical environment on the H-bond lengths and chemical shifts. All three DMAN compounds exhibit significantly elongated N-H distances compared to the covalent bond length, and the (1)H(N) chemical shifts are larger than ∼17 ppm, consistent with strong NHN H-bonds in the DMAN cation. However, the (15)N and (1)H chemical shifts and the precise N-H distances differ among the three compounds, and the (15)N chemical shifts show opposite dependences on the proton localization from the general trend in organic compounds, indicating the significant effects of the counteranions on the electronic structure of the H-bond. These data provide useful NMR benchmarks for strong H-bonds and caution against the sole reliance on chemical shifts for identifying strong H-bonds in proteins since neighboring side chains can exert influences on chemical shifts similar to those of the bulky organic anions in DMAN. Instead, N-H bond lengths should be measured, in conjunction with chemical shifts, as a more fundamental parameter of H-bond strength.
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Affiliation(s)
- Paul B White
- Department of Chemistry, Massachusetts Institute of Technology , 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology , 170 Albany Street, Cambridge, Massachusetts 02139, United States
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94
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Haraguchi S, Hara M, Shingae T, Kumauchi M, Hoff WD, Unno M. Experimental Detection of the Intrinsic Difference in Raman Optical Activity of a Photoreceptor Protein under Preresonance and Resonance Conditions. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201505466] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shojiro Haraguchi
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840‐8502 (Japan)
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 (USA)
| | - Takahito Shingae
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840‐8502 (Japan)
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 (USA)
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 (USA)
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840‐8502 (Japan)
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95
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Haraguchi S, Hara M, Shingae T, Kumauchi M, Hoff WD, Unno M. Experimental Detection of the Intrinsic Difference in Raman Optical Activity of a Photoreceptor Protein under Preresonance and Resonance Conditions. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505466] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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96
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Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith E, Wang KK, Prati F, Renslo AR, Woodcock HL, Chen Y. Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography. J Am Chem Soc 2015; 137:8086-95. [PMID: 26057252 PMCID: PMC4530788 DOI: 10.1021/jacs.5b00749] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M β-lactamase, directly visualizing protonation state changes along the enzymatic pathway: apo protein at 0.79 Å, precovalent complex with nonelectrophilic ligand at 0.89 Å, and acylation transition state (TS) analogue at 0.84 Å. Binding of the noncovalent ligand induces a proton transfer from the catalytic Ser70 to the negatively charged Glu166, and the formation of a low-barrier hydrogen bond (LBHB) between Ser70 and Lys73, with a length of 2.53 Å and the shared hydrogen equidistant from the heteroatoms. QM/MM reaction path calculations determined the proton transfer barrier to be 1.53 kcal/mol. The LBHB is absent in the other two structures although Glu166 remains neutral in the covalent complex. Our data represents the first X-ray crystallographic example of a hydrogen engaged in an enzymatic LBHB, and demonstrates that desolvation of the active site by ligand binding can provide a protein microenvironment conducive to LBHB formation. It also suggests that LBHBs may contribute to stabilization of the TS in general acid/base catalysis together with other preorganized features of enzyme active sites. These structures reconcile previous experimental results suggesting alternatively Glu166 or Lys73 as the general base for acylation, and underline the importance of considering residue protonation state change when modeling protein-ligand interactions. Additionally, the observation of another LBHB (2.47 Å) between two conserved residues, Asp233 and Asp246, suggests that LBHBs may potentially play a special structural role in proteins.
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Affiliation(s)
- Derek A. Nichols
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
| | | | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - Emmanuel Smith
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
| | - Kenneth K. Wang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620
| | - Yu Chen
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
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97
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Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
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98
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Oltrogge LM, Boxer SG. Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP). ACS CENTRAL SCIENCE 2015; 1:148-56. [PMID: 27162964 PMCID: PMC4827562 DOI: 10.1021/acscentsci.5b00160] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 05/16/2023]
Abstract
Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor-acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy.
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99
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Kumar A, Woolley GA. Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein. Photochem Photobiol 2015; 91:985-91. [PMID: 25946641 DOI: 10.1111/php.12464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/26/2015] [Indexed: 12/11/2022]
Abstract
Numerous single-site mutants of photoactive yellow protein (PYP) from Halorhodospira halophila and as well as PYP homologs from other species exhibit a shoulder on the short wavelength side of the absorbance maximum in their dark-adapted states. The structural basis for the occurrence of this shoulder, called the "intermediate spectral form," has only been investigated in detail for the Y42F mutation. Here we explore the structural basis for occurrence of the intermediate spectral form in a M121E derivative of a circularly permuted H. halophila PYP (M121E-cPYP). The M121 site in M121E-cPYP corresponds to the M100 site in wild-type H. halophila PYP. High-resolution NMR measurements with a salt-tolerant cryoprobe enabled identification of those residues directly affected by increasing concentrations of ammonium chloride, a salt that greatly enhances the fraction of the intermediate spectra form. Residues in the surface loop containing the M121E (M100E) mutation were found to be affected by ammonium chloride as well as a discrete set of residues that link this surface loop to the buried hydroxyl group of the chromophore via a hydrogen bond network. Localized changes in the conformational dynamics of a surface loop can thereby produce structural rearrangements near the buried hydroxyl group chromophore while leaving the large majority of residues in the protein unaffected.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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100
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Kaledhonkar S, Hara M, Stalcup TP, Xie A, Hoff WD. Strong ionic hydrogen bonding causes a spectral isotope effect in photoactive yellow protein. Biophys J 2014; 105:2577-85. [PMID: 24314088 DOI: 10.1016/j.bpj.2013.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/07/2013] [Accepted: 10/16/2013] [Indexed: 10/25/2022] Open
Abstract
Standard hydrogen bonds are of great importance for protein structure and function. Ionic hydrogen bonds often are significantly stronger than standard hydrogen bonds and exhibit unique properties, but their role in proteins is not well understood. We report that hydrogen/deuterium exchange causes a redshift in the visible absorbance spectrum of photoactive yellow protein (PYP). We expand the range of interpretable isotope effects by assigning this spectral isotope effect (SIE) to a functionally important hydrogen bond at the active site of PYP. The inverted sign and extent of this SIE is explained by the ionic nature and strength of this hydrogen bond. These results show the relevance of ionic hydrogen bonding for protein active sites, and reveal that the inverted SIE is a novel, to our knowledge, tool to probe ionic hydrogen bonds. Our results support a classification of hydrogen bonds that distinguishes the properties of ionic hydrogen bonds from those of both standard and low barrier hydrogen bonds, and show how this classification helps resolve a recent debate regarding active site hydrogen bonding in PYP.
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