1
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Hui P, Shi Y, Xu Z, Xu J, Zhu B, Xu L, Liu B, Zhang E. Innovative indenone-derivative colorimetric fluorescent probe: A approach for copper ion detection in water. LUMINESCENCE 2024; 39:e4857. [PMID: 39129422 DOI: 10.1002/bio.4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/13/2024]
Abstract
Copper (Cu2+) is a metal chemical element closely related to human life and is widely used in many fields. However, with the discharge of copper wastewater, the water quality will be seriously affected, leading to excessive intake of Cu2+ and a variety of diseases. Hence, there is a pressing need for an effective detection method for Cu2+ in aqueous environments. Leveraging the remarkable attributes of GFP chromophores and indenone derivatives, we have created a novel colorimetric fluorescent probe P-Cu2+, tailored for efficient copper ion detection. The addition of Cu2+ causes the solution to visibly change from colorless to a pronounced yellow, enabling naked-eye detection and offering promise for real sample analysis.
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Affiliation(s)
- Peichen Hui
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
| | - Yanfeng Shi
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Zhenghe Xu
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
| | - Jing Xu
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
| | - Baocun Zhu
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
| | - Lirong Xu
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
| | - Bowen Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
| | - Erchi Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan, China
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2
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Hassan A, Akram W, Rizwana H, Aftab ZEH, Hanif S, Anjum T, Alwahibi MS. The Imperative Use of Bacillus Consortium and Quercetin Contributes to Suppress Fusarium Wilt Disease by Direct Antagonism and Induced Resistance. Microorganisms 2023; 11:2603. [PMID: 37894261 PMCID: PMC10609423 DOI: 10.3390/microorganisms11102603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Fusarium wilt diseases severely influence the growth and productivity of numerous crop plants. The consortium of antagonistic rhizospheric Bacillus strains and quercetin were evaluated imperatively as a possible remedy to effectively manage the Fusarium wilt disease of tomato plants. The selection of Bacillus strains was made based on in-vitro antagonistic bioassays against Fusarium oxysporum f.sp. lycoprsici (FOL). Quercetin was selected after screening a library of phytochemicals during in-silico molecular docking analysis using tomato LysM receptor kinases "SILKY12" based on its dual role in symbiosis and plant defense responses. After the selection of test materials, pot trials were conducted where tomato plants were provided consortium of Bacillus strains as soil drenching and quercetin as a foliar spray in different concentrations. The combined application of consortium (Bacillus velezensis strain BS6, Bacillus thuringiensis strain BS7, Bacillus fortis strain BS9) and quercetin (1.0 mM) reduced the Fusarium wilt disease index up to 69%, also resulting in increased plant growth attributes. Likewise, the imperative application of the Bacillus consortium and quercetin (1.0 mM) significantly increased total phenolic contents and activities of the enzymes of the phenylpropanoid pathway. Non-targeted metabolomics analysis was performed to investigate the perturbation in metabolites. FOL pathogen negatively affected a range of metabolites including carbohydrates, amino acids, phenylpropanoids, and organic acids. Thereinto, combined treatment of Bacillus consortium and quercetin (1.0 mM) ameliorated the production of different metabolites in tomato plants. These findings prove the imperative use of Bacillus consortium and quercetin as an effective and sustainable remedy to manage Fusarium wilt disease of tomato plants and to promote the growth of tomato plants under pathogen stress conditions.
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Affiliation(s)
- Ali Hassan
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Waheed Akram
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Humaira Rizwana
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Zill-E-Huma Aftab
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Sana Hanif
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Tehmina Anjum
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Mona S Alwahibi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
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3
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Tarai A, Mallick J, Singh P, Conradie J, Kar S, Ghosh A. Free-Base Corrole Anion. J Org Chem 2023; 88:13022-13029. [PMID: 37647416 PMCID: PMC10763984 DOI: 10.1021/acs.joc.3c01125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 09/01/2023]
Abstract
Free-base corroles have long been known to be acidic, readily undergoing deprotonation by mild bases and in polar solvents. The conjugate base, however, has not been structurally characterized until now. Presented here is a first crystal structure of a free-base corrole anion, derived from tris(p-cyanophenyl)corrole, as the tetrabuylammonium salt. The low-temperature (100 K) structure reveals localized hydrogens on a pair of opposite pyrrole nitrogens. DFT calculations identify such a structure as the global minimum but also point to two cis tautomers only 4-7 kcal/mol above the ground state. In terms of free energy, however, the cis tautomers are above or essentially flush with the trans-to-cis barrier so the cis tautomers are unlikely to exist or be observed as true intermediates. Thus, the hydrogen bond within each dipyrrin unit on either side of the molecular pseudo-C2 axis through C10 (i.e., between pyrrole rings A and B or between C and D) qualifies as or closely approaches a low-barrier hydrogen bond. Proton migration across the pseudo-C2 axis entails much higher activation energies >20 kcal/mol, reflecting the relative rigidity of the molecule along the C1-C19 pyrrole-pyrrole linkage.
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Affiliation(s)
- Arup Tarai
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Jyotiprakash Mallick
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Pranjali Singh
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Jeanet Conradie
- Department
of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, Republic
of South Africa
- Department
of Chemistry, UiT − The Arctic University
of Norway, N-9037 Tromsø, Norway
| | - Sanjib Kar
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhubaneswar 752050, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Abhik Ghosh
- Department
of Chemistry, UiT − The Arctic University
of Norway, N-9037 Tromsø, Norway
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4
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Zhou S, Liu Y, Wang S, Wang L. Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds. Sci Rep 2023; 13:13741. [PMID: 37612311 PMCID: PMC10447522 DOI: 10.1038/s41598-023-40614-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
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Affiliation(s)
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
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5
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Chen MS, Mao Y, Snider A, Gupta P, Montoya-Castillo A, Zuehlsdorff TJ, Isborn CM, Markland TE. Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure. J Phys Chem Lett 2023; 14:6610-6619. [PMID: 37459252 DOI: 10.1021/acs.jpclett.3c01444] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. We show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.
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Affiliation(s)
- Michael S Chen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Andrew Snider
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Prachi Gupta
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Andrés Montoya-Castillo
- Department of Chemistry, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, United States
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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6
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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Affiliation(s)
- Vishal
Annasaheb Adhav
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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7
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Perrin CL. Symmetry of Hydrogen Bonds: Application of NMR Method of Isotopic Perturbation and Relevance of Solvatomers. Molecules 2023; 28:molecules28114462. [PMID: 37298938 DOI: 10.3390/molecules28114462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Short, strong, symmetric, low-barrier hydrogen bonds (H-bonds) are thought to be of special significance. We have been searching for symmetric H-bonds by using the NMR technique of isotopic perturbation. Various dicarboxylate monoanions, aldehyde enols, diamines, enamines, acid-base complexes, and two sterically encumbered enols have been investigated. Among all of these, we have found only one example of a symmetric H-bond, in nitromalonamide enol, and all of the others are equilibrating mixtures of tautomers. The nearly universal lack of symmetry is attributed to the presence of these H-bonded species as a mixture of solvatomers, meaning isomers (or stereoisomers or tautomers) that differ in their solvation environment. The disorder of solvation renders the two donor atoms instantaneously inequivalent, whereupon the hydrogen attaches to the less well solvated donor. We therefore conclude that there is no special significance to short, strong, symmetric, low-barrier H-bonds. Moreover, they have no heightened stability or else they would have been more prevalent.
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Affiliation(s)
- Charles L Perrin
- Department of Chemistry & Biochemistry University of California, La Jolla, San Diego, CA 92093, USA
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8
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Zhou S, Liu Y, Wang S, Wang L. Chemical Features and Machine Learning Assisted Predictions of Protein-Ligand Short Hydrogen Bonds. RESEARCH SQUARE 2023:rs.3.rs-2895170. [PMID: 37292822 PMCID: PMC10246099 DOI: 10.21203/rs.3.rs-2895170/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 A closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
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Affiliation(s)
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
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9
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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10
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True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat Struct Mol Biol 2022; 29:440-450. [PMID: 35484235 DOI: 10.1038/s41594-022-00762-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/14/2022] [Indexed: 12/21/2022]
Abstract
Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.
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11
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Mohamed HI, Gao C, Gui Z, Song Z, Wei D. A novel fluorescent probe with a pyrazolo[4,3- c]quinoline core selectively recognizes c-MYC promoter G-quadruplexes. NEW J CHEM 2022. [DOI: 10.1039/d1nj00098e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer combined with a c-MYC-selective fluorophore could work as the fluorescent core of nucleic acid mimics of fluorescent proteins to locate and image functional biomolecules in cells.
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Affiliation(s)
- Hany I. Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Chao Gao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhikun Gui
- College of Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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12
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Nunthaboot N, Tanaka F, Borst JW, Visser AJ. Simultaneous analyses of fluorescence decay and anisotropy decay in green fluorescent protein dimer from jellyfish Clytia gregaria: FRET and molecular dynamics simulation. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Xu S, Pan W, Ren T, Huan S, Yuan L, Zhang X. Molecular Engineering of Novel Fluorophores for
High‐Contrast
Bioimaging. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shuai Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Wenjing Pan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Tian‐Bing Ren
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Shuang‐Yan Huan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Lin Yuan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Xiao‐Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
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14
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Chen C, Tutol JN, Tang L, Zhu L, Ong WSY, Dodani SC, Fang C. Excitation ratiometric chloride sensing in a standalone yellow fluorescent protein is powered by the interplay between proton transfer and conformational reorganization. Chem Sci 2021; 12:11382-11393. [PMID: 34667546 PMCID: PMC8447875 DOI: 10.1039/d1sc00847a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Natural and laboratory-guided evolution has created a rich diversity of fluorescent protein (FP)-based sensors for chloride (Cl−). To date, such sensors have been limited to the Aequorea victoria green fluorescent protein (avGFP) family, and fusions with other FPs have unlocked ratiometric imaging applications. Recently, we identified the yellow fluorescent protein from jellyfish Phialidium sp. (phiYFP) as a fluorescent turn-on, self-ratiometric Cl− sensor. To elucidate its working mechanism as a rare example of a single FP with this capability, we tracked the excited-state dynamics of phiYFP using femtosecond transient absorption (fs-TA) spectroscopy and target analysis. The photoexcited neutral chromophore undergoes bifurcated pathways with the twisting-motion-induced nonradiative decay and barrierless excited-state proton transfer. The latter pathway yields a weakly fluorescent anionic intermediate , followed by the formation of a red-shifted fluorescent state that enables the ratiometric response on the tens of picoseconds timescale. The redshift results from the optimized π–π stacking between chromophore Y66 and nearby Y203, an ultrafast molecular event. The anion binding leads to an increase of the chromophore pKa and ESPT population, and the hindrance of conversion. The interplay between these two effects determines the turn-on fluorescence response to halides such as Cl− but turn-off response to other anions such as nitrate as governed by different binding affinities. These deep mechanistic insights lay the foundation for guiding the targeted engineering of phiYFP and its derivatives for ratiometric imaging of cellular chloride with high selectivity. We discovered an interplay between proton transfer and conformational reorganization that powers a standalone fluorescent-protein-based excitation-ratiometric biosensor for chloride imaging.![]()
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| | - Jasmine N Tutol
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA https://lab.utdallas.edu/dodani/
| | - Longteng Tang
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
| | - Whitney S Y Ong
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA https://lab.utdallas.edu/dodani/
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA https://lab.utdallas.edu/dodani/
| | - Chong Fang
- Department of Chemistry, Oregon State University 153 Gilbert Hall Corvallis OR 97331-4003 USA https://fanglab.oregonstate.edu/
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15
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Gleason PR, Kolbaba-Kartchner B, Henderson JN, Stahl EP, Simmons CR, Mills JH. Structural Origins of Altered Spectroscopic Properties upon Ligand Binding in Proteins Containing a Fluorescent Noncanonical Amino Acid. Biochemistry 2021; 60:2577-2585. [PMID: 34415744 DOI: 10.1021/acs.biochem.1c00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent noncanonical amino acids (fNCAAs) could serve as starting points for the rational design of protein-based fluorescent sensors of biological activity. However, efforts toward this goal are likely hampered by a lack of atomic-level characterization of fNCAAs within proteins. Here, we describe the spectroscopic and structural characterization of five streptavidin mutants that contain the fNCAA l-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) at sites proximal to the binding site of its substrate, biotin. Many of the mutants exhibited altered fluorescence spectra in response to biotin binding, which included both increases and decreases in fluorescence intensity as well as red- or blue-shifted emission maxima. Structural data were also obtained for three of the five mutants. The crystal structures shed light on interactions between 7-HCAA and functional groups, contributed either by the protein or by the substrate, that may be responsible for the observed changes in the 7-HCAA spectra. These data could be used in future studies aimed at the rational design of fluorescent, protein-based sensors of small molecule binding or dissociation.
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16
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Langeland J, Persen NW, Gruber E, Kiefer HV, Kabylda AM, Bochenkova AV, Andersen LH. Controlling Light-Induced Proton Transfer from the GFP Chromophore. Chemphyschem 2021; 22:833-841. [PMID: 33591586 DOI: 10.1002/cphc.202100068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Green Fluorescent Protein (GFP) is known to undergo excited-state proton transfer (ESPT). Formation of a short H-bond favors ultrafast ESPT in GFP-like proteins, such as the GFP S65T/H148D mutant, but the detailed mechanism and its quantum nature remain to be resolved. Here we study in vacuo, light-induced proton transfer from the GFP chromophore in hydrogen-bonded complexes with two anionic proton acceptors, I- and deprotonated trichloroacetic acid (TCA- ). We address the role of the strong H-bond and the quantum mechanical proton-density distribution in the excited state, which determines the proton-transfer probability. Our study shows that chemical modifications to the molecular network drastically change the proton-transfer probability and it can become strongly wavelength dependent. The proton-transfer branching ratio is found to be 60 % for the TCA complex and 10 % for the iodide complex, being highly dependent on the photon energy in the latter case. Using high-level ab initio calculations, we show that light-induced proton transfer takes place in S1 , revealing intrinsic photoacid properties of the isolated GFP chromophore in strongly bound H-bonded complexes. ESPT is found to be very sensitive to the topography of the highly anharmonic potential in S1 , depending on the quantum-density distribution upon vibrational excitation. We also show that the S1 potential-energy surface, and hence excited-state proton transfer, can be controlled by altering the chromophore microenvironment.
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Affiliation(s)
- Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Natascha W Persen
- Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Elisabeth Gruber
- Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Hjalte V Kiefer
- Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Adil M Kabylda
- Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | | | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, DK-8000, Aarhus C, Denmark
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17
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Kumar P, Agarwal PK, Cuneo MJ. On the Case of the Misplaced Hydrogens. Chembiochem 2021; 22:288-297. [PMID: 32706524 PMCID: PMC7952024 DOI: 10.1002/cbic.202000376] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Indexed: 12/30/2022]
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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18
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Dereka B, Yu Q, Lewis NHC, Carpenter WB, Bowman JM, Tokmakoff A. Crossover from hydrogen to chemical bonding. Science 2021; 371:160-164. [DOI: 10.1126/science.abe1951] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/20/2020] [Indexed: 11/02/2022]
Affiliation(s)
- Bogdan Dereka
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Qi Yu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Nicholas H. C. Lewis
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - William B. Carpenter
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
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19
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Tang L, Zhang S, Zhao Y, Rozanov ND, Zhu L, Wu J, Campbell RE, Fang C. Switching between Ultrafast Pathways Enables a Green-Red Emission Ratiometric Fluorescent-Protein-Based Ca 2+ Biosensor. Int J Mol Sci 2021; 22:E445. [PMID: 33466257 PMCID: PMC7794744 DOI: 10.3390/ijms22010445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 01/25/2023] Open
Abstract
Ratiometric indicators with long emission wavelengths are highly preferred in modern bioimaging and life sciences. Herein, we elucidated the working mechanism of a standalone red fluorescent protein (FP)-based Ca2+ biosensor, REX-GECO1, using a series of spectroscopic and computational methods. Upon 480 nm photoexcitation, the Ca2+-free biosensor chromophore becomes trapped in an excited dark state. Binding with Ca2+ switches the route to ultrafast excited-state proton transfer through a short hydrogen bond to an adjacent Glu80 residue, which is key for the biosensor's functionality. Inspired by the 2D-fluorescence map, REX-GECO1 for Ca2+ imaging in the ionomycin-treated human HeLa cells was achieved for the first time with a red/green emission ratio change (ΔR/R0) of ~300%, outperforming many FRET- and single FP-based indicators. These spectroscopy-driven discoveries enable targeted design for the next-generation biosensors with larger dynamic range and longer emission wavelengths.
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Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
| | - Shuce Zhang
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
| | - Yufeng Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
| | - Nikita D. Rozanov
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
| | - Jiahui Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (S.Z.); (Y.Z.); (J.W.); or
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA; (L.T.); (N.D.R.); (L.Z.)
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20
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Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2021; 1869:140557. [PMID: 33148530 PMCID: PMC7736181 DOI: 10.1016/j.bbapap.2020.140557] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023]
Abstract
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States.
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21
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Lin CY, Boxer SG. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. J Phys Chem B 2020; 124:9513-9525. [DOI: 10.1021/acs.jpcb.0c07730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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22
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Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail. Angew Chem Int Ed Engl 2020; 59:18619-18626. [PMID: 32533629 DOI: 10.1002/anie.202005505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 11/08/2022]
Abstract
DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.
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Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
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23
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Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chad R. Simmons
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
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24
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Romei MG, Lin CY, Boxer SG. Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms. J Photochem Photobiol A Chem 2020; 401. [PMID: 32753830 PMCID: PMC7402594 DOI: 10.1016/j.jphotochem.2020.112738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. Here we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore's photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-theart time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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25
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Oscar BG, Zhu L, Wolfendeen H, Rozanov ND, Chang A, Stout KT, Sandwisch JW, Porter JJ, Mehl RA, Fang C. Dissecting Optical Response and Molecular Structure of Fluorescent Proteins With Non-canonical Chromophores. Front Mol Biosci 2020; 7:131. [PMID: 32733917 PMCID: PMC7358599 DOI: 10.3389/fmolb.2020.00131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/02/2020] [Indexed: 12/21/2022] Open
Abstract
Tracking the structural dynamics of fluorescent protein chromophores holds the key to unlocking the fluorescence mechanisms in real time and enabling rational design principles of these powerful and versatile bioimaging probes. By combining recent chemical biology and ultrafast spectroscopy advances, we prepared the superfolder green fluorescent protein (sfGFP) and its non-canonical amino acid (ncAA) derivatives with a single chlorine, bromine, and nitro substituent at the ortho site to the phenolate oxygen of the embedded chromophore, and characterized them using an integrated toolset of femtosecond transient absorption and tunable femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations of the vibrational normal modes. A dominant vibrational cooling time constant of ~4 and 11 ps is revealed in Cl-GFP and Br-GFP, respectively, facilitating a ~30 and 12% increase of the fluorescent quantum yield vs. the parent sfGFP. Similar time constants were also retrieved from the transient absorption spectra, substantiating the correlated electronic and vibrational motions on the intrinsic molecular timescales. Key carbon-halogen stretching motions coupled with phenolate ring motions of the deprotonated chromophores at ca. 908 and 890 cm-1 in Cl-GFP and Br-GFP exhibit enhanced activities in the electronic excited state and blue-shift during a distinct vibrational cooling process on the ps timescale. The retrieved structural dynamics change due to targeted site-specific halogenation of the chromophore thus provides an effective means to design new GFP derivatives and enrich the bioimaging probe toolset for life and medical sciences.
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Affiliation(s)
- Breland G. Oscar
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Hayati Wolfendeen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| | - Nikita D. Rozanov
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR, United States
| | - Alvin Chang
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR, United States
| | - Kenneth T. Stout
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR, United States
| | - Jason W. Sandwisch
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Joseph J. Porter
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
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26
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Wang L, Ceriotti M, Markland TE. Quantum kinetic energy and isotope fractionation in aqueous ionic solutions. Phys Chem Chem Phys 2020; 22:10490-10499. [PMID: 31942581 DOI: 10.1039/c9cp06483d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
At room temperature, the quantum contribution to the kinetic energy of a water molecule exceeds the classical contribution by an order of magnitude. The quantum kinetic energy (QKE) of a water molecule is modulated by its local chemical environment and leads to uneven partitioning of isotopes between different phases in thermal equilibrium, which would not occur if the nuclei behaved classically. In this work, we use ab initio path integral simulations to show that QKEs of the water molecules and the equilibrium isotope fractionation ratios of the oxygen and hydrogen isotopes are sensitive probes of the hydrogen bonding structures in aqueous ionic solutions. In particular, we demonstrate how the QKE of water molecules in path integral simulations can be decomposed into translational, rotational and vibrational degrees of freedom, and use them to determine the impact of solvation on different molecular motions. By analyzing the QKEs and isotope fractionation ratios, we show how the addition of the Na+, Cl- and HPO42- ions perturbs the competition between quantum effects in liquid water and impacts their local solvation structures.
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Affiliation(s)
- Lu Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
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27
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Romei MG, Lin CY, Mathews II, Boxer SG. Electrostatic control of photoisomerization pathways in proteins. Science 2020; 367:76-79. [PMID: 31896714 DOI: 10.1126/science.aax1898] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/04/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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28
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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29
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Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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30
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Chang J, Romei MG, Boxer SG. Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins. J Am Chem Soc 2019; 141:15504-15508. [PMID: 31533429 PMCID: PMC7036281 DOI: 10.1021/jacs.9b08356] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of cis and trans rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the trans state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas, in a tighter packing (7% smaller unit cell size), the hula-twist occurs.
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Affiliation(s)
- Jeffrey Chang
- Department of Physics, Stanford University, Stanford, California 94305, United States
| | - Matthew G. Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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31
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Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG. Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. J Am Chem Soc 2019; 141:15250-15265. [PMID: 31450887 DOI: 10.1021/jacs.9b07152] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Matthew G Romei
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Luke M Oltrogge
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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32
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Yang L, Nian S, Zhang G, Sharman E, Miao H, Zhang X, Chen X, Luo Y, Jiang J. Role of Hydrogen Bonding in Green Fluorescent Protein-like Chromophore Emission. Sci Rep 2019; 9:11640. [PMID: 31406231 PMCID: PMC6690883 DOI: 10.1038/s41598-019-47660-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022] Open
Abstract
The fluorescence emission from green fluorescent protein (GFP) is known to be heavily influenced by hydrogen bonding between the core fluorophore and the surrounding side chains or water molecules. Yet how to utilize this feature for modulating the fluorescence of GFP chromophore or GFP-like fluorophore still remains elusive. Here we present theoretical calculations to predict how hydrogen bonding could influence the excited states of the GFP-like fluorophores. These studies provide both a new perspective for understanding the photophysical properties of GFP as well as a solid basis for the rational design of GFP-based fluorophores.
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Affiliation(s)
- Li Yang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, P. R. China.,Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shifeng Nian
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Guozhen Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Edward Sharman
- Department of Neurology, University of California, Irvine, California, 92697, United States
| | - Hui Miao
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xuepeng Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China.
| | - Xiaofeng Chen
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, China.
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Centre of Chemistry for Energy Materials), CAS Centre for Excellence in Nanoscience, Department of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China.
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33
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Zhou S, Wang L. Unraveling the structural and chemical features of biological short hydrogen bonds. Chem Sci 2019; 10:7734-7745. [PMID: 31588321 PMCID: PMC6764281 DOI: 10.1039/c9sc01496a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/30/2019] [Indexed: 02/06/2023] Open
Abstract
Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.
The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
| | - Lu Wang
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
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34
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Shedge SV, Zuehlsdorff TJ, Servis MJ, Clark AE, Isborn CM. Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores. J Phys Chem A 2019; 123:6175-6184. [DOI: 10.1021/acs.jpca.9b03163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sapana V. Shedge
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Tim J. Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Michael J. Servis
- Department of Chemistry and the Material Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
| | - Aurora E. Clark
- Department of Chemistry and the Material Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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35
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Thomson B, Both J, Wu Y, Parrish RM, Martínez TJ, Boxer SG. Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. J Phys Chem B 2019; 123:4844-4849. [PMID: 31117606 PMCID: PMC7061054 DOI: 10.1021/acs.jpcb.9b01571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.
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Affiliation(s)
| | | | | | - Robert M. Parrish
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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36
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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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37
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Ren TB, Xu W, Zhang QL, Zhang XX, Wen SY, Yi HB, Yuan L, Zhang XB. Enhancing the Anti-Solvatochromic Two-Photon Fluorescence for Cirrhosis Imaging by Forming a Hydrogen-Bond Network. Angew Chem Int Ed Engl 2018; 57:7473-7477. [PMID: 29682856 DOI: 10.1002/anie.201800293] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/10/2023]
Abstract
Two-photon imaging is an emerging tool for biomedical research and clinical diagnostics. Electron donor-acceptor (D-A) type molecules are the most widely employed two-photon scaffolds. However, current D-A type fluorophores suffer from solvatochromic quenching in aqueous biological samples. To address this issue, we devised a novel class of D-A type green fluorescent protein (GFP) chromophore analogues that form a hydrogen-bond network in water to improve the two-photon efficiency. Our design results in two-photon chalcone (TPC) dyes with 0.80 quantum yield and large two-photon action cross section (210 GM) in water. This strategy to form hydrogen bonds can be generalized to design two-photon materials with anti-solvatochromic fluorescence. To demonstrate the improved in vivo imaging, we designed a sulfide probe based on TPC dyes and monitored endogenous H2 S generation and scavenging in the cirrhotic rat liver for the first time.
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Affiliation(s)
- Tian-Bing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Wang Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Qian-Ling Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xing-Xing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Si-Yu Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Hai-Bo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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38
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Ren TB, Xu W, Zhang QL, Zhang XX, Wen SY, Yi HB, Yuan L, Zhang XB. Enhancing the Anti-Solvatochromic Two-Photon Fluorescence for Cirrhosis Imaging by Forming a Hydrogen-Bond Network. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tian-Bing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Wang Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Qian-Ling Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Xing-Xing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Si-Yu Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Hai-Bo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
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39
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Crystal Structure of Green Fluorescent Protein Clover and Design of Clover-Based Redox Sensors. Structure 2018; 26:225-237.e3. [PMID: 29307487 DOI: 10.1016/j.str.2017.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/31/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022]
Abstract
We have determined the crystal structure of Clover, one of the brightest fluorescent proteins, and found that its T203H/S65G mutations relative to wild-type GFP lock the critical E222 side chain in a fixed configuration that mimics the major conformer of that in EGFP. The resulting equilibrium shift to the predominantly deprotonated chromophore increases the extinction coefficient (EC), opposes photoactivation, and is responsible for the bathochromic shift. Clover's brightness can further be attributed to a π-π stacking interaction between H203 and the chromophore. Consistent with these observations, the Clover G65S mutant reversed the equilibrium shift, dramatically decreased the EC, and made Clover photoactivatable under conditions that activated photoactivatable GFP. Using the Clover structure, we rationally engineered a non-photoactivatable redox sensor, roClover1, and determined its structure as well as that of its parental template, roClover0.1. These high-resolution structures provide deeper insights into structure-function relationships in GFPs and may aid the development of excitation-improved ratiometric biosensors.
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40
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Klinman JP, Offenbacher AR, Hu S. Origins of Enzyme Catalysis: Experimental Findings for C-H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs. J Am Chem Soc 2017; 139:18409-18427. [PMID: 29244501 PMCID: PMC5812730 DOI: 10.1021/jacs.7b08418] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases. The data necessitate a reformulation of the dominant textbook definition of biological catalysis. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor-acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site. The available model also suggests a physical framework for understanding the empirical enthalpic barrier in enzyme-catalyzed processes. We conclude by addressing the often conflicting interface between computational and experimental chemists, emphasizing the need for computation to predict experimental results in advance of their measurement.
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Affiliation(s)
- Judith P Klinman
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Adam R Offenbacher
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
| | - Shenshen Hu
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States
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41
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Chen C, Liu W, Baranov MS, Baleeva NS, Yampolsky IV, Zhu L, Wang Y, Shamir A, Solntsev KM, Fang C. Unveiling Structural Motions of a Highly Fluorescent Superphotoacid by Locking and Fluorinating the GFP Chromophore in Solution. J Phys Chem Lett 2017; 8:5921-5928. [PMID: 29148819 DOI: 10.1021/acs.jpclett.7b02661] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Superphotoacidity involves ultrafast proton motions implicated in numerous chemical and biological processes. We used conformational locking and strategic addition of electron-withdrawing substituents to synthesize a new GFP chromophore analogue: p-HO-3,5-diF-BDI:BF2 (diF). It is highly fluorescent and exhibits excited-state proton transfer (ESPT) in various solvents, placing it among the strongest photoacids. Tunable femtosecond stimulated Raman spectroscopy with unique resonance conditions and transient absorption are complementarily employed to elucidate the structural basis for superphotoacidity. We reveal a multistep ESPT reaction from diF to methanol with an initial proton dissociation on the ∼600 fs time scale that forms a charge-separated state, stabilized by solvation, and followed by a diffusion-controlled proton transfer on the ∼350 ps time scale. A ∼1580 cm-1 phenolic ring motion is uncovered to accompany ESPT before 1 ps. This study provides a vivid movie of the photoinduced proton dissociation of a superphotoacid with bright fluorescence, effectively bridging fundamental mechanistic insights to precise control of macroscopic functions.
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Weimin Liu
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ilia V Yampolsky
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1, Moscow 117997, Russia
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Yanli Wang
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Alexandra Shamir
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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42
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Athokpam B, Ramesh SG, McKenzie RH. Effect of hydrogen bonding on the infrared absorption intensity of OH stretch vibrations. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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43
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Platisa J, Vasan G, Yang A, Pieribone VA. Directed Evolution of Key Residues in Fluorescent Protein Inverses the Polarity of Voltage Sensitivity in the Genetically Encoded Indicator ArcLight. ACS Chem Neurosci 2017; 8:513-523. [PMID: 28045247 PMCID: PMC5355904 DOI: 10.1021/acschemneuro.6b00234] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
![]()
Genetically encoded
calcium indicators (GECIs) produce unprecedentedly
large signals that have enabled routine optical recording of single
neuron activity in vivo in rodent brain. Genetically encoded voltage
indicators (GEVIs) offer a more direct measure of neuronal electrical
status, however the signal-to-noise characteristics and signal polarity
of the probes developed to date have precluded routine use in vivo.
We applied directed evolution to target modulable areas of the fluorescent
protein in GEVI ArcLight to create the first GFP-based GEVI (Marina)
that exhibits a ΔF/ΔV with a positive slope relationship. We found that only three rounds
of site-directed mutagenesis produced a family of “brightening”
GEVIs with voltage sensitivities comparable to that seen in the parent
probe ArcLight. This shift in signal polarity is an essential first
step to producing voltage indicators with signal-to-noise characteristics
comparable to GECIs to support widespread use in vivo.
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Affiliation(s)
- Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
| | - Ganesh Vasan
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
| | - Amy Yang
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
| | - Vincent A. Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, United States
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44
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Sappati S, Hassanali A, Gebauer R, Ghosh P. Nuclear quantum effects in a HIV/cancer inhibitor: The case of ellipticine. J Chem Phys 2017; 145:205102. [PMID: 27908111 DOI: 10.1063/1.4968046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak.
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Affiliation(s)
- Subrahmanyam Sappati
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ali Hassanali
- Condensed Matter and Statistical Physics Section, The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Ralph Gebauer
- Condensed Matter and Statistical Physics Section, The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Prasenjit Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
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45
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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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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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Wu Y, Boxer SG. A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase. J Am Chem Soc 2016; 138:11890-5. [PMID: 27545569 PMCID: PMC5063566 DOI: 10.1021/jacs.6b06843] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with ΔG(⧧) in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations. A linear relationship is observed between the electric field and ΔG(⧧) that interpolates between wild-type and more drastic conventional mutations, reinforcing the evaluation of the electrostatic contribution to catalysis in KSI. A simplified model and calculation are developed to estimate changes in the electric field accompanying changes in the extended hydrogen-bond network in the active site. The results are consistent with a model in which the O-H group of a key active site tyrosine functions by imposing a static electrostatic potential onto the carbonyl bond. The model suggests that the contribution to catalysis from the active site hydrogen bonds is of similar weight to the distal interactions from the rest of the protein. A similar linear correlation was also observed between the proton affinity of KSI's active site and the catalytic rate, suggesting a direct connection between the strength of the H-bond and the electric field it exerts.
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Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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48
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Bose S, Chakrabarty S, Ghosh D. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant. J Phys Chem B 2016; 120:4410-20. [DOI: 10.1021/acs.jpcb.6b03723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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Wu Y, Fried SD, Boxer SG. Dissecting Proton Delocalization in an Enzyme's Hydrogen Bond Network with Unnatural Amino Acids. Biochemistry 2015; 54:7110-9. [PMID: 26571340 DOI: 10.1021/acs.biochem.5b00958] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extended hydrogen bond networks are a common structural motif of enzymes. A recent analysis proposed quantum delocalization of protons as a feature present in the hydrogen bond network spanning a triad of tyrosines (Y(16), Y(32), and Y(57)) in the active site of ketosteroid isomerase (KSI), contributing to its unusual acidity and large isotope shift. In this study, we utilized amber suppression to substitute each tyrosine residue with 3-chlorotyrosine to test the delocalization model and the proton affinity balance in the triad. X-ray crystal structures of each variant demonstrated that the structure, notably the O-O distances within the triad, was unaffected by 3-chlorotyrosine substitutions. The changes in the cluster's acidity and the acidity's isotope dependence in these variants were assessed via UV-vis spectroscopy and the proton sharing pattern among individual residues with (13)C nuclear magnetic resonance. Our data show pKa detuning at each triad residue alters the proton delocalization behavior in the H-bond network. The extra stabilization energy necessary for the unusual acidity mainly comes from the strong interactions between Y(57) and Y(16). This is further enabled by Y(32), which maintains the right geometry and matched proton affinity in the triad. This study provides a rich picture of the energetics of the hydrogen bond network in enzymes for further model refinement.
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Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Stephen D Fried
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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McKenzie RH, Athokpam B, Ramesh SG. Isotopic fractionation in proteins as a measure of hydrogen bond length. J Chem Phys 2015; 143:044309. [DOI: 10.1063/1.4927391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Ross H. McKenzie
- School of Mathematics and Physics, University of Queensland, Brisbane 4072, Australia
| | - Bijyalaxmi Athokpam
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sai G. Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
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