1
|
Giudetti G, Polyakov I, Grigorenko BL, Faraji S, Nemukhin AV, Krylov AI. How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur. J Chem Theory Comput 2022; 18:5056-5067. [PMID: 35797455 DOI: 10.1021/acs.jctc.2c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work explores the level of transparency in reporting the details of computational protocols that is required for practical reproducibility of quantum mechanics/molecular mechanics (QM/MM) simulations. Using the reaction of an essential SARS-CoV-2 enzyme (the main protease) with a covalent inhibitor (carmofur) as a test case of chemical reactions in biomolecules, we carried out QM/MM calculations to determine the structures and energies of the reactants, the product, and the transition state/intermediate using analogous QM/MM models implemented in two software packages, NWChem and Q-Chem. Our main benchmarking goal was to reproduce the key energetics computed with the two packages. Our results indicate that quantitative agreement (within the numerical thresholds used in calculations) is difficult to achieve. We show that rather minor details of QM/MM simulations must be reported in order to ensure the reproducibility of the results and offer suggestions toward developing practical guidelines for reporting the results of biosimulations.
Collapse
Affiliation(s)
- Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Igor Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG The Netherlands
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
2
|
Skúpa K, Urban J. Modifications of the chromophore of Spinach aptamer based on QM:MM calculations. J Mol Model 2017; 23:46. [PMID: 28154983 DOI: 10.1007/s00894-017-3232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/13/2017] [Indexed: 10/20/2022]
Abstract
Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.
Collapse
Affiliation(s)
- Katarína Skúpa
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia.
| | - Ján Urban
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| |
Collapse
|
3
|
Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
Collapse
Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| |
Collapse
|
4
|
Bogdanov AM, Acharya A, Titelmayer AV, Mamontova AV, Bravaya KB, Kolomeisky AB, Lukyanov KA, Krylov AI. Turning On and Off Photoinduced Electron Transfer in Fluorescent Proteins by π-Stacking, Halide Binding, and Tyr145 Mutations. J Am Chem Soc 2016; 138:4807-17. [DOI: 10.1021/jacs.6b00092] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alexey M. Bogdanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603005, Russia
| | - Atanu Acharya
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | | | - Ksenia B. Bravaya
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | | | - Konstantin A. Lukyanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603005, Russia
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
5
|
Long- and Short-Range Electrostatic Fields in GFP Mutants: Implications for Spectral Tuning. Sci Rep 2015; 5:13223. [PMID: 26286372 PMCID: PMC4541067 DOI: 10.1038/srep13223] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/20/2015] [Indexed: 12/27/2022] Open
Abstract
The majority of protein functions are governed by their internal local electrostatics. Quantitative information about these interactions can shed light on how proteins work and allow for improving/altering their performance. Green fluorescent protein (GFP) and its mutation variants provide unique optical windows for interrogation of internal electric fields, thanks to the intrinsic fluorophore group formed inside them. Here we use an all-optical method, based on the independent measurements of transition frequency and one- and two-photon absorption cross sections in a number of GFP mutants to evaluate these internal electric fields. Two physical models based on the quadratic Stark effect, either with or without taking into account structural (bond-length) changes of the chromophore in varying field, allow us to separately evaluate the long-range and the total effective (short- and long-range) fields. Both types of the field quantitatively agree with the results of independent molecular dynamic simulations, justifying our method of measurement.
Collapse
|
6
|
Grigorenko BL, Nemukhin AV, Polyakov IV, Khrenova MG, Krylov AI. A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins. J Phys Chem B 2015; 119:5444-52. [PMID: 25867185 DOI: 10.1021/acs.jpcb.5b02271] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photobleaching and photostability of proteins of the green fluorescent protein (GFP) family are crucially important for practical applications of these widely used biomarkers. On the basis of simulations, we propose a mechanism for irreversible bleaching in GFP-type proteins under intense light illumination. The key feature of the mechanism is a photoinduced reaction of the chromophore with molecular oxygen (O2) inside the protein barrel leading to the chromophore's decomposition. Using quantum mechanics/molecular mechanics (QM/MM) modeling we show that a model system comprising the protein-bound Chro(-) and O2 can be excited to an electronic state of the intermolecular charge-transfer (CT) character (Chro(•)···O2(-•)). Once in the CT state, the system undergoes a series of chemical reactions with low activation barriers resulting in the cleavage of the bridging bond between the phenolic and imidazolinone rings and disintegration of the chromophore.
Collapse
Affiliation(s)
- Bella L Grigorenko
- †Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation.,‡N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
| | - Alexander V Nemukhin
- †Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation.,‡N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
| | - Igor V Polyakov
- †Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Maria G Khrenova
- †Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Anna I Krylov
- §Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
7
|
Sala M, Guérin S, Gatti F. Quantum dynamics of the photostability of pyrazine. Phys Chem Chem Phys 2015; 17:29518-30. [DOI: 10.1039/c5cp04605j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We propose a new mechanism for the radiationless decay of photoexcited pyrazine to its ground electronic state involving a conical intersection between the dark Au(nπ) state and the ground state.
Collapse
Affiliation(s)
- Matthieu Sala
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 6303 CNRS
- Université de Bourgogne Franche-Comté
- F-21078 Dijon
- France
| | - Stéphane Guérin
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 6303 CNRS
- Université de Bourgogne Franche-Comté
- F-21078 Dijon
- France
| | - Fabien Gatti
- CTMM
- Institut Charles Gerhardt UMR 5253 CNRS
- F-34095 Montpellier
- France
| |
Collapse
|
8
|
Vegh R, Bravaya KB, Bloch DA, Bommarius A, Tolbert L, Verkhovsky M, Krylov AI, Solntsev KM. Chromophore photoreduction in red fluorescent proteins is responsible for bleaching and phototoxicity. J Phys Chem B 2014; 118:4527-34. [PMID: 24712386 PMCID: PMC4010289 DOI: 10.1021/jp500919a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/05/2014] [Indexed: 12/11/2022]
Abstract
Red fluorescent proteins (RFPs) are indispensable tools for deep-tissue imaging, fluorescence resonance energy transfer applications, and super-resolution microscopy. Using time-resolved optical spectroscopy this study investigated photoinduced dynamics of three RFPs, KillerRed, mRFP, and DsRed. In all three RFPs, a new transient absorption intermediate was observed, which decays on a microsecond-millisecond time scale. This intermediate is characterized by red-shifted absorption at 1.68-1.72 eV (λmax = 720-740 nm). On the basis of electronic structure calculations, experimental evidence, and published literature, the chemical nature of the intermediate is assigned to an unusual open-shell dianionic chromophore (dianion-radical) formed via photoreduction. A doubly charged state that is not stable in the isolated (gas phase) chromophore is stabilized by the electrostatic field of the protein. Mechanistic implications for photobleaching, blinking, and phototoxicity are discussed.
Collapse
Affiliation(s)
- Russell
B. Vegh
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
- Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0363, United States
| | - Ksenia B. Bravaya
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Dmitry A. Bloch
- Institute
of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Andreas
S. Bommarius
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
- Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0363, United States
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0100, United States
| | - Laren
M. Tolbert
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
| | | | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Kyril M. Solntsev
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0400, United States
| |
Collapse
|
9
|
Sala M, Kirkby OM, Guérin S, Fielding HH. New insight into the potential energy landscape and relaxation pathways of photoexcited aniline from CASSCF and XMCQDPT2 electronic structure calculations. Phys Chem Chem Phys 2014; 16:3122-33. [DOI: 10.1039/c3cp54418d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
New insight into the nonadiabatic relaxation dynamics of aniline following excitation to its first three singlet excited states, 11ππ*, 11π3s/πσ* and 21ππ*.
Collapse
Affiliation(s)
- Matthieu Sala
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 5209 CNRS
- Université de Bourgogne
- F-21078 Dijon, France
| | - Oliver M. Kirkby
- Department of Chemistry
- University College London
- London WC1H 0AJ, UK
| | - Stéphane Guérin
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 5209 CNRS
- Université de Bourgogne
- F-21078 Dijon, France
| | | |
Collapse
|
10
|
Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
Collapse
Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| |
Collapse
|
11
|
Gozem S, Krylov AI, Olivucci M. Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods. J Chem Theory Comput 2012; 9:284-92. [DOI: 10.1021/ct300759z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Anna I. Krylov
- Department of Chemistry, University
of Southern California, Los Angeles, California 90089-0482, United
States
| | - Massimo Olivucci
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica,
Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
| |
Collapse
|
12
|
Ghosh D, Acharya A, Tiwari SC, Krylov AI. Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects. J Phys Chem B 2012; 116:12398-405. [PMID: 22978512 DOI: 10.1021/jp305022t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (E(red)(0)) of the anionic (Chr•/Chr–) and neutral (Chr+•/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and −0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values.
Collapse
Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | | | | |
Collapse
|
13
|
Mooney CRS, Sanz ME, McKay AR, Fitzmaurice RJ, Aliev AE, Caddick S, Fielding HH. Photodetachment Spectra of Deprotonated Fluorescent Protein Chromophore Anions. J Phys Chem A 2012; 116:7943-9. [DOI: 10.1021/jp3058349] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ciarán R. S. Mooney
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - M. Eugenia Sanz
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
- Department of Chemistry, School of Biomedical Sciences, King’s College London, Guy’s Campus,
London SE1 1UL, U.K
| | - Adam R. McKay
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Richard J. Fitzmaurice
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Abil E. Aliev
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Stephen Caddick
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Helen H. Fielding
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| |
Collapse
|
14
|
Bravaya KB, Grigorenko BL, Nemukhin AV, Krylov AI. Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores. Acc Chem Res 2012; 45:265-75. [PMID: 21882809 DOI: 10.1021/ar2001556] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The unique properties of green fluorescent protein (GFP) have been harnessed in a variety of bioimaging techniques, revolutionizing many areas of the life sciences. Molecular-level understanding of the underlying photophysics provides an advantage in the design of new fluorescent proteins (FPs) with improved properties; however, because of its complexity, many aspects of the GFP photocycle remain unknown. In this Account, we discuss computational studies of FPs and their chromophores that provide qualitative insights into mechanistic details of their photocycle and the structural basis for their optical properties. In a reductionist framework, studies of well-defined model systems (such as isolated chromophores) help to understand their intrinsic properties, while calculations including protein matrix and/or solvent demonstrate, on the atomic level, how these properties are modulated by the environment. An interesting feature of several anionic FP chromophores in the gas phase is their low electron detachment energy. For example, the bright excited ππ* state of the model GFP chromophore (2.6 eV) lies above the electron detachment continuum (2.5 eV). Thus, the excited state is metastable with respect to electron detachment. This autoionizing character needs to be taken into account in interpreting gas-phase measurements and is very difficult to describe computationally. Solvation (and even microsolvation by a single water molecule) stabilizes the anionic states enough such that the resonance excited state becomes bound. However, even in stabilizing environments (such as protein or solution), the anionic chromophores have relatively low oxidation potentials and can act as light-induced electron donors. Protein appears to affect excitation energies very little (<0.1 eV), but alters ionization or electron detachment energies by several electron volts. Solvents (especially polar ones) have a pronounced effect on the chromophore's electronic states; for example, the absorption wavelength changes considerably, the ground-state barrier for cis-trans isomerization is reduced, and fluorescence quantum yield drops dramatically. Calculations reveal that these effects can be explained in terms of electrostatic interactions and polarization, as well as specific interactions such as hydrogen bonding. The availability of efficient computer implementations of predictive electronic structure methods is essential. Important challenges include developing faster codes (to enable better equilibrium sampling and excited-state dynamics modeling), creating algorithms for properties calculations (such as nonlinear optical properties), extending standard excited-state methods to autoionizing (resonance) states, and developing accurate QM/MM schemes. The results of sophisticated first-principle calculations can be interpreted in terms of simpler, qualitative molecular orbital models to explain general trends. In particular, an essential feature of the anionic GFP chromophore is an almost perfect resonance (mesomeric) interaction between two Lewis structures, giving rise to charge delocalization, bond-order scrambling, and, most importantly, allylic frontier molecular orbitals spanning the methine bridge. We demonstrate that a three-center Hückel-like model provides a useful framework for understanding properties of FPs. It can explain changes in absorption wavelength upon protonation or other structural modifications of the chromophore, the magnitude of transition dipole moment, barriers to isomerization, and even non-Condon effects in one- and two-photon absorption.
Collapse
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Bella L. Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander V. Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
15
|
Bravaya KB, Subach OM, Korovina N, Verkhusha VV, Krylov AI. Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealed. J Am Chem Soc 2012; 134:2807-14. [PMID: 22239269 PMCID: PMC3310345 DOI: 10.1021/ja2114568] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the chromophore maturation process in fluorescent proteins is important for the design of proteins with improved properties. Here, we present the results of electronic structure calculations identifying the nature of a blue intermediate, a key species in the process of the red chromophore formation in DsRed, TagRFP, fluorescent timers, and PAmCherry. The chromophore of the blue intermediate has a structure in which the π-system of the imidazole ring is extended by the acylimine bond, which can be represented by the model N-[(5-hydroxy-1H-imidazole-2yl)methylidene]acetamide (HIMA) compound. Ab initio and QM/MM calculations of the isolated model and protein-bound (mTagBFP) chromophores identify the anionic form of HIMA as the only structure that has absorption that is consistent with the experiment and is stable in the protein binding pocket. The anion and zwitterion are the only protonation forms of HIMA whose absorption (421 and 414 nm, or 2.95 and 3.00 eV) matches the experimental spectrum of the blue form in DsRed (the absorption maximum is 408 nm or 3.04 eV) and mTagBFP (400 nm or 3.10 eV). The QM/MM optimization of the protein-bound anionic form results in a structure that is close to the X-ray one, whereas the zwitterionic chromophore is unstable in the protein binding pocket and undergoes prompt proton transfer. The computed excitation energy of the protein-bound anionic form of the mTagBFP-like chromophore (3.04 eV) agrees with the experimental absorption spectrum of the protein. The DsRed-like chromophore formation in red fluorescent proteins is revisited on the basis of ab initio results and verified by directed mutagenesis revealing a key role of the amino acid residue 70, which is the second after the chromophore tripeptide, in the formation process.
Collapse
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0482
| | - Oksana M. Subach
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Nadezhda Korovina
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0482
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0482
| |
Collapse
|
16
|
Horke DA, Verlet JRR. Photoelectron spectroscopy of the model GFP chromophore anion. Phys Chem Chem Phys 2012; 14:8511-5. [DOI: 10.1039/c2cp40880e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
17
|
Hasegawa JY, Fujimoto KJ, Nakatsuji H. Color tuning in photofunctional proteins. Chemphyschem 2011; 12:3106-15. [PMID: 21990164 DOI: 10.1002/cphc.201100452] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/24/2011] [Indexed: 11/11/2022]
Abstract
Depending on protein environment, a single photofunctional chromophore shows a wide variation of photoabsorption/emission energies. This photobiological phenomenon, known as color tuning, is observed in human visual cone pigments, firefly luciferase, and red fluorescent protein. We investigate the origin of color tuning by quantum chemical calculations on the excited states: symmetry-adapted cluster-configuration interaction (SAC-CI) method for excited states and a combined quantum mechanical (QM)/molecular mechanical (MM) method for protein environments. This Minireview summarizes our theoretical studies on the above three systems and explains a common feature of their color-tuning mechanisms. It also discuss the possibility of artificial color tuning toward a rational design of photoabsorption/emission properties.
Collapse
Affiliation(s)
- Jun-ya Hasegawa
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
| | | | | |
Collapse
|
18
|
Zuev D, Bravaya KB, Makarova MV, Krylov AI. Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins. J Chem Phys 2011; 135:194304. [DOI: 10.1063/1.3660350] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
19
|
Granovsky AA. Extended multi-configuration quasi-degenerate perturbation theory: The new approach to multi-state multi-reference perturbation theory. J Chem Phys 2011; 134:214113. [DOI: 10.1063/1.3596699] [Citation(s) in RCA: 519] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
20
|
Bravaya KB, Khrenova MG, Grigorenko BL, Nemukhin AV, Krylov AI. Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore. J Phys Chem B 2011; 115:8296-303. [DOI: 10.1021/jp2020269] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Maria G. Khrenova
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander V. Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
21
|
Kalies S, Kuetemeyer K, Heisterkamp A. Mechanisms of high-order photobleaching and its relationship to intracellular ablation. BIOMEDICAL OPTICS EXPRESS 2011; 2:805-816. [PMID: 21483605 PMCID: PMC3072123 DOI: 10.1364/boe.2.000816] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/18/2011] [Accepted: 02/20/2011] [Indexed: 05/30/2023]
Abstract
In two-photon laser-scanning microscopy using femtosecond laser pulses, the dependence of the photobleaching rate on excitation power may have a quadratic, cubic or even biquadratic order. To date, there are still many open questions concerning this so-called high-order photobleaching. We studied the photobleaching kinetics of an intrinsic (enhanced Green Fluorescent Protein (eGFP)) and an extrinsic (Hoechst 33342) fluorophore in a cellular environment in two-photon microscopy. Furthermore, we examined the correlation between bleaching and the formation of reactive oxygen species. We observed bleaching-orders of three and four for eGFP and two and three for Hoechst increasing step-wise at a certain wavelength. An increase of reactive oxygen species correlating with the bleaching over time was recognized. Comparing our results to the mechanisms involved in intracellular ablation with respect to the amount of interacting photons and involved energetic states, we found that a low-density plasma is formed in both cases with a smooth transition in between. Photobleaching, however, is mediated by sequential-absorption and multiphoton-ionization, while ablation is dominated by the latter and cascade-ionization processes.
Collapse
Affiliation(s)
- S. Kalies
- Laser Zentrum Hannover e.V., Hollerithallee 8, 30419 Hannover, Germany
| | - K. Kuetemeyer
- Laser Zentrum Hannover e.V., Hollerithallee 8, 30419 Hannover, Germany
| | - A. Heisterkamp
- Laser Zentrum Hannover e.V., Hollerithallee 8, 30419 Hannover, Germany
| |
Collapse
|
22
|
Kalies S, Kuetemeyer K, Heisterkamp A. Mechanisms of high-order photobleaching and its relationship to intracellular ablation. BIOMEDICAL OPTICS EXPRESS 2011; 2:805-816. [PMID: 21483605 DOI: 10.1364/boe.2.000805] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/18/2011] [Accepted: 02/20/2011] [Indexed: 05/27/2023]
Abstract
In two-photon laser-scanning microscopy using femtosecond laser pulses, the dependence of the photobleaching rate on excitation power may have a quadratic, cubic or even biquadratic order. To date, there are still many open questions concerning this so-called high-order photobleaching. We studied the photobleaching kinetics of an intrinsic (enhanced Green Fluorescent Protein (eGFP)) and an extrinsic (Hoechst 33342) fluorophore in a cellular environment in two-photon microscopy. Furthermore, we examined the correlation between bleaching and the formation of reactive oxygen species. We observed bleaching-orders of three and four for eGFP and two and three for Hoechst increasing step-wise at a certain wavelength. An increase of reactive oxygen species correlating with the bleaching over time was recognized. Comparing our results to the mechanisms involved in intracellular ablation with respect to the amount of interacting photons and involved energetic states, we found that a low-density plasma is formed in both cases with a smooth transition in between. Photobleaching, however, is mediated by sequential-absorption and multiphoton-ionization, while ablation is dominated by the latter and cascade-ionization processes.
Collapse
|
23
|
Zuev D, Bravaya KB, Crawford TD, Lindh R, Krylov AI. Electronic structure of the two isomers of the anionic form ofp-coumaric acid chromophore. J Chem Phys 2011; 134:034310. [DOI: 10.1063/1.3516211] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
24
|
Lukyanov KA, Serebrovskaya EO, Lukyanov S, Chudakov DM. Fluorescent proteins as light-inducible photochemical partners. Photochem Photobiol Sci 2010; 9:1301-6. [PMID: 20672171 DOI: 10.1039/c0pp00114g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 07/14/2010] [Indexed: 01/19/2023]
Abstract
Green Fluorescent Protein (GFP) and other related fluorescent proteins are generally used as genetically encoded, chemically inert labels in vivo. This review focuses on the emerging application of fluorescent proteins as light-inducible intracellular photochemical partners. The first example of a chemically active GFP-like protein was the phototoxic red fluorescent protein KillerRed, which can be used for precise light-induced killing of cells, protein inactivation, and studying reactive oxygen species signaling in different cellular compartments. Moreover, recent studies revealed that various GFPs can act as light-induced electron donors in photochemical reactions with biologically relevant electron acceptors. These findings have important implications for practical uses of fluorescent proteins as well as for our understanding of the evolution and biology of this protein family.
Collapse
|
25
|
Polyakov IV, Grigorenko BL, Epifanovsky EM, Krylov AI, Nemukhin AV. Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections. J Chem Theory Comput 2010; 6:2377-87. [PMID: 26613493 DOI: 10.1021/ct100227k] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the results of quantum chemical calculations of the transition energies and conical intersection points for the two lowest singlet electronic states of the green fluorescent protein chromophore, 4'-hydroxybenzylidene-2,3-dimethylimidazolinone, in the vicinity of its cis conformation in the gas phase. Four protonation states of the chromophore, i.e., anionic, neutral, cationic, and zwitterionic, were considered. Energy differences were computed by the perturbatively corrected complete active space self-consistent field (CASSCF)-based approaches at the corresponding potential energy minima optimized by density functional theory and CASSCF (for the ground and excited states, respectively). We also report the EOM-CCSD and SOS-CIS(D) results for the excitation energies. The minimum energy S0/S1 conical intersection points were located using analytic state-specific CASSCF gradients. The results reproduce essential features of previous ab initio calculations of the anionic form of the chromophore and provide an extension for the neutral, cationic, and zwitterionic forms, which are important in the protein environment. The S1 PES of the anion is fairly flat, and the barrier separating the planar bright conformation from the dark twisted one as well as the conical intersection point with the S0 surface is very small (less than 2 kcal/mol). On the cationic surface, the barrier is considerably higher (∼13 kcal/mol). The PES of the S1 state of the zwitterionic form does not have a planar minimum in the Franck-Condon region. The S1 surface of the neutral form possesses a bright planar minimum; the energy barrier of about 9 kcal/mol separates it from the dark twisted conformation as well as from the conical intersection point leading to the cis-trans chromophore isomerization.
Collapse
Affiliation(s)
- I V Polyakov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - B L Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - E M Epifanovsky
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - A I Krylov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - A V Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| |
Collapse
|
26
|
|