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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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Fujimoto KJ, Minowa F, Nishina M, Nakamura S, Ohashi S, Katayama K, Kandori H, Yanai T. Molecular Mechanism of Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual Pigment. J Phys Chem Lett 2023; 14:1784-1793. [PMID: 36762971 DOI: 10.1021/acs.jpclett.2c03619] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The visual pigments of the cones perceive red, green, and blue colors. The monkey green (MG) pigment possesses a unique Cl- binding site; however, its relationship to the spectral tuning in green pigments remains elusive. Recently, FTIR spectroscopy revealed the characteristic structural modifications of the retinal binding site by Cl- binding. Herein, we report the computational structural modeling of MG pigments and quantum-chemical simulation to investigate its spectral redshift and physicochemical relevance when Cl- is present. Our protein structures reflect the previously suggested structural changes. AlphaFold2 failed to predict these structural changes. Excited-state calculations successfully reproduced the experimental red-shifted absorption energies, corroborating our protein structures. Electrostatic energy decomposition revealed that the redshift results from the His197 protonation state and conformations of Glu129, Ser202, and Ala308; however, Cl- itself contributes to the blueshift. Site-directed mutagenesis supported our analysis. These modeled structures may provide a valuable foundation for studying cone pigments.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Fumika Minowa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Michiya Nishina
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
| | - Shunta Nakamura
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Sayaka Ohashi
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Gokiso-cho, Showa, Nagoya, 466-8555, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan
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3
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Shtyrov AA, Nikolaev DM, Mironov VN, Vasin AV, Panov MS, Tveryanovich YS, Ryazantsev MN. Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima. Int J Mol Sci 2021; 22:ijms22063029. [PMID: 33809708 PMCID: PMC8002287 DOI: 10.3390/ijms22063029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/22/2023] Open
Abstract
A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties.
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Affiliation(s)
- Andrey A. Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
| | - Dmitrii M. Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
| | - Vladimir N. Mironov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
| | - Andrey V. Vasin
- Institute of Biomedical Systems and Botechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Street, 195251 St. Petersburg, Russia;
| | - Maxim S. Panov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
| | - Yuri S. Tveryanovich
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
| | - Mikhail N. Ryazantsev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.)
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.)
- Correspondence:
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4
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Abstract
For nearly a century adaptive landscapes have provided overviews of the evolutionary process and yet they remain metaphors. We redefine adaptive landscapes in terms of biological processes rather than descriptive phenomenology. We focus on the underlying mechanisms that generate emergent properties such as epistasis, dominance, trade-offs and adaptive peaks. We illustrate the utility of landscapes in predicting the course of adaptation and the distribution of fitness effects. We abandon aged arguments concerning landscape ruggedness in favor of empirically determining landscape architecture. In so doing, we transform the landscape metaphor into a scientific framework within which causal hypotheses can be tested.
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Affiliation(s)
- Xiao Yi
- BioTechnology Institute, University of Minnesota, St. Paul, MN
| | - Antony M Dean
- BioTechnology Institute, University of Minnesota, St. Paul, MN
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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5
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Orozco-Gonzalez Y, Kabir MP, Gozem S. Electrostatic Spectral Tuning Maps for Biological Chromophores. J Phys Chem B 2019; 123:4813-4824. [DOI: 10.1021/acs.jpcb.9b00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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6
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Grabarek D, Andruniów T. Initial excited-state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations. J Comput Chem 2018; 39:1720-1727. [PMID: 29727036 DOI: 10.1002/jcc.25346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 11/07/2022]
Abstract
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers. Therefore, a strong coupling between bonds length inversion and backbone out-of-plane deformation resulting in a very steep S1 energy profile predicted by CASSCF/CASPT2 calculations is in clear contradiction with the reference XMCQDPT2 results. Even though CC2 method predicts good quality ground-state structures, the excited-state structures display more advanced torsional deformation leading to ca. 0.2 eV exaggerated energy relaxation and significantly red shifted (0.4-0.7 eV) emission maxima. According to our findings, the initial photoisomerization process in locked-11.8, and possibly in other RPSB analogs, studied fully (both geometries and energies) by multireference perturbation theory may be somewhat slower than predicted by CASSCF/CASPT2 or CC2 methods. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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7
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Wolański Ł, Grabarek D, Andruniów T. Is the choice of a standard zeroth-order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal? J Comput Chem 2018; 39:1470-1480. [PMID: 29635695 DOI: 10.1002/jcc.25217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 11/07/2022]
Abstract
To account for systematic error of CASPT2 method empirical modification of the zeroth-order Hamiltonian with Ionization Potential-Electron Affinity (IPEA) shift was introduced. The optimized IPEA value (0.25 a.u.), called standard IPEA (S-IPEA), was recommended but due to its unsatisfactory performance in multiple metallic and organic compounds it has been questioned lately as a general parameter working properly for all molecules under CASPT2 study. As we are interested in Schiff bases of retinal, an important question emerging from this conflict of choice, to use or not to use S-IPEA, is whether the introduction of the modified zeroth-order Hamiltonian into CASPT2 ansatz does really improve their energetics. To achieve this goal, we assessed an impact of the IPEA shift value, in a range of 0-0.35 a.u., on vertical excitation energies to low-lying singlet states of two protonated (RPSBs) and two unprotonated (RSBs) Schiff bases of retinal for which experimental data in gas phase are available. In addition, an effect of geometry, basis set, and active space on computed VEEs is also reported. We find, that for these systems, the choice of S-IPEA significantly overestimates both S0 →S1 and S0 →S2 energies and the best theoretical estimate, in reference to the experimental data, is provided with either unmodified zeroth-order Hamiltonian or small value of the IPEA shift in a range of 0.05-0.15 a.u., depending on active space and basis set size, equilibrium geometry, and character of the excited state. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Łukasz Wolański
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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8
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Loco D, Buda F, Lugtenburg J, Mennucci B. The Dynamic Origin of Color Tuning in Proteins Revealed by a Carotenoid Pigment. J Phys Chem Lett 2018; 9:2404-2410. [PMID: 29683674 DOI: 10.1021/acs.jpclett.8b00763] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the microscopic origin of the color tuning in pigment-protein complexes is a challenging yet fundamental issue in photoactive biological systems. Here, we propose a possible interpretation by using a state-of-the-art multiscale strategy based on the integration of quantum chemistry and polarizable atomistic embeddings into a dynamic description. By means of such a strategy we are able to resolve the long-standing dispute over the coloration mechanism in the crustacyanin protein. It is shown that the combination of the dynamical flexibility of the carotenoid pigments (astaxanthin) with the responsive protein environment is essential to obtain quantitative predictions of the spectral tuning. The strong linear correlation between the excitation energies and the bond length alternation in the long-chain carotenoids modulated by the dynamical protein environment is a novel finding explaining the high color tunability in crustacyanin.
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Affiliation(s)
- Daniele Loco
- Dipartimento di Chimica e Chimica Industriale , University of Pisa , via G. Moruzzi 13 , 56124 , Pisa , Italy
| | - Francesco Buda
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2300 RA Leiden , The Netherlands
| | - Johan Lugtenburg
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2300 RA Leiden , The Netherlands
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , University of Pisa , via G. Moruzzi 13 , 56124 , Pisa , Italy
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9
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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10
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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11
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Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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12
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Chen H, Zhu H, Liu P, Li L. A study on the conformational space of the all-trans retinal deprotonated Schiff base. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Hedegård ED, Reiher M. Polarizable Embedding Density Matrix Renormalization Group. J Chem Theory Comput 2016; 12:4242-53. [PMID: 27537835 DOI: 10.1021/acs.jctc.6b00476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The polarizable embedding (PE) approach is a flexible embedding model where a preselected region out of a larger system is described quantum mechanically, while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG). This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces. Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment. Moreover, we study the environment effect on the first excited state of a retinylidene Schiff base within a channelrhodopsin protein. For this system, we also investigate the effect of dynamical correlation included through short-range density functional theory.
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Affiliation(s)
- Erik D Hedegård
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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14
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Yokoyama S, Tada T, Liu Y, Faggionato D, Altun A. A simple method for studying the molecular mechanisms of ultraviolet and violet reception in vertebrates. BMC Evol Biol 2016; 16:64. [PMID: 27001075 PMCID: PMC4802639 DOI: 10.1186/s12862-016-0637-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/16/2016] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Many vertebrate species use ultraviolet (UV) reception for such basic behaviors as foraging and mating, but many others switched to violet reception and improved their visual resolution. The respective phenotypes are regulated by the short wavelength-sensitive (SWS1) pigments that absorb light maximally (λmax) at ~360 and 395-440 nm. Because of strong epistatic interactions, the biological significance of the extensive mutagenesis results on the molecular basis of spectral tuning in SWS1 pigments and the mechanisms of their phenotypic adaptations remains uncertain. RESULTS The magnitudes of the λmax-shifts caused by mutations in a present-day SWS1 pigment and by the corresponding forward mutations in its ancestral pigment are often dramatically different. To resolve these mutagenesis results, the A/B ratio, in which A and B are the areas formed by amino acids at sites 90, 113 and 118 and by those at sites 86, 90 and 118 and 295, respectively, becomes indispensable. Then, all critical mutations that generated the λmax of a SWS1 pigment can be identified by establishing that 1) the difference between the λmax of the ancestral pigment with these mutations and that of the present-day pigment is small (3 ~ 5 nm, depending on the entire λmax-shift) and 2) the difference between the corresponding A/B ratios is < 0.002. CONCLUSION Molecular adaptation has been studied mostly by using comparative sequence analyses. These statistical results provide biological hypotheses and need to be tested using experimental means. This is an opportune time to explore the currently available and new genetic systems and test these statistical hypotheses. Evaluating the λmaxs and A/B ratios of mutagenized present-day and their ancestral pigments, we now have a method to identify all critical mutations that are responsible for phenotypic adaptation of SWS1 pigments. The result also explains spectral tuning of the same pigments, a central unanswered question in phototransduction.
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Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - Takashi Tada
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Yang Liu
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | | | - Ahmet Altun
- Department of Physics, Fatih University, Istanbul, 34500, Turkey.,Department of Genetics and Bioengineering, Fatih University, Istanbul, 34500, Turkey
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15
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Hofmann L, Palczewski K. Advances in understanding the molecular basis of the first steps in color vision. Prog Retin Eye Res 2015; 49:46-66. [PMID: 26187035 DOI: 10.1016/j.preteyeres.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
Abstract
Serving as one of our primary environmental inputs, vision is the most sophisticated sensory system in humans. Here, we present recent findings derived from energetics, genetics and physiology that provide a more advanced understanding of color perception in mammals. Energetics of cis-trans isomerization of 11-cis-retinal accounts for color perception in the narrow region of the electromagnetic spectrum and how human eyes can absorb light in the near infrared (IR) range. Structural homology models of visual pigments reveal complex interactions of the protein moieties with the light sensitive chromophore 11-cis-retinal and that certain color blinding mutations impair secondary structural elements of these G protein-coupled receptors (GPCRs). Finally, we identify unsolved critical aspects of color tuning that require future investigation.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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16
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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17
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 752] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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18
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Yokoyama S, Xing J, Liu Y, Faggionato D, Altun A, Starmer WT. Epistatic adaptive evolution of human color vision. PLoS Genet 2014; 10:e1004884. [PMID: 25522367 PMCID: PMC4270479 DOI: 10.1371/journal.pgen.1004884] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/10/2014] [Indexed: 11/18/2022] Open
Abstract
Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic) interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV)-free retinal environment, the short wavelength-sensitive (SWS1) visual pigment in human (human S1) switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45-30 million years ago, the middle and long wavelength-sensitive (MWS/LWS) pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.
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Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
| | - Jinyi Xing
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- College of Life Science, Linyi University, Linyi, Shandong, China
| | - Yang Liu
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Davide Faggionato
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Ahmet Altun
- Department of Physics, Fatih University, Istanbul, Turkey
| | - William T. Starmer
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
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19
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Altun A, Breidung J, Neese F, Thiel W. Correlated Ab Initio and Density Functional Studies on H2 Activation by FeO+. J Chem Theory Comput 2014; 10:3807-20. [DOI: 10.1021/ct500522d] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ahmet Altun
- Department
of Physics, Fatih University, 34500 B.Çekmece, Istanbul, Turkey
| | - Jürgen Breidung
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz
1, D-45470 Mülheim
an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz
1, D-45470 Mülheim
an der Ruhr, Germany
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20
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Hauser FE, van Hazel I, Chang BSW. Spectral tuning in vertebrate short wavelength-sensitive 1 (SWS1) visual pigments: Can wavelength sensitivity be inferred from sequence data? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:529-39. [DOI: 10.1002/jez.b.22576] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/05/2014] [Accepted: 05/06/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Ilke van Hazel
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Belinda S. W. Chang
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario Canada
- Centre for the Analysis of Genome Evolution & Function; University of Toronto; Toronto Ontario Canada
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21
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Zhou P, Liu J, Han K, He G. The photoisomerization of 11-cis-retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory. J Comput Chem 2013; 35:109-20. [DOI: 10.1002/jcc.23463] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/12/2013] [Accepted: 09/24/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Guozhong He
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
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22
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Hernández-Rodríguez EW, Montero-Alejo AL, López R, Sánchez-García E, Montero-Cabrera LA, García de la Vega JM. Electron density deformations provide new insights into the spectral shift of rhodopsins. J Comput Chem 2013; 34:2460-71. [DOI: 10.1002/jcc.23414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 11/08/2022]
Affiliation(s)
| | - Ana Lilian Montero-Alejo
- Laboratorio de Química Computacional y Teórica; Departamento de Química Física; Universidad de La Habana; Havana; 10400; Cuba
| | - Rafael López
- Departamento de Química Física Aplicada; Facultad de Ciencias, Universidad Autónoma de Madrid; Madrid; 28049; Spain
| | - Elsa Sánchez-García
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1; Mülheim an der Ruhr; 45470; Germany
| | - Luis Alberto Montero-Cabrera
- Laboratorio de Química Computacional y Teórica; Departamento de Química Física; Universidad de La Habana; Havana; 10400; Cuba
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23
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Frähmcke JS, Wanko M, Elstner M. Building a model of the blue cone pigment based on the wild type rhodopsin structure with QM/MM methods. J Phys Chem B 2012; 116:3313-21. [PMID: 22332756 DOI: 10.1021/jp2086472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the mechanism of color tuning of the retinal chromophore by its host protein became one of the key issues in the research on rhodopsins. While early mutation studies addressed its genetic origin, recent studies advanced to investigate its structural origin, based on X-ray crystallographic structures. For the human cone pigments, no crystal structures have been produced, and homology models were employed to elucidate the origin of its blue-shifted absorption. In this theoretical study, we take a different route to establish a structural model for human blue. Starting from the well-resolved structure of bovine rhodopsin, we derive multiple mutant models by stepwise mutation and equilibration using molecular dynamics simulations in a hybrid quantum mechanics/molecular mechanics framework. Our 30fold mutant reproduces the experimental UV-vis absorption shift of 0.45 eV and provides new insights about both structural and genetic factors that affect the excitation energy. Electrostatic effects of individual amino acids and collaborative structural effects are analyzed using semiempirical (OM2/MRCI) and ab initio (SORCI) multireference approaches.
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Affiliation(s)
- Jan S Frähmcke
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Strasse 10, D-38106 Braunschweig, Germany
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24
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Bernini C, Pogni R, Basosi R, Sinicropi A. The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations. Proteins 2012; 80:1476-83. [DOI: 10.1002/prot.24046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/18/2012] [Accepted: 01/25/2012] [Indexed: 01/21/2023]
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25
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Conductivity by Electron Pairs. Chem Phys 2012. [DOI: 10.1201/b11524-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Kaila VRI, Send R, Sundholm D. The effect of protein environment on photoexcitation properties of retinal. J Phys Chem B 2012; 116:2249-58. [PMID: 22166007 DOI: 10.1021/jp205918m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.
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Affiliation(s)
- Ville R I Kaila
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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27
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Send R, Kaila VRI, Sundholm D. Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems. J Chem Phys 2012; 134:214114. [PMID: 21663351 DOI: 10.1063/1.3596729] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.
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Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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28
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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.
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Affiliation(s)
- Jun-ya Hasegawa
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
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29
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Welke K, Frähmcke JS, Watanabe HC, Hegemann P, Elstner M. Color tuning in binding pocket models of the chlamydomonas-type channelrhodopsins. J Phys Chem B 2011; 115:15119-28. [PMID: 22077286 DOI: 10.1021/jp2085457] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We examined the shift of absorption maxima between the chlamydomonas-type channelrhodopsins (ChRs) and bacteriorhodopsin (BR). Starting from the BR X-ray structure, we modeled the color tuning in the binding pockets of the ChRs by mutating up to 28 amino acids in the vicinity of the chromophore. By applying the efficient self-consistent charge density functional tight binding (SCC-DFTB) method in a quantum mechanical/molecular mechanical (QM/MM) framework, including explicit polarization and calculating excitation energies with the semiempirical OM2/MRCI method and the ab initio SORCI method, we have shown that multiple mutations in the binding pocket of BR causes large hypsochromic shifts that are of the same order as the experimentally observed shifts of the absorption maxima between BR and the ChRs. This study further demonstrates that mutations in the proximity of the Schiff base and complex counterion lead to a stronger but more flexible interaction with the retinal, which could serve as a possible explanation for the spectral patterns found in the ChRs.
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Affiliation(s)
- Kai Welke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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30
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Altun A, Morokuma K, Yokoyama S. H-bond network around retinal regulates the evolution of ultraviolet and violet vision. ACS Chem Biol 2011; 6:775-80. [PMID: 21650174 DOI: 10.1021/cb200100f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ancestors of vertebrates used ultraviolet vision. Some descendants preserved ultraviolet vision, whereas some others replaced it with violet vision, and then, some of avian lineages reinvented ultraviolet vision. Ultraviolet (absorption at ∼360 nm) and violet (410-440 nm) sensitivities of visual pigments are known to be affected by around 20 amino acid substitutions. The present quantum mechanical/molecular mechanical calculations show that these substitutions modify a H-bond network formed by two waters and sites 86, 90, 113, 114, 118, and 295, which determines the protonation state of Schiff base linked 11-cis-retinal. A pigment is ultraviolet-sensitive when it is more stable with an unprotonated retinal (SBR) form than with its protonated analogue (PSBR) and is violet-sensitive when the PSBR form is more stable. These results establish for the first time the chemical basis of ultraviolet and violet vision in vertebrates.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, United States
- Department of Physics, Fatih University, 34900 B. Cekmece, Istanbul, Turkey
| | - Keiji Morokuma
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34−4 Takano Nishihiraki-cho, Sakyo, Kyoto 606−8103, Japan
| | - Shozo Yokoyama
- Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, United States
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31
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Hirao H, Morokuma K. [Recent progress in the theoretical studies of structure, function, and reaction of biological molecules]. YAKUGAKU ZASSHI 2011; 131:1151-61. [PMID: 21804318 DOI: 10.1248/yakushi.131.1151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Essential biomolecular functions often involve electron-related events such as chemical reactions and photoluminescence phenomena. Theoretical description of such electronic processes requires the use of quantum mechanics (QM), but the number of atoms that can be handled with QM is usually smaller than the number of atoms present in a single protein. A reasonable strategy is therefore to give priority to a few tens or hundreds of atoms in the system and deal with them quantum mechanically. Lower-priority atoms influence the event occurring in the higher-priority area; therefore, their effect should also be taken into account. Under these circumstances, a reasonable approach is to apply two or more different theoretical methods to differently prioritized subsystems. QM can be combined, for example, with less accurate yet much less demanding molecular mechanics (MM). Our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method allows for such hybrid calculations, and our group has been applying it to a wide range of biology-related problems. In this paper, we briefly explain the theoretical background and the procedure for the theoretical investigation of biological systems. Subsequently, we provide an overview of some of our recent studies of metalloenzymes and photobiology-related problems.
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Affiliation(s)
- Hajime Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Japan
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32
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Nishizaka M, Mori T, Inoue Y. Axial chirality of donor-donor, donor-acceptor, and tethered 1,1'-binaphthyls: a theoretical revisit with dynamics trajectories. J Phys Chem A 2011; 115:5488-95. [PMID: 21557592 DOI: 10.1021/jp202776g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The circular dichroism (CD) spectra of (R)-2,2'-dimethoxy-1,1'-binaphthyl (DD) and its untethered and tethered donor-acceptor analogues (DA and DA7-DA9) were investigated experimentally and theoretically. The experimental CD spectra of DD and DA resembled each other in several aspects, displaying a positive-positive-negative Cotton effect pattern in the (1)L(b)-(1)L(a) region and a strong negative couplet at the (1)B(b) band, but significantly differed in transition energy and rotatory strength. The couplet amplitude (A) of the main band was 1.6 times larger in DA than in DD, despite the comparable extinction coefficients and seemingly analogous conformations. An additional positive Cotton effect was observed at the CT (CT) band for donor-acceptor binaphthyl DA. Our theoretical prediction of the CD spectra of binaphthyls involves three sequential first principle quantum mechanics (QM) calculations. Thus, the geometry optimizations of a series of conformers with varying dihedral angles were performed by the dispersion-corrected DFT-D method using the B97-D functional and the TZV2P basis set. The potential curve as a function of the dihedral angle (θ) was obtained by using the SCS-MP2/TZVPP single-point energy calculations with and without application of the solvent correction. The CD spectrum of each conformer was independently calculated by the second-order approximate coupled cluster calculation (CC2 method) using the TZVPP basis sets and the resolution of the identity (RI-J) approximation. The (net) theoretical CD spectrum was obtained by averaging over all possible conformers, where the dynamics trajectories based on the relative SCS-MP2 energies were taken into account. By using 17 possible conformers at θ varying from 50 to 130° by 5° intervals, the experimental CD spectra were successfully reproduced in a quantitative manner, enabling us to characterize properly almost all of the important spectral features and chiroptical properties. The two-state model, reported previously, turned out to have led to the right answer with wrong reasons. The couplet sign and amplitude A are critical functions of θ and can be used not only for (qualitatively) determining the absolute configuration but also for quantitatively analyzing the binaphthyl conformations. The angle dependence of A was already argued in the classical coupled oscillator and exciton chirality theories to provide reasonable structure elucidations but only in a qualitative or semiquantitative manner. Our method is able to predict the A value quantitatively as a function of θ. For tethered binaphthyls DA7-DA9, particular care should be exercised in the conformational assessment based on the classical treatment because the amplitude A was shown to be significantly affected by the existence of the tether itself. In the present method, the couplet amplitude A was nicely related to the dihedral angle θ of DA and DD by the state-of-the-art ab initio calculations, enabling us to gain the quantitative information about the conformation of axially chiral binaphthyls. The Cotton effect at the CT band also serves as a complementary clue for elucidating the conformation of donor-acceptor binaphthyls.
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Affiliation(s)
- Masaki Nishizaka
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
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33
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Bernini C, Pogni R, Ruiz-Dueñas FJ, Martínez AT, Basosi R, Sinicropi A. EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level. Phys Chem Chem Phys 2011; 13:5078-98. [DOI: 10.1039/c0cp02151b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Sekharan S, Altun A, Morokuma K. QM/MM study of dehydro and dihydro β-ionone retinal analogues in squid and bovine rhodopsins: implications for vision in salamander rhodopsin. J Am Chem Soc 2010; 132:15856-9. [PMID: 20964383 DOI: 10.1021/ja105050p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Visual pigment rhodopsin provides a decisive crossing point for interaction between organisms and environment. Naturally occurring visual pigments contain only PSB11 and 3,4-dehydro-PSB11 as chromophores. Therefore, the ability of visual opsin to discriminate between the retinal geometries is investigated by means of QM/MM incorporation of PSB11, 6-s-cis and 6-s-trans forms of 3,4-dehydro-PSB11, and 3,4-dehydro-5,6-dihydro-PSB11 and 5,6-dihydro-PSB11 analogues into squid and bovine rhodopsin environments. The analogue-protein interaction reveals the binding site of squid rhodopsin to be malleable and ductile, while that of bovine rhodopsin is rigid and stiff. On the basis of these studies, a tentative model of the salamander rhodopsin binding site is also proposed.
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Affiliation(s)
- Sivakumar Sekharan
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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Rostov IV, Amos RD, Kobayashi R, Scalmani G, Frisch MJ. Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP. J Phys Chem B 2010; 114:5547-55. [PMID: 20369810 DOI: 10.1021/jp911329g] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.
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Affiliation(s)
- Ivan V Rostov
- Australian National University Supercomputer Facility, Mills Road, Canberra, ACT 0200, Australia
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Valsson O, Filippi C. Photoisomerization of Model Retinal Chromophores: Insight from Quantum Monte Carlo and Multiconfigurational Perturbation Theory. J Chem Theory Comput 2010. [DOI: 10.1021/ct900692y] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Omar Valsson
- Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Claudia Filippi
- Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Neugebauer J. Subsystem-Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies. Chemphyschem 2009; 10:3148-73. [DOI: 10.1002/cphc.200900538] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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