1
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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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2
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Corbo JC. Vitamin A 1/A 2 chromophore exchange: Its role in spectral tuning and visual plasticity. Dev Biol 2021; 475:145-155. [PMID: 33684435 DOI: 10.1016/j.ydbio.2021.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023]
Abstract
Vertebrate rod and cone photoreceptors detect light via a specialized organelle called the outer segment. This structure is packed with light-sensitive molecules known as visual pigments that consist of a G-protein-coupled, seven-transmembrane protein known as opsin, and a chromophore prosthetic group, either 11-cis retinal ('A1') or 11-cis 3,4-didehydroretinal ('A2'). The enzyme cyp27c1 converts A1 into A2 in the retinal pigment epithelium. Replacing A1 with A2 in a visual pigment red-shifts its spectral sensitivity and broadens its bandwidth of absorption at the expense of decreased photosensitivity and increased thermal noise. The use of vitamin A2-based visual pigments is strongly associated with the occupation of aquatic habitats in which the ambient light is red-shifted. By modulating the A1/A2 ratio in the retina, an organism can dynamically tune the spectral sensitivity of the visual system to better match the predominant wavelengths of light in its environment. As many as a quarter of all vertebrate species utilize A2, at least during a part of their life cycle or under certain environmental conditions. A2 utilization therefore represents an important and widespread mechanism of sensory plasticity. This review provides an up-to-date account of the A1/A2 chromophore exchange system.
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Affiliation(s)
- Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, United States.
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3
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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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4
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Altun A, Neese F, Bistoni G. Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study. Beilstein J Org Chem 2018; 14:919-929. [PMID: 29765473 PMCID: PMC5942370 DOI: 10.3762/bjoc.14.79] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/06/2018] [Indexed: 11/23/2022] Open
Abstract
The local energy decomposition (LED) analysis allows for a decomposition of the accurate domain-based local pair natural orbital CCSD(T) [DLPNO-CCSD(T)] energy into physically meaningful contributions including geometric and electronic preparation, electrostatic interaction, interfragment exchange, dynamic charge polarization, and London dispersion terms. Herein, this technique is employed in the study of hydrogen-bonding interactions in a series of conformers of water and hydrogen fluoride dimers. Initially, DLPNO-CCSD(T) dissociation energies for the most stable conformers are computed and compared with available experimental data. Afterwards, the decay of the LED terms with the intermolecular distance (r) is discussed and results are compared with the ones obtained from the popular symmetry adapted perturbation theory (SAPT). It is found that, as expected, electrostatic contributions slowly decay for increasing r and dominate the interaction energies in the long range. London dispersion contributions decay as expected, as r-6. They significantly affect the depths of the potential wells. The interfragment exchange provides a further stabilizing contribution that decays exponentially with the intermolecular distance. This information is used to rationalize the trend of stability of various conformers of the water and hydrogen fluoride dimers.
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Affiliation(s)
- Ahmet Altun
- Max Planck Institute for Chemical Energy Conversion, Stifstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Max Planck Institute for Coal Research, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stifstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Max Planck Institute for Coal Research, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max Planck Institute for Chemical Energy Conversion, Stifstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Max Planck Institute for Coal Research, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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5
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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6
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Toomey MB, Corbo JC. Evolution, Development and Function of Vertebrate Cone Oil Droplets. Front Neural Circuits 2017; 11:97. [PMID: 29276475 PMCID: PMC5727011 DOI: 10.3389/fncir.2017.00097] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 11/24/2022] Open
Abstract
To distinguish colors, the nervous system must compare the activity of distinct subtypes of photoreceptors that are maximally sensitive to different portions of the light spectrum. In vertebrates, a variety of adaptations have arisen to refine the spectral sensitivity of cone photoreceptors and improve color vision. In this review article, we focus on one such adaptation, the oil droplet, a unique optical organelle found within the inner segment of cone photoreceptors of a diverse array of vertebrate species, from fish to mammals. These droplets, which consist of neutral lipids and carotenoid pigments, are interposed in the path of light through the photoreceptor and modify the intensity and spectrum of light reaching the photosensitive outer segment. In the course of evolution, the optical function of oil droplets has been fine-tuned through changes in carotenoid content. Species active in dim light reduce or eliminate carotenoids to enhance sensitivity, whereas species active in bright light precisely modulate carotenoid double bond conjugation and concentration among cone subtypes to optimize color discrimination and color constancy. Cone oil droplets have sparked the curiosity of vision scientists for more than a century. Accordingly, we begin by briefly reviewing the history of research on oil droplets. We then discuss what is known about the developmental origins of oil droplets. Next, we describe recent advances in understanding the function of oil droplets based on biochemical and optical analyses. Finally, we survey the occurrence and properties of oil droplets across the diversity of vertebrate species and discuss what these patterns indicate about the evolutionary history and function of this intriguing organelle.
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Affiliation(s)
- Matthew B Toomey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
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7
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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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8
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Nikolaev DM, Emelyanov A, Boitsov VM, Panov MS, Ryazantsev MN. A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. F1000Res 2017; 6:33. [PMID: 28435665 PMCID: PMC5381632 DOI: 10.12688/f1000research.10541.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 12/25/2022] Open
Abstract
It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. While it has already shown encouraging results, there is still a large room for improvement. One of possible directions is increasing the intensity of the protein's fluorescent signal. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.
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Affiliation(s)
- Dmitrii M Nikolaev
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Anton Emelyanov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Vitaly M Boitsov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Maxim S Panov
- Saint-Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail N Ryazantsev
- Saint-Petersburg State University, St. Petersburg, Russian Federation.,Saint-Petersburg Scientific Center of the Russian Academy of Sciences, St. Petersburg, Russian Federation
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9
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Toomey MB, Lind O, Frederiksen R, Curley RW, Riedl KM, Wilby D, Schwartz SJ, Witt CC, Harrison EH, Roberts NW, Vorobyev M, McGraw KJ, Cornwall MC, Kelber A, Corbo JC. Complementary shifts in photoreceptor spectral tuning unlock the full adaptive potential of ultraviolet vision in birds. eLife 2016; 5:e15675. [PMID: 27402384 PMCID: PMC4947394 DOI: 10.7554/elife.15675] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/13/2016] [Indexed: 01/01/2023] Open
Abstract
Color vision in birds is mediated by four types of cone photoreceptors whose maximal sensitivities (λmax) are evenly spaced across the light spectrum. In the course of avian evolution, the λmax of the most shortwave-sensitive cone, SWS1, has switched between violet (λmax > 400 nm) and ultraviolet (λmax < 380 nm) multiple times. This shift of the SWS1 opsin is accompanied by a corresponding short-wavelength shift in the spectrally adjacent SWS2 cone. Here, we show that SWS2 cone spectral tuning is mediated by modulating the ratio of two apocarotenoids, galloxanthin and 11’,12’-dihydrogalloxanthin, which act as intracellular spectral filters in this cell type. We propose an enzymatic pathway that mediates the differential production of these apocarotenoids in the avian retina, and we use color vision modeling to demonstrate how correlated evolution of spectral tuning is necessary to achieve even sampling of the light spectrum and thereby maintain near-optimal color discrimination.
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Affiliation(s)
- Matthew B Toomey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - Olle Lind
- Department of Philosophy, Lund University, Lund, Sweden
| | - Rikard Frederiksen
- Department of Physiology and Biophysics, Boston University, Boston, United States
| | - Robert W Curley
- College of Pharmacy, The Ohio State University, Columbus, United States
| | - Ken M Riedl
- Department of Food Science and Technology, The Ohio State University, Columbus, United States
- Nutrient and Phytochemical Shared Resource of the OSU-Comprehensive Cancer Center, Columbus, United States
| | - David Wilby
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Steven J Schwartz
- Department of Food Science and Technology, The Ohio State University, Columbus, United States
| | - Christopher C Witt
- Department of Biology, University of New Mexico, Albuquerque, United States
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, United States
| | - Earl H Harrison
- Department of Human Nutrition, The Ohio State University, Columbus, United States
| | - Nicholas W Roberts
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Misha Vorobyev
- Department of Optometry and Vision Science, University of Auckland, Auckland, New Zealand
| | - Kevin J McGraw
- School of Life Sciences, Arizona State University, Tempe, United States
| | - M Carter Cornwall
- Department of Physiology and Biophysics, Boston University, Boston, United States
| | - Almut Kelber
- Department of Biology, Lund University, Lund, Sweden
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
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10
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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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11
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Yokoyama S, Altun A, Jia H, Yang H, Koyama T, Faggionato D, Liu Y, Starmer WT. Adaptive evolutionary paths from UV reception to sensing violet light by epistatic interactions. SCIENCE ADVANCES 2015; 1:e1500162. [PMID: 26601250 PMCID: PMC4643761 DOI: 10.1126/sciadv.1500162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/02/2015] [Indexed: 06/05/2023]
Abstract
Ultraviolet (UV) reception is useful for such basic behaviors as mate choice, foraging, predator avoidance, communication, and navigation, whereas violet reception improves visual resolution and subtle contrast detection. UV and violet reception are mediated by the short wavelength-sensitive (SWS1) pigments that absorb light maximally (λmax) at ~360 nm and ~395 to 440 nm, respectively. Because of strong nonadditive (epistatic) interactions among amino acid changes in the pigments, the adaptive evolutionary mechanisms of these phenotypes are not well understood. Evolution of the violet pigment of the African clawed frog (Xenopus laevis, λmax = 423 nm) from the UV pigment in the amphibian ancestor (λmax = 359 nm) can be fully explained by eight mutations in transmembrane (TM) I-III segments. We show that epistatic interactions involving the remaining TM IV-VII segments provided evolutionary potential for the frog pigment to gradually achieve its violet-light reception by tuning its color sensitivity in small steps. Mutants in these segments also impair pigments that would cause drastic spectral shifts and thus eliminate them from viable evolutionary pathways. The overall effects of epistatic interactions involving TM IV-VII segments have disappeared at the last evolutionary step and thus are not detectable by studying present-day pigments. Therefore, characterizing the genotype-phenotype relationship during each evolutionary step is the key to uncover the true nature of epistasis.
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Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Ahmet Altun
- Department of Physics and Department of Genetics and Bioengineering, Fatih University, Istanbul 34500, Turkey
| | - Huiyong Jia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Hui Yang
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Takashi Koyama
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Yang Liu
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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12
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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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13
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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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14
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Kubli-Garfias C, Vázquez-Ramírez R, Cabrera-Vivas BM, Gómez-Reyes B, Ramírez JC. Atomic and molecular analysis highlights the biophysics of unprotonated and protonated retinal in UV and scotopic vision. Photochem Photobiol Sci 2015; 14:1660-72. [DOI: 10.1039/c5pp00091b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unprotonated (UR) and protonated (PR) retinal have marked atomic and molecular differences in cis and trans configurations. In conclusion, UR and PR uphold UV and light vision through their different biophysical properties.
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Affiliation(s)
- Carlos Kubli-Garfias
- Instituto de Investigaciones Biomédicas
- Universidad Nacional Autónoma de México
- México
- Mexico
| | | | | | | | - Juan Carlos Ramírez
- Facultad de Ciencias Químicas
- Benemérita Universidad Autónoma de Puebla
- Puebla 72530
- Mexico
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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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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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Abstract
For over the last 2 decades, positively selected amino acid sites have been inferred almost exclusively by showing that the number of nonsynonymous substitutions per nonsynonymous site (dn) is greater than that of synonymous substitutions per synonymous site (ds). However, virtually none of these statistical results have been experimentally tested and remain as hypotheses. To perform such experimental tests, we must connect genotype and phenotype and relate the phenotypic changes to the environmental and behavioral changes of the organism. The genotype-phenotype relationship can be established only by synthesizing and manipulating "proper" ancestral phenotypes, whereas the actual functions of adaptive mutations can be learned by studying their chemical roles in phenotypic changes.
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YOKOYAMA SHOZO. Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision. Bioscience 2012; 62:939-948. [PMID: 23483186 PMCID: PMC3593118 DOI: 10.1525/bio.2012.62.11.3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Natural selection has played an important role in establishing various phenotypes, but the molecular mechanisms of phenotypic adaptation are not well understood. The slow progress is a consequence of mutagenesis experiments in which present-day molecules were used and of the limited scope of statistical methods used to detect adaptive evolution. To fully appreciate phenotypic adaptation, the precise roles of adaptive mutations during phenotypic evolution must be elucidated through the engineering and manipulation of ancestral phenotypes. Experimental and quantum chemical analyses of dim-light vision reveal some surprising results and provide a foundation for a productive study of the adaptive evolution of various phenotypes.
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Affiliation(s)
- SHOZO YOKOYAMA
- Department of Biology at Emory University, in Atlanta, Georgia
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Ryazantsev MN, Altun A, Morokuma K. Color Tuning in rhodopsins: the origin of the spectral shift between the chloride-bound and anion-free forms of halorhodopsin. J Am Chem Soc 2012; 134:5520-3. [PMID: 22397521 DOI: 10.1021/ja3009117] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Detailed knowledge of the molecular mechanisms that control the spectral properties in the rhodopsin protein family is important for understanding the functions of these photoreceptors and for the rational design of artificial photosensitive proteins. Here we used a high-level ab initio QM/MM method to investigate the mechanism of spectral tuning in the chloride-bound and anion-free forms of halorhodopsin from Natronobacterium pharaonis (phR) and the interprotein spectral shift between them. We demonstrate that the chloride ion tunes the spectral properties of phR via two distinct mechanisms: (i) electrostatic interaction with the chromophore, which results in a 95 nm difference between the absorption maxima of the two forms, and (ii) induction of a structural reorganization in the protein, which changes the positions of charged and polar residues and reduces this difference to 29 nm. The present study expands our knowledge concerning the role of the reorganization of the internal H-bond network for color tuning in general and provides a detailed investigation of the tuning mechanism in phR in particular.
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Affiliation(s)
- Mikhail N Ryazantsev
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Plasser F, Barbatti M, Aquino AJA, Lischka H. Electronically excited states and photodynamics: a continuing challenge. Theor Chem Acc 2012. [DOI: 10.1007/s00214-011-1073-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sekharan S, Yokoyama S, Morokuma K. Quantum mechanical/molecular mechanical structure, enantioselectivity, and spectroscopy of hydroxyretinals and insights into the evolution of color vision in small white butterflies. J Phys Chem B 2011; 115:15380-8. [PMID: 22087641 DOI: 10.1021/jp208107r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since Vogt's discovery of A(3)-retinal or 3-hydroxyretinal in insects in 1983 and Matsui's discovery of A(4)-retinal or 4-hydroxyretinal in firefly squid in 1988, hydroxyretinal-protein interactions mediating vision have remained largely unexplored. In the present study, A(3)- and A(4)-retinals are theoretically incorporated into squid and bovine visual pigments by use of the hybrid quantum mechanics/molecular mechanics [SORCI+Q//B3LYP/6-31G(d):Amber96] method, and insights into structure, enantioselectivity, and spectroscopy are gathered and presented for the first time. Contrary to general perception, our findings rule out the formation of a hydrogen bond between the hydroxyl-bearing β-ionone ring portion of retinal and opsin. Compared to A(1)-pigments, A(3)- and A(4)-pigments exhibit slightly blue-shifted absorption maxima due to increase in bond-length alternation of the hydroxyretinal. We suggest that (i) the binding site of firefly squid (Watasenia scintillans) opsin is very similar to that of the Japanese common squid (Todarodes pacificus) opsin; (ii) the molecular mechanism of spectral tuning in small white butterflies involve sites S116 and T185 and breaking of a hydrogen bond between sites E180 and T185; and finally (iii) A(3)-retinal may have occurred during the conversion of A(1)- to A(2)-retinal and insects may have acquired them, in order to absorb light in the blue-green wavelength region and to speed up the G-protein signaling cascade.
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Affiliation(s)
- Sivakumar Sekharan
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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