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Guo Y, Hendrickson HP, Videla PE, Chen YN, Ho J, Sekharan S, Batista VS, Tully JC, Yan ECY. Probing the remarkable thermal kinetics of visual rhodopsin with E181Q and S186A mutants. J Chem Phys 2017; 146:215104. [DOI: 10.1063/1.4984818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ying Guo
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Heidi P. Hendrickson
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Pablo E. Videla
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Ya-Na Chen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Junming Ho
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Sivakumar Sekharan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - John C. Tully
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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2
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Singhal A, Guo Y, Matkovic M, Schertler G, Deupi X, Yan EC, Standfuss J. Structural role of the T94I rhodopsin mutation in congenital stationary night blindness. EMBO Rep 2016; 17:1431-1440. [PMID: 27458239 DOI: 10.15252/embr.201642671] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/07/2016] [Indexed: 11/09/2022] Open
Abstract
Congenital stationary night blindness (CSNB) is an inherited and non-progressive retinal dysfunction. Here, we present the crystal structure of CSNB-causing T94I2.61 rhodopsin in the active conformation at 2.3 Å resolution. The introduced hydrophobic side chain prolongs the lifetime of the G protein activating metarhodopsin-II state by establishing a direct van der Waals contact with K2967.43, the site of retinal attachment. This is in stark contrast to the light-activated state of the CSNB-causing G90D2.57 mutation, where the charged mutation forms a salt bridge with K2967.43 To find the common denominator between these two functional modifications, we combined our structural data with a kinetic biochemical analysis and molecular dynamics simulations. Our results indicate that both the charged G90D2.57 and the hydrophobic T94I2.61 mutation alter the dark state by weakening the interaction between the Schiff base (SB) and its counterion E1133.28 We propose that this interference with the tight regulation of the dim light photoreceptor rhodopsin increases background noise in the visual system and causes the loss of night vision characteristic for CSNB patients.
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Affiliation(s)
- Ankita Singhal
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Ying Guo
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Milos Matkovic
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Deparment of Biology, ETH Zurich, Zürich, Switzerland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland
| | - Elsa Cy Yan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Joerg Standfuss
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
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3
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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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Morrow JM, Chang BSW. Comparative Mutagenesis Studies of Retinal Release in Light-Activated Zebrafish Rhodopsin Using Fluorescence Spectroscopy. Biochemistry 2015; 54:4507-18. [PMID: 26098991 DOI: 10.1021/bi501377b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rhodopsin is the visual pigment responsible for initiating scotopic (dim-light) vision in vetebrates. Once activated by light, release of all-trans-retinal from rhodopsin involves hydrolysis of the Schiff base linkage, followed by dissociation of retinal from the protein moiety. This kinetic process has been well studied in model systems such as bovine rhodopsin, but not in rhodopsins from cold-blooded animals, where physiological temperatures can vary considerably. Here, we characterize the rate of retinal release from light-activated rhodopsin in an ectotherm, zebrafish (Danio rerio), demonstrating in a fluorescence assay that this process occurs more than twice as fast as bovine rhodopsin at similar temperatures in 0.1% dodecyl maltoside. Using site-directed mutagenesis, we found that differences in retinal release rates can be attributed to a series of variable residues lining the retinal channel in three key structural motifs: an opening in metarhodopsin II between transmembrane helix 5 (TM5) and TM6, in TM3 near E122, and in the "retinal plug" formed by extracellular loop 2 (EL2). The majority of these sites are more proximal to the β-ionone ring of retinal than the Schiff base, indicating their influence on retinal release is more likely due to steric effects during retinal dissociation, rather than alterations to Schiff base stability. An Arrhenius plot of zebrafish rhodopsin was consistent with this model, inferring that the activation energy for Schiff base hydrolysis is similar to that of bovine rhodopsin. Functional variation at key sites identified in this study is consistent with the idea that retinal release might be an adaptive property of rhodopsin in vertebrates. Our study is one of the few investigating a nonmammalian rhodopsin, which will help establish a better understanding of the molecular mechanisms contributing to vision in cold-blooded vertebrates.
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Mooney V, Sekharan S, Liu J, Guo Y, Batista VS, Yan ECY. Kinetics of thermal activation of an ultraviolet cone pigment. J Am Chem Soc 2014; 137:307-13. [PMID: 25514632 DOI: 10.1021/ja510553f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Visual pigments can be thermally activated via isomerization of the retinyl chromophore and hydrolysis of the Schiff base (SB) through which the retinyl chromophore is bound to the opsin protein. Here, we present the first combined experimental and theoretical study of the thermal activation of a Siberian hamster ultraviolet (SHUV) pigment. We measured the rates of thermal isomerization and hydrolysis in the SHUV pigment and bovine rhodopsin. We found that these rates were significantly faster in the UV pigment than in rhodopsin due to the difference in the structural and electrostatic effects surrounding the unprotonated Schiff base (USB) retinyl chromophore in the UV pigment. Theoretical (DFT-QM/MM) calculations of the cis-trans thermal isomerization revealed a barrier of ∼23 kcal/mol for the USB retinyl chromophore in SHUV compared to ∼40 kcal/mol for protonated Schiff base (PSB) chromophore in rhodopsin. The lower barrier for thermal isomerization in the SHUV pigment is attributed to the (i) lessening of the steric restraints near the β-ionone ring and SB ends of the chromophore, (ii) displacement of the transmembrane helix 6 (TM6) away from the binding pocket toward TM5 due to absence of the salt bridge between the USB and the protonated E113 residue, and (iii) change in orientation of the hydrogen-bonding networks (HBNs) in the extracellular loop 2 (EII). The results in comparing thermal stability of UV cone pigment and rhodopsin provide insight into molecular evolution of vertebrate visual pigments in achieving low discrete dark noise and high photosensitivity in rod pigments for dim-light vision.
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Affiliation(s)
- Victoria Mooney
- Department of Chemistry, Yale University , New Haven, Connecticut 06520 United States
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6
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Unusual kinetics of thermal decay of dim-light photoreceptors in vertebrate vision. Proc Natl Acad Sci U S A 2014; 111:10438-43. [PMID: 25002518 DOI: 10.1073/pnas.1410826111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present measurements of rate constants for thermal-induced reactions of the 11-cis retinyl chromophore in vertebrate visual pigment rhodopsin, a process that produces noise and limits the sensitivity of vision in dim light. At temperatures of 52.0-64.6 °C, the rate constants fit well to an Arrhenius straight line with, however, an unexpectedly large activation energy of 114 ± 8 kcal/mol, which is much larger than the 60-kcal/mol photoactivation energy at 500 nm. Moreover, we obtain an unprecedentedly large prefactor of 10(72±5) s(-1), which is roughly 60 orders of magnitude larger than typical frequencies of molecular motions! At lower temperatures, the measured Arrhenius parameters become more normal: Ea = 22 ± 2 kcal/mol and Apref = 10(9±1) s(-1) in the range of 37.0-44.5 °C. We present a theoretical framework and supporting calculations that attribute this unusual temperature-dependent kinetics of rhodopsin to a lowering of the reaction barrier at higher temperatures due to entropy-driven partial breakup of the rigid hydrogen-bonding network that hinders the reaction at lower temperatures.
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7
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Tsai FK, Fu HY, Yang CS, Chu LK. Photochemistry of a Dual-Bacteriorhodopsin System in Haloarcula marismortui: HmbRI and HmbRII. J Phys Chem B 2014; 118:7290-301. [DOI: 10.1021/jp503629v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fu-Kuo Tsai
- Department
of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Hsu-Yuan Fu
- Department
of Biochemical Science and Technology, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chii-Shen Yang
- Department
of Biochemical Science and Technology, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
- Institute
of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Li-Kang Chu
- Department
of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
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8
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Chiang HK, Chu LK. Solvent isotope effect on the dark adaptation of bacteriorhodopsin in purple membrane: viewpoints of kinetics and thermodynamics. J Phys Chem B 2014; 118:2662-9. [PMID: 24533671 DOI: 10.1021/jp412475u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermal retinal isomerization from all-trans, 15-anti to 13-cis, 15-syn of bacteriorhodopsin in purple membrane in H2O and D2O during dark adaptation was investigated at 30-55 °C at neutral pH. In this temperature range, phase transition of purple membrane and destruction of the tertiary structure of bacteriorhodopsin did not take place. We found that the solvent isotope effect is inverted below about 45 °C; i.e., k(f)(D2O)/k(f)(H2O) > 1. Applying the transition state theory, the changes in enthalpy from the initial state to the transition state along the thermal trans-to-cis forward reaction coordinate, ΔH(f)*, were determined to be 24.7 ± 1.2 and 20.1 ± 0.4 kcal mol(-1) in H2O and D2O, respectively. The relative entropic change of the transition state in H2O and D2O, ΔΔS(f)* = ΔS(f)*(D2O) - ΔS(f)*(H2O), was -14.4 ± 3.9 cal mol(-1) K(-1). In addition, the Gibbs free energy of trans-to-cis thermal isomerization reaction in D2O is 0.4-0.7 kcal mol(-1) lower than that in H2O. It is the first time the entropy and enthalpy of the transition state have been quantified to elucidate the solvent isotope effect in the retinal thermal isomerization of bacteriorhodopsin during dark adaptation. The solvent isotope effect on the thermodynamics properties and kinetics implied that the hydrogen bonding in the transition state during the dark adaptation of bR is stronger than that in the initial state.
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Affiliation(s)
- Han-Kuei Chiang
- Department of Chemistry, National Tsing Hua University , 101, Sec. 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
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Park PSH. Constitutively active rhodopsin and retinal disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2014; 70:1-36. [PMID: 24931191 DOI: 10.1016/b978-0-12-417197-8.00001-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells of the retina that initiates scotopic vision. In the dark, rhodopsin is bound to the chromophore 11-cis retinal, which locks the receptor in an inactive state. The maintenance of an inactive rhodopsin in the dark is critical for rod photoreceptor cells to remain highly sensitive. Perturbations by mutation or the absence of 11-cis retinal can cause rhodopsin to become constitutively active, which leads to the desensitization of photoreceptor cells and, in some instances, retinal degeneration. Constitutive activity can arise in rhodopsin by various mechanisms and can cause a variety of inherited retinal diseases including Leber congenital amaurosis, congenital night blindness, and retinitis pigmentosa. In this review, the molecular and structural properties of different constitutively active forms of rhodopsin are overviewed, and the possibility that constitutive activity can arise from different active-state conformations is discussed.
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Affiliation(s)
- Paul Shin-Hyun Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio, USA.
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Liu MY, Liu J, Mehrotra D, Liu Y, Guo Y, Baldera-Aguayo PA, Mooney VL, Nour AM, Yan ECY. Thermal stability of rhodopsin and progression of retinitis pigmentosa: comparison of S186W and D190N rhodopsin mutants. J Biol Chem 2013; 288:17698-712. [PMID: 23625926 DOI: 10.1074/jbc.m112.397257] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Over 100 point mutations in the rhodopsin gene have been associated with retinitis pigmentosa (RP), a family of inherited visual disorders. Among these, we focused on characterizing the S186W mutation. We compared the thermal properties of the S186W mutant with another RP-causing mutant, D190N, and with WT rhodopsin. To assess thermal stability, we measured the rate of two thermal reactions contributing to the thermal decay of rhodopsin as follows: thermal isomerization of 11-cis-retinal and hydrolysis of the protonated Schiff base linkage between the 11-cis-retinal chromophore and opsin protein. We used UV-visible spectroscopy and HPLC to examine the kinetics of these reactions at 37 and 55 °C for WT and mutant rhodopsin purified from HEK293 cells. Compared with WT rhodopsin and the D190N mutant, the S186W mutation dramatically increases the rates of both thermal isomerization and dark state hydrolysis of the Schiff base by 1-2 orders of magnitude. The results suggest that the S186W mutant thermally destabilizes rhodopsin by disrupting a hydrogen bond network at the receptor's active site. The decrease in the thermal stability of dark state rhodopsin is likely to be associated with higher levels of dark noise that undermine the sensitivity of rhodopsin, potentially accounting for night blindness in the early stages of RP. Further studies of the thermal stability of additional pathogenic rhodopsin mutations in conjunction with clinical studies are expected to provide insight into the molecular mechanism of RP and test the correlation between rhodopsin's thermal stability and RP progression in patients.
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Affiliation(s)
- Monica Yun Liu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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Sancho-Pelluz J, Tosi J, Hsu CW, Lee F, Wolpert K, Tabacaru MR, Greenberg JP, Tsang SH, Lin CS. Mice with a D190N mutation in the gene encoding rhodopsin: a model for human autosomal-dominant retinitis pigmentosa. Mol Med 2012; 18:549-55. [PMID: 22252712 DOI: 10.2119/molmed.2011.00475] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/10/2012] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin is the G protein-coupled receptor in charge of initiating signal transduction in rod photoreceptor cells upon the arrival of the photon. D190N (Rho(D190n)), a missense mutation in rhodopsin, causes autosomal-dominant retinitis pigmentosa (adRP) in humans. Affected patients present hyperfluorescent retinal rings and progressive rod photoreceptor degeneration. Studies in humans cannot reveal the molecular processes causing the earliest stages of the condition, thus necessitating the creation of an appropriate animal model. A knock-in mouse model with the D190N mutation was engineered to study the pathogenesis of the disease. Electrophysiological and histological findings in the mouse were similar to those observed in human patients, and the hyperfluorescence pattern was analogous to that seen in humans, confirming that the D190N mouse is an accurate model for the study of adRP.
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Affiliation(s)
- Javier Sancho-Pelluz
- Bernard and Shirlee Brown Glaucoma Laboratory, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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