Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Valsson, Ómar; Campomanes, Pablo; Tavernelli, Ivano; Röthlisberger, Ursula; Filippi, Claudia

doi:10.1021/ct3010408

Cited by 89 publications

(131 citation statements)

References 115 publications

(273 reference statements)

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“…In fact, the predicted scattering wavelengths for each single structure sampled during QM/MM simulations at a temperature of 300 K can differ by more than 100 nm. This outcome agrees with the results of 1PO excitation calculations for the same system, where the position of the absorption band is strongly dependent on the instantaneous thermal deformation of the protein and chromophore structures (68). It should be noted that our calculations refer to the ideal vertical transition, where concomitant absorption of the two photons takes place, and thus no structural relaxation on the virtual state occurs.…”

Section: Methodssupporting

confidence: 89%

Human infrared vision is triggered by two-photon chromophore isomerization

Palczewska

Vinberg

Stremplewski

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Vision relies on photoactivation of visual pigments in rod and cone photoreceptor cells of the retina. The human eye structure and the absorption spectra of pigments limit our visual perception of light. Our visual perception is most responsive to stimulating light in the 400-to 720-nm (visible) range. First, we demonstrate by psychophysical experiments that humans can perceive infrared laser emission as visible light. Moreover, we show that mammalian photoreceptors can be directly activated by near infrared light with a sensitivity that paradoxically increases at wavelengths above 900 nm, and display quadratic dependence on laser power, indicating a nonlinear optical process. Biochemical experiments with rhodopsin, cone visual pigments, and a chromophore model compound 11-cis-retinyl-propylamine Schiff base demonstrate the direct isomerization of visual chromophore by a two-photon chromophore isomerization. Indeed, quantum mechanics modeling indicates the feasibility of this mechanism. Together, these findings clearly show that human visual perception of near infrared light occurs by twophoton isomerization of visual pigments.visual pigment | two-photon absorption | rhodopsin | transretinal electrophysiology | multiscale modeling H uman vision is generally believed to be restricted to a visible light range, although >50% of the sun's radiation energy that reaches earth is in the infrared (IR) range (1). Human rod and cone visual pigments with the 11-cis-retinylidene chromophore absorb in the visible range, with absorption monotonically declining from their maxima of 430-560 nm toward longer wavelengths. The spectral sensitivity of human dim light perception matches well with the absorption spectrum of the rod visual pigment, rhodopsin (2, 3). Activation of visual pigments is temperature independent around their absorption peaks (λ max ), but at longer wavelengths, the lower energy photons must be supplemented by heat to achieve chromophore photoisomerization (4). Long wavelength-sensitive visual pigments of vertebrates exhibit maximal absorption at the ∼500-to ∼625-nm range. Pigments with λ max > 700 nm are theoretically possible, but the high noise due to spontaneous thermal activation would render them impractical (5). At human body temperature and with 1,050-nm stimulation, the sensitivity of the peripheral retina to one-photon (1PO) stimulation is less than 10 −12 of its maximum value at 505 nm (4, 6). Indeed, reports about human IR vision can be found in the literature, although they are fragmentary and do not describe the mechanism of this phenomenon.With the invention of radar during World War II, it was immediately questioned if pilots could detect high intensity radiation in the IR range of the spectrum. Wald and colleagues reported that at wavelengths above 800 nm, rod photoreceptors become more sensitive than cones, resulting in perception of IR signals as white light selectively in the peripheral retina (6). They proposed that relative spectral sensitivity declines monotonically toward longer wavele...

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Section: Methodssupporting

confidence: 89%

Human infrared vision is triggered by two-photon chromophore isomerization

Palczewska

Vinberg

Stremplewski

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…In contrast, the original FF does not account for the changes of the bond lengths between carbon−carbon single and double bonds in the RPSB chromophore and produces, as expected, a BLA close to 0. Since in the derivation As reported in previous studies, 44 we observe considerable differences in the counterion distances. In the crystal structure the NZ-H moiety appears to be involved in two equivalent hydrogen bonds with the carboxylate oxygens OE of the Glu113 counterion with a R NZ−OEGlu113 distance of 3.45 Å.…”

Section: Journal Of Chemical Theory and Computationsupporting

confidence: 65%

“…43 Currently, one has to rely on QM/MM methods in order to generate realistic structural models for a calculation of optical properties. 44 In order to overcome the time scale limitations associated with the QM/MM approach we apply the newly implemented QM/MM force matching protocol to derive a consistent set of FF parameters that reproduce the structural and dynamical properties at the QM/MM level. In particular, the new parameter set correctly captures thermal variations of the BLA in dark state RPSB.…”

Section: Introductionmentioning

confidence: 99%

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

Doemer

Maurer

Campomanes

et al. 2013

J. Chem. Theory Comput.

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We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.

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“…Solid lines: fit function f(x) = a·x + b with coefficients a = 0.59(11) and b = −0.059(13) for the A form, and a = 0.82(13) and b = −0.027(14) for the B form. Dashed lines: b = 0 with a = 1.06(9) for the A form and 1.07(4) for the B form.…”

mentioning

confidence: 99%

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein

Daday

Curutchet

Sinicropi

et al. 2015

J. Chem. Theory Comput.

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122

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The nature of the coupling of the photoexcited chromophore with the environment in a prototypical system like green fluorescent protein (GFP) is to date not understood, and its description still defies state-of-the-art multiscale approaches. To identify which theoretical framework of the chromophore-protein complex can realistically capture its essence, we employ here a variety of electronic-structure methods, namely, time-dependent density functional theory (TD-DFT), multireference perturbation theory (NEVPT2 and CASPT2), and quantum Monte Carlo (QMC) in combination with static point charges (QM/MM), DFT embedding (QM/DFT), and classical polarizable embedding through induced dipoles (QM/MMpol). Since structural modifications can significantly affect the photophysics of GFP, we also account for thermal fluctuations through extensive molecular dynamics simulations. We find that a treatment of the protein through static point charges leads to significantly blue-shifted excitation energies and that including thermal fluctuations does not cure the coarseness of the MM description. While TDDFT calculations on large cluster models indicate the need of a responsive protein, this response is not simply electrostatic: An improved description of the protein in the ground state or in response to the excitation of the chromophore via ground-state or state-specific DFT and MMpol embedding does not significantly modify the results obtained with static point charges. Through the use of QM/MMpol in a linear response formulation, a different picture in fact emerges in which the main environment response to the chromophore excitation is the one coupling the transition density and the corresponding induced dipoles. Such interaction leads to significant red-shifts and a satisfactory agreement with full QM cluster calculations at the same level of theory. Our findings demonstrate that, ultimately, faithfully capturing the effects of the environment in GFP requires a quantum treatment of large photoexcited regions but that a QM/classical model can be a useful approximation when extended beyond the electrostatic-only formulation.

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Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Cited by 89 publications

References 115 publications

Human infrared vision is triggered by two-photon chromophore isomerization

Human infrared vision is triggered by two-photon chromophore isomerization

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein

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