Photoactive Yellow Protein:  A Prototypic PAS Domain Sensory Protein and Development of a Common Signaling Mechanism

Cusanovich, Michael A.; Meyer, Terry E.

doi:10.1021/bi020690e

Cited by 157 publications

(192 citation statements)

References 85 publications

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“…2 (see later). As emphasized in a previous comparison of pCA 2 Scheme 1). The amplitude of the fluorescence redshift is smaller than that of the absorption, which leads to a progressive decrease of the large fluorescence Stokes shift from 6800 cm −1 for pCA 2− to 5200 cm −1 for pCT − .…”

Section: Steady-state Absorption and Fluorescence Spectramentioning

confidence: 74%

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Ultrafast light-induced response of photoactive yellow protein chromophore analogues

Espagne

Paik

Changenet‐Barret

et al. 2007

Photochem Photobiol Sci

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The fluorescence decays of several analogues of the photoactive yellow protein (PYP) chromophore in aqueous solution have been measured by femtosecond fluorescence up-conversion and the corresponding time-resolved fluorescence spectra have been reconstructed. The native chromophore of PYP is a thioester derivative of p-coumaric acid in its trans deprotonated form. Fluorescence kinetics are reported for a thioester phenyl analogue and for two analogues where the thioester group has been changed to amide and carboxylate groups. The kinetics are compared to those we previously reported for the analogues bearing ketone and ester groups. The fluorescence decays of the full series are found to lie in the 1-10 ps range depending on the electron-acceptor character of the substituent, in good agreement with the excited-state relaxation kinetics extracted from transient absorption measurements. Steady-state photolysis is also examined and found to depend strongly on the nature of the substituent. While it has been shown that the ultrafast light-induced response of the chromophore in PYP is controlled by the properties of the protein nanospace, the present results demonstrate that, in solution, the relaxation dynamics and pathway of the chromophore is controlled by its electron donor-acceptor structure: structures of stronger electron donor-acceptor character lead to faster decays and less photoisomerisation.

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Section: Steady-state Absorption and Fluorescence Spectramentioning

confidence: 74%

“…1-5 Its chromophore is a thioester derivative of p-coumaric acid in its trans deprotonated form (see pCA 2 phenolate group connected to a thioester group via a single ethylenic bond. It is covalently bound to the unique cystein residue of the protein (Cys69) through the thioester bond (see PYP, Scheme 1).…”

Section: Introductionmentioning

confidence: 99%

Ultrafast light-induced response of photoactive yellow protein chromophore analogues

Espagne

Paik

Changenet‐Barret

et al. 2007

Photochem Photobiol Sci

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“…Photoactive yellow protein (PYP) (27,28), in both its ground and photoexcited states, is examined as a test case. PYP from the halophilic photosynthetic bacterium Halorhodopsira halophila is a blue light receptor involved in negative phototaxis (29).…”

Section: Background On the Photoactive Yellow Protein Systemmentioning

confidence: 99%

Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation

Nome

Zhao

Hoff

et al. 2007

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

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We present a comprehensive study that integrates experimental and theoretical nonequilibrium techniques to map energy landscapes along well defined pull-axis specific coordinates to elucidate mechanisms of protein unfolding. Single-molecule force-extension experiments along two different axes of photoactive yellow protein combined with nonequilibrium statistical mechanical analysis and atomistic simulation reveal energetic and mechanistic anisotropy. Steered molecular dynamics simulations and free-energy curves constructed from the experimental results reveal that unfolding along one axis exhibits a transition-state-like feature where six hydrogen bonds break simultaneously with weak interactions observed during further unfolding. The other axis exhibits a constant (unpeaked) force profile indicative of a noncooperative transition, with enthalpic (e.g., H-bond) interactions being broken throughout the unfolding process. Striking qualitative agreement was found between the force-extension curves derived from steered molecular dynamics calculations and the equilibrium freeenergy curves obtained by Jarzynski-Hummer-Szabo analysis of the nonequilibrium work data. The anisotropy persists beyond pulling distances of more than twice the initial dimensions of the folded protein, indicating a rich energy landscape to the mechanically fully unfolded state. Our findings challenge the notion that cooperative unfolding is a universal feature in protein stability.nonequilibrium dynamics ͉ photoactive yellow protein ͉ biophysics A key step toward connecting protein structure, dynamics, and function is the insightful mapping of energy landscapes (1). A proper set of reaction coordinates encodes the progress of a transition through the dynamical bottleneck region and correlates energetics with structure. Significant advances, both experimental and computational, have been made to map energy landscapes and understand protein (un)folding mechanisms (2). Experimental methods such as fluorescence quenching (3), fluorescence resonance energy transfer (4), hydrogen exchange (5), and small-angle x-ray scattering (6) yielded insights into the rates and structures of folding intermediates. A common result emerging from these studies on a range of small water-soluble proteins is that protein unfolding occurs in a cooperative, all-or-none, transition with a single dominant barrier separating the native and unfolded states (7,8). However, these approaches tend to sample thermodynamically favorable pathways and do not address why other paths are not preferred. For example, a gradual progression of partially unfolded intermediates is usually not detected for these small proteins, possibly because such conformational states are not populated to a measurable extent. Recently, thermal unfolding studies exhibited thermodynamically noncooperative behavior (9, 10). Hence, the molecular basis for the cooperativity of protein folding is a matter of considerable debate (11).In addition, unfolding (i.e., both chemical and mechanical) is a highly nonequ...

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“…PYP serves as the structural prototype of the Per-Arnt-Sim (PAS) sensory domain and has provided a powerful system to dissect the physical mechanisms of light-activated signal transduction (9)(10)(11). Upon absorption of light at 446 nm and rapid charge rearrangement within its thioester-linked p-coumaric acid chromophore, PYP initiates a complex photocycle that couples the local trans-cis isomerization of a double bond within the chromophore to global conformational restructuring of the protein on the picosecond-to-millisecond time scale (12)(13)(14).…”

mentioning

confidence: 99%

Hydrogen bond dynamics in the active site of photoactive yellow protein

Sigala

Tsuchida

Herschlag

2009

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

144

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Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. We report the NMR detection of the hydrogen-bonded protons donated by Tyr-42 and Glu-46 to the chromophore oxygen in the active site of the bacterial photoreceptor, photoactive yellow protein (PYP). We have used the NMR resonances for these hydrogen bonds to probe their conformational properties and ability to rearrange in response to nearby electronic perturbation. The detection of geometric isotope effects transmitted between the Tyr-42 and Glu-46 hydrogen bonds provides strong evidence for robust coupling of their equilibrium conformations. Incorporation of a modified chromophore containing an electron-withdrawing cyano group to delocalize negative charge from the chromophore oxygen, analogous to the electronic rearrangement detected upon photon absorption, results in a lengthening of the Tyr-42 and Glu-46 hydrogen bonds and an attenuated hydrogen bond coupling. The results herein elucidate fundamental properties of hydrogen bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of hydrogen bonds observed in the PYP active site may facilitate the larger-scale dynamical coupling and signal transduction inherent to the biological function that PYP has evolved to carry out and may provide a model for other coupled dynamic systems.charge delocalization ͉ hydrogen bond coupling ͉ protein structure ͉ signal transduction

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Photoactive Yellow Protein: A Prototypic PAS Domain Sensory Protein and Development of a Common Signaling Mechanism

Cited by 157 publications

References 85 publications

Ultrafast light-induced response of photoactive yellow protein chromophore analogues

Ultrafast light-induced response of photoactive yellow protein chromophore analogues

Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation

Hydrogen bond dynamics in the active site of photoactive yellow protein

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