Conformational Changes in the N-Terminal Region of Photoactive Yellow Protein: A Time-Resolved Diffusion Study

Hoshihara, Yuji; Imamoto, Yasushi; Kataoka, Mikio; Tokunaga, Fumio; Terazima, Masahide

doi:10.1529/biophysj.107.115253

Cited by 33 publications

(48 citation statements)

References 38 publications

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“…[25] In addition, the light induced changes of the radius of gyration of the M100L mutant of the full length PYP as observed by smallangle X-ray scattering are 5% [36] and are also small for truncated variants. [37] [38] Single molecule studies have additionally shown that the PAS domain is extended by several nm in the I 2 ′ state. [39] This is in line with the calculated radii of gyration of the P and (DEER and NMR derived) I 2 ′ structural ensembles which are 13.3 ± 0.08 Å and 15.4 ± 0.41 Å respectively.…”

Section: Discussionmentioning

confidence: 99%

The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes

Lovett²,

et al. 2011

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J.J.v.T. is a Royal Society University Research Fellow. We thank Gunnar Jeschke for help with initial experiments, for help with DEER data analysis and for valuable discussions. We thank Peter Höfer for access to facilities at Bruker BioSpin, Rheinstetten. We thank Jim McDonnell for help with acquiring NMR data. We acknowledge access to beamline ID09B at the European Synchrotron Radiation Facility under access number SC2438. We thank Michael Wulff for support at beamline ID09B at ESRF. We thank Jungkweon Choi for help with collecting TR-WAXS data. We thank Alexander Grishaev for help with the NIH CNS-SAXS program. J.J.v. Supporting information:Nuclear magnetic resonance, double electron electron resonance, and small angle X-ray scattering tables; figures; and experimental details. This material is available free of charge via the Internet at http://pubs.acs.org reduced folding of the I 2 ′ state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I 2 ′ state, which is structurally modeled by dynamical annealing and refinement calculations.

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Section: Discussionmentioning

confidence: 99%

The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes

Lovett²,

et al. 2011

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“…20,[31][32][33][34][35][36][37][38] Origins of D-change have been investigated and can be classified into two categories. The first category is related to photo-induced dimeriza- tion.…”

Section: Concentration Dependence Of the Diffusion Signalmentioning

confidence: 99%

Oligomeric-State-Dependent Conformational Change of the BLUF Protein TePixD (Tll0078)

Tanaka

Nakasone

Okajima

et al. 2009

Journal of Molecular Biology

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“…The prediction that a salt bridge is correlated with the unfolding route can also be addressed experimentally. Recently, a time-resolved diffusion study suggested that the Nterminal region, including Asp20, loses α-helical content after the proton transfer (35). Varying the ionic strength of the environment of PYP has a profound effect on the formation of pB, as shown by time-resolved absorption and fluorescence spectroscopy (36).…”

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Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein

Vreede

Juraszek

Bolhuis

2010

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

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Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the α-helical region 43-51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge that is part of the N-terminal domain. Additional molecular dynamics simulations indicate that the exposure of the chromophore does not result in a productive pathway. We discuss several possibilities for experimental validation of these predictions. Our results open the way for studying millisecond conformational changes in other medium-sized (signaling) proteins. molecular dynamics | protein unfolding mechanism | transition path sampling | transition state ensemble | committor analysis I nvestigation of the dynamics of large conformational changes in proteins leads to a better understanding of their functioning. Molecular simulation can complement experiments by modeling the dynamical time evolution of biomolecular systems in atomistic detail. Yet, even though straightforward all-atom molecular dynamics (MD) can now access the microsecond regime, simulating the kinetics of folding and other large conformational changes in proteins at ambient conditions has been limited to relatively small (model) proteins (1). Here we show how the transition path sampling technique enables investigation of the atomistic dynamical pathways for the millisecond timescale partial unfolding transition in a biologically relevant signaling protein, the photoactive yellow protein (PYP). Moreover, analysis of the ensembles of unbiased molecular trajectories allows the extraction of the (possibly complex) reaction coordinates.PYP is a water soluble blue-light photo receptor from Halorhodospira halophila (2, 3) composed of 125 amino acids and a covalently bound chromophore (para-coumaric acid, pCA) (4). The protein folds into a Per-Arnt-Sim core capped by an Nterminal domain (5, 6). Upon the absorption of a blue-light photon, PYP undergoes many different conformational rearrangements, culminating in the formation of the signaling state. The first steps in signaling state formation are the isomerization of pCA, on a picosecond timescale (7), followed by a proton transfer, taking place within microseconds (8, 9). These reactions result in an intermediate pB 0 with pCA in a strained configuration and a negative charge on a buried glutamate (Glu46) (10, 11). As a consequence, the protein partially unfolds to expose pCA and Glu46 to bulk water (12-14), completing ...

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Conformational Changes in the N-Terminal Region of Photoactive Yellow Protein: A Time-Resolved Diffusion Study

Cited by 33 publications

References 38 publications

The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes

The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes

Oligomeric-State-Dependent Conformational Change of the BLUF Protein TePixD (Tll0078)

Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein

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