The Solution Structure of a Transient Photoreceptor Intermediate: Δ25 Photoactive Yellow Protein

Bernard, Cédric; Houben, Klaartje; Derix, N.M.; Marks, David I.; Horst, Michael; Hellingwerf, Klaas J.; Boelens, Rolf; Kaptein, Robert; Nuland, Nico A. J. van

doi:10.1016/j.str.2005.04.017

Cited by 72 publications

(125 citation statements)

References 46 publications

Supporting

Mentioning

114

Contrasting

Order By: Relevance

supporting

confidence: 61%

“…Replica exchange MD (REMD) simulations indicated that the formation of pB involves the unfolding of the α-helical region 43-51 and the solvent exposure of Glu46 and pCA (14). The predicted signaling state showed remarkable agreement with the NMR structure of the pB state of the N-terminally truncated mutant Δ 25 -PYP (13,19).Notwithstanding the success of the signaling state prediction, the room temperature kinetic mechanism by which pB is formed remained hidden due to the nature of the REMD sampling method. In this work we aim to provide mechanistic details at atomistic resolution of the submillisecond unfolding process of PYP by molecular simulation.…”

mentioning

confidence: 70%

“…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)(13)(14), completing the formation of the signaling state pB.…”

mentioning

confidence: 99%

See 2 more Smart Citations

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.

View full text Add to dashboard Cite

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 ...

show abstract

supporting

confidence: 61%

mentioning

confidence: 70%

See 1 more Smart Citation

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.

View full text Add to dashboard Cite

show abstract

“…H͞D exchange monitored by NMR spectroscopy indicates that, although pB formation involves a significant loss of structure, it retains a well folded core (31). NMR measurements on a PYP derivative lacking the 25 N-terminal amino acids indicate that the central ␤-sheet in pB is still intact, whereas much of the remainder of the protein becomes highly flexible (16), implying an increase in the linear dimension of PYP of up to 4.5 Å along the two axes studied here. Small-angle x-ray scattering experiments on PYP and Nterminally truncated mutants revealed that the N-terminal 15 residues in PYP move away from the core of PYP upon pB formation, whereas the remainder of PYP swells by 0.7 Å (15).…”

Section: Force-extension Curves In the Dark And Under Illuminationmentioning

confidence: 99%

“…Previous solution spectroscopy experiments indicate that unfolding of the two N-terminal helices of PYP is involved (10,(13)(14)(15). Recent NMR measurements on a PYP mutant lacking the 25 N-terminal residues indicate that regions outside the central ␤-sheet also undergo a significant increase in flexibility (16). Interestingly, activation of LOV, a PAS domain blue-light receptor in plants, involves partial unfolding of a C-terminal helix immediately beyond the PAS domain core of the receptor (17), suggesting that the unfolding of N-or C-terminal helices is a general theme in PAS domain activation.…”

mentioning

confidence: 99%

Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation

Zhao

Lee²,

Nome

et al. 2006

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

View full text Add to dashboard Cite

The Per-Arnt-Sim (PAS) domain is a ubiquitous protein module with a common three-dimensional fold involved in a wide range of regulatory and sensory functions in all domains of life. The activation of these functions is thought to involve partial unfolding of N-or C-terminal helices attached to the PAS domain. Here we use atomic force microscopy to probe receptor activation in single molecules of photoactive yellow protein (PYP), a prototype of the PAS domain family. Mechanical unfolding of Cys-linked PYP multimers in the presence and absence of illumination reveals that, in contrast to previous studies, the PAS domain itself is extended by Ϸ3 nm (at the 10-pN detection limit of the measurement) and destabilized by Ϸ30% in the light-activated state of PYP. Comparative measurements and steered molecular dynamics simulations of two double-Cys PYP mutants that probe different regions of the PAS domain quantify the anisotropy in stability and changes in local structure, thereby demonstrating the partial unfolding of their PAS domain upon activation. These results establish a generally applicable single-molecule approach for mapping functional conformational changes to selected regions of a protein. In addition, the results have profound implications for the molecular mechanism of PAS domain activation and indicate that stimulusinduced partial protein unfolding can be used as a signaling mechanism.atomic force spectroscopy ͉ photoactive yellow protein ͉ receptor activation B iological signaling starts with the activation of receptor proteins, in which stimuli trigger protein conformational changes that relay a signal to an associated signal transduction chain. A central question concerns the nature of the structural changes that activate a receptor protein. The mechanism of signaling by PerArnt-Sim (PAS) domain-containing proteins is of considerable interest, because these structural domains occur in many signaling proteins (1). In addition, incorrect signaling by PAS domains is associated with a range of diseases. Important examples are mutations in the human ERG potassium channel, which causes cardiac arrhythmias (2), and the involvement of hypoxia-inducible factors in myocardial and cerebral ischemia (3).We investigate the photoinduced structural changes in the bacterial blue light receptor, photoactive yellow protein (PYP), a prototype for PAS domains (4). As shown in Fig. 1, PYP consists of two N-terminal ␣-helices (residues 1-25), followed by a typical PAS domain (1, 5) fold (residues 26-125) that contains a central six-stranded ␤-sheet flanked by ␣-helices (6). The protein exhibits photochemistry based on its p-coumaric acid chromophore (7). Blue light converts the initial pG state of PYP into the photoactivated pB state in milliseconds, whereas pB decays back to pG in Ϸ0.5 s (8). The pB state is believed to trigger negative phototaxis in purple bacteria (9).The structural changes that occur upon pB formation involve partial unfolding of the receptor, indicating partial protein unfolding as a novel signaling m...

show abstract

Changes in Active Site Hydrogen Bonding upon Formation of the Electronically Excited State of Photoactive Yellow Protein

Hoff

Kang

Kumauchi

et al. 2010

Hydrogen Bonding and Transfer in the Excited State

View full text Add to dashboard Cite

Light plays three main roles in biology. First, light from the sun provides the main source of energy driving the biosphere through chlorophyll-based electron transfer in photosynthetic reaction centers and retinal-based proton pumping in rhodopsins [1]. Second, light is a source of information about the environment for many organisms using photosensory proteins, including animals, plants, fungi and bacteria [2,3]. Third, light can cause damage to biological systems. Light from the near-UV region can damage DNA [4], and excess visible light can damage the photosynthetic machinery in photoinhibition [5]. Thus, light is of great importance for a wide range of biological processes.Proteins that perform photosynthesis or light sensing consist of an apoprotein and a bound chromophore. Only a small number of chromophores account for most known processes in photobiology: chlorophyll and linear tetrapyrroles, caretoids and retinal, flavins and p-coumaric acid [2]. In many cases the chromophore has strong and functionally important interactions with the protein binding pocket, particularly charge-charge interactions and hydrogen bonding interactions. While many different proteins interact with light in a wide range of organisms, almost all of these systems are based on key types of photochemical processes, including electron transfer, C¼C double bond isomerization and the formation of chemical bonds [2,6]. These photochemical events often trigger a cascade of thermal reactions in the protein that extends to the millisecond and minute range, and that result in a biologically relevant output. If the cascade of thermal reactions results in the re-formation of the initial state, the process is referred to as a photocycle. It is the initial ultrafast

show abstract

The Solution Structure of a Transient Photoreceptor Intermediate: Δ25 Photoactive Yellow Protein

Cited by 72 publications

References 46 publications

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

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

Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation

Changes in Active Site Hydrogen Bonding upon Formation of the Electronically Excited State of Photoactive Yellow Protein

Contact Info

Product

Resources

About