Temperature and cryoprotectant influence secondary quinone binding position in bacterial reaction centers

Pokkuluri, P.R.; Laible, Philip D.; Crawford, Adam E; Mayfield, Joy F; Yousef, Mohammed; Ginell, Stephan L.; Hanson, Deborah K.; Schiffer, M.

doi:10.1016/j.febslet.2004.06.042

Cited by 21 publications

(35 citation statements)

References 29 publications

(71 reference statements)

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“…In X-ray diffraction and spectroscopic studies, cryoprotectants, such as ethylene glycol or glycerol, are commonly used to keep the RC protein intact at cryogenic temperatures. This procedure, however, might introduce artifacts into the RC structure with respect to cofactor and side-chain positions [45,[58][59][60][61]. In this respect, the use of trehalose matrices at room temperature, to condition the RC protein dynamics, represents an attractive alternative to the low-temperature approach for structure determination.…”

Section: Conformational Substates and Dynamicsmentioning

confidence: 99%

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

et al. 2015

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The structural and dynamical interaction of proteins with their microenvironment in disordered matrices plays a decisive role for their function; EPR spectroscopy is a powerful tool for shading light onto the molecular mechanisms of this protein-matrix interplay. To clarify the molecular mechanisms of disaccharide bioprotection, we studied the structure and dynamics of spin-labeled systems and photosynthetic reaction centers (RCs) in sucrose and trehalose matrices at different hydration levels by means of cw and pulse high-field 95 GHz (W-band) EPR as well as by FTIR. In this minireview, we summarize and discuss EPR and FTIR experiments showing that the anhydrobiotic state of the RC-trehalose system (1) is not the result of matrix-induced changes of the local structure of the charge-separated radical-pair cofactors, P Áþ 865 and Q ÁÀ A , and (2) is not the result of changes of local dynamics and local hydrogen bonding of Q A in its binding pocket. Rather, the extreme impairment of RC dynamics caused by incorporation into the dehydrated trehalose matrix, which also protects it against thermal denaturation, originates in the high rigidity, already at room temperature, of the dry trehalose glass matrix coating the RC protein surface. This surface hydrogen-bonding scaffold shifts the correlation time of thermal conformational fluctuations into the non-biological time domain. Another intriguing aspect of disaccharide bioprotection is the superior The authors dedicate this work to Giovanni Giacometti on the occasion of his 85th birthday. AppliedMagnetic Resonance efficiency of trehalose versus sucrose matrices in stabilizing the anhydrobiotic state of proteins. To clarify the molecular basis of this specificity, glassy trehalose-water and sucrose-water binary systems, incorporating a nitroxide radical as spin probe, have been studied by high-field W-band EPR spectroscopy at different water contents. Analysis of the EPR spectra revealed a different structural and dynamical organization in the sucrose and trehalose matrix, only the trehalose being homogeneous in terms of residual water and nitroxide distribution.

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Section: Conformational Substates and Dynamicsmentioning

confidence: 99%

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

et al. 2015

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“…34 For the bRC of R. sphaeroides, only the proximal position of Q B is used for the calculations since the distal position is thought to be unproductive. [49][50][51][52] For both structures, the lipids of the crystal structures were included in the calculations. Hydrogen atoms are placed with the HBUILD module 53 of CHARMM, 54 followed by energy optimization of the hydrogen positions, while the heavy-atom positions are kept fixed.…”

Section: Structure Preparationmentioning

confidence: 99%

Proton-Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations

Krammer

Till

Sebban

et al. 2009

Journal of Molecular Biology

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“…Since binding to these two sites is nearly isoenergetic, small changes in the binding free energy resulting from temperature or external solvent could lead to a change in the relatively occupancy. This may be one reason for the reported differences in the binding position of Q B (26)(27)(28)(29)(30)69) and the FTIR observation that Q B prefers to bind at the proximal position at room temperature (46). …”

Section: Conformational Assignments Of the Q B States In The Mutant Rcsmentioning

confidence: 99%

Trapped Conformational States of Semiquinone (D⁺^•Q_B^-^•) Formed by B-Branch Electron Transfer at Low Temperature in Rhodobacter sphaeroides Reaction Centers

et al. 2006

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The reaction center (RC) from Rhodobacter sphaeroides captures light energy by electron transfer between quinones Q A and Q B , involving a conformational gating step. In this work, conformational states of D +• Q B −• were trapped (80K) and studied using EPR spectroscopy in mutant RCs that lack Q A in which Q B was reduced by the bacteriopheophytin along the B-branch. In mutant RCs frozen in the dark, a light induced EPR signal due to D +• Q B −• formed in 30% of the sample with low quantum yield (0.2%-20%) and decayed in 6 s. A small signal with similar characteristics was also observed in native RCs. In contrast, the EPR signal due to D + Q B − in mutant RCs illuminated while freezing formed in ~ 95% of the sample that did not decay (τ >10 7 s) at 80K. In all samples, the observed gvalues were the same (g=2.0026) indicating that all active Q B −• was located in a proximal conformation coupled with the non-heme Fe 2+ . We propose that before electron transfer at 80K, the majority (~70%) of Q B , structurally located in the distal site, cannot be stably reduced, while the minor ( can be considered to be the initial and final states along the reaction coordinate for conformationallygated electron transfer.

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Temperature and cryoprotectant influence secondary quinone binding position in bacterial reaction centers

Cited by 21 publications

References 29 publications

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

Proton-Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations

Trapped Conformational States of Semiquinone (D⁺^•Q_B^-^•) Formed by B-Branch Electron Transfer at Low Temperature in Rhodobacter sphaeroides Reaction Centers

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Temperature and cryoprotectant influence secondary quinone binding position in bacterial reaction centers

Cited by 21 publications

References 29 publications

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

Proton-Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations

Trapped Conformational States of Semiquinone (D+•QB-•) Formed by B-Branch Electron Transfer at Low Temperature in Rhodobacter sphaeroides Reaction Centers

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Trapped Conformational States of Semiquinone (D⁺^•Q_B^-^•) Formed by B-Branch Electron Transfer at Low Temperature in Rhodobacter sphaeroides Reaction Centers