Exploring the primary electron acceptor (Q<sub>A</sub>)‐site of the bacterial reaction center from <i>Rhodobacter sphaeroides</i>

Hucke, Oliver; Schmid, Ralf; Labahn, Andreas

doi:10.1046/j.0014-2956.2001.02699.x

Cited by 9 publications

(5 citation statements)

References 54 publications

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“…Likewise, the affinity of many compounds for the Q A site of Rb. sphaeroides RCs have been measured, providing a qualitative picture of the importance of the quinone ring substituents and the tail structure 5, 38–44. However, there has been little computational analysis of quinone affinity.…”

Section: Introductionmentioning

confidence: 99%

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis

Jalak

Väljamaë

2010

Biotech & Bioengineering

134

157

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Despite intensive research, the mechanism of the rapid retardation in the rates of cellobiohydrolase (CBH) catalyzed cellulose hydrolysis is still not clear. Interpretation of the hydrolysis data has been complicated by the inability to measure the catalytic constants for CBH-s acting on cellulose. We developed a method for measuring the observed catalytic constant (k(obs)) for CBH catalyzed cellulose hydrolysis. It relies on in situ measurement of the concentration of CBH with the active site occupied by the cellulose chain. For that we followed the specific inhibition of the hydrolysis of para-nitrophenyl-beta-D-lactoside by cellulose. The method was applied to CBH-s TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium and their isolated catalytic domains. Bacterial microcrystalline cellulose, Avicel, amorphous cellulose, and lignocellulose were used as substrates. A rapid decrease of k(obs) in time was observed on all substrates. The k(obs) values for PcCel7D were about 1.5 times higher than those for TrCel7A. In case of both TrCel7A and PcCel7D, the k(obs) values for catalytic domains were similar to those for intact enzymes. A model where CBH action is limited by the average length of obstacle-free way on cellulose chain is proposed. Once formed, productive CBH-cellulose complex proceeds with a constant rate determined by the true catalytic constant. After encountering an obstacle CBH will "get stuck" and the rate of further cellulose hydrolysis will be governed by the dissociation rate constant (k(off)), which is low for processive CBH-s.

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Section: Introductionmentioning

confidence: 99%

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis

Jalak

Väljamaë

2010

Biotech & Bioengineering

134

157

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“…sphaeroides and Rp. viridis ( − ) as well as in mutant RCs ( − ). In particular, FTIR studies of Rb.…”

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confidence: 99%

Vibrational Spectroscopy Favors a Unique Q_BBinding Site at the Proximal Position in Wild-Type Reaction Centers and in the Pro-L209 → Tyr Mutant fromRhodobacter sphaeroides

et al. 2002

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In the various X-ray structures of native reaction centers (RCs) from the photosynthetic bacterium Rhodobacter sphaeroides, two distinct main binding sites (distal and proximal) for the secondary quinone Q(B) have been described in the literature. The movement of Q(B) from its distal to proximal position has been proposed to account for the conformational gate limiting the rate of the first electron transfer from the primary quinone Q(A-) to Q(B). Recently, Q(B) was found to bind in the proximal binding site in the dark-adapted crystals of a mutant RC where Pro-L209 was changed to Tyr [Kuglstatter, A., Ermler, U., Michel, H., Baciou, L., and Fritzsch, G. (2001) Biochemistry 40, 4253-4260]. To test the structural and functional implications of the distal and proximal sites, a comparison of the FTIR vibrational properties of Q(B) in native RCs and in the Pro-L209 --> Tyr mutant was performed. Light-induced FTIR absorption changes associated with the reduction of Q(B) in Pro-L209 --> Tyr RCs reconstituted with 13C-labeled ubiquinone (Q3) at the 1 or 4 position show a highly specific IR fingerprint for the C=O and C=C modes of Q(B) upon selective labeling at C1 or C4. This IR fingerprint is very similar to that of native RCs, demonstrating that equivalent interactions occur between neutral Q(B) and the protein in native and mutant RCs. Consequently, Q(B) occupies the same binding site in all RCs. Since the FTIR data fit the description of Q(B) bonding interactions in the proximal site, it is therefore concluded that neutral Q(B) also binds to the proximal site in native functional RCs. The implication of these new results for the conformational gate of the first electron transfer to Q(B) is outlined.

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“…DMNQ and VK structures were constructed starting from the UQ structure, by replacing the methoxy groups with the NQ aromatic ring, without alteration of the quinone ring (Figure 2F). This orientation of the NQ ring (of DMNQ and VK) was chosen as previous docking calculations have suggested it is the most favorable (Hucke et al, 2002). …”

Section: Methodsmentioning

confidence: 99%

Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site

Zhao¹,

Lamichhane²,

Hastings³

2013

Front. Plant Sci.

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Previously we have shown that ONIOM type (QM/MM) calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and 18O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0), 2,3,5,6-tetramethyl-1, 4-benzoquinone (duroquinone, DQ), and 2,3-dimethyl-l,4-naphthoquinone (DMNQ) incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites. The normal modes that contribute to the bands in the calculated spectra, their composition, frequency, and intensity, and how these quantities are modified upon 18O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10–13 cm−1 separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry in H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are “tail-less.” Spectra were also calculated for reaction centers with corresponding “tail” containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated spectra.

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Exploring the primary electron acceptor (Q_A)‐site of the bacterial reaction center from Rhodobacter sphaeroides

Cited by 9 publications

References 54 publications

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis

Vibrational Spectroscopy Favors a Unique Q_BBinding Site at the Proximal Position in Wild-Type Reaction Centers and in the Pro-L209 → Tyr Mutant fromRhodobacter sphaeroides

Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site

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Exploring the primary electron acceptor (QA)‐site of the bacterial reaction center from Rhodobacter sphaeroides

Cited by 9 publications

References 54 publications

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis

Vibrational Spectroscopy Favors a Unique QBBinding Site at the Proximal Position in Wild-Type Reaction Centers and in the Pro-L209 → Tyr Mutant fromRhodobacter sphaeroides

Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site

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Exploring the primary electron acceptor (Q_A)‐site of the bacterial reaction center from Rhodobacter sphaeroides

Vibrational Spectroscopy Favors a Unique Q_BBinding Site at the Proximal Position in Wild-Type Reaction Centers and in the Pro-L209 → Tyr Mutant fromRhodobacter sphaeroides