Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate

Rouhani, Shahab; Cartailler, Jean‐Philippe; Facciotti, Marc T.; Walian, Peter J.; Needleman, Richard; Lanyi, Janos Κ.; Glaeser, Robert M.; Luecke, Hartmut

doi:10.1006/jmbi.2001.5066

Cited by 96 publications

(143 citation statements)

References 51 publications

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“…The apparent mixture of conformations for Y83 in this structure suggests that, although the conformational states of R82 and Y83 may in some way be linked, changing the conformation of Y83 is also dependent on events other than a change in conformation of R82, such as the larger repacking of helices on the extracellular side of the protein that was seen earlier by Rouhani et al. (7).…”

Section: Structure Of the Anion-free Form Of Br(d85s)mentioning

confidence: 52%

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Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin

et al. 2004

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The structure of the D85S mutant of bacteriorhodopsin with a nitrate anion bound in the Schiff base binding site and the structure of the anion-free protein have been obtained in the same crystal form. Together with the previously solved structures of this anion pump, in both the anion-free state and bromide-bound state, these new structures provide insight into how this mutant of bacteriorhodopsin is able to bind a variety of different anions in the same binding pocket. The structural analysis reveals that the main structural change that accommodates different anions is the repositioning of the polar side chain of S85. On the basis of these X-ray crystal structures, the prediction is then made that the D85S/D212N double mutant might bind similar anions and do so over a broader pH range than does the single mutant. Experimental comparison of the dissociation constants, K d, for a variety of anions confirms this prediction and demonstrates, in addition, that the binding affinity is dramatically improved by the D212N substitution.

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Section: Structure Of the Anion-free Form Of Br(d85s)mentioning

confidence: 52%

“…The direction of movement is towards the position adopted in the crystals grown by Rouhani et al (7). In addition, the end of helix C is better ordered in the halide-free crystals grown in the presence of halide than in either the bromide or nitrate-bound forms.…”

Section: Structure Of the Anion-free Form Of Br(d85s)mentioning

confidence: 69%

Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin

et al. 2004

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“…It also contains a tryptophan residue at position 138, which is known from high-resolution crystal structures of bacteriorhodopsin and its mutants to be a key component of the complex hydrogen-bond network on the extracellular side of the protein, which undergoes substantial rearrangements late in the photocycle (Supplemental Fig. E; Luecke et al 2001;Rouhani et al 2001;Facciotti et al 2003). Thus, although it seems that Xop1 may function as a second bacteriorhodopsin, the significance of evolutionarily maintaining two such genes is difficult to explain unless there is some further differentiation of function.…”

Section: Photobiology: Opsins Cryptochrome/photolyase Clock Regulatmentioning

confidence: 99%

Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea

Baliga¹,

Bonneau²,

Facciotti³

et al. 2004

Genome Res.

278

210

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We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a halophilic archaeal isolate from the Dead Sea. The genome is organized into nine circular replicons of varying G+C compositions ranging from 54% to 62%. Comparison of the genome architectures of Halobacterium sp. NRC-1 and H. marismortui suggests a common ancestor for the two organisms and a genome of significantly reduced size in the former. Both of these halophilic archaea use the same strategy of high surface negative charge of folded proteins as means to circumvent the salting-out phenomenon in a hypersaline cytoplasm. A multitiered annotation approach, including primary sequence similarities, protein family signatures, structure prediction, and a protein function association network, has assigned putative functions for at least 58% of the 4242 predicted proteins, a far larger number than is usually achieved in most newly sequenced microorganisms. Among these assigned functions were genes encoding six opsins, 19 MCP and/or HAMP domain signal transducers, and an unusually large number of environmental response regulators-nearly five times as many as those encoded in Halobacterium sp. NRC-1-suggesting H. marismortui is significantly more physiologically capable of exploiting diverse environments. In comparing the physiologies of the two halophilic archaea, in addition to the expected extensive similarity, we discovered several differences in their metabolic strategies and physiological responses such as distinct pathways for arginine breakdown in each halophile. Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1.

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“…The energy-level calculations for the O-like conformer are based on a hybrid of the resting-state structure of the D85S mutant 23 for the Asp85 to Asp96 region and the M-state structural model for the extracellular-side groups, Arg82 through RG, as detailed in Methods. Re-isomerization of the retinal brings the positively charged SB closer to the proton on Asp85, making this O-like protonation microstate, in which both SB and Asp85 are occupied, unfavorable (Figure 4(C)).…”

Section: The O State and Completion Of The Cyclementioning

confidence: 99%

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

Onufriev

Smondyrev

Bashford

2003

Journal of Molecular Biology

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Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the photocycle, and affinity-switch models, which focus on changes in proton affinity of groups along the transport chain during the photocycle. Using newly available structural data, and adapting current methods of protein protonation-state prediction to the non-equilibrium case, we have calculated the relative free energies of protonation microstates of groups on the transport chain during key conformational states of the photocycle. Proton flow is modeled using accessibility limitations that do not change during the photocycle. The results show that changes in affinity (microstate energy) calculable from the structural models are sufficient to drive unidirectional proton transport without invoking an accessibility switch. Modeling studies for the N state relative to late M suggest that small structural re-arrangements in the cytoplasmic side may be enough to produce the crucial affinity change of Asp96 during N that allows it to participate in the reprotonation of the Schiff base from the cytoplasmic side. Methodologically, the work represents a conceptual advance compared to the usual calculations of pK a using macroscopic electrostatic models. We operate with collective states of protonation involving all key groups, rather than the individualgroup pK a values traditionally used. When combined with state-to-state transition rules based on accessibility considerations, a model for nonequilibrium proton flow is obtained. Such methods should also be applicable to other active proton-transport systems.

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Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate

Cited by 96 publications

References 51 publications

Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin

Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin

Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

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