2
|
Faramarzi S, Feng J, Mertz B. Allosteric Effects of the Proton Donor on the Microbial Proton Pump Proteorhodopsin. Biophys J 2018; 115:1240-1250. [PMID: 30219284 DOI: 10.1016/j.bpj.2018.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 11/17/2022] Open
Abstract
Proteorhodopsin (PR) is a microbial proton pump that is ubiquitous in marine environments and may play an important role in the oceanic carbon cycle. Photoisomerization of the retinal chromophore in PR leads to a series of proton transfers between specific acidic amino acid residues and the Schiff base of retinal, culminating in a proton motive force to facilitate ATP synthesis. The proton donor in a similar retinal protein, bacteriorhodopsin, acts as a latch to allow the influx of bulk water. However, it is unclear if the proton donor in PR, E108, utilizes the same latch mechanism to become internally hydrated. Here, we used molecular dynamics simulations to model the changes in internal hydration of the blue variant of PR during photoactivation with the proton donor in protonated and deprotonated states. We find that there is a stark contrast in the levels of internal hydration of the cytoplasmic half of PR based on the protonation state of E108. Instead of a latch mechanism, deprotonation of E108 acts as a gate, taking advantage of a nearby polar residue (S61) to promote the formation of a stable water wire from bulk cytoplasm to the retinal-binding pocket over hundreds of nanoseconds. No large-scale conformational changes occur in PR over the microsecond timescale. This subtle yet clear difference in the effect of deprotonation of the proton donor in PR may help explain why the photointermediates that involve the proton donor (i.e., M and N states) have timescales that are orders of magnitude different from the archaeal proton pump, bacteriorhodopsin. In general, our study highlights the importance of understanding how structural fluctuations lead to differences in the way that retinal proteins accomplish the same task.
Collapse
Affiliation(s)
- Sadegh Faramarzi
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Jun Feng
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Blake Mertz
- C. Eugene Department of Chemistry, West Virginia University, Morgantown, West Virginia.
| |
Collapse
|
3
|
Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT. A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site. PLoS One 2016; 11:e0156543. [PMID: 27327432 PMCID: PMC4915679 DOI: 10.1371/journal.pone.0156543] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/19/2016] [Indexed: 11/24/2022] Open
Abstract
Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. We report phylogenetic analyses, structural modeling, genomic context analysis and biochemistry, to describe the evolutionary relationship of these recently described proteins with other opsins, show that they are expressed and do not bind retinal in a canonical manner. Given these data, we propose a hypothesis that these abnormal opsin homologs may represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. If true, this finding would challenge our current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.
Collapse
Affiliation(s)
- Erin A. Becker
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Microbiology Graduate Group, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Andrew I. Yao
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Phillip M. Seitzer
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Proteome Software, 1340 SW Bertha Blvd., Portland, Oregon, United States of America
| | - Tobias Kind
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Ting Wang
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Rich Eigenheer
- California Department of Food and Agriculture, 1220 N St., Sacramento, CA, 95814, United States of America
| | - Katie S. Y. Shao
- William’s College, 880 Main St., Williamstown, MA, 01267, United States of America
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| | - Marc T. Facciotti
- Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Microbiology Graduate Group, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
- Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America
| |
Collapse
|