Download Bacterial Rhodopsin Light-driven Proton Pump

BIMM130
Dr. Milton Saier
Week 7
Bacterial Rhodopsin Light-driven Proton Pump
Brho 3-D structure known to 1.55 Å.
1. Retinal (VitA aldehyde or retinaldehyde; one of 3 forms of VitA) is parallel to the plane of the membrane,
bound to K216 in the middle of helix 7.
2. The internal cavity is divided into two half channels, cytoplasmic and external (the H+ pathway)
3. The internal half channel is more hydrophobic.
4. The external half channel is more hydrophilic.
5. The N-terminus of the protein is outside; the C-terminus is inside.
Rhodopsin: K296 (out of 348aas for the bovine rhodopsin) is covalently linked to retinal via a Schiff’s base.
Bacterio-Rhodopsin: K216 (of 262aas) is covalently linked to retinal via a Schiff’s base.
1. Energy cycling: h absorption  photoisomerization (all-trans  13-cis)
2. This causes pKa changes in the Schiff’s base and amino acid residues. Sequential conformational changes 
differential access to the two half channels (each step is fast but has its own characteristic half life).
3. These changes allow access of the Schiff’s base (SB) to protonation only from the cytoplasm or deprotonation
to the external medium at any point in time.
4. Thermal reisomerization allows 13-cis  all-trans (slow)  cycle repeat.
hυ-driven bacterio-rhodopsin pumping: H+
D96
SB
D 85
(All-trans)
+
hυ
13-cis
E204
E194
H 2O
Steps
Outer
half
channel
Inner
half
channel











1.
2.
3.
4.
5.
6.
7.
 8.
 9.
 10.


 11.
 12.
h absorption
all-trans  13-cis
The protein changes geometry: D85 approaches SB.
The Schiff’s base donates H+ to D85.
A conformational change (dependent on SB protonation) causes helix 6 to tilt. Helices 3 and
7 also change conformation.
Then D85  E204  E194  H2O (out).
This is essentially irreversible because the external pH is low.
Helix 6 (& 7) tilt   hydration of the inner half channel (decreased contact with D85;
increased contact with D96).
 hydration of D96   pKa; it becomes an H+ donor.
The SB is reprotonated (SB deprotonation “opens” the inner 1/2 channel).
Reversal of the helix 6 tilt  restoration of the original pKa of D96. This restores the more
hydrophobic environment of D96; contact with the SB is lost.
D96 is reprotonated from the cytoplasm.
Retinal undergoes slow thermal reisomerization to all-trans.
Additional References
Essen LO (2002) Halorhodopsin: light-driven ion pumping made simple? Curr Opin Struct Biol 12:516-22
Hirai T, Subramaniam S, Lanyi JK (2009) Structural snapshots of conformational changes in a seven-helix
membrane protein: lessons from bacteriorhodopsin. Curr Opin Struct Biol 19:433-9
Lanyi JK (1997) Mechanism of ion transport across membranes. Bacteriorhodopsin as a prototype for proton
pumps. J Biol Chem 272:31209-12
Nagel G, Szellas T, Kateriya S, Adeishvili N, Hegemann P, Bamberg E (2005) Channelrhodopsins: directly
light-gated cation channels. Biochem Soc Trans 33:863-6
Zhai Y, Heijne WH, Smith DW, Saier MH, Jr. (2001) Homologues of archaeal rhodopsins in plants, animals and
fungi: structural and functional predications for a putative fungal chaperone protein. Biochim Biophys
Acta 1511:206-23
References for H+-specific Transporters
H+ Channels
Viral H+ Channels (PC# 1.A.19; 1.A.40): Cause acidification of the viral particle inside the viral envelope
(plants, fungi, etc.).
Cady SD, Luo W, Hu F, Hong M (2009) Structure and function of the influenza A M2 proton channel.
Biochemistry 48:7356-64
Fischer WB, Kruger J (2009) Viral channel-forming proteins. Int Rev Cell Mol Biol 275:35-63
DeCoursey TE (2008) Voltage-gated proton channels: what's next? J Physiol 586:5305-24
Mot/Exb (1.A.30): The motor for bacterial flagellar rotation.
Cascales, E., Lloubes, R., and Sturgis, J.N. (2001). The TolQ-TolR proteins energize TolA and share
homologies with the flagellar motor proteins MotA-MotB. Mol. Microbiol. 42, 795–807.
H+ Carriers
MC (2.A.29) – “Uncoupling” Proteins. They may shuttle the carboxylate end of fatty acids to facilitate
downhill H+ transport
Porter RK (2008) Uncoupling protein 1: a short-circuit in the chemiosmotic process. J Bioeng Biomembr
40:457-61
H+ Pumps
F-ATPase (3.A.2): These are rotary machines.
Arechaga, I. and Jones, P.C. (2001). The rotor in the membrane of the ATP synthase and relatives. FEBS
Lett. 494, 1–5.
Saroussi S, Nelson N (2009) The little we know on the structure and machinery of V-ATPase. J Exp
Biol 212:1604-10
P-ATPase (3.A.3): Two families of these enzyme/transporters contain proton translocating functions, one in
the stomachs of animals and one in plants, fungi and lower eukaryotes.
Duby G, Boutry M (2009) The plant plasma membrane proton pump ATPase: a highly regulated P-type
ATPase with multiple physiological roles. Pflugers Arch 457:645-55
Dunbar, L.A. and Caplan, M.J. (2001). Ion pumps in polarized cells: sorting and regulation of the Na+,K+and H+,K+-ATPases. J. Biol. Chem. 276, 29617–29620.
H+-PPase (3.A.10): These enzyme/transporters have 16 TMSs in a 6+4+6 arrangement, where the three
segments are repeat units.
Baltscheffsky, M., Schultz, A., and Baltscheffsky, H. (1999). H+-PPases: a tightly membrane-bound
family. FEBS Lett. 457, 527–533.
Miranda K, de Souza W, Plattner H, Hentschel J, Kawazoe U, Fang J, Moreno SN (2008)
Acidocalcisomes in Apicomplexan parasites. Exp Parasitol 118:2-9
Redox-coupled H+ Pumps (3.D.1-4): Protons are pumped out, coupled to electron flow, down the electron
transfer chain; a primary source of chemiosmotic energy.
Schultz, B.E. and Chan, S.I. (2001). Structures and proton-pumping strategies of mitochondrial
respiratory enzymes. Annu. Rev. Biophys. Biomol. Struct. 30, 23–65.
Yoshikawa S, Muramoto K, Shinzawa-Itoh K, Aoyama H, Tsukihara T, Shimokata K, Katayama Y,
Shimada H (2006) Proton pumping mechanism of bovine heart cytochrome c oxidase. Biochim Biophys
Acta 1757:1110-6
Note: Numbers in parentheses represent identification numbers on the Transporter Classification DataBase
(TCDB; www.TCDB.org)