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How similar tridimensional structures could have different biological functionality

Alejandro G´mez Espinosa o
Escuela Polit´cnica Nacional e Quito - Ecuador

June 23, 2010

Abstract Bacteriorhodopsin and Rhodopsin are two Opsin proteins that have similar tridimensional structure, share the same chromophore but have different primary structure. During the study of each protein could be found that both respond different to light absorption processes and because of it have different biological functionality.

In nature, it is possible to find many examples of molecules which share similar structures but have different biological functionality and primary structure, such as retinal proteins or chlorophills. For example, chlorophyll, the vital pigment found in most plants and algae cells, has five different structures; they differ only on the position of a couple of hydrogen and oxygen atoms in their molecules and this subtle change determines the specific properties and function of these structures in the process of photosynthesis [14]. On the other hand, retinylidene proteins (RP), also called Opsins, are a family of proteins found in photoreceptor cells that have a similar tridimensional structure of a seven transmembrane helices that enclose a chromophore called retinal. Nature uses this chromophore in processes such as vision, bioenergetics or phototaxis which is the movement of organisms in response to light stimuli (Hayashi et al 2003). Bacteriorhodopsins (bR) and Rhodopsins (Rh) are good examples of such RP. Figure 1 shows the similar tridimensional structure of the proteins. Hoffmann et al (2006) point out that such lightabsorbing chromophore triggers the response of the protein to light. Free retinal absorbs light at maximal wavelength of 370nm but retinal inside Rh absorbs light at 500nm and inside bR at 560 nm

[14]. It suggests that the environment surrounding a protein could modulate drastically the process of absorption made by retinal because this significant change in the wavelegth of light absorption; although it is known that these two RP contain the same chromophore. When a protein absorbs light, it changes the retinal’s conformation from cis to all-trans or vice versa. bR makes use of it to activate energy storages processes whereas Rh uses it as a photosensorial signal.

Figure 1: Graphical representation of bR and Rh. [7]


Retinylidene Protein
As said before, RP is a family of proteins within which it is possible to locate a retinal chromophore inside their seven transmembrane helices bundled structure. A graphical representation of this chromophore is shown in Figure 2. Such RP are activated by light via a process called photoisomerization, which changes the retinal conformation from cis to trans or vice versa in order to activate a signal transduction mechanism within the cell (Terakita et al. 2005). Depending on the purpose of the photoisomerization and their sequence, RP can be divided into two groups: Ion channels and proton pumps, and G protein-coupled receptors The first ones consist in RP with their retinal in an all-trans conformation at their ground state that isomerizes to 13-cis upon light activation (Balu et al 2008), shown in Figure 3. Bacteriorhodopsin is one of these proteins that acts as a proton pump in order to perform a processes inside the archaea similar to photosynthesis in plants. A proton pump is a kind of protein that moves protons across the cytoplasmic side to the extracellular side of the membrane in bacteria and other ATP-producing organelles (Hayashi et al 2003).

Figure 3: Retinal chromophores and their light-induced isomerizations in Rh (left) and bR (right). [4]

bR is a protein in the cell membrane of Halobacteria archaea which are unicellular organisms who live where the salt concentration is very high; they possess the simplest known biological device of energy conversion (Lanyi 1997 and Tajkhorshid et al. 2000) and the best understood ion pump (Luecke et al. 199) bR carries out the simplest known form of biological photosynthetic energy storage (BenNun et al 1998). A graphical representation of bR is shown in Figure 4

Figure 2: Graphical representation of Retinal with a linked base Lys216 in bR. [7]
The other ones, G protein-coupled receptors sometimes called seven-transmembrane domain receptors or GPCRs, sense molecules or particles outside the cell and activate a signal transduction inside the cell producing a cellular response (Fotiadis et al 2004). Opsins have their retinal in a 11cis conformations in their ground state and photoisomerize it to an all-trans conformation upon light activation (Balu et al 2008), shown in Figure 3. Rhodopsin belongs to these kind of proteins which after photoisomerization take place they change the conformation of the protein that activate the G protein (Terakita et al. 2005).

Figure 4: Graphical representation of bR. Alpha Helix are shown in purple in a New Cartoon representation and retinal in green in a WdV rep. [7]
This transmembrane protein can be found in a purple membrane for the Halobacterium salinarium and weighs about 26 kDa according to Humphrey et al 1998. As a RP, bR is arranged


in a seven transmembrane helix with the retinal linked via a protonated Schiff base to Lys216 (lysine216) close to the middle of helix G as shown in Figure 4 and Figure 5. bR secondary structure is shown as well in Figure 5. The extracellular and cytoplasmic sides are divided inside the interhelical cavity by the Schiff base, this channel describes the trajectory of the proton (Lanyi 1998).

bR acts as a light-driven proton pump in the purple membrane, i.e. it absorbs light and converts it into a proton gradient across the cellular membrane (Hayashi et al 2003). This proton gradient drives the synthesis of adenine triphosphate (ATP) by the ATP syntase (Luecke et al 1999; Humphrey et al 1998). Due to its unusual stability, the exhibition of a strong spectral shifts within the 500-650 nm range and the possibility of measure its vibrational spectra, bR is an ideal system resource for research.

Figure 6: Graphical representation of Rh. Alpha Helices are shown in purple in a New Cartoon representation and retinal in green in a WdV rep. [7]

Kandori et al 2001 and Saam et al 2002 stated that Rh is a well studied protein due to its abundance and importance as the unique photoreceptor in the external segment of rod cells and cones of vertebrate and invertebrate retinas universally. Rh accounts for more than 90% of the protein in retinal rod cells (Khorana 1993). Rh is the only member of GPCRs for which a high-resolution crystal structure is available too. Figure 6 shows the tridimensional structure of Rh, it consists of seven transmembrane helices as described before, and Figure 7 shows its secondary structure. As a RP, inside Rh is located the retinal chomophore that is the responsible of a very efficient light absorption processes in the middle of the visible spectrum (close to 500 nm) in this case [14]. Retinal in Rh is bound to the protein through a protonated Schiff base linkage to Lys296. In its ground state in Rh, retinal is in a 11-cis conformation that stabilizes the inactive conformation of Rh and because of light absorption processes, retinal changes to all-trans conformation. This photoisomerization of retinal initiates a photocycle that is conducted in a series of interconvertions between different conformational states of Rh (Saam et al 2002). This photocycle transforms the light energy into atomic motion which leads to the closing of ion channels and the generation of a nerve impulse [14]. Kandori et al 2001, indicate that Rh produces chemical signals outside the

Figure 5: A secondary structure model of bR showing the amino acids involved in proton translocation. Retinal is linked to Lys216 as a Schiff base. The arrow indicates the direction of proton transport. [4]
Photoisomerization processes of the all-trans to 13-cis retinal conformation produce a large displacement of the methyl group C13 that makes a conformational change in E and F helices of bR and its cytoplasmic loops. When bR is activated by light, it opens a cytoplasmic channel that allows a proton to enter into the protein (Balu et al 2008).


cell, mechanisms that identifies it as a G proteincoupled receptor or GPCR.

tion of retinal in bacteriorhodopsin. Faraday Discuss. 110. pp:447-462. [3] Fortiadis, D., et al, 2004. The G proteincoupled receptor rhodopsin in tehe native membrane. FEBS Letters. 564. pp:281-288. [4] Khorana, G. H., 1993. Two lighttransducing membrane proteins: Bacteriorhodopsin and the mammalian rhodopsin. Proc. Natl. Acad. Sci. USA. 90. pp:1166-1171. [5] Hayashi, S., Tajkhorshid, E., Schulten, K., 2003. Molecular Dynamics Simulation of Bacteriorhodopsin’s Photoisomerization Using Ab Initio Forces for the Excited Chromophore. Biophysical Journal. 85(3). pp:1440-1449. [6] Hayashi, S., Tajkhorshid, E., Schulten, K., 2009. Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation. Biophysical Journal. 96(2). pp:403-416. [7] Humphrey, W., Dalke, A., Schulten, K. 1996. VMD - Visual Molecular Dynamics, J. Molec. Graphics 14. pp:33-38. [8] Humphrey, W., et al, 1998. Three Electronic State Model of the Primary Phototransformation of Bacteriorhodopsin. Biophysical Journal. 75. pp:1689-1699. [9] Hoffmann, M., et al, 2006. Color Tuning in Rhodopsins: The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin II. J. Am. Chem. Soc. 128(33). pp:10808-10818. [10] Kandori, H., Shichida, Y., Yoshizawa, T., 2001. Photoisomerization in Rhodopsin. Biochemistry (Moskow). 66(11). pp:11971209. [11] Lanyi, J., 1997. Mechanims of ion transport across membranes. Bacteriorhodopsin as a prototype for proton pumps. J. Biol. Chem. 272. pp:31209-31212. [12] Luecke, H., et al, 1999. Structure of bacteriorhodopsin at 1.55 A resolution. J. Mol. Biol. 291. pp:899-911. [13] Saam, J., Tajkhorshid, E., Hayashi, S., Schulten, K., 2002. Molecular Dynamics Investigation of Primary Photoinduced Events in the Activation of Rhodopsin. Biophysical Journal. 83(6). pp: 3097-3112. [14] Stryer, L., 1995. Biochemistry. 4th Ed. W.H. Freeman & Company. pp: 1319-1355.

Figure 7: A secondary structure model of Rh. [4]

Conclusions and Discusion
Following the description of these two proteins it was observed some radical differences and similarities. Both structures are Opsins which hold the same chromophore and the similar tridimensional structure. But each one presents different primary structure; they also allocate the retinal in a different conformation at its ground state and one of the most important differences between these two rhodopsins is the way they interact with light. bR induces a process similar to photosyntesis and Rh a process of transmitting chemical signals. Isomerization processes change in a dissimilar way in each protein as well. These subtle differences suggest being the main reason of Rhodopsins’ specific biological functionality. It can be further considered the idea of these two structures sharing a common ancestor protein which, by evolution and adaptation, managed to alter their primary sequence but somehow conserved their overall appearance.

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