In biological membranes the signal detection and transmission is initiated by the interaction of a chemical or physical stimulus with a specific membrane receptor which, in turn, becomes activated and initiates a chain of intracellular reactions that result in modulation of target protein activity. G-Protein Coupled Receptors are a superfamily of such membrane proteins that transmit a signal by coupling to heterotrimeric-binding proteins, which consist of three subunits (α, β and γ). Rhodopsin is a member of GPCRs superfamily which is pharmacologically important.
GPCRs share a common heptahelical transmembrane structure and therefore is also known as 7-TM Receptors. In the cell membrane these proteins are embedded and have both regions i.e. outside and inside of the cell. The protein chain winds back and forth through the cell membrane. Each of these helical shaped seven transmembrane sections is hydrophobic and usually roman numerals are used to assign these helices (I, II etc.) starting from the N-terminal end of the protein. Three extracellular and intracellular loops are the results of winding of protein back and forth through the membrane. Intracellular loops connecting helices V and VI varies, depending on the specific receptor, rest all the loops are fairly constant in length. The N-terminal chain is extracellular and is variable in length depending on the receptor, while the C-terminal chain is intracellular.
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Here structure of g protein coupled receptors................
As the receptors for hormones, neurotransmitters, ions, photons, and other stimuli, GPCRs are amongst the essential nodes of communication between the internal and external environments of cells. The classical role of GPCRs is to couple the binding of agonists to the activation of specific heterotrimeric G proteins, leading to the modulation of downstream effector proteins.
Rhodopsin, a chromoprotein is basically a protein which is linked to a pigment carrying substance that is contained in the light- sensitive cells of the rod type in the retina of the eye. The pigment which contains the portion of rhodopsin is retinal, a substance formed by oxidation of vitamin-A. opsin is the protein part. Retinal and opsin in dark makes rhodopsin but the process is reversed in a bright light.
In ribbon diagram of rhodopsin, seven transmembrane helical segments are linked together by extracellular and cytoplasmic loops. The carboxy- terminal tail is cytoplasmic and the amino-terminal tail is extracellular. The 11-cis-retinal chromophore is situated more towards the extracellular boundary of the plane of putative membrane bilayer.
Rhodopsin works as G-Protein Coupled Receptors and it leads to the activation of G-Protein called transducin. This gives rise to a process which is known as visual cascade which transfers an electrical signals to the brain. The chromophore retinal absorbs the light photon and isomerizes from 11-cis-retinal to all-trans-retinal. This process leads to a conformational change in opsin protein which inturn activates G-Protein. Rhodopsin is composed of a membrane-embedded chromophore, 11-cis-retinal, which is covalently bound to the opsin. It is membrane protein of the disk membrane and occupies 50% of the disk surface area, the remainder of which is filled with phospholipids and cholestrol
For the interaction of drugs with its target, water and hydrophobic interactions plays an important role. When hydrophobic region of a drug interacts with a hydrophobic region of a binding site , water molecules added to a drug are freed and increase in entropy and binding energy takes place which is substantial. In rhodopsin the amino acids alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, tyrosine, proline all have hydrophobic residues capable of interacting with each other by van der waals interactions. Hydrophobic interactions are also important in the coming together of hydrophobic residues
Figure 2 surface of a protein. Colour coding; grey= hydrophobic residues, yellow=polar residues, red=acidic residues, blue=basic residues.
Figure 2 shows the surface of a rhodopsin protein with a specific colour coding for particular residues. In this protein the polar residues are much more spread 6across the protein. The orange colour residues are retinal residues. Lysine forms the schiffs base with retinal. At the junction between retinal and lys-296, there is an acidic residue i.e. Glu 113 which is an important residue for rhodopsin`s function, and is coloured as cyan. Figure 3 shows the surface of a protein with Glu 113 coloured as cyan.
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Figure 3 surface of a protein with Glu 113 residue coloured as cyan.
Activation of rhodopsin is initiated by photoisomerization of its 11-cis-retinal chromophore which is linked to the protein by a protonated schiff base (PSB), to an all-trans-retinal. This photoconversion brings conformational changes in the protein to give series of intermediates Meta-I and Meta-II. Meta-I is in conformational eqilibrium with Meta-II. Meta-II is an intermediate which leads to the activation of heterotrimeric G-Protein, transducin. The transition to Meta-II involves a deprotonation of protonated schiff base which was protonated for each of the intermediate. Protonation of Glu113 is an essential step which leads to the activation of receptor. The protonation occurs in dark state and a proton is transferred to Glu113 during transition to Meta-I. Mutation of glutamate to alanine is carried out by breaking the salt bridge between the protonated and a complex counterion formed by the protein. Mutation changes the H-bonded network of helices and conformation of retinal.
Hyperchem was used to compare the spectrum of retinal in its protonated and mutated form. Semi -empirical calculations were performed using a small part of protein consisting of retinal ligand and protein residues Ala-295, Lys-296, Thr-297, and Leu-112, Glu-113, Gly-114. The spectra was calculated by a semi-empirical method ZINDO/S'. The calculations were performed by choosing polarizabilities and computing it by using single point CI followed by singly excited, orbital criterion. The calculations were performed by taking occupied and unoccupied values as 8. The electronic spectrum was adjsuted between wavelength of 400 to 600nm using 'zoom' and 'pan' sliders.
Figure4 spectra of protein consisting retinal.
Maximum wavelength: 494nm
Figure 4 shows the spectrum of protein consisting retinal with few residues mentioned above. The pink line gives the centre frequency of the band as maximum wavelength which is 494nm in this case.
Figure 5 spectra after protonation of schiff`s base
Maximum wavelength: 404nm
Figure 5 shows the spectrum of protonation of schiff`s base, which can be done by removing one proton from the fragment. The electronic spectra was computed by semi-empirical method by setting the total charge as -1 and spin multiplicity as 1. The calculated maximum wavelength for this spectra is 404nm.
Figure 6 spectra after mutation of Glu113
Figure 6 shows the spectra for mutation of Glu-113. Mutation is carried out by replacing glutamate residue by alanine. This spectra is also computed by semi-empirical method by setting the total charge as -1 and spin multiplicity as 1. The calculated maximum wavelength for this spectra is 553nm.
When rhodopsin receives a visible light , it triggers a G-Protein coupled receptors. The trigger is a change in a shape of a signal molecule. When the molecule absorbs a photon C11-C12 double bond of retinal is switched from cis to trans. This means that on receiving a signal, rhodopsin goes from 'off' to its 'on' state. Figure 7 shows the structure of rhodopsin in its 'on' state.
Figure 7 structure of rhodopsin in its 'on' configuration