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G protein coupled receptors are some of the most important drug targets in medicinal chemistry. It was first describe by Alfred gilman and martin rodbell. harmones and neurotransmitter activates the g protein coupled receptor. They include muscarinic receptors and adrenergic receptors and opioid receptors. These are also known as membrane bound protein that are important for activating proteins called G- proteins. These protein act as signal proteins. They have potency of activating and deactivating membrane bound enzymes. Rhodopsin is a g protein coupled receptor which when activated interacts with a heterotrimetric g protein to convert an extracellular signal in to an intracellular signal. It is a first receptor to have a crystal structure and rhodopsin is also known as retinal photoreceptor. It can form dimers and other higher order oligomers. Its structure and function will be discussed further.
Materials and methods-:
We have done this practical by using a software hyperchem release 8.0. we have worked on the ribbon diagram by downloading the file from e learning portal. After downloading the file we got a 3D model of the protein, together with its ribbon diagram in red, yellow and green. We have done some semi- empirical quantum calculations to see how the structure of rhodopsin enables it to carry out its biological function. For this we have used ZINDO /S , this is a semi-empirical method that has been developed particularly for calculating spectra.
Structure description of G protein coupled receptor and rhodopsin coupled receptor-:
G PROTEIN COUPLED RECEPTOR consist of 3 subunits alpha , beta and gamma. There are various types of g protein eg G0, GQ/G11,/GS, GI . and several subtypes of these. specific g protein act on specific receptors. When neurotransmitter or harmone binds to the receptor as a result, receptor changes shape and there will be new binding site on its inner surface. The newly exposed binding site now observed and binds a specific G protein. The binding process between newly exposed binding site and particular g protein causes to change shape , which in turn changes the shape of the nucleotide binding site. Receptor binding to G protein coupled receptors activates G alpha subunit of a stimulatory G protein to replace its bound GDP with GTP, release its associated G beta gamma subunit and activate adenyl cyclase to give CAMP activation.
G protein coupled receptors has seven transmembrane regions,the G protein are also known as 7- TM receptors. Each of the seven transmembrane sections is hydrophobic and helical in shape and is assign with roman numerals( I,II, ETC) starting from the N terminal end of the protein. The binding site for the G protein is situated on the intracellular side of the proteins and includes part of C terminal chain and the part of intracellular loop.
STRUCTURE OF RHODOPSIN-:
G protein coupled receptor consist of different light sensing proteins in the retina, which are known as rhodopsins. It consist of the 348- residue protein opsin which is covalently bind to the chromophore retinal via a Schiff base to lys 296,much as occurs in related bacteriorhodopsin, which is a heptahelical light driven proton pumb. Rhodopsin absorbs photon and causes bound retinal to isomerizes from its ground state 11-cis form to its all trans form. Rhodopsin are different from G protein coupled receptors in that their 11-cis retinal ââ‚¬Å“agonistââ‚¬Â is covalently bound to the protein.
Rhodopsin structure consist of cytoplasmic helix 8 which form dimer formation. In the structure the sciffs base linkage between the lys 296 residue and the chromophore was predicted to be deprotonated based on the analysis of the retinal content and the absorption maxima of these light exposed crystals. As we compare the structure of activated and inactivated rhodopsin, the transmembrane helices do not encounter a dramtic conformational change.
FIG-1 STRUCTURE OF RHODOPSIN
FUNCTION of rhodopsin-:
Proteins merge with other molecules such as substrates,inhibitors, ions,nucleic acids, carbohydrates, lipids in which they perform their various functions. When rhodopsin reaches its membrane location in the outer segment, it has already interacted with many proteins which involves activities such as biosynthesis, acetylation, glycosylation and transportation. Two molecules of palmitate and 1 molecule of 11-cis retinal bounds with it and has become enclosed in a membrane lipid bilayer. Rhodopsin is now ready to carry out its function in phototransduction. After photoactivation, rhodopsin show its impact on rod cell biochemistry by combining with rod cell proteins through its cytoplasmic surface.
G protein receptor rhodopsin lies within the cell membrane which means most of its structure is hydrophobic. Polar groups are added to a drug to increase its water solubility. It is crucial that such groups are arrange in such a way that they extend from the binding site when the drug binds. Sometimes hydrophobic region in drug is not that close to hydrophobic region in the binding site, and water may be trapped between the two surfaces. Van der waals interactions are weaker interactions than hydrogen bonds and can take place between two hydrophobic regions of the protein. For example they can take place between two alkyl groups. The amino acids alanine, valine, leucine,isoleucine,phenylalanine, and proline all have hydrophobic residues capable of interacting with each other by van der waals interactions. The residue of amino acids contain polar fuctional groups, amino acids such as methionine, tryptophan, threonine and tyrosine . Residues also have hydrophobic character and hydrophobic interactions are plays an key role in the coming together of the hydrophobic residues.
FIG-2 . surface of a typical water-soluble protein. colour coding; grey= hydrophobic residues, yellow= polar residues, red= acidic residues, blue= basic residues.
Fig-2 explains the surface of rhodopsin protein with a specific colour coding for particular residues. In this protein the polar residues are much more spread over the protein. The orange colour residue are retinal residue. Lysine has Schiff base with retinal. At the junction between retinal and lysine-296, there is an acidic residue known as glu 113 which is an important residue for rhodopsin function and is colour is cyan.
Fig-3, surface of a protein with glu-113 coloured as cyan.
Changes upon the SIGNAL TRANSDUCTION-:
When the chromophore absorbs a photon it converts in to the trans- configuration with out any change in the structure of protein. Rhodopsin containing the all trans isomers of retinal is called bathorhodopsin.Due to the prolonged, inflexible shape of the protein, trans isomer does not fit well in to the protein. Twisted conformation is adopted by the trans chromophore when it is contained in the protein, which is energetically unfavourable. Therefore number of changes occurs to pass the chromophore from the protein. The rhodopsin isomerizes the 11-cis retinal to all trans, which activates a chain of conformational changes in the opsin that cause enzymatic cascade leading to vision.
FIG- 4 Rhodopsin in its on state.
Here we will discuss about the three different graphs of retinal and calculating its maximum wavelength. The calculations were performed by taking occupied and unoccupied value 8. The electronic spectrum was adjusted between wavelength 400 to 600 nm using zoom pan sliders.
Semi ââ‚¬" empirical quantum calculations have been carried out by using hyperchem release 8.0 to compare the wavelength of retinal ligand containing residues ALA-295, LYS-296, THR-297, and Leu-112, glu-113, gly-114. Fig -5 shows the spectrum of retinal before protonation and mutation. The maximum wavelength is 490nm.
Fig-6 spectrum of retinal ligand after the protonation of Schiff base. The maximum wavelength is 403.93nm, which is smaller than the wavelength of retinal ligand of fig 1. This is due to loss of the proton which causes conformational changes. Its spin multiplicity is 1.
Fig-7 shows spectrum of retinal ligand after the mutation of glu-113. The maximum wavelength is 551.90nm, which is larger than wavelength of protonation of Schiff base and the neutral ligand.In the mutation of glu-113 negatively charged glutamate sidechain replaced by alanine, therefore overall charge on the structure was +1. Its spin multiciplity is 1.
This practical have given an overview of G-protein coupled receptor rhodopsin. After studying the detailed study about rhodopsin we come to the conclusion that rhodopsin is only receptor for which crystal structures are available representing the conformations of both the active and inactive states. Most important is rhodopsin is a retinal photoreceptor, which is very sensitive to light, facultative vision in low light condition.