Sandbox Reserved 955: Difference between revisions
No edit summary |
No edit summary |
||
| Line 9: | Line 9: | ||
The structure of HIV-1 protease with protein bound can't be solved as it would be cleaved before, we analyse how inhibitors bind to the active site to solve the structure. | The structure of HIV-1 protease with protein bound can't be solved as it would be cleaved before, we analyse how inhibitors bind to the active site to solve the structure. | ||
Inhibitors like the hydroxyethylamine bind to the active site mimicking the tetrahedral transition state of the proteolytic reaction <ref>http://biology.kenyon.edu/BMB/Jmol2008/2uxz/index.html#Inhibitor</ref>. The inhibitor interacts with the active site by direct hydrogen bonds and indirect hydrogen bonds through water molecules. | Inhibitors like the hydroxyethylamine bind to the active site mimicking the tetrahedral transition state of the proteolytic reaction <ref>http://biology.kenyon.edu/BMB/Jmol2008/2uxz/index.html#Inhibitor</ref>. The inhibitor interacts with the active site by direct hydrogen bonds and indirect hydrogen bonds through water molecules. | ||
== Structure == | == Structure == | ||
The crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site is a 3 chains structure which contains 203 amino acid alpha carbons. | The crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site is a 3 chains structure which contains 203 amino acid alpha carbons. | ||
'''Inhibitor structure''' | '''Inhibitor structure''' | ||
The sequence of the inhibitor JG-365 is <scene name='60/604474/Inhibitor/1'>Ac-Ser-Leu-Asn-Phe-psi[CH(OH)CH2N]-Pro-Ile-Val-OMe</scene>; the Ki is 0.24 nM. It's a protein with a length of 7 amino acid residues, composed of a C chain.<ref>http://www.rcsb.org/pdb/explore/explore.do?structureId=7hvp</ref>.The orientation of the inhibitor is a particular one in the protease active site, in fact its flaps are folded directly over it in order to protect it from bulk solvent. | The sequence of the inhibitor JG-365 is <scene name='60/604474/Inhibitor/1'>Ac-Ser-Leu-Asn-Phe-psi[CH(OH)CH2N]-Pro-Ile-Val-OMe</scene>; the Ki is 0.24 nM. It's a protein with a length of 7 amino acid residues, composed of a C chain.<ref>http://www.rcsb.org/pdb/explore/explore.do?structureId=7hvp</ref>.The orientation of the inhibitor is a particular one in the protease active site, in fact its flaps are folded directly over it in order to protect it from bulk solvent. | ||
'''HIV 1 protease structure''' | '''HIV 1 protease structure''' | ||
HIV-1 protease is a dimer of identical polypeptide chains : it's composed of two symmetrically related subunits, each consisting of 99 amino acid residues. Its structure is composed of A,B chains,<scene name='60/604474/Helix/1'>two helix</scene> (one in each subunit)and <scene name='60/604474/Sheets/2'>16 bêta sheets</scene>(8 in each subunits). | HIV-1 protease is a dimer of identical polypeptide chains : it's composed of two symmetrically related subunits, each consisting of 99 amino acid residues. Its structure is composed of A,B chains,<scene name='60/604474/Helix/1'>two helix</scene> (one in each subunit)and <scene name='60/604474/Sheets/2'>16 bêta sheets</scene>(8 in each subunits). | ||
The active site of the protease is localised inside the tunnel forms by the two subunits of the protein which come together, and it consists of two <scene name='60/604474/Catalytic/5'>Asp-Thr-Gly</scene> conserved sequences, making it the member of the aspartyl protease family.On the top of this tunnel are txo flexible flaps which move to allow proteins to enter the tunnel and thus the catalytic site : they shift from an open to a closed conformation in order to bind the target in a correct conformation for cleavage. The two Asp's are essential catalytic residues either interact with the incoming water or protonate the carbonyl to make the carbon more electrophilic for the incoming water. <ref>http://proteopedia.org/wiki/index.php/HIV-1_protease</ref> | The active site of the protease is localised inside the tunnel forms by the two subunits of the protein which come together, and it consists of two <scene name='60/604474/Catalytic/5'>Asp-Thr-Gly</scene> conserved sequences, making it the member of the aspartyl protease family.On the top of this tunnel are txo flexible flaps which move to allow proteins to enter the tunnel and thus the catalytic site : they shift from an open to a closed conformation in order to bind the target in a correct conformation for cleavage. The two Asp's are essential catalytic residues either interact with the incoming water or protonate the carbonyl to make the carbon more electrophilic for the incoming water. <ref>http://proteopedia.org/wiki/index.php/HIV-1_protease</ref> | ||
'''Binding site''' | '''Binding site''' | ||
| Line 24: | Line 32: | ||
The binding is not symmetric between the two Asp residues : Asp-25 is a little closer than Asp-125. Another aspect of this structure is that only one substituent atom of the Asn-203 side chain makes a polar contact, plus the contact between the hydroxyl group on the tetrahedral carbon and the active site apspartates.<ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55048/pdf/pnas01047-0128.pdf</ref> | The binding is not symmetric between the two Asp residues : Asp-25 is a little closer than Asp-125. Another aspect of this structure is that only one substituent atom of the Asn-203 side chain makes a polar contact, plus the contact between the hydroxyl group on the tetrahedral carbon and the active site apspartates.<ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55048/pdf/pnas01047-0128.pdf</ref> | ||
The monomers are directly related to inhibitor binding as this region, <scene name='60/604474/Loop/1'>the loop 49-52</scene>,shows it.The difference between the alpha carbons upon superposition of Gly-49 and Gly-149 is 1.6 A. These loop regions correspond to the extremity of the flaps that close over the inhibitor and provide some side-chain contacts to the hydrophobic binding pockets. As <scene name='60/604474/Loop/3'>the picture</scene> shows, their position are not equivalent because of peptide bond between residues Ile-50 and Gly-51 is turned of 180° compared with Ile-150 and Gly-151 (the symmetrical residues in the other chain).In consequence a direct hydrogen bond between the extremity of the flaps is possible. | The monomers are directly related to inhibitor binding as this region, <scene name='60/604474/Loop/1'>the loop 49-52</scene>,shows it.The difference between the alpha carbons upon superposition of Gly-49 and Gly-149 is 1.6 A. These loop regions correspond to the extremity of the flaps that close over the inhibitor and provide some side-chain contacts to the hydrophobic binding pockets. As <scene name='60/604474/Loop/3'>the picture</scene> shows, their position are not equivalent because of peptide bond between residues Ile-50 and Gly-51 is turned of 180° compared with Ile-150 and Gly-151 (the symmetrical residues in the other chain).In consequence a direct hydrogen bond between the extremity of the flaps is possible. | ||
== Biological and Biotechnological Relevance == | == Biological and Biotechnological Relevance == | ||
HIV-1 protease has a crucial importance in drug design as inhbition of it makes the virus noninfective. It prevents formation of mature protein of the HIV virus. The most encouraging inhibtors are the hydroxyethylamine substrate-based inhibitors <ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55048/pdf/pnas01047-0128.pdf</ref> which led to the discovery of the first protease inhibitor, saquinavir. But mutations coding for alteration of the active site conformation facilitates resistance to protease inhibitors. Structure comprehension of HIV protease through structural analysis is crucial to design inhibitors to slow down worldwide AIDS spreading epidemic. | HIV-1 protease has a crucial importance in drug design as inhbition of it makes the virus noninfective. It prevents formation of mature protein of the HIV virus. The most encouraging inhibtors are the hydroxyethylamine substrate-based inhibitors <ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55048/pdf/pnas01047-0128.pdf</ref> which led to the discovery of the first protease inhibitor, saquinavir. But mutations coding for alteration of the active site conformation facilitates resistance to protease inhibitors. Structure comprehension of HIV protease through structural analysis is crucial to design inhibitors to slow down worldwide AIDS spreading epidemic. | ||
== | |||
== Headline text == | |||
== | |||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||