Sandbox GGC4
From Proteopedia
(Difference between revisions)
| (30 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | = | + | ==HIV-1 Protease== |
| - | + | An infection of the Human Immuno-deficiency Virus can cause Acquired Immunodeficiency Syndrome (AIDS). HIV attacks the CD4 T cells that are an essential part of the cell-mediated immune response, without which the immune system cannot fight against other infections or cancers, causing AIDS. There are currently 37 million people worldwide living with HIV/AIDS, with approximately 1 million new cases each year along with approximately 1 million deaths a year. | |
| - | + | ||
| - | + | Antiretroviral Therapy is one of the HIV treatments that is most effective as the combinations of different medicines reduce the viral load to become undetectable and non-transmissible and also allows the immune system to recuperate and increase the CD4 count. Protease Inhibitors are one of the FDA approved medicines that target the viral Aspartyl Protease to prevent the HIV from making more copies of itself. | |
| - | + | ||
| - | + | <StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''> | |
| + | |||
| + | |||
== Function == | == Function == | ||
| - | + | HIV-1 Aspartyl Proteases are homo-dimeric proteolytic enzymes, also known as endopeptidases that allow water molecules to act as nucleophiles during catalysis when activated by 2 aspartic acid residues that make up the <scene name='75/752268/Active_site_without_inhibitor/1'>active site</scene>. Usually, the active site consists of a triad (ASP-THR-GLY) on each monomer with the catalytic residue being D25. | |
| - | + | Aspartyl Protease cleaves the Gag and Gag-Pol polyproteins that encode for other structural proteins and enzymes crucial for viral maturation. Hence, HIV-1 Protease Inhibitors have been developed to inhibit the viral protease enzyme to prevent the production and release of mature, infectious HIV virions. Here is how an inhibitor binds to the protease to form a <scene name='75/752268/Hiv-1_protease-inhibitor/1'>HIV-1 protease-inhibitor complex</scene>. | |
| - | + | ||
| - | + | ||
| - | '''Apolipoprotein A-I (Milano)''' is a mutant form of apolipoprotein A-I associated in reducing coronary artery disease to those genetically predisposition. <ref>CR;, C. (n.d.). Apolipoprotein A-I(Milano): Current perspectives. Retrieved November 14, 2020, from https://pubmed.ncbi.nlm.nih.gov/12642784/</ref> Mutation Milano was first discovered in from a patient in Limone sul Garda, Northern Italy or alarming elevated triglycerides and low HDL with no signs of atherosclerosis or cardiovascular disease. Mutation occurs at 173 residue of <scene name='75/752268/Milano/1'>arginine</scene> replaced with cysteine. <ref>Lowe, D. (2016, November 16). The Long Saga of Apo-A1 Milano. Retrieved November 14, 2020, from https://blogs.sciencemag.org/pipeline/archives/2016/11/16/the-long-saga-of-apo-a1-milano</ref> | ||
| - | == | + | == Disease == |
| - | '' | + | Protease inhibitors along with reverse transcriptase inhibitors have been proven to be effective in reducing the viral load to slow the development of AIDS, however in recent years, mutations on the HIV-1 Protease have become a new challenge for researchers and pharmaceutical companies. Here is an image of a <scene name='75/752268/Mdr_protease_18_mutation/1'>multi-drug resistant HIV-1 Protease enzyme</scene> from a patient for whom the protease inhibitor regimen is no longer effective. The HIV-1 strain from this patient has 9 mutations per monomer. The ineffectiveness of the protease inhibitors can allow the viral load to increase and allow the progression of AIDS. |
| - | + | == Relevance == | |
| + | Once again, if the structure of the protease enzyme changes due to mutations, the protease inhibitors will not be effective in preventing viral maturation. The relevance of these mutations can be seen in the active site expansion that takes place, especially at <scene name='75/752268/Mutations_v82a_and_i84v/1'>residue positions 82 and 84</scene>, among others. Here, it can be seen that the V82A and the I84V mutation causes the distance between the active site flap to become wider as the amino acid side chains become shorter. The change in the distance of amino acid 83,84,182 and 184 is approximately 1.5 A each in amino acid residues according to Logsdon et al, 2004.This conformational change reduces the binding affinity of the protease inhibitor to the active site. | ||
== Structural highlights == | == Structural highlights == | ||
| + | Other notable structural highlights include the 1. <scene name='75/752268/Inhibitor_binding_site_of_mut1/1'>Inhibitor Binding Site of Mutated HIV-1 Protease</scene>, | ||
| + | 2. <scene name='75/752268/Active_site_flap/1'>Active Site Flap of Mutated HIV-1 Protease</scene>, | ||
| + | 3. <scene name='75/752268/Alpha-d-glucose/1'>Interaction with Alpha-D-glucose</scene>, and | ||
| + | 4. <scene name='75/752268/Catalytic_residue_shift/1'>Catalytic Residue Shift | ||
| + | </scene> | ||
| - | Apolipoprotein a-1 (apoA-I) is a fairly small molecule that consists of a total of 243 residues and is 29-kD polypeptide in size. Its structure consists of two helical domains that include a four-helix of antiparallel bundle by N terminal and two helix bundle at the C terminal end. ApoA-I consists of <scene name='75/752268/Chains/1'>four chains</scene> alpha helices including chain A (orange), B (blue), C (red), and D (green) as displayed, in which an infinity like structure. C terminal domain of carboxyl group is known to participate in role in lipid binding for transport, found following between residues <scene name='75/752268/Cterm_binding/1'>(190-243).</scene> At the central region, two antiparallel helices form a flexible domain of connected bundles of each end of helices.<ref>And, X. (2011, November 04). Crystal Structure of C-terminal Truncated Apolipoprotein A-I Reveals the Assembly of High Density Lipoprotein (HDL) by Dimerization. Retrieved November 14, 2020, from https://www.jbc.org/content/286/44/38570.abstract?sid=eee11503-e692-438c-a298-52d329852b25</ref> | ||
| - | |||
| - | Apolipoprotein a-1 in the monomer form <scene name='75/752268/Truncated/4'>truncated</scene> (lacking 1-43 residues) consists of unique pseudo-continuous alpha helix highlighted by kinks at <scene name='75/752268/Truncated/3'>Pro residues</scene>, spaced approximately every 22 residues.<ref>Nagao, K., Hata, M., Tanaka, K., Takechi, Y., Nguyen, D., Dhanasekaran, P., . . . Saito, H. (2014, January). The roles of C-terminal helices of human apolipoprotein A-I in formation of high-density lipoprotein particles. Retrieved November 14, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863607/</ref> | ||
| - | |||
| - | Biomarkers of coronary artery disease are also found to be of modification at glutamate residue 243 of truncated APOA1 of single amino acid. | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
| - | + | Logsdon BC, Vickrey JF, Martin P, Proteasa G, Koepke JI, Terlecky SR, Wawrzak Z, Winters MA, Merigan TC, Kovari LC. Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity. J Virol. 2004 Mar;78(6):3123-32. doi: 10.1128/jvi.78.6.3123-3132.2004. PMID: 14990731; PMCID: PMC354404. | |
| - | + | <references/> | |
| - | + | Munshi S, Chen Z, Li Y, Olsen DB, Fraley ME, Hungate RW, Kuo LC. Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme. Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):1053-60. doi: 10.1107/s0907444998003588. PMID: 9757136. | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | 6. | + | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
HIV-1 Protease
An infection of the Human Immuno-deficiency Virus can cause Acquired Immunodeficiency Syndrome (AIDS). HIV attacks the CD4 T cells that are an essential part of the cell-mediated immune response, without which the immune system cannot fight against other infections or cancers, causing AIDS. There are currently 37 million people worldwide living with HIV/AIDS, with approximately 1 million new cases each year along with approximately 1 million deaths a year.
Antiretroviral Therapy is one of the HIV treatments that is most effective as the combinations of different medicines reduce the viral load to become undetectable and non-transmissible and also allows the immune system to recuperate and increase the CD4 count. Protease Inhibitors are one of the FDA approved medicines that target the viral Aspartyl Protease to prevent the HIV from making more copies of itself.
| |||||||||||
References
Logsdon BC, Vickrey JF, Martin P, Proteasa G, Koepke JI, Terlecky SR, Wawrzak Z, Winters MA, Merigan TC, Kovari LC. Crystal structures of a multidrug-resistant human immunodeficiency virus type 1 protease reveal an expanded active-site cavity. J Virol. 2004 Mar;78(6):3123-32. doi: 10.1128/jvi.78.6.3123-3132.2004. PMID: 14990731; PMCID: PMC354404.
Munshi S, Chen Z, Li Y, Olsen DB, Fraley ME, Hungate RW, Kuo LC. Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme. Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):1053-60. doi: 10.1107/s0907444998003588. PMID: 9757136.
