Sandbox Reserved 1123: Difference between revisions

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=== Quaternary structure ===

CA hexamers formation is due to intermolecular highly cooperative and noncovalent interactions, between the NTD of one subunit and the CTD of the neighbouring subunit within the same hexameric ring. These NTD-CTD interactions are crucial for the HIV-1 capsid assembly. CTD-CTD contacts and NTD-NTD contacts also exist for CA hexamers and pentamers formation. <ref name="C">[http://www.ncbi.nlm.nih.gov/pubmed/?term=%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BCStructural+basis+of+HIV-1+capsid+recognition+by+PF74+and+CPSF6 Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18625-30. doi: 10.1073/pnas.1419945112. Epub 2014 Dec 17.

CA hexamers formation is due to intermolecular highly cooperative and noncovalent interactions, between the NTD of one subunit and the CTD of the neighbouring subunit within the same hexameric ring. These '''NTD-CTD interactions are crucial for the HIV-1 capsid assembly'''. CTD-CTD contacts and NTD-NTD contacts also exist for CA hexamers and pentamers formation. <ref name="C">[http://www.ncbi.nlm.nih.gov/pubmed/?term=%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BCStructural+basis+of+HIV-1+capsid+recognition+by+PF74+and+CPSF6 Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18625-30. doi: 10.1073/pnas.1419945112. Epub 2014 Dec 17.

Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Bhattacharya A, Alam SL, Fricke T, Zadrozny K, Sedzicki J, Taylor AB, Demeler B, Pornillos O, Ganser-Pornillos BK, Diaz-Griffero F, Ivanov DN, Yeager M.] </ref>

NTD forms both hexameric or pentameric rings, while CTD forms symmetric homodimers which connect the rings into a hexagonal lattice. Moreover, the formation of hexamers and pentamers is controlled by an electrostatic switch, thanks to this process, hexamers are favored compared to pentamers. Pentamer and hexamer structures are very close to each other, in either case, the CTDs form a belt which encircles the inner ring of NTDs.

NTD forms both hexameric or pentameric rings, while CTD forms symmetric homodimers which connect the rings into a hexagonal lattice. Moreover, the formation of hexamers and pentamers is controlled by an electrostatic switch, thanks to this process, hexamers are favored compared to pentamers. '''Pentamer and hexamer structures are very close to each other''', in either case, the CTDs form a belt which encircles the inner ring of NTDs.

Intermolecular NTD-NTD contacts facilitate the formation of the NTD rings, while NTD-CTD contacts maintain the CTD subunits in the belts. There is no intramolecular interaction between the NTD and CTD of each subunit, except the peptidic linkage between these two domains of course. Furthermore, the flexible linker is able to adopt different conformations, which is very useful because the monomers can position themselves in an optimal manner to permit the interaction surfaces in pentamer and hexamer. NTD rings form a rigid structure, this is not the case of CTDs in belts which are mobile and able to rotate, relative to the NTD ring. CTD pivotes such as a rigid body about four intermolecular helix-capping hydrogen bounds at the NTD-CTD interface.

Thus, each hexameric ring can have slightly different dihedral angles relative to its adjacent rings thanks to the CTDs movments. NTD rings interactions are possible thanks to the first three α-helices of each subunit, they forme a 15-helix barrel in the pentamer and a 18-helix barrel in the hexamer. A small hydrophobic core is located at the center of the bundle thanks to the presence of aliphatic residues, while polar sidechains are present at the periphery and do hydrophilic interactions. <ref name="B"/> <ref>[http://www.ncbi.nlm.nih.gov/pubmed/?term=nature09640 Nature. 2011 Jan 20;469(7330):424-7. doi: 10.1038/nature09640. Atomic-level modelling of the HIV capsid. Pornillos O, Ganser-Pornillos BK, Yeager M.] </ref>

Intermolecular '''NTD-NTD contacts facilitate the formation of the NTD rings''', while '''NTD-CTD contacts maintain the CTD subunits in the belts'''. There is no intramolecular interaction between the NTD and CTD of each subunit, except the peptidic linkage between these two domains of course. Furthermore, the flexible linker is able to adopt different conformations, which is very useful because the monomers can position themselves in an optimal manner to permit the interaction surfaces in pentamer and hexamer. '''NTD rings form a rigid structure''', this is not the case of '''CTDs in belts''' which '''are mobile and able to rotate''', relative to the NTD ring. CTD pivotes such as a rigid body about four intermolecular helix-capping hydrogen bounds at the NTD-CTD interface.

Thus, each hexameric ring can have slightly different dihedral angles relative to its adjacent rings thanks to the CTDs movments. '''NTD rings interactions are possible thanks to the first three α-helices of each subunit''', they forme a 15-helix barrel in the pentamer and a 18-helix barrel in the hexamer. A small hydrophobic core is located at the center of the bundle thanks to the presence of aliphatic residues, while polar sidechains are present at the periphery and do hydrophilic interactions. <ref name="B"/> <ref>[http://www.ncbi.nlm.nih.gov/pubmed/?term=nature09640 Nature. 2011 Jan 20;469(7330):424-7. doi: 10.1038/nature09640. Atomic-level modelling of the HIV capsid. Pornillos O, Ganser-Pornillos BK, Yeager M.] </ref>

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This approach is interesting because, based on structural information, we are able to build such ligands using drug design. However, we are still far away from the "miraculous HIV drug", because the pathway from design to approved drug is not an easy way at all.

Sandbox Reserved 1123: Difference between revisions

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@@ Line 35: / Line 35: @@
 === Quaternary structure ===
-CA hexamers formation is due to intermolecular highly cooperative and noncovalent interactions, between the NTD of one subunit and the CTD of the neighbouring subunit within the same hexameric ring. These NTD-CTD interactions are crucial for the HIV-1 capsid assembly. CTD-CTD contacts and NTD-NTD contacts also exist for CA hexamers and pentamers formation. <ref name="C">[http://www.ncbi.nlm.nih.gov/pubmed/?term=%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BCStructural+basis+of+HIV-1+capsid+recognition+by+PF74+and+CPSF6  Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18625-30. doi: 10.1073/pnas.1419945112. Epub 2014 Dec 17.
+CA hexamers formation is due to intermolecular highly cooperative and noncovalent interactions, between the NTD of one subunit and the CTD of the neighbouring subunit within the same hexameric ring. These '''NTD-CTD interactions are crucial for the HIV-1 capsid assembly'''. CTD-CTD contacts and NTD-NTD contacts also exist for CA hexamers and pentamers formation. <ref name="C">[http://www.ncbi.nlm.nih.gov/pubmed/?term=%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BC%EF%BF%BCStructural+basis+of+HIV-1+capsid+recognition+by+PF74+and+CPSF6  Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18625-30. doi: 10.1073/pnas.1419945112. Epub 2014 Dec 17.
 Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Bhattacharya A, Alam SL, Fricke T, Zadrozny K, Sedzicki J, Taylor AB, Demeler B, Pornillos O, Ganser-Pornillos BK, Diaz-Griffero F, Ivanov DN, Yeager M.] </ref>
-NTD forms both hexameric or pentameric rings, while CTD forms symmetric homodimers which connect the rings into a hexagonal lattice. Moreover, the formation of hexamers and pentamers is controlled by an electrostatic switch, thanks to this process, hexamers are favored compared to pentamers. Pentamer and hexamer structures are very close to each other, in either case, the CTDs form a belt which encircles the inner ring of NTDs.
+NTD forms both hexameric or pentameric rings, while CTD forms symmetric homodimers which connect the rings into a hexagonal lattice. Moreover, the formation of hexamers and pentamers is controlled by an electrostatic switch, thanks to this process, hexamers are favored compared to pentamers. '''Pentamer and hexamer structures are very close to each other''', in either case, the CTDs form a belt which encircles the inner ring of NTDs.
-Intermolecular NTD-NTD contacts facilitate the formation of the NTD rings, while NTD-CTD contacts maintain the CTD subunits in the belts. There is no intramolecular interaction between the NTD and CTD of each subunit, except the peptidic linkage between these two domains of course. Furthermore, the flexible linker is able to adopt different conformations, which is very useful because the monomers can position themselves in an optimal manner to permit the interaction surfaces in pentamer and hexamer. NTD rings form a rigid structure, this is not the case of CTDs in belts which are mobile and able to rotate, relative to the NTD ring. CTD pivotes such as a rigid body about four intermolecular helix-capping hydrogen bounds at the NTD-CTD interface.
-Thus, each hexameric ring can have slightly different dihedral angles relative to its adjacent rings thanks to the CTDs movments. NTD rings interactions are possible thanks to the first three α-helices of each subunit, they forme a 15-helix barrel in the pentamer and a 18-helix barrel in the hexamer. A small hydrophobic core is located at the center of the bundle thanks to the presence of aliphatic residues, while polar sidechains are present at the periphery and do hydrophilic interactions. <ref name="B"/> <ref>[http://www.ncbi.nlm.nih.gov/pubmed/?term=nature09640 Nature. 2011 Jan 20;469(7330):424-7. doi: 10.1038/nature09640. Atomic-level modelling of the HIV capsid. Pornillos O, Ganser-Pornillos BK, Yeager M.] </ref>
+Intermolecular '''NTD-NTD contacts facilitate the formation of the NTD rings''', while '''NTD-CTD contacts maintain the CTD subunits in the belts'''. There is no intramolecular interaction between the NTD and CTD of each subunit, except the peptidic linkage between these two domains of course. Furthermore, the flexible linker is able to adopt different conformations, which is very useful because the monomers can position themselves in an optimal manner to permit the interaction surfaces in pentamer and hexamer. '''NTD rings form a rigid structure''', this is not the case of '''CTDs in belts''' which '''are mobile and able to rotate''', relative to the NTD ring. CTD pivotes such as a rigid body about four intermolecular helix-capping hydrogen bounds at the NTD-CTD interface.
+Thus, each hexameric ring can have slightly different dihedral angles relative to its adjacent rings thanks to the CTDs movments. '''NTD rings interactions are possible thanks to the first three α-helices of each subunit''', they forme a 15-helix barrel in the pentamer and a 18-helix barrel in the hexamer. A small hydrophobic core is located at the center of the bundle thanks to the presence of aliphatic residues, while polar sidechains are present at the periphery and do hydrophilic interactions. <ref name="B"/> <ref>[http://www.ncbi.nlm.nih.gov/pubmed/?term=nature09640 Nature. 2011 Jan 20;469(7330):424-7. doi: 10.1038/nature09640. Atomic-level modelling of the HIV capsid. Pornillos O, Ganser-Pornillos BK, Yeager M.] </ref>
@@ Line 71: / Line 73: @@
 This approach is interesting because, based on structural information, we are able to build such ligands using drug design. However, we are still far away from the "miraculous HIV drug", because the pathway from design to approved drug is  not an easy way at all.