Sandbox Reserved 1105: Difference between revisions

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The TTR gene is located on chromosome 18 <ref> Wallace MR, Naylor SL, Kluve-Beckerman B, Long GL, McDonald L, Shows TB, Benson MD, Localization of the human prealbumin gene to chromosome 18 [archive], Biochem Biophys Res Commun, 1985;129:753–758</ref>.

== ~~Structure~~ TTR structure with natural ligand : T4 and retinol ==

== Human TTR structure with natural ligand : T4 and retinol ==

=== Human TTR: ===

Human TTR is a 54 kDa homo-tetramer, described as a dimer of dimer, rich in β-sheet. It is composed of 127 amino acids assembled around the central channel of the protein, resulting in a 222 symmetry protein. This tetramer contains a channel divided into two symmetry-related L-T4-binding sites. The channel has three sets of small depressions, termed halogen binding pockets (HBPs). They have a two-fold symmetry and confer a hydrophobic surface to the protein. But then, when the side chain of the TTR changes of conformation, these pockets can realise more hydrogen bonds with other molecules, they can be donor or acceptor. Thus, they are involved in the binding of the natural ligand, the thyroxine (T4).

Each monomer is composed of an α-helix and two four stranded β-sheets, which results in two eight-stranded β-sheets per dimer (5). There is a large solvent channel which passes between the two sheets in which two molecules of T4 can bind. Monomers associate via the formation of an eight-stranded anti-parallel β-sheet to which each monomer contributes four β-strands. These β-sheets are situated at the center of the tetramer and positioned back to back. Ile107 and Val122 of monomer A are in direct van der Waals contact with the phenol ring of Phe87 from monomer B. * And Phe64 is in van der Waals contact with Cys10 via Pro11 in monomer A.** Each monomer contain a single cysteine (Cys10), which is usually bound to various sulfhydryls or sulfite from plasma. S-oxidation of Cys10 to cysteic acid has a stabilizing effect on the monomer. It may be derived from hydrogen bonds between the sulfonic oxygens of Cys10–SO3 – and Gly57 N, His56 NE and Arg104 NH1 (6).

Monomers of TTR will be called A, B, C, D. And as we consider the TTR as a dimer of dimer, we have A and B the upper part of the protein and C and D the lower part. The contact between upper and lower dimers is made via β-sheet contacts, creating hydrogen bonds between main-chain atoms. In contrast to the monomer associations, contacts between the upper and lower parts are much less important so that the dimer assembly unit of TTR is best defined as the monomers which are joined by β-strand hydrogen bonding. Two funnel-shaped hormone binding sites are located at the dimer–dimer region.

At the entry of the binding site, the TTR has a hydrophilic tail, into which the four iodine atoms of the ligand are placed. The innermost binding pocket, HBP-3, is located between the side chains of Ser 117, Thr 119, Ala 108 and Leu 110. Its surface is composed of aliphatic methyl and methylene groups, as well as the Ser 117 hydroxyl group, the carbonyl groups of Ser 117, Thr 118 and Ala 108, and the main chain NH groups of Thr 119, Ala 109 and Leu 110. The central HBP-2 is formed by the side chains of Leu 110, Ala 109, Lys 15, and Leu 17, it is primarily hydrophobic with polar or electrostatic contributions from the carbonyl groups of Lys 15, Ala 108 and Ala 109. The outermost pocket HBP-1 is located between the side chains of Ala 108, Thr 106, Met 13 and Lys 15. This pocket is lined with the methyl and methylene groups of Lys 15, Ala 108 and Thr 106 [[[[1]]]] (1).

=== TTR-ligand complex ===

The TTR – ligand interaction provides kinetic stabilization the protein. The more the affinity is high, the more the ligand stabilizes the complex. The dissociation constants with T4 and retinol-binding protein (RBP) are respectively from 1,1.10-7 to 1,5.10-7 M (7)

==== TTR-T4 complex =====

The crystal structure of this complex is orthorhombic (4).

Two hormone binding sites are located at the dimer–dimer region bind T4 with negative cooperativity. Under physiological conditions, the bound between the natural ligand and the tetramer can’t be broken down. Moreover, there is only one hormone bound per tetramer. The negative cooperativity mechanism explain the fact that the affinity constants (Ka) for the binding of the first and the second T4 changes, they are respectively 108 and 106 M-1 [[[[1]]]] (1).

For the TTR-T4 complex, the HBP play a key role. The HBP interact with the four iodine groups of the thyroxine. HBPs bind the iodine of the ligands in two different ways: 3 2’ 1 1’ or 3’ 2 1 1’ with prime indicating the HBP symmetry [[[[1]]]] (1). PICTURE

A significant contribution of T4 binding to TTR comes from charged groups near the periphery of the binding site. Glu 54 and Lys15 are located near the HBP-1 pocket allowing potential electrostatic interactions with the ligands [[[[1]]]] (1).

P1, 2 and 3 represent the three HBPs.

Thyroxine is bound deep in the cleft of the channel surface between the side chains of residues Leu17, Alal8 and Leull0, with interactions of its phenolic ring with Ser117 and Thr119 in the P2 pocket which has a more nucleophilic character than the P1 pocket, and with its alanyl moiety interacting with Glu54 and Lysl5 near the channel entrance.

T 4 interactions with TTR side chains shows that it can make good hydrogen-bonding contacts with Lysl5 and Glu54.

The P3 pocket forms close contacts between iodine and Leu110 backbone N atom, while the shortest contacts for 3'-I are formed with the carbonyl of Alal09. These contacts for the low-occupancy model of the hormone are shifted toward the tetramer center and toward the carbonyl and hydroxyl of Ser117, as well as Alal09.

==== TTR-RBP complex =====

TTR is a specific carrier of retinol-binding protein (RBP). This one has the following composition (8):

RBPs have a molecular mass of 21 kDa. They are composed of an eight-stranded β-barrel and a C-terminal α-helix.

One tetramer of TTR can bind two molecules of RBP in vitro (1:2 stoichiometry). However, when we isolate the TTR-RBP complex from the plasma (in vivo) we find a 1:1 stoichiometry (9). The β-barrel entrance loop involved in A-B strands binding (amino acids from 31 to 38, hairpin1) is also implicated in the TTR-RBP interaction.

RBP-TTR complex stale at high ionic strength and dissociate at low ionic strength (8). It is explained by the presence of a hydrophobic surface in the contact region, represented by hairpin 1,2,3 (include Leu35, 63, 64 and 67). Trp67 (close to hairpin1) seems to be involved in the binding (8). The dissociation constant of this complex is around 0.4 µM (9).

RBP has two polypeptide chains, E and F, which are bound to “opposite dimers” of TTR, the main TTR-RBP contact region is made between TTR-D / RBP-E and TTR-B / RBP-F. Thus, we observe an asymmetry in RBP-TTR relationship: RBP-E has more extensive interactions with TTR than molecule RBP-F (9).

The specific protein – protein recognition of this complex is classified in the three-dimensional docking model. The recognition site between RBP and TTR implies the positioning of the open end on the RBP β-barrel. For each interface 21 amino acids are involved from both proteins. At the periphery of the site there is charged amino acids. Half of the amino acid side chains are hydrophobic or aromatic in this area. Then, at the center of the site, we find hydrophobic amino acids, Leu and Ile are the predominant amino acids. RBPs present two different complementary surfaces to a dimeric surface. Indeed, at the core of the RBP-E interface, we find Ile84 from TTR-A and TTR-D, as well as Val20 and Ala81. Moreover, Trp67, Phe96, and Leu63 and 97 from RBP are surrounded by Val20, Leu82, and Ile84 from TTR-A and D.

All mammalian RBP’s have a carboxy-terminal extension of eight amino acids (9). This region interacts with TTR and the carboxy-extension of RBP-E is deeply located in the RBP-TTR interface. Indeed, the two terminal Leu182 and Leu183 are embedded in a hydrophobic region which includes Leu82 from TTR-A monomer and Val69 of RBP-E. Moreover, the terminal carboxylate group of RBP-E extension adopts a position to be neutralized by Arg21 of TTR-A. This interaction allows to bury more than 40% of the surface area, compared to the area buried without the carboxy terminal group of RBP-E (9).

== Disease ==

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== References ==

[[[[1]]]]Klabunde T, Petrassi HM, Oza VB, Raman P, Kelly JW, Sacchettini JC. Rational design of potent human transthyretin amyloid disease inhibitors. Nat Struct Biol. 2000 Apr;7(4):312-21. PMID:10742177 doi:http://dx.doi.org/10.1038/74082

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@@ Line 11: / Line 11: @@
 The TTR gene is located on chromosome 18 <ref> Wallace MR, Naylor SL, Kluve-Beckerman B, Long GL, McDonald L, Shows TB, Benson MD, Localization of the human prealbumin gene to chromosome 18 [archive], Biochem Biophys Res Commun, 1985;129:753–758</ref>.
-== Structure TTR structure with natural ligand :  T4 and retinol ==
+== Human TTR structure with natural ligand :  T4 and retinol ==
+=== Human TTR: ===
+Human TTR is a 54 kDa homo-tetramer, described as a dimer of dimer, rich in β-sheet. It is composed of 127 amino acids assembled around the central channel of the protein, resulting in a 222 symmetry protein. This tetramer contains a channel divided into two symmetry-related L-T4-binding sites.  The channel has three sets of small depressions, termed halogen binding pockets (HBPs). They have a two-fold symmetry and confer a hydrophobic surface to the protein. But then, when the side chain of the TTR changes of conformation, these pockets can realise more hydrogen bonds with other molecules, they can be donor or acceptor.  Thus, they are involved in the binding of the natural ligand, the thyroxine (T4).
+Each monomer is composed of an α-helix and two four stranded β-sheets, which results in two eight-stranded β-sheets per dimer (5). There is a large solvent channel which passes between the two sheets in which two molecules of T4 can bind. Monomers associate via the formation of an eight-stranded anti-parallel β-sheet to which each monomer contributes four β-strands. These β-sheets are situated at the center of the tetramer and positioned back to back. Ile107 and Val122 of monomer A are in direct van der Waals contact with the phenol ring of Phe87 from monomer B. * And Phe64 is in van der Waals contact with Cys10 via Pro11 in monomer A.** Each monomer contain a single cysteine (Cys10), which is usually bound to various sulfhydryls or sulfite from plasma. S-oxidation of Cys10 to cysteic acid has a stabilizing effect on the monomer. It may be derived from hydrogen bonds between the sulfonic oxygens of Cys10–SO3 – and Gly57 N, His56 NE and Arg104 NH1 (6).
+ Monomers of TTR will be called A, B, C, D. And as we consider the TTR as a dimer of dimer, we have A and B the upper part of the protein and C and D the lower part. The contact between upper and lower dimers is made via β-sheet contacts, creating hydrogen bonds between main-chain atoms. In contrast to the monomer associations, contacts between the upper and lower parts are much less important so that the dimer assembly unit of TTR is best defined as the monomers which are joined by β-strand hydrogen bonding. Two funnel-shaped hormone binding sites are located at the dimer–dimer region.
+At the entry of the binding site, the TTR has a hydrophilic tail, into which the four iodine atoms of the ligand are placed. The innermost binding pocket, HBP-3, is located between the side chains of Ser 117, Thr 119, Ala 108 and Leu 110. Its surface is composed of aliphatic methyl and methylene groups, as well as the Ser 117 hydroxyl group, the carbonyl groups of Ser 117, Thr 118 and Ala 108, and the main chain NH groups of Thr 119, Ala 109 and Leu 110. The central HBP-2 is formed by the side chains of Leu 110, Ala 109, Lys 15, and Leu 17, it is primarily hydrophobic with polar or electrostatic contributions from the carbonyl groups of Lys 15, Ala 108 and Ala 109. The outermost pocket HBP-1 is located between the side chains of Ala 108, Thr 106, Met 13 and Lys 15. This pocket is lined with the methyl and methylene groups of Lys 15, Ala 108 and Thr 106 [[[[1]]]] (1).
+=== TTR-ligand complex ===
+The TTR – ligand interaction provides kinetic stabilization the protein. The more the affinity is high, the more the ligand stabilizes the complex. The dissociation constants with T4 and retinol-binding protein (RBP) are respectively from 1,1.10-7 to 1,5.10-7 M (7)
+==== TTR-T4 complex =====
+The crystal structure of this complex is orthorhombic (4).
+Two hormone binding sites are located at the dimer–dimer region bind T4 with negative cooperativity. Under physiological conditions, the bound between the natural ligand and the tetramer can’t be broken down. Moreover, there is only one hormone bound per tetramer. The negative cooperativity mechanism explain the fact that the affinity constants (Ka) for the binding of the first and the second T4 changes, they are respectively 108 and 106 M-1 [[[[1]]]] (1).
+For the TTR-T4 complex, the HBP play a key role. The HBP interact with the four iodine groups of the thyroxine. HBPs bind the iodine of the ligands in two different ways: 3 2’ 1 1’ or 3’ 2 1 1’ with prime indicating the HBP symmetry [[[[1]]]] (1). PICTURE
+A significant contribution of T4 binding to TTR comes from charged groups near the periphery of the binding site. Glu 54 and Lys15 are located near the HBP-1 pocket allowing potential electrostatic interactions with the ligands [[[[1]]]] (1).
+P1, 2 and 3 represent the three HBPs.
+Thyroxine is bound deep in the cleft of the channel surface between the side chains of residues Leu17, Alal8 and Leull0, with interactions of its phenolic ring with Ser117 and Thr119 in the P2 pocket which has a more nucleophilic character than the P1 pocket, and with its alanyl moiety interacting with Glu54 and Lysl5 near the channel entrance.
+T 4 interactions with TTR side chains shows that it can make good hydrogen-bonding contacts with Lysl5 and Glu54.
+The P3 pocket forms close contacts between iodine and Leu110 backbone N atom, while the shortest contacts for 3'-I are formed with the carbonyl of Alal09. These contacts for the low-occupancy model of the hormone are shifted toward the tetramer center and toward the carbonyl and hydroxyl of Ser117, as well as Alal09.
+==== TTR-RBP complex =====
+TTR is a specific carrier of retinol-binding protein (RBP). This one has the following composition (8):
+RBPs have a molecular mass of 21 kDa. They are composed of an eight-stranded β-barrel and a C-terminal α-helix.
+One tetramer of TTR can bind two molecules of RBP in vitro (1:2 stoichiometry). However, when we isolate the TTR-RBP complex from the plasma (in vivo) we find a 1:1 stoichiometry (9). The β-barrel entrance loop involved in A-B strands binding (amino acids from 31 to 38, hairpin1) is also implicated in the TTR-RBP interaction.
+RBP-TTR complex stale at high ionic strength and dissociate at low ionic strength (8). It is explained by the presence of a hydrophobic surface in the contact region, represented by hairpin 1,2,3 (include Leu35, 63, 64 and 67). Trp67 (close to hairpin1) seems to be involved in the binding (8). The dissociation constant of this complex is around 0.4 µM (9).
+RBP has two polypeptide chains, E and F, which are bound to “opposite dimers” of TTR, the main TTR-RBP contact region is made between TTR-D / RBP-E and TTR-B / RBP-F. Thus, we observe an asymmetry in RBP-TTR relationship: RBP-E has more extensive interactions with TTR than molecule RBP-F (9).
+The specific protein – protein recognition of this complex is classified in the three-dimensional docking model. The recognition site between RBP and TTR implies the positioning of the open end on the RBP β-barrel. For each interface 21 amino acids are involved from both proteins. At the periphery of the site there is charged amino acids. Half of the amino acid side chains are hydrophobic or aromatic in this area. Then, at the center of the site, we find hydrophobic amino acids, Leu and Ile are the predominant amino acids.  RBPs present two different complementary surfaces to a dimeric surface. Indeed, at the core of the RBP-E interface, we find Ile84 from TTR-A and TTR-D, as well as Val20 and Ala81. Moreover, Trp67, Phe96, and Leu63 and 97 from RBP are surrounded by Val20, Leu82, and Ile84 from TTR-A and D.
+All mammalian RBP’s have a carboxy-terminal extension of eight amino acids (9). This region interacts with TTR and the carboxy-extension of RBP-E is deeply located in the RBP-TTR interface. Indeed, the two terminal Leu182 and Leu183 are embedded in a hydrophobic region which includes Leu82 from TTR-A monomer and Val69 of RBP-E. Moreover, the terminal carboxylate group of RBP-E extension adopts a position to be neutralized by Arg21 of TTR-A. This interaction allows to bury more than 40% of the surface area, compared to the area buried without the carboxy terminal group of RBP-E (9).
 == Disease ==
@@ Line 127: / Line 174: @@
 == References ==
 <references/>
+[[[[1]]]]Klabunde T, Petrassi HM, Oza VB, Raman P, Kelly JW, Sacchettini JC. Rational design of potent human transthyretin amyloid disease inhibitors. Nat Struct Biol. 2000 Apr;7(4):312-21. PMID:10742177 doi:http://dx.doi.org/10.1038/74082