PDBsum entry 3djs

Transport protein

PDB id: 3djs

Contents

Protein chain

116 a.a.

Waters ×184

References listed in PDB file

Key reference

Title

Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.

Authors

L.Cendron, A.Trovato, F.Seno, C.Folli, B.Alfieri, G.Zanotti, R.Berni.

Ref.

J Biol Chem, 2009, 284, 25832-25841.

PubMed id

19602727

Abstract

Human transthyretin (TTR) is an amyloidogenic protein whose mild amyloidogenicity is enhanced by many point mutations affecting considerably the amyloid disease phenotype. To ascertain whether the high amyloidogenic potential of TTR variants may be explained on the basis of the conformational change hypothesis, an aim of this work was to determine structural alterations for five amyloidogenic TTR variants crystallized under native and/or destabilizing (moderately acidic pH) conditions. While at acidic pH structural changes may be more significant because of a higher local protein flexibility, only limited alterations, possibly representing early events associated with protein destabilization, are generally induced by mutations. This study was also aimed at establishing to what extent wild-type TTR and its amyloidogenic variants are intrinsically prone to beta-aggregation. We report the results of a computational analysis predicting that wild-type TTR possesses a very high intrinsic beta-aggregation propensity which is on average not enhanced by amyloidogenic mutations. However, when located in beta-strands, most of these mutations are predicted to destabilize the native beta-structure. The analysis also shows that rat and murine TTR have a lower intrinsic beta-aggregation propensity and a similar native beta-structure stability compared with human TTR. This result is consistent with the lack of in vitro amyloidogenicity found for both murine and rat TTR. Collectively, the results of this study support the notion that the high amyloidogenic potential of human pathogenic TTR variants is determined by the destabilization of their native structures, rather than by a higher intrinsic beta-aggregation propensity.

Secondary reference #1

Title

Acidic ph-Induced conformational changes in amyloidogenic mutant transthyretin.

Authors

N.Pasquato, R.Berni, C.Folli, B.Alfieri, L.Cendron, G.Zanotti.

Ref.

J Mol Biol, 2007, 366, 711-719. [DOI no: 10.1016/j.jmb.2006.11.076]

PubMed id

17196219

Figure 1.
Figure 1. (a) Stereo view of the C^α chain trace of I84A TTR crystallized at pH 4.6 (red) superimposed on the C^α chain traces of the same mutant form crystallized at pH 7.5 (green) and of I84S TTR crystallized at pH 4.6 (light blue). The regions of each monomer involving the mutation are labeled. It can be seen from the tetramer model that the large loops generated at low pH in monomers B and B′ point towards the α-helices of monomers A′ and A, respectively, whose conformation remains unaltered. (b) Stereo view of the C^α chain trace of the dimer, formed by monomers A and B, for I84A TTR crystallized at pH 4.6 (red) superimposed on the C^α chain trace of the same mutant crystallized at pH 7.5 (green). The large conformational change affecting the region from residues 75–90 in monomer B is clearly visible. Figure 1. (a) Stereo view of the C^α chain trace of I84A TTR crystallized at pH 4.6 (red) superimposed on the C^α chain traces of the same mutant form crystallized at pH 7.5 (green) and of I84S TTR crystallized at pH 4.6 (light blue). The regions of each monomer involving the mutation are labeled. It can be seen from the tetramer model that the large loops generated at low pH in monomers B and B′ point towards the α-helices of monomers A′ and A, respectively, whose conformation remains unaltered. (b) Stereo view of the C^α chain trace of the dimer, formed by monomers A and B, for I84A TTR crystallized at pH 4.6 (red) superimposed on the C^α chain trace of the same mutant crystallized at pH 7.5 (green). The large conformational change affecting the region from residues 75–90 in monomer B is clearly visible.

Figure 2.
Figure 2. (a) Stereo view of the region around residues 88–90 for monomer B of I84A TTR at pH 4.6 (yellow) superimposed on the same region of I84A TTR at pH 7.5 (green), showing details of the conformational change occurring at acidic pH. (b) Stereo view of the electron density map of the region shown in (a) for I84A TTR at pH 4.6. The map was calculated with coefficients 2 |F[obs]–F[calc]| and contoured at 1.5 σ. (c) Stereo view of the network of H-bonded water molecules (red spheres) stabilizing the conformation of the newly formed loop in the region around residues 74–80 in I84A TTR at pH 4.6. (d) Stereo view of a detail of the hydrophobic cluster at the interface between monomers B (green) and A′ (yellow) in I84A TTR at pH 4.6. van der Waals spheres highlight hydrophobic residues that are present in the cluster. Figure 2. (a) Stereo view of the region around residues 88–90 for monomer B of I84A TTR at pH 4.6 (yellow) superimposed on the same region of I84A TTR at pH 7.5 (green), showing details of the conformational change occurring at acidic pH. (b) Stereo view of the electron density map of the region shown in (a) for I84A TTR at pH 4.6. The map was calculated with coefficients 2 |F[obs]–F[calc]| and contoured at 1.5 σ. (c) Stereo view of the network of H-bonded water molecules (red spheres) stabilizing the conformation of the newly formed loop in the region around residues 74–80 in I84A TTR at pH 4.6. (d) Stereo view of a detail of the hydrophobic cluster at the interface between monomers B (green) and A′ (yellow) in I84A TTR at pH 4.6. van der Waals spheres highlight hydrophobic residues that are present in the cluster.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

A comparative analysis of 23 structures of the amyloidogenic protein transthyretin.

Authors

A.Hörnberg, T.Eneqvist, A.Olofsson, E.Lundgren, A.E.Sauer-Eriksson.

Ref.

J Mol Biol, 2000, 302, 649-669. [DOI no: 10.1006/jmbi.2000.4078]

PubMed id

10986125

Figure 1.
Figure 1. Ribbon drawing of the transthyretin structure. (a) The structure of the dimer with monomer A colored in dark gray and monomer B in light gray. The b-strands from each monomer are denoted A-H as suggested by [Blake et al 1978]. Two b-sheets (D-A-G-H and C-B-E-F) in each monomer form a b-barrel. Two monomers dimerize through an intermolecular main-chain interaction involving the H-strands from each monomer to form a continuous eight-stranded b-sheet. The two paths of the FG-loop in the B monomer are shown in red. (b) The structure of the tetramer generated by applying the 2-fold crystallographic symmetry operator on the dimer in the asymmetric unit. The two dimers interact through hydrophobic contacts involving the loop regions between b-strands G and H and b-strands A and B. The thyroxine-binding sites are situated in one large hydrophobic channel formed between the two dimers. The positions of 36 buried water molecules are indicated as blue spheres. The pictures were generated using the program MOLSCRIPT [Kraulis 1991] and RENDER [Merritt and Bacon 1997].

Figure 7.
Figure 7. Charge distribution in the TTR molecule at two different orientations (a) facing the dimer-dimer interface at the FF' interaction site (under the saddle) and (b) a 180° rotation from the orientation in (a) and facing the dimer-dimer interface at the HH' interaction site. Charged residues are highlighted (red and blue for negatively and positively charged residues, respectively), with a concentration of negatively charged residues in the canyon between the two BC-loops from each monomer. (c) and (d) Electrostatic potential mapped onto the molecular surface of TTR with the same orientation as in (a) and (b). Positive potential is colored in blue and negative in red. The Figures were generated using the program ICM [Abagyan et al 1994].

The above figures are reproduced from the cited reference with permission from Elsevier