The putative role of some conserved water molecules in the structure and function of human transthyretin

Abstract

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and Aβ peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH ≤ 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.

Fluorotryptophan Incorporation Modulates the Structure and Stability of Transthyretin in a Site-Specific Manner

“…9B). 63, 64 Alternatively, the 6F atom could potentially hydrogen bond to V20NH based on their proximity in the modeled structure (Fig. 9A).…”

“…The chemical shift changes in the AB loop, which forms part of the weak dimer interface, most likely reflect subtle structural perturbations that arise from steric clash between the 6-fluoro atom on W79 and the side chains of D18 and R21 (Figure A). The perturbations appear to propagate from the AB loop across the DAGH β-sheet to S117 in the H strand, which forms part of the strong dimer interface (Figure B). , Alternatively, the 6F atom could potentially hydrogen bond to V20NH based on their proximity in the modeled structure (Figure A). However, this mechanism is less likely given that fluorine is a very weak hydrogen bond acceptor .…”

“…Alternatively, perturbations of the AB loop could propagate to H88. The 6F-W79 substitution also appears to perturb a water-bridged hydrogen bond network involving H88 , (Figure B), which has been suggested to play a role in stabilizing tetrameric TTR and may serve as a structural basis for pH-dependent conformational changes. , Notably, four of these perturbed distal sites (V71, H88, A109, and S117) are associated with pathogenic TTR variants. − In addition, mutations of residues L111, S112, P113, and Y114 in the GH loop, which packs against the W79 indole ring and contacts the AB loop to form part of the weak dimer interface, are also pathogenic. , …”

“…The perturbations appear to propagate from the AB loop across the DAGH βsheet to S117 in the H strand, which forms part of the strong dimer interface (Figure 9B). 63,64 Alternatively, the 6F atom could potentially hydrogen bond to V20NH based on their proximity in the modeled structure (Figure 9A). However, this mechanism is less likely given that fluorine is a very weak hydrogen bond acceptor.…”

Putative role of conserved water molecules in the hydration and inter-domain recognition of mono nuclear copper centers in O2-bound human ceruloplasmin: A comparative study between X-ray and MD simulated structures

“…After superposition of the simulated structures, the water molecules which were within 1.8 Å and formed at least one hydrogen bond with the protein or coordinated to T-1 copper centers were considered to be conserved or semi-conserved 27. But at certain instances, water molecules were considered to be equivalent where a similar type of hydrogen bonding pattern was encountered even if the pair-wise distance criterion was not satisfied due to varying side-chain conformation 28.…”