Molecular modeling of the amyloid-β-peptide using the homology to a fragment of triosephosphate isomerase that forms amyloid in vitro

Abstract

The main component of the amyloid senile plaques found in Alzheimer's brain is the amyloid-beta-peptide (A beta), a proteolytic product of a membrane precursor protein. Previous structural studies have found different conformations for the A beta peptide depending on the solvent and pH used. In general, they have suggested an alpha-helix conformation at the N-terminal domain and a beta-sheet conformation for the C-terminal domain. The structure of the complete A beta peptide (residues 1-40) solved by NMR has revealed that only helical structure is present in A beta. However, this result cannot explain the large beta-sheet A beta aggregates known to form amyloid under physiological conditions. Therefore, we investigated the structure of A beta by molecular modeling based on extensive homology using the Smith and Waterman algorithm implemented in the MPsrch program (Blitz server). The results showed a mean value of 23% identity with selected sequences. Since these values do not allow a clear homology to be established with a reference structure in order to perform molecular modeling studies, we searched for detailed homology. A 28% identity with an alpha/beta segment of a triosephosphate isomerase (TIM) from Culex tarralis with an unsolved three-dimensional structure was obtained. Then, multiple sequence alignment was performed considering A beta, TIM from C.tarralis and another five TIM sequences with known three-dimensional structures. We found a TIM segment with secondary structure elements in agreement with previous experimental data for A beta. Moreover, when a synthetic peptide from this TIM segment was studied in vitro, it was able to aggregate and to form amyloid fibrils, as established by Congo red binding and electron microscopy. The A beta model obtained was optimized by molecular dynamics considering ionizable side chains in order to simulate A beta in a neutral pH environment. We report here the structural implications of this study.

Accumulation of Triosephosphate Isomerase, with Sequence Homology to β Amyloid Peptides, in Vessel Walls of the Newborn Piglet Hippocampus

“…These also indicated that detectable expression of Ab proteins were not seen in the piglet brains. It seems likely that the crossreactivity between Ab and TPI was a synergic consequence of a homologous amino acid sequence and their similar three-dimensional conformational epitopes, as assumed by Contreras et al (Contreras et al, 1999) and also by Tamaoka et al (1996) on the crossreactivity between Ab and GAPDH. Table 1 shows that TPI has the limited local identity to parts of Ab(1-42) peptides, namely, Ab(11-13) and…”

“…Second, N-terminal amino acid sequencing, mass fingerprint and Western blotting analyses revealed that the immunoreactive protein recognized by the anti-Ab protein antibodies was TPI, showing sequence homology to the Ab(1-28) peptide (Contreras et al, 1999). The findings on the protein analyzed by Western blotting and 2-DE were also compatible with the previously published information on TPI, having a 26.7 kDa molecular weight and pI of 7.19 (Poon et al, 2004), and on Ab(1-42), having a 4.5 kDa molecular weight and pI of 5.31.…”

“…Also, it is known that Ab binds in nanomolar concentrations to phosphofructokinase and decreases its activity (Bigl and Eschrich, 1995). In addition, Contreras et al (1999) modeled the complete structure of the Ab peptide based on the 1-28 segment of Ab solved by nuclear magnetic resonance spectroscopy and by homology of the peptide to a segment of triosephosphate isomerase (TPI). They have also shown that this segment of TPI, with sequence homology to the Ab peptide, is able to form amyloid in vitro.…”

Acetylcholinesterase-amyloid-β-peptide interaction and Wnt signaling involvement in Aβ neurotoxicity

“…Two Aβ models, built by homology modeling from a fragment of the enzyme triosephosphate isomerase (12), were used for docking. All modeled structures were positioned arbitrarily, adjacent to the high‐resolution structure of Torpedo californica AChE (TcAChE; PDB code: 2ACE), and according to the requirements of GRAMM, they contained coordinates for hydrogen atoms.…”

The Oligomeric Nature of Triosephosphate Isomerase. Studies of Monomerization

“…Comparison of amino acid sequence of TIM illustrates their high degree of evolutionary conservation throughout evolution; for example, the sequence around the active site residue (the glutamic acid 168) is totally conserved. The crystallographic structures of wild-type TIMs and engineered mutants have been determined for some species comprising from Archaea (6,7) and Bacteria (8)(9)(10)(11) to Eukarya (12)(13)(14)(15)(16)(17)(18)(19)(20)(21). Each TIM subunit has ~250 amino acid residues with a molecular mass close to 27 kDa and folds into a (β/α) 8 scaffold denominated "TIM barrel" (22).…”