Neurological update: dementia

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.

Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

Replica exchange molecular dynamics simulations (300 ns) were used to study the dimerization of amyloid β(1-40) (Aβ(1-40)) polypeptide. Configurational entropy calculations revealed that at physiological temperature (310 K, 37°C) dynamic dimers are formed by randomly docked monomers. Free energy of binding of the two chains to each other was -93.56 ± 6.341 kJ mol^-1 . Prevalence of random coil conformations was found for both chains with the exceptions of increased β-sheet content from residues 16-21 and 29-32 of chain A and residues 15-21 and 30-33 of chain B with β-turn/β-bend conformations in both chains from residues 1-16, 21-29 of chain A, 1-16, and 21-29 of chain B. There is a mixed β-turn/β-sheet region from residues 33-38 of both chains. Analysis of intra- and interchain residue distances shows that, although the individual chains are highly flexible, the dimer system stays in a loosely packed antiparallel β-sheet configuration with contacts between residues 17-21 of chain A with residues 17-21 and 31-36 of chain B as well as residues 31-36 of chain A with residues 17-21 and 31-36 of chain B. Based on dihedral principal component analysis, the antiparallel β-sheet-loop-β-sheet conformational motif is favored for many low energy sampled conformations. Our results show that Aβ(1-40) can form dynamic dimers in aqueous solution that have significant conformational flexibility and are stabilized by collapse of the central and C-terminal hydrophobic cores with the expected β-sheet-loop-β-sheet conformational motif. Proteins 2017; 85:1024-1045. © 2017 Wiley Periodicals, Inc.

Association between comorbidities and dementia in diabetes mellitus patients: population-based retrospective cohort study

AIMS

Most diabetes mellitus (DM) patients have several comorbidities; the correlation of these comorbidities with dementia in DM requires clarification.

METHODS

Using claims data from Taiwan National Health Insurance, we identified 33,709 DM adults before the year 2000 and randomly selected 67,066 non-DM patients matched by sex and age. Subjects were followed until diagnosis with dementia, excluded due to death/withdrawal from the insurance program, or followed until 2011. We compared the incidence and hazard ratio (HR) for dementia in both cohorts.

RESULTS

Comorbidities were more prevalent in DM patients, including hypertension, hyperlipidemia, stroke, coronary artery and/or kidney disease. The HR was higher for the DM cohort with comorbidities than those without: 1.88 vs. 1.46 with hypertension; 1.56 vs. 1.39 with hyperlipidemia; 1.73 vs. 1.37 with coronary artery disease; 2.36 vs. 2.29 with stroke and 1.88 vs. 1.50 with kidney disease. The HR for dementia in diabetics rose from 1.41 in those without comorbidities to 2.49 in those with ≥4 comorbidities. In the DM cohort, HR was 1.22 for non-insulin-users and 1.41 for insulin-users, and 1.49 for type 1 DM and 1.23 for type 2 DM.

CONCLUSION

Diabetic patients have an elevated risk of dementia, and comorbidity increases this risk.