Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation.
Recent experiments have shown that the congener Abeta(1-40)[D23-K28], in which the side chains of charged residues Asp23 and Lys28 are linked by a lactam bridge, forms amyloid fibrils that are structurally similar to the wild type (WT) Abeta peptide, but at a rate that is nearly 1000 times faster. We used all atom molecular dynamics simulations in explicit water, and two force fields, of the WT dimer, a monomer with the lactam bridge (Abeta(10-35)-lactam[D23-K28]), and the monomer and dimers with harmonically constrained D23-K28 salt bridge (Abeta(10-35)[D23-K28]) to understand the origin of the enhanced fibril rate formation. The simulations show that the assembly competent fibril-like monomer (N*) structure, which is present among the conformations sampled by the isolated monomer, with strand conformations in the residues spanning the N and C termini and a bend involving residues D(23) VGSNKG(29), are populated to a much greater extent in Abeta(10-35)[D23-K28] and Abeta(10-35)-lactam[D23-K28] than in the WT, which has negligible probability of forming N*. The salt bridge in N* of Abeta(10-35)[D23-K28], whose topology is similar to that found in the fibril, is hydrated. The reduction in the free energy barrier to fibril formation in Abeta(10-35)[D23-K28] and in Abeta(10-35)-lactam[D23-K28], compared to the WT, arises largely due to entropic restriction which enables the bend formation. A decrease in the entropy of the unfolded state and the lesser penalty for conformational rearrangement including the formation of the salt bridge in Abeta peptides with D23-K28 constraint results in a reduction in the kinetic barrier in the Abeta(1-40)-lactam[D23-K28] congener compared to the WT. The decrease in the barrier, which is related to the free energy cost of forming a bend, is estimated to be in the range (4-7)k(B)T. Although a number of factors determine the growth of fibrils, the decrease in the free energy barrier, relative to the WT, to N* formation is a major factor in the rate enhancement in the fibril formation of Abeta(1-40)[D23-K28] congener. Qualitatively similar results were obtained using simulations of Abeta(9-40) peptides and various constructs related to the Abeta(10-35) systems that were probed using OPLS and CHARMM force fields. We hypothesize that mutations or other constraints that preferentially enhance the population of the N* species would speed up aggregation rates. Conversely, ligands that lock it in the fibril-like N* structure would prevent amyloid formation.
Reddy
Govardhan
G
Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA.
Straub
John E
JE
Thirumalai
D
D
D000682:Amyloid / Q000737:chemistry*; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D001216:Asparagine; D003198:Computer Simulation; D019281:Dimerization; D007769:Lactams / Q000737:chemistry; D008239:Lysine; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D012492:Salts / Q000737:chemistry; D013816:Thermodynamics
D000682:Amyloid; D016229:Amyloid beta-Peptides; D007769:Lactams; D010446:Peptide Fragments; D012492:Salts; D001216:Asparagine; D008239:Lysine