Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations.
We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Abeta(21-30) peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer's disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants ((3)J(H(N)H(alpha))), chemical-shift values, (13)C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Abeta(21-30). We find robust prediction of the (13)C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Abeta(21-30) peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Abeta(21-30) conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Abeta(21-30) peptide involves a majority population (approximately 60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a beta-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Abeta(1-40) and Abeta(1-42), for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high-quality NMR experiments has reached a fruitful stage for characterizing structural ensembles of disordered peptides and proteins in general.
Fawzi
Nicolas L
NL
UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 94720, USA.
Phillips
Aaron H
AH
Ruscio
Jory Z
JZ
Doucleff
Michaeleen
M
Wemmer
David E
DE
Head-Gordon
Teresa
T
D016229:Amyloid beta-Peptides / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; C501831:amyloid beta-protein (21-30)