Chemistry

Peptide plane can flip in two opposite directions: Implication in amyloid formation of transthyretin

Document Type

Article

Abstract

Transthyretin (TTR) is one of the known 20 or so human proteins that form fibrils in vivo, which is a hallmark of amyloid diseases. Recently, molecular dynamics simulations using ENCAD force field have revealed that under low pH conditions, the peptide planes of several amyloidogenic proteins can flip in one direction to form an α-pleated structure which may be a common conformational transition in the fibril formation. We performed molecular dynamics simulations with AMBER force fields on a recently engineered double mutant TTR, which was shown experimentally to form amyloid fibrils even under close to physiological conditions. Our simulations have demonstrated that peptide-plane flipping can occur even under neutral pH and room temperature for this amyloidogenic TTR variant. Unlike previously reported peptide-plane flipping of TTR using ENCAD force field, we have found two-way flipping using AMBER force field. We propose a new mechanism of amyloid formation based on the two-way flipping, which gives a better explanation of various experimental and computational results. In principle, the residual dipolar and hydrogen-bond scalar coupling techniques can be applied to the wild-type TTR and the variant to study the peptide-plane flipping of amyloidogenic proteins. © 2006 American Chemical Society.

Publication Title

Journal of Physical Chemistry B

Publication Date

3-30-2006

Volume

110

Issue

12

First Page

5829

Last Page

5833

ISSN

1520-6106

DOI

10.1021/jp0570420

Keywords

computer simulation, conformations, diseases, molecular dynamics, pH effects

Cross Post Location

Student Publications

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