Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations

Joan-Emma Shea; Zachary A Levine

doi:10.1007/978-1-4939-2978-8_15

Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations

Methods Mol Biol. 2016:1345:225-50. doi: 10.1007/978-1-4939-2978-8_15.

Authors

Joan-Emma Shea^{1

2}, Zachary A Levine^{3

4}

Affiliations

¹ Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA. [email protected].
² Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA. [email protected].
³ Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
⁴ Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.

PMID: 26453216
DOI: 10.1007/978-1-4939-2978-8_15

Abstract

The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.

Keywords: Alzheimer’s disease; Amyloid fibrils; Intrinsically disordered proteins; Molecular dynamics simulations; Protein aggregation; Protein folding; Replica exchange molecular dynamics; Tau protein.

MeSH terms

Amyloid beta-Peptides / chemistry*
Amyloid beta-Peptides / genetics
Humans
Molecular Dynamics Simulation*
Protein Aggregation, Pathological / genetics*
Protein Conformation
Temperature
Thermodynamics

Substances

Amyloid beta-Peptides