@article {351, title = {Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations}, journal = {The Journal of Chemical Physics}, volume = {132}, year = {2010}, pages = {165104}, publisher = {AIP}, abstract = {Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.}, keywords = {aggregation, biochemistry, diseases, macromolecules, molecular biophysics, Proteins, self-assembly}, doi = {10.1063/1.3415372}, url = {http://link.aip.org/link/?JCP/132/165104/1}, author = {Hoang Bao Nam and Maksim Kouza and Hoang Zung and Mai Suan Li} } @article {352, title = {Protein mechanical unfolding: Importance of non-native interactions}, journal = {The Journal of Chemical Physics}, volume = {131}, year = {2009}, pages = {215103}, publisher = {AIP}, keywords = {biomechanics, elasticity, Hydrogen Bonds, molecular biophysics, molecular dynamics method, Proteins}, doi = {10.1063/1.3272275}, url = {http://link.aip.org/link/?JCP/131/215103/1}, author = {Maksim Kouza and Chin-Kun Hu and Hoang Zung and Mai Suan Li} }