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Molecular dynamics studies of protei...

Ding, Feng.

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Molecular dynamics studies of protein folding and aggregation.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Molecular dynamics studies of protein folding and aggregation./
作者:	Ding, Feng.
面頁冊數:	104 p.
附註:	Source: Dissertation Abstracts International, Volume: 65-01, Section: B, page: 0261.
Contained By:	Dissertation Abstracts International65-01B.
標題:	Physics, Condensed Matter. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3118804

Molecular dynamics studies of protein folding and aggregation.
Ding, Feng.

Molecular dynamics studies of protein folding and aggregation. - 104 p.

Source: Dissertation Abstracts International, Volume: 65-01, Section: B, page: 0261.

Thesis (Ph.D.)--Boston University, 2004.

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation.Subjects--Topical Terms:

1018743
Physics, Condensed Matter.

Molecular dynamics studies of protein folding and aggregation.
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245 1 0 $a Molecular dynamics studies of protein folding and aggregation.
300 $a 104 p.
500 $a Source: Dissertation Abstracts International, Volume: 65-01, Section: B, page: 0261.
500 $a Major Professor: H. Eugene Stanley.
502 $a Thesis (Ph.D.)--Boston University, 2004.
520 $a This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation.
520 $a Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability &prop; exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition.
520 $a Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.
590 $a School code: 0017.
650 4 $a Physics, Condensed Matter. $3 1018743
650 4 $a Biophysics, General. $3 1019105
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773 0 $t Dissertation Abstracts International $g 65-01B.
790 1 0 $a Stanley, H. Eugene, $e advisor
790 $a 0017
791 $a Ph.D.
792 $a 2004
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