Linked Life Data

21289072

Source:http://linkedlifedata.com/resource/pubmed/id/21289072

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2011-2-21
pubmed:abstractText
The structural and thermodynamics characters of ?-syn12 (residues 1-12 of the human ?-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational ?-helix and an irregular structure, respectively. Each replica was run for 300 ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded ?-hairpin structure, and favorite conformations. The results showed that the isolated ?-syn12 peptide in water adopted four different conformational states: the first state was a ?-hairpin ensemble with Turn(9-6) and four hydrogen bonds, the second state was a ?-hairpin ensemble with two turns (Turn(9-6) and Turn(5-2)) and three hydrogen bonds, the third state was a disordered structure with both Turn(8-5) and Turn(5-2), and the last state was a ?-helix ensemble. Meanwhile, we studied the free energy change of ?-syn12 peptide from the unfolded state to the ?-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition. The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated ?-syn12 peptide in water by T-REMD.
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
1745-7270
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
43
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
172-80
pubmed:dateRevised
2011-5-9
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution.
pubmed:affiliation
Key Lab of Biophysics in Universities of Shandong, Dezhou, China.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't