| pubmed-article:18479708 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C0030956 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C0596988 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C0678607 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C1883559 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C0678594 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C0870781 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C0962722 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C1723136 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C1869507 | lld:lifeskim |
| pubmed-article:18479708 | lifeskim:mentions | umls-concept:C2354310 | lld:lifeskim |
| pubmed-article:18479708 | pubmed:issue | 4 | lld:pubmed |
| pubmed-article:18479708 | pubmed:dateCreated | 2008-6-2 | lld:pubmed |
| pubmed-article:18479708 | pubmed:abstractText | The initial events in protein aggregation involve fluctuations that populate monomer conformations, which lead to oligomerization and fibril assembly. The highly populated structures, driven by a balance between hydrophobic and electrostatic interactions in the protease-resistant wild-type Abeta(21-30) peptide and mutants E22Q (Dutch), D23N (Iowa), and K28N, are analyzed using molecular dynamics simulations. Intrapeptide electrostatic interactions were connected to calculated pK(a) values that compare well with the experimental estimates. The pK(a) values of the titratable residues show that E22 and D23 side chains form salt bridges only infrequently with the K28 side chain. Contacts between E22-K28 are more probable in "dried" salt bridges, whereas D23-K28 contacts are more probable in solvated salt bridges. The strength of the intrapeptide hydrophobic interactions increases as D23N<WT<E22Q<K28A. Free-energy profiles and disconnectivity representation of the energy landscapes show that the monomer structures partition into four distinct basins. The hydrophobic interactions cluster the Abeta(21-30) peptide into two basins, differentiated by the relative position of the DVG(23-25) and GSN(25-27) fragments about the G25 residue. The E22Q mutation increases the population with intact VGSN turn compared to the wild-type (WT) peptide. The increase in the population of the structures in the aggregation-prone Basin I in E22Q, which occurs solely due to the difference in charge states between the Dutch mutant and the WT, gives a structural explanation of the somewhat larger aggregation rate in the mutant. The D23N mutation dramatically reduces the intrapeptide interactions. The K28A mutation increases the intrapeptide hydrophobic interactions that promote population of structures in Basin I and Basin II whose structures are characterized by hydrophobic interaction between V24 and K28 side chains but with well-separated ends of the backbone atoms in the VGSN turn. The intrapeptide electrostatic interactions in the WT and E22Q peptides roughen the free-energy surface compared to the K28A peptide. The D23N mutation has a flat free-energy surface, corresponding to an increased population of random coil-like structures with weak hydrophobic and electrostatic interactions. We propose that mutations or sequences that enhance the probability of occupying Basin I would promote aggregation of Abeta peptides. | lld:pubmed |
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| pubmed-article:18479708 | pubmed:language | eng | lld:pubmed |
| pubmed-article:18479708 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:18479708 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:18479708 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
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| pubmed-article:18479708 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:18479708 | pubmed:month | Jun | lld:pubmed |
| pubmed-article:18479708 | pubmed:issn | 1089-8638 | lld:pubmed |
| pubmed-article:18479708 | pubmed:author | pubmed-author:ThirumalaiDD | lld:pubmed |
| pubmed-article:18479708 | pubmed:author | pubmed-author:StraubJohn... | lld:pubmed |
| pubmed-article:18479708 | pubmed:author | pubmed-author:TarusBogdanB | lld:pubmed |
| pubmed-article:18479708 | pubmed:issnType | Electronic | lld:pubmed |
| pubmed-article:18479708 | pubmed:day | 13 | lld:pubmed |
| pubmed-article:18479708 | pubmed:volume | 379 | lld:pubmed |
| pubmed-article:18479708 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:18479708 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:18479708 | pubmed:pagination | 815-29 | lld:pubmed |
| pubmed-article:18479708 | pubmed:dateRevised | 2010-11-18 | lld:pubmed |
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