A Folding Pathway Model of Mini-Protein BBA5.
We present the folding pathway model of mini-protein BBA5, a bundle of secondary structures, α-helix and β-hairpin, by using action-derived molecular dynamics (ADMD) simulations. From ten independent ADMD simulations, we extracted common features of the folding pathway of BBA5, from which we found t...
| Publicado en: | BioMed Research International Vol. 2015; pp. 1 - 10 |
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| Autores principales: | , , |
| Formato: | equations & formulas pictorial research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
9/20/2015
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=110155485&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 110155485 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 9/20/2015 vid: 2015 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 110155485 110155485 NLM26457304 110155485 10.1155/2015/828095 NLM26457304 PMC4592707 110155485 ppf: 1 ppct: 9 formats: fmt: @attributes: type: P tig: atl: A Folding Pathway Model of Mini-Protein BBA5. aug: au: Lee, In-Ho Kim, Seung-Yeon Lee, Jooyoung affil: Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea sug: subj: Models, Theoretical Computer Simulation Proteins Biochemical Phenomena Factor Analysis Molecular Structure Funding Source Human ab: We present the folding pathway model of mini-protein BBA5, a bundle of secondary structures, α-helix and β-hairpin, by using action-derived molecular dynamics (ADMD) simulations. From ten independent ADMD simulations, we extracted common features of the folding pathway of BBA5, from which we found that the early stage chain compaction was followed by the formation of C-terminal α-helix. The N-terminal β-hairpin was observed to form only after α-helix was stabilized. This result is in good agreement with the experimental observation that BBA5 mutants were moderately cooperative folders, and their C-terminal helical fragments were of higher secondary structure propensity while the N-terminal hairpin fragments were of a random coil spectrum. We found that the most flexible part of BBA5 is the N-terminal four residues. Although both are made of the identical ββα motif, the secondary structure formation sequence of BBA5 is found to be different from that of FSD-1. Finally, a description of the folding pathway in terms of principal component analysis is presented to characterize the folding dynamics in reduced dimensions. With only three principal components, we were able to describe 83.4% of the pathway. pubtype: Academic Journal doctype: equations & formulas pictorial research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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