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Systematic Approach to Find the Global Minimum of Relaxation Dispersion Data for Protein-Induced B-Z Transition of DNA.
Oh, Kwang-Im; Lee, Ae-Ree; Choi, Seo-Ree; Go, Youyeon; Ryu, Kyoung-Seok; Kim, Eun-Hee; Lee, Joon-Hwa.
Afiliação
  • Oh KI; Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea.
  • Lee AR; Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea.
  • Choi SR; Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea.
  • Go Y; Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea.
  • Ryu KS; Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 28119, Korea.
  • Kim EH; Center for Research Equipment, Korea Basic Science Institute, Ochang, Chungbuk 28119, Korea.
  • Lee JH; Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea.
Int J Mol Sci ; 22(7)2021 Mar 29.
Article em En | MEDLINE | ID: mdl-33805331
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in µs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZαADAR1)-DNA complex. The global search results indicated that a α-helical segment of hZαADAR1 provided the main contribution to the three-state conformational changes of a hZαADAR1-DNA complex with a slow B-Z exchange process. The two global exchange rate constants, kex and kZB, were found to be 844 and 9.8 s-1, respectively, in agreement with two regimes of residue-dependent chemical shift differences-the "dominant oscillatory regime" and "semi-oscillatory regime". We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Modelos Moleculares / Adenosina Desaminase / Proteínas de Ligação a RNA / DNA Forma Z / DNA de Forma B Limite: Humans Idioma: En Revista: Int J Mol Sci Ano de publicação: 2021 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Modelos Moleculares / Adenosina Desaminase / Proteínas de Ligação a RNA / DNA Forma Z / DNA de Forma B Limite: Humans Idioma: En Revista: Int J Mol Sci Ano de publicação: 2021 Tipo de documento: Article