A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory

Shaghaghi, H ; Sharif University of Technology | 2016

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  1. Type of Document: Article
  2. DOI: 10.1002/jcc.24323
  3. Publisher: John Wiley and Sons Inc , 2016
  4. Abstract:
  5. The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of 13Cα ADCC plots are independent of computational method but not of basis set valence shell type
  6. Keywords:
  7. 13C chemical shifts ; DFT ; Dihedral angle ; protein ; Secondary structure ; Amino acids ; Chemical shift ; Computation theory ; Dihedral angle ; Proteins ; Absolute deviations ; Graphical approach ; NMR chemical shifts ; ONIOM ; Protein structures ; Secondary structure of proteins ; Secondary structures ; Structural refinement ; Density functional theory
  8. Source: Journal of Computational Chemistry ; Volume 37, Issue 14 , 2016 , Pages 1296-1305 ; 01928651 (ISSN)
  9. URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.24323/abstract;jsessionid=35D624CC9F6F4ED7B48E9DE6080ACDD2.f04t01?systemMessage=Wiley+Online+Library+will+be+unavailable+on+Saturday+7th+Oct+from+03.00+EDT+%2F+08%3A00+BST+%2F+12%3A30+IST+%2F+15.00+SGT+to+08.00+EDT+%2F+13.00+BST+%2F+17%3A30+IST+%2F+20.00+SGT+and+Sunday+8th+Oct+from+03.00+EDT+%2F+08%3A00+BST+%2F+12%3A30+IST+%2F+15.00+SGT+to+06.00+EDT+%2F+11.00+BST+%2F+15%3A30+IST+%2F+18.00+SGT+for+essential+maintenance.+Apologies+for+the+inconvenience+caused+