Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics
 
research article

SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics

Grell, D
•
Richardson, JS
•
Richardson, DC
Show more
2000
Journal of Molecular Graphics and Modelling

Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein, A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains. including hydrogens. while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids, ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.

  • Details
  • Metrics
Type
research article
Author(s)
Grell, D
Richardson, JS
Richardson, DC
Mutter, M  
Date Issued

2000

Published in
Journal of Molecular Graphics and Modelling
Volume

18

Issue

3

Start page

290

End page

298

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBP  
Available on Infoscience
February 9, 2006
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/222273
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés