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Biomolecular Concepts

Editor-in-Chief: Jollès, Pierre / Mansuy, Isabelle

Editorial Board Member: Avila, Jesus / Bonetto, Valentina / Cera, Enrico / Jorgensen, Erik / Jörnvall, Hans / Lagasse, Eric / Norman, Robert / Pinna, Lorenzo / Raghavan, K. Vijay / Venetianer, Pal / Wahli, Walter

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1868-503X
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A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

Scott A. Hollingsworth
  • Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
/ P. Andrew Karplus
  • Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
Published Online: 2010-09-08 | DOI: https://doi.org/10.1515/bmc.2010.022

Abstract

The Ramachandran plot is among the most central concepts in structural biology, seen in publications and textbooks alike. However, with the increasing numbers of known protein structures and greater accuracy of ultra-high resolution protein structures, we are still learning more about the basic principles of protein structure. Here, we use high-fidelity conformational information to explore novel ways, such as geo-style and wrapped Ramachandran plots, to convey some of the basic aspects of the Ramachandran plot and of protein conformation. We point out the pressing need for a standard nomenclature for peptide conformation and propose such a nomenclature. Finally, we summarize some recent conceptual advances related to the building blocks of protein structure. The results for linear groups imply the need for substantive revisions in how the basics of protein structure are handled.

Keywords: linear groups; polypeptide conformation; Ramachandran plot, secondary structure; torsion angles

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Corresponding author


Published Online: 2010-09-08

Published in Print: 2010-10-01


Citation Information: BioMolecular Concepts, ISSN (Online) 1868-503X, ISSN (Print) 1868-5021, DOI: https://doi.org/10.1515/bmc.2010.022. Export Citation

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