A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

Scott A. Hollingsworth 1  and P. Andrew Karplus 1
  • 1 Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA

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.

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BioMolecular Concepts is a peer-reviewed journal fostering the integration of different fields of biomolecular research. The journal provides expert summaries and conclusive extensions of research data leading to new and original, testable hypotheses. Aspects of research that can promote related fields and lead to novel insight into biological mechanisms are of special interest.

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