Jump to ContentJump to Main Navigation
Show Summary Details

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

6 Issues per year

SCImago Journal Rank (SJR) 2015: 0.519
Source Normalized Impact per Paper (SNIP) 2015: 0.395
Impact per Publication (IPP) 2015: 1.289

See all formats and pricing

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


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

About the article

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

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Sara R. R. Campos, Olga Iranzo, and António M. Baptista
The Journal of Physical Chemistry B, 2016
Robert P. Bywater and Valera Veryazov
SpringerPlus, 2015, Volume 4, Number 1
Roberto Improta, Luigi Vitagliano, and Luciana Esposito
Proteins: Structure, Function, and Bioinformatics, 2015, Page n/a
Panagiotis I. Koukos and Nicholas M. Glykos
The Journal of Physical Chemistry B, 2014, Volume 118, Number 34, Page 10076
Neha V. Kalmankar, C. Ramakrishnan, and P. Balaram
Proteins: Structure, Function, and Bioinformatics, 2014, Volume 82, Number 7, Page 1101
Chakresh Kumar Jain, Money Gupta, Yamuna Prasad, Gulshan Wadhwa, and Sanjeev Kumar Sharma
Molecular Simulation, 2015, Volume 41, Number 7, Page 592
Francisco Carrascoza, Snezana Zaric, and Radu Silaghi-Dumitrescu
Journal of Molecular Graphics and Modelling, 2014, Volume 50, Page 125
Oleksandr O. Grygorenko, Sergey Zhersh, Bohdan V. Oliinyk, Oleg V. Shishkin, and Andrey A. Tolmachev
Tetrahedron: Asymmetry, 2014, Volume 25, Number 3, Page 229
Jan Zacharias and Ernst Walter Knapp
Protein Science, 2013, Volume 22, Number 11, Page 1669
Andrew Morin, Piotr Sliz, and Alfred Wittinghofer
Biopolymers, 2013, Volume 99, Number 11, Page 809
James T Koerber, Nathan D Thomsen, Brett T Hannigan, William F Degrado, and James A Wells
Nature Biotechnology, 2013, Volume 31, Number 10, Page 916
Oliviero Carugo and Kristina Djinović-Carugo
Acta Crystallographica Section D Biological Crystallography, 2013, Volume 69, Number 8, Page 1333
Sinosh Skariyachan, Nisha Jayaprakash, Navya Bharadwaj, and Rajeswari Narayanappa
Journal of Biomolecular Structure and Dynamics, 2014, Volume 32, Number 9, Page 1379
Yarrow Madrona, Scott A. Hollingsworth, Bushra Khan, and Thomas L. Poulos
Biochemistry, 2013, Volume 52, Number 30, Page 5039
Oleksandr O. Grygorenko, Sergey Zhersh, Bohdan V. Oliinyk, Oleg V. Shishkin, and Andrey A. Tolmachev
Org. Biomol. Chem., 2013, Volume 11, Number 6, Page 975
Mahdieh Nazari-Robati, Khosro Khajeh, Mahdi Aminian, Nasrin Mollania, and Abolfazl Golestani
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013, Volume 1834, Number 2, Page 479
Scott A. Hollingsworth, Matthew C. Lewis, Donald S. Berkholz, Weng-Keen Wong, and P. Andrew Karplus
Journal of Molecular Biology, 2012, Volume 416, Number 1, Page 78
Richard B. Cooley, Daniel J. Arp, and P. Andrew Karplus
Journal of Molecular Biology, 2011, Volume 413, Number 1, Page 177

Comments (0)

Please log in or register to comment.
Log in