Deciphering the preference and predicting the viability of circular permutations in proteins.

PloS One
Wei-Cheng LoPing-Chiang Lyu

Abstract

Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. The...Continue Reading

References

Feb 20, 1991·Journal of Molecular Biology·D Bordo, P Argos
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
May 1, 1995·Trends in Biochemical Sciences·C P Ponting, R B Russell
Feb 1, 1995·Protein Engineering·A C WallaceJ M Thornton
Feb 1, 1995·Protein Science : a Publication of the Protein Society·B E Jones, C R Matthews
May 1, 1994·Protein Science : a Publication of the Protein Society·A ChakrabarttyR L Baldwin
Oct 1, 1993·Protein Science : a Publication of the Protein Society·S F Betz
Jan 1, 1995·Progress in Biophysics and Molecular Biology·U Heinemann, M Hahn
Jun 1, 1997·Current Opinion in Structural Biology·Y Lindqvist, G Schneider
Jun 25, 1998·European Journal of Radiology·A R van Erkel, P M Pattynama
Jun 16, 1999·Journal of Molecular Evolution·A Jeltsch
Sep 3, 1999·FEBS Letters·S TopellR Glockshuber
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·G S BairdR Y Tsien
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 27, 2001·Protein Science : a Publication of the Protein Society·M ZavodszkyR Krishnamoorthi
Oct 2, 2001·Protein Engineering·S UlielR Unger
Jan 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Bertil Halle
Mar 27, 2002·BMC Evolutionary Biology·Janusz M Bujnicki
Apr 27, 2002·Acta Crystallographica. Section D, Biological Crystallography·Sven HovmöllerTomas Ohlson
Jul 19, 2002·Biophysical Journal·Sibsankar KunduGeorge N Phillips
Aug 2, 2002·Trends in Biochemical Sciences·Annabel E ToddJanet M Thornton
Apr 2, 2003·Biophysical Journal·Alessandro PintarSándor Pongor
Feb 12, 2004·Journal of Molecular Recognition : JMR·Christelle PommiéMarie-Paule Lefranc
Apr 21, 2004·Protein Science : a Publication of the Protein Society·Grzegorz BulajDavid P Goldenberg
Aug 25, 2004·Proteins·Jie ChenWei Wang
Sep 2, 2004·Protein Science : a Publication of the Protein Society·Thomas U SchwartzGünter Blobel
Nov 17, 2004·Journal of Molecular Biology·Gil AmitaiShmuel Pietrokovski
Dec 21, 2004·Proteins·Jianhua Zhu, Zhiping Weng
Feb 3, 2005·Proteins·Han-Kuen LiangJenn-Kang Hwang
Feb 5, 2005·BMC Evolutionary Biology·Anna R Panchenko, Thomas Madej
Feb 8, 2005·Proteins·Minh N Nguyen, Jagath C Rajapakse
Mar 25, 2005·Bioinformatics·January WeinerErich Bornberg-Bauer

❮ Previous
Next ❯

Methods Mentioned

BETA
protein folding
RSA
PCA

Software Mentioned

REPRDB
LIGPLOT
teLeap
DSSP
ZooBank
GANGSTA
align
FASTA
Perl
pygnm

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.

Related Papers

Nucleic Acids Research
Wei-Cheng LoPing-Chiang Lyu
PLoS Computational Biology
Spencer Bliven, Andreas Prlić
Protein Science : a Publication of the Protein Society
J Jung, B Lee
© 2022 Meta ULC. All rights reserved