Spencer Bliven July 11, 2014 3DSIG 2014 Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic Detection of Internal Symmetry in Proteins Using CE- Symm. Journal of Molecular Biology, 426(11), 2255–2268. PMID 24681267
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3DSIG 2014 Poster: Systematic detection of internal symmetry in proteins
These slides are from 3DSIG 2014, presented on July 11.
I describe our investigation of internal symmetry in protein structures. This is quite common (24% of domains), and has many implications for function, folding, and evolution.
I introduce the CE-Symm method, described in
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic Detection of Internal Symmetry in Proteins Using CE-Symm. Journal of Molecular Biology, 426(11), 2255–2268. doi:10.1016/j.jmb.2014.03.010
I discuss the results from running CE-Symm across the PDB, as well as some particularly compelling examples.
See also my poster by the same title for more details.
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Transcript
Spencer Bliven July 11, 2014 3DSIG 2014
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic Detection of Internal Symmetry in Proteins Using CE-Symm. Journal of Molecular Biology, 426(11), 2255–2268. PMID 24681267
Shindyalov, I. N., & Bourne, P. E. (1998). Protein Engineering, 11(9), 739–747.
Jia, Y., Dewey, T. G., Shindyalov, I. N., & Bourne, P. E. (2004). J Comput Biol, 11(5), 787–799.
Fibroblast Growth Factor [3JUT]
120° 120°
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Journal of Molecular Biology, 426(11), 2255–2268.
Fibroblast Growth Factor [3JUT]
120° 120°
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Journal of Molecular Biology, 426(11), 2255–2268.
! 1007 structures from SCOP superfamilies
! Manually curated ! Excludes small proteins
(<4 SSEs) ! 24% of superfamilies
have internal symmetry or large structural repeats
Order Superfamilies % Asymmetric 766 76.10%
Rotational
2 166 16.5%
3 10 1.0%
4 2 0.2%
5 3 0.3%
6 9 0.9%
7 9 0.9%
8 21 2.1%
Dihedral
2 2 0.2%
4 1 0.1%
Helical
2 9 0.9%
3 2 0.2%
Non-integral 2 0.2%
Superhelical 2 0.2%
Translational 3 0.3%
! AUC = .95 ! 86% True Positive
Rate ! 3.3% False
Positive Rate
SymD: Kim, C., Basner, J., & Lee, B. (2010). BMC Bioinformatics, 11, 303.
! All domains from SCOPe 2.03 ! Interactive results:
source.rcsb.org/jfatcatserver/scopResults.jsp ! Underestimate based on conservative thresholds
! PTS sorbitol transporter subunit IIA ! Novel fold ! Solved by the Protein Structure Initiative ! Structural alignment reveals a conserved sequence
motif between halves
[2F9H]
! 18-24% of domains have internal symmetry ! Symmetry gives clues about duplication events ! Symmetry is deeply tied to protein function ! CE-Symm can accurately detect internal symmetry
d1su3a2 D1pt2a_ d1c5ka1 d1k3ia3 d1h9ya2
! UC San Diego/RCSB ! Douglas Myers-Turnbull ! Andreas Prlić ! Peter Rose ! Zaid Aziz ! Milton Saier ! RCSB & Bourne Lab
members ! NIH
! Philip Bourne ! Philippe Youkharibache ! David Landsman