Understanding the role and evolution of internal symmetry in protein structure is a fundamental question in structural biology. We present here CE-Symm 2.0, a key tool to address that question, which is able to detect all types of protein internal symmetry and provides a robust and intuitive sequence-to-structure analysis of all repeats. Notable features compared to the previous version include an optimized multiple alignment between repeats, determination of the full point group, and identification of multiple symmetry axes. We expect CE-Symm to find ample use in evolutionary studies, functional annotation, and structural classification of proteins. This work was presented at the 3DSIG 2016 conference in Orlando, FL, on July 8, 2016. See also the poster form: http://www.slideshare.net/sbliven/3dsig-2016-poster-exploring-internal-symmetry-and-structural-repeats-with-cesymm

1. EXPLORING INTERNAL SYMMETRY AND
STRUCTURAL REPEATS WITH CE-SYMM
Spencer Bliven
July 8, 2016
3DSIG. Orlando, FL

2. LEVELS OF SYMMETRY: QUATERNARY SYMMETRY
 DNA Clamps are found as
dimers in bacteria or
trimers in eukaryotes
 DNA is bound in the
central channel
Proliferating Cell Nuclear Antigen [1VYM]
(DNA modeled from 1BNA)
Stoichiometry: A3
Symmetry: C3
1

3. LEVELS OF SYMMETRY: SYMMETRY OF DOMAINS
 6 “processivity fold”
domains
Proliferating Cell Nuclear Antigen [1VYM]
Stoichiometry: A6
Symmetry: C6
2

4. LEVELS OF SYMMETRY: INTERNAL SYMMETRY
Kelman, Z., & O'Donnell, M. (1995). Nucleic Acids Research, 23(18), 3613–3620.
Neuwald, A. F., & Poleksic, A. (2000). Nucleic Acids Research, 28(18), 3570–3580.
Stoichiometry: A12
Symmetry: D6
3

5. SIGNIFICANCE
 Evolution
 Identify duplications & fusions
 Many examples of homologous quaternary symmetric/internally
symmetric proteins
 Tradeoff between monomer & oligomer
4
Ancient protomer (x2?)
x6
Bacterial DimerEukaryotic/Archaeal/Viral
Trimer
x2x3
DNA polymerase IIIβ
E. coli
[1MMI]
Proliferating Cell
Nuclear Antigen
Human
[1VYM]

6. SIGNIFICANCE
 Function
 Allosteric regulation/cooperativity
 Bind ligands symmetrically (e.g. metals,
palindromic DNA, channels)
Monod, J., Wyman, J., & Changeux, J.-P. (1965). J Mol Biol, 12, 88–118.
TATA Binding Protein
[1TGH]
Hemoglobin
[4HHB]
5

7. SIGNIFICANCE
 Function
 Allosteric regulation/cooperativity
 Bind ligands symmetrically (e.g. metals,
palindromic DNA, channels)
 Folding
 Prevent infinite assembly
 Subunits fold quasi-independently
TATA Binding Protein
[1TGH]
Monod, J., Wyman, J., & Changeux, J.-P. (1965). J Mol Biol, 12, 88–118.
Wolynes, P. G. (1996). PNAS, 93(25), 14249–14255.
Hemoglobin
[4HHB]
6

8. TYPES OF SYMMETRY
Cyclic (C8)
TIM barrel
[1TIM]
Dihedral (D2)
Glyoxalase
[3B59]
Helical (H3)
Antifreeze Protein
[1L0S]
Translational (R)
Ankyrin Repeat
[1N0R]
7

9. HIERARCHICAL SYMMETRY
ɣB-Crystallin
[4GCR]
C2+C2
Vitamin C transporter
[4RP8]
C2+C2/Broken D2
8

10. CE-SYMM 2.0
 Multiple alignment between all repeats
 Open and Closed symmetry
 Multiple Axes and hierarchical symmetry
 Point Group detection
 Monte Carlo alignment optimization
 https://github.com/rcsb/symmetry (LGPL)
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
Glyoxalase
[3B59]
D2
9

11. Monoamine Oxidase Regulatory Protein [1Q6W]
DIFFERENT STOICHIOMETRY, SAME STRUCTURE
10

12. Monoamine Oxidase Regulatory Protein [1Q6W]
DIFFERENT STOICHIOMETRY, SAME STRUCTURE
11

13. Monoamine Oxidase Regulatory Protein [1Q6W]
MaoC domain protein dehydratase [4E3E]
DIFFERENT STOICHIOMETRY, SAME STRUCTURE
12

14. Monoamine Oxidase Regulatory Protein [1Q6W]
MaoC domain protein dehydratase [4E3E]
DIFFERENT STOICHIOMETRY, SAME STRUCTURE
13
A6 stoichiometry
D3 symmetry
A3 stoichiometry
C3 symmetry?

15. Monoamine Oxidase Regulatory Protein [1Q6W]
MaoC domain protein dehydratase [4E3E]
DIFFERENT STOICHIOMETRY, SAME STRUCTURE
14
[ND]xxxxH

16. PROMINENT IN MEMBRANE PROTEINS
 Major Facilitator Superfamily
 Lactose/Proton symporter
 Lactose binds at center
 4 repeats (2 inverted)
periplasm
cytosol
15
LacY
[1Q6W]

17. CE-SYMM 2.0 ALGORITHM
Structure
1. Structural Self
Alignment
Self-Alignment
TM-Score
2.Order Detection
Order
3. Refinement
Multiple
Alignment
4. Optimization
TM-ScoreAsymmetry Symmetry
6. Point Group
Detection
5. Iterate
16

18. CE-SYMM 2.0 ALGORITHM
Structure
1. Structural Self
Alignment
Self-Alignment
TM-Score
2.Order Detection
Order
3. Refinement
Multiple
Alignment
4. Optimization
TM-ScoreAsymmetry Symmetry
6. Point Group
Detection
5. Iterate
Keap1 Kelch domain
[1U6D]
17

19. CE-SYMM 2.0 ALGORITHM
Structure
1. Structural Self
Alignment
Self-Alignment
TM-Score
Order
Multiple
Alignment
4. Optimization
TM-ScoreAsymmetry Symmetry
6. Point Group
Detection
5. Iterate
3. Refinement
Keap1 Kelch domain
[1U6D]
18
2.Order Detection

20. CE-SYMM 2.0 ALGORITHM
Structure
1. Structural Self
Alignment
Self-Alignment
TM-Score
2.Order Detection
Order
3. Refinement
Multiple
Alignment
TM-ScoreAsymmetry Symmetry
6. Point Group
Detection
5. Iterate
4. Optimization
Keap1 Kelch domain
[1U6D]
19

21. CE-SYMM 2.0 ALGORITHM
Structure
1. Structural Self
Alignment
Self-Alignment
TM-Score
2.Order Detection
Order
3. Refinement
Multiple
Alignment
4. Optimization
TM-ScoreAsymmetry Symmetry
6. Point Group
Detection
5. Iterate
Keap1 Kelch domain
[1U6D]
20

22. CENSUS
 All domains from SCOPe 2.06
 Underestimate based on conservative thresholds
21
Order Number of Superfamilies % symmetric
Asymmetric 1051 75.39%
Rotational 302 21.66%
C2 237 78.48%
C3 19 6.29%
C4 12 3.97%
C5 2 0.66%
C6 8 2.65%
C7 16 5.30%
C8 8 2.65%
Dihedral 19 1.36%
D2 17 89.47%
D3 2 10.53%
Helical 7 0.50%
Translational 15 1.08%

23. SUMMARY
 Nature utilizes symmetry at multiple levels
 Internal symmetry can reveal evolutionary history of folds
 Duplications & fusions can preserve the overall biological assembly
 Internal symmetry is a multiple alignment problem
 CE-Symm is able to automatically detect most types of structural
repeats
22

24. ACKNOWLEDGEMENTS
 Paul Scherrer Institute
 Guido Capitani
 Aleix Lafita
 UC San Diego/RCSB
 Douglas Myers-Turnbull
 Andreas Prlić
 Peter Rose
 Jose Duarte
 RCSB & Bourne Lab members
 NIH
 Philip Bourne
 Philippe Youkharibache
 David Landsman
Resources:
 github.com/rcsb/symmetry
 source.rcsb.org/jfatcatserver/sy
mmetry.jsp
 www.slideshare.net/sbliven
Funding: NCBI/NLM/NIH
RCSB: NSF, NIH, DOE
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25. 24

26. RNA INTERNAL SYMMETRY
FMN Riboswitch [3F4E]
25

27. PTSIIA/GUTA-LIKE DOMAIN
 PTS sorbitol transporter subunit IIA
 Novel fold
 Solved by the Protein Structure Initiative
 Structural alignment reveals a conserved sequence motif between
halves
2F9H
26

28. ABC TRANSPORTER
BtuF
BtuC
BtuD
Vitamin B12 transporter BtuCD–F from E. coli [4FI3]
Periplasmic-binding protein
Transmembrane domain
Nucleotide-binding domain
27

29. ABC TRANSPORTER
BtuF [1N4A]
BtuF
BtuC
BtuD
Vitamin B12 transporter BtuCD–F from E. coli [4FI3]
28

30. BENCHMARK
 1007 structures from SCOP
superfamilies
 Manually curated
 Excludes small proteins (<4
SSEs)
 26% of superfamilies have
internal symmetry or large
structural repeats
Order Superfamilies %
Asymmetric 747 74.2%
Rotational 214 21.2%
2 160 74.8%
3 10 4.7%
4 2 0.9%
5 3 1.4%
6 9 4.2%
7 10 4.7%
8 20 9.3%
Dihedral 18 1.8%
D2 14 77.8%
D3 1 5.6%
D4 2 11.1%
D5 1 5.6
Helical 11 1.1%
H2 9 81.8%
H3 2 18.2%
H10 1 9.1%
Superhelical 2 0.2%
Translational 15 1.5%
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31. PERFORMANCE
30

32. PERFORMANCE
31

33. CE-SYMM: SELF-ALIGNMENT
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.
32

34. CE-SYMM: SELF-ALIGNMENT
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.
33

35. βγ-CRYSTALLIN FAMILY
34
Aravind, P., Mishra, A., Suman, S. K., Jobby, M. K., Sankaranarayanan, R., & Sharma, Y. (2009). The betagamma-
crystallin superfamily contains a universal motif for binding calcium. Biochemistry, 48(51), 12180–12190.
M-Crystallin
[3HZ2.A]
C2
Bovine ɣB-Crystallin
[4GCR]
C2+C2

36. This work is licensed under a
Creative Commons Attribution-ShareAlike 3.0 Unported License.
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