Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further...
Transcript of Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further...
![Page 1: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/1.jpg)
Simulating supercoilingin DNA minicirclesGeorge Watson
![Page 2: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/2.jpg)
Introduction
![Page 3: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/3.jpg)
Supercoiling● Supercoiling is the addition of extra twists to a length of DNA
● Relaxed B-DNA has ~10.5 bp/turn
Adding or removing twists induces strain, which causes the
DNA to contort into different shapes
● Supercoiling has many biological functions, including gene
regulation, and prokaryotic & eukaryotic genomes are
persistently supercoiled
![Page 4: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/4.jpg)
Supercoiling II: Twist & Writhe● Supercoiling is characterised by
○ Twist, Tw, the number of times the two strands coil around one another
(typically N / 10.5); often given in degrees per base pair (relaxed = 34.3 ° / bp)
○ Writhe, Wr, the number of times the helix axis coils around itself
● The linking number, Lk = Tw + Wr, is usually constant, but twist
and writhe can vary smoothly
● The linking number of relaxed B-DNA is denoted Lk0
ΔLk = Lk − Lk0
![Page 5: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/5.jpg)
Kornberg 1980 DNA replication (San Francisco: W. H. Freeman) 29
![Page 6: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/6.jpg)
Irobalieva et al. 2015 Nat. Commun. 6 8440 [CC-BY]
![Page 7: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/7.jpg)
DNA-bending proteins: IHF & HU● Histone-like nucleoid-associated
proteins present in virtually all known
prokaryotes
● Bend DNA (up to 160°) by binding;
intercalating prolines disrupt stacking,
causing kinks
● IHF binds specifically to a known
sequence; HU binds nonspecifically but
prefers damaged DNA E. coli IHFPDB: 5J0N
![Page 8: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/8.jpg)
Method
![Page 9: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/9.jpg)
Molecular Dynamics● Simulation technique that can provide atomistic insight
● Construct a potential based on the properties of each atom;
integrate to find the force on each atom at every time step
● Powerful, but very computationally expensive!
● Simulating water atomistically would be prohibitively slow, so
treat solvent implicitly using generalised Born model
● Many potentials and packages (AMBER, GROMACS, CHARMM…)
![Page 10: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/10.jpg)
Method
29 + IHFt = 0
● 336 bp minicircles with 29–34 turns (Lk
0 = 32 ⇒ −3 ≤ ΔLk ≤ +2)
● Insert IHF binding site (11 bp) &
minimise with/without protein
(E. coli)
● Simulate in implicit solvent for
20 ns using AMBER (pmemd.CUDA)○ Temperature: 300 K○ Salt concentration: 0.8 mol/l
○ Potential: ff14SB + parmbsc1
![Page 11: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/11.jpg)
Results
![Page 12: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/12.jpg)
336bp minicircles + IHF
ΔLk = −2 ΔLk = −3
![Page 13: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/13.jpg)
Results● Supercoiling can condense DNA & bring distal sites closer
together; this effect appears to be enhanced by bound IHF,
especially in highly supercoiled systems
● IHF is always positioned at the apex of the plectoneme
● IHF can bridge distal sites in supercoiled DNA, forming closed
loops — linked to stability of biofilms?
● The amino acids that form these bridges are not present in
HU- — are they conserved in other (non-E. coli) IHFs?
![Page 14: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/14.jpg)
Twist, Writhe, Radius of gyration
Tw / ° Wr
Lk Rg / Å
Irobalieva et al. 2015 Nat. Commun. 6 8440 [CC-BY]
/ °
![Page 15: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/15.jpg)
Hydrogen bonds
Data for 29 + IHF
![Page 16: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/16.jpg)
The DNA–IHF interaction is
asymmetric
One side of the protein always
binds first & more strongly
Is this due to the protein structure
or the sequence of this DNA?
IHF is a heterodimer, so
asymmetry is possible33 + IHFt = 20 ns
![Page 17: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/17.jpg)
IHF surface charge● Surface charge distribution
is patchy
● Contrast with, e.g., RNA
polymerase
Cramer, Bushnell, Kornberg 2001 Science 292 1863–76(Used under licence)
![Page 18: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/18.jpg)
Discussion
![Page 19: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/19.jpg)
The Future● Replicas (running...)
● HU (requires crystal structure)
● H bonds; effect of supercoiling on interaction
● Formation of protein bridges between distal sites; dependence
on supercoiling?
● Link to experimental work (Seb) — go bigger?
![Page 20: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/20.jpg)
Acknowledgements● Supervision — Agnes Noy, Mark Leake
● Complementary experiments (soon) — Sébastien Guilbaud
![Page 21: Simulating supercoiling in DNA minicirclesgw639/2018-01-30_group... · 2018. 1. 30. · Further Reading Supercoiling: Irobalieva et al. 2015 Nat. Commun. 6 8440 Noy, Sutthibutpong,](https://reader035.fdocuments.net/reader035/viewer/2022071512/6131aa171ecc51586944e0a3/html5/thumbnails/21.jpg)
Further Reading● Supercoiling:
○ Irobalieva et al. 2015 Nat. Commun. 6 8440○ Noy, Sutthibutpong, Harris 2016 Biophys. Rev. 8 145–55○ Noy, Maxwell, Harris 2017 Biophys. J. 112 523–31
● DNABII proteins (IHF, HU):○ Swinger, Rice 2004 Curr. Opin. Struct. Biol. 14 28–35
● Software:○ AMBER/AmberTools: http://ambermd.org/
○ Curves+/Canal: Lavery et al. 2009 Nucleic Acids Res. 37 5917–29
○ WrLINE: Sutthibutpong, Harris, Noy 2015 J. Chem. Theory Comput. 11 2768–75