topological methods in physical virology fsu-uf topology meeting feb. 23, 2013 de witt sumners...
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TOPOLOGICAL METHODS IN PHYSICAL VIROLOGY
FSU-UF TOPOLOGY MEETINGFEB. 23, 2013
De Witt SumnersDepartment of Mathematics
Florida State University
Tallahassee, FL 32306
DNA Replication
TOPOLOGICAL VIROLOGY
• Using DNA plasmids as an assay for site-specific recombination—deduce viral enzyme binding and mechanism
• Using DNA knots to elucidate packing geometry and ejection of DNA in viral capsids
A Little Entanglement Can Go a Long Way
DNA KNOTTING IS LETHAL IN BACTERIA
• Promotes replicon loss by blocking DNA replication
• Blocks gene transcription
• Causes mutation at a rate 3 to 4 orders of magnitude higher than an unknotted plasmid
Diebler et al, BMC Molecular Biology (2007) 8:44
Crossover Number
CHIRALITY
Knots and Catenanes
Prime and Composite Knots
http://www.pims.math.ca/knotplot/zoo/
A Knot Zoo By Robert G. Scharein
© 2005 Jennifer K. Mann
T ORUS KNOTS
TWIST KNOTS
Topological Enzymology
Mathematics: Deduce enzyme binding and mechanism from
observed products
Strand PassageStrand Passage
TopoisomeraseTopoisomerase
Strand ExchangeStrand Exchange
RecombinaseRecombinase
GEL ELECTROPHORESIS
RecA Coated DNA
DNA Trefoil Knot
Dean et al., J BIOL. CHEM. Dean et al., J BIOL. CHEM. 260260(1985), 4975(1985), 4975
DNA (2,13) TORUS KNOT
Spengler et al. CELL Spengler et al. CELL 4242 (1985), 325 (1985), 325
T4 TOPOISOMERASE TWIST KNOTS
Wassserman & Cozzarelli, J. Biol. Chem. 266 (1991), 20567Wassserman & Cozzarelli, J. Biol. Chem. 266 (1991), 20567
PHAGE GIN KNOTS
Kanaar et al. CELL Kanaar et al. CELL 6262(1990), 553(1990), 553
Topoisomerase Knots
DDeeaann eett aall..,, JJ BBIIOOLL.. CCHHEEMM.. 226600((11998855)),, 44997755
Topoisomerase Knots
Dean et al., J BIOL. CHEM. Dean et al., J BIOL. CHEM. 260260(1985), 4975(1985), 4975
GEL VELOCITY IDENTIFIES KNOT COMPLEXITY
Vologodskii et al, JMB Vologodskii et al, JMB 278278 (1988), 1 (1988), 1
SITE-SPECIFIC RECOMBINATION
Biology of Site-Specific Recombination
• Integration and excision of viral genome into and out of host genome
• DNA inversion--regulate gene expression & mediate phage host specificity
• Segregation of DNA progeny at cell division
• Plasmid copy number regulation
RESOLVASE SYNAPTIC COMPLEX
DNA 2-STRING TANGLES
2-STRING TANGLES
3 KINDS OF TANGLES
A A tangle tangle is a configuration of a pair of strands in a 3-ball. We consider all is a configuration of a pair of strands in a 3-ball. We consider alltangles to have the SAME boundary. There are 3 kinds of tangles:tangles to have the SAME boundary. There are 3 kinds of tangles:
RATIONAL TANGLES
TANGLE OPERATIONS
RATIONAL TANGLES AND 4-PLATS
4-PLATS (2-BRIDGE KNOTS AND LINKS)
4-PLATS
TANGLE EQUATIONS
RECOMBINATION TANGLES
SUBSTRATE EQUATION
PRODUCT EQUATION
TANGLE MODEL SCHEMATIC
Ernst & Sumners, Math. Proc. Camb. Phil. Soc. 108 (1990), 489
Tn3 RESOLVASE PRODUCTS
RESOLVASE MAJOR PRODUCT
• MAJOR PRODUCT is Hopf link [2], which does not react with Tn3
• Therefore, ANY iterated recombination must begin with 2 rounds of processive recombination
RESOLVASE MINOR PRODUCTS
• Figure 8 knot [1,1,2] (2 rounds of processive recombination)
• Whitehead link [1,1,1,1,1] (either 1 or 3 rounds of recombination)
• Composite link ( [2] # [1,1,2]--not the result of processive recombination, because assumption of tangle addition for iterated recombination implies prime products (Montesinos knots and links) for processive recombination
1st and 2nd ROUND PRODUC TS
RESOLVASE SYNAPTIC COMPLEX
Of = 0
THEOREM 1
PROOF OF THEOREM 1
• Analyze 2-fold branched cyclic cover T* of tangle T--T is rational iff T* = S1 x D2
• Use Cyclic Surgery Theorem to show T* is a Seifert Fiber Space
• Use results of Dehn surgery on SFS to show T* is a solid torus--hence T is a rational tangle
• Use rational tangle calculus to solve tangle equations posed by resolvase experiments
3rd ROUND PRODUCT
THEOREM 2
4th ROUND PRODUCT
UTILITY OF TANGLE MODEL
• Precise mathematical language for recombination-allows hypothesis testing
• Calculates ALL alternative mechanisms for processive recombination
• Model can be used with incomplete experimental evidence (NO EM)--crossing # of products, questionable relationship between product and round of recombination
• Proof shows there is NO OTHER explanation of the data
REFERENCES
JMB COVER
Crisona et al, J. Mol. Biol. 289 (1999), 747
BACTERIOPHAGE STRUCTURE
T4 EM
HOW IS THE DNA PACKED?
SPOOLING MODEL
RANDOM PACKING
P4 DNA has cohesive ends that form closed circular molecules
GGCGAGGCGGGAAAGCAC
CCGCTCCGCCCTTTCGTG…...
….
GGCGAGGCGGGAAAGCAC CCGCTCCGCCCTTTCGTG
Liu et al P2 Knots (33kb)
VIRAL KNOTS REVEAL PACKING
• Compare observed DNA knot spectrum to simulation of knots in confined volumes
EFFECTS OF CONFINEMENT ON DNA KNOTTING
• No confinement--3% knots, mostly trefoils
• Viral knots--95% knots, very high complexity--average crossover number 27!
MATURE vs TAILLESS PHAGE
Mutants--48% of knots formed inside capsidMutants--48% of knots formed inside capsid
Arsuaga et al, PNAS Arsuaga et al, PNAS 99 99 (2002), 5373(2002), 5373
P4 KNOT SPECTRUM
97% of DNA knots had crossing number > 10!97% of DNA knots had crossing number > 10!Arsuaga et al, PNAS Arsuaga et al, PNAS 99 99 (2002), 5373(2002), 5373
2D GEL RESOLVES SMALL KNOTS
Arsuaga et al, PNAS Arsuaga et al, PNAS 102 (2005), 9165102 (2005), 9165
PIVOT ALGORITHM
• Ergodic—can include volume exclusion and bending rigidity
• Knot detector—knot polynomials (Alexander, Jones, KNOTSCAPE)
VOLUME EFFECTS ON KNOT SIMULATION
• On average, 75% of crossings are extraneous
Arsuaga et al, PNAS Arsuaga et al, PNAS 99 99 (2002), 5373(2002), 5373
SIMULATION vs EXPERIMENT
Arsuaga et al, PNAS Arsuaga et al, PNAS 102 (2005), 9165102 (2005), 9165
n=90, R=4n=90, R=4
EFFECT OF WRITHE-BIASED SAMPLING
Arsuaga et al, PNAS Arsuaga et al, PNAS 102 (2005), 9165102 (2005), 9165
n=90, R=4n=90, R=4
CONCLUSIONS
• Viral DNA not randomly embedded (41and 52 deficit, 51 and 71 excess in observed knot spectrum)
• Viral DNA has a chiral packing mechanism--writhe-biased simulation close to observed spectrum
• Torus knot excess favors toroidal or spool-like packing conformation of capsid DNA
• Next step--EM (AFM) of 3- and 5- crossing knots to see if they all have same chirality
NEW PACKING DATA—4.7 KB COSMID
• Trigeuros & Roca, BMC Biotechnology 7 (2007) 94
CRYO EM VIRUS STRUCTUREJiang et al NATURE 439 (2006) 612
DNA-DNA INTERACTIONS GENERATE KNOTTING AND SURFACE ORDER
• Contacting DNA strands (apolar cholosteric interaction) assume preferred twist angle
Marenduzzo et al PNAS 106 (2009) 22269
SIMULATED PACKING GEOMETRY
Marenduzzo et al PNAS 106 (2009) 22269
THE BEAD MODEL
• Semiflexible chain of 640 beads--hard core diameter 2.5 nm
• Spherical capsid 45 nm
• Kink-jump stochastic dynamic scheme for simulating packing
KNOTS DELOCALIZED
Marenduzzo et al PNAS 106 (2009) 22269
Black—unknot; 91—red; complex knot--green
SIMULATED KNOT SPECTRUM
Marenduzzo et al PNAS 106 (2009) 22269
DNA-DNA INTERACTION CONCLUSIONS
• Reproduce cryo-em observed surface order
• Reproduce observed knot spectrum—excess of torus knots over twist knots
• Handedness of torus knots—no excess of right over left at small twist angles—some excess at larger twist angles and polar interaction
REFERENCES
• Nucleic Acids Research 29(2001), 67-71.• Proc. National Academy of Sciences USA
99(2002), 5373-5377.• Biophysical Chemistry 101-102 (2002), 475-484.• Proc. National Academy of Sciences USA
102(2005), 9165-9169.• J. Chem. Phys 124 (2006), 064903• Biophys. J. 95 (2008), 3591-3599• Proc. National Academy of Sciences USA
106(2009), 2269-2274.
JAVIER ARSUAGA, MARIEL VAZQUEZ, CEDRIC, EITHNE
CHRISTIAN MICHELETTI, ENZO ORLANDINI, DAVIDE MARENDUZZO
ANDRZEJ STASIAK
COLLABORATORS
Mathematics: Claus Ernst, Mariel Vazquez, Javier Arsuaga, Steve Harvey, Yuanan Diao, Christian Laing, Nick Pippenger, Stu Whittington, Chris Soteros, Enzo Orlandini, Christian Micheletti, Davide Marenduzzo
Biology: Nick Cozzarelli, Nancy Crisona, Sean Colloms, Joaquim Roca, Sonja Trigeuros, Lynn Zechiedrich, Jennifer Mann, Andrzej Stasiak
Thank You
•National Science Foundation
•Burroughs Wellcome Fund
UNKNOWN P4 KNOT
UNKNOWN P4 KNOTS
AFM Images of Simple DNA Knots (Mg2+)
μmμm
μm
Ercolini, Ercolini, Dietler EPFL LausanneDietler EPFL Lausanne