-
1
-
-
0034703226
-
Topologically linked protein rings in the bacteriophage HK97 capsid
-
Wikoff, W.R., Liljas, L., Duda, R.L., Tsuruta, H., Hendrix, R.W. and Johnson, J.E. (2000) Topologically linked protein rings in the bacteriophage HK97 capsid. Science, 289, 2129-2133.
-
(2000)
Science
, vol.289
, pp. 2129-2133
-
-
Wikoff, W.R.1
Liljas, L.2
Duda, R.L.3
Tsuruta, H.4
Hendrix, R.W.5
Johnson, J.E.6
-
2
-
-
0034797254
-
Combined EM/X-Ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions
-
DOI 10.1016/S0969-2126(01)00642-6, PII S0969212601006426
-
Martn, C.S., Burnett, R.M., de Haas, F., Heinkel, R., Rutten, T., Fuller, S.D., Butcher, S.J. and Bamford, D.H. (2001) Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure, 9, 917-930. (Pubitemid 32972158)
-
(2001)
Structure
, vol.9
, Issue.10
, pp. 917-930
-
-
Martin, C.S.1
Burnett, R.M.2
De Haas, F.3
Heinkel, R.4
Rutten, T.5
Fuller, S.D.6
Butcher, S.J.7
Bamford, D.H.8
-
3
-
-
17044395121
-
Conservation of the capsid structure in tailed dsDNA bacteriophages: The pseudoatomic structure of phi29
-
Morais, M.C., Choi, K.H., Koti, J.S., Chipman, P.R., Anderson, D.L. and Rossmann, M.G. (2005) Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29. Mol. Cell, 18, 149-159.
-
(2005)
Mol. Cell
, vol.18
, pp. 149-159
-
-
Morais, M.C.1
Choi, K.H.2
Koti, J.S.3
Chipman, P.R.4
Anderson, D.L.5
Rossmann, M.G.6
-
4
-
-
31844435708
-
Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus
-
DOI 10.1038/nature04487, PII NATURE04487
-
Jiang, W., Chang, J., Jakana, J., Weigele, P., King, J. and Chiu, W. (2006) Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature, 439, 612-616. (Pubitemid 43185387)
-
(2006)
Nature
, vol.439
, Issue.7076
, pp. 612-616
-
-
Jiang, W.1
Chang, J.2
Jakana, J.3
Weigele, P.4
King, J.5
Chiu, W.6
-
5
-
-
38649114349
-
Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process
-
DOI 10.1016/j.virol.2007.07.035, PII S0042682207004990
-
Comolli, L.R., Spakowitz, A.J., Siegerist, C.E., Jardine, P.J., Grimes, S., Anderson, D.L., Bustamante, C. and Downing, K.H. (2008) Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology, 371, 267-277. (Pubitemid 351173222)
-
(2008)
Virology
, vol.371
, Issue.2
, pp. 267-277
-
-
Comolli, L.R.1
Spakowitz, A.J.2
Siegerist, C.E.3
Jardine, P.J.4
Grimes, S.5
Anderson, D.L.6
Bustamante, C.7
Downing, K.H.8
-
6
-
-
0037058959
-
Investigation of viral DNA packaging using molecular mechanics models
-
DOI 10.1016/S0301-4622(02)00197-7, PII S0301462202001977
-
Arsuaga, J., Tan, R.K., Vazquez, M., Sumners, D.W. and Harvey, S.C. (2002) Investigation of viral DNA packaging using molecular mechanics models. Biophys. Chem., 101-102, 475-484. (Pubitemid 35462066)
-
(2002)
Biophysical Chemistry
, vol.101-102
, pp. 475-484
-
-
Arsuaga, J.1
Tan, R.K.-Z.2
Vazquez, M.3
Sumners, D.W.4
Harvey, S.C.5
-
7
-
-
35148817067
-
The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape
-
DOI 10.1016/j.jsb.2007.08.012, PII S1047847707002018
-
Petrov, A.S., Boz, M.B. and Harvey, S.C. (2007) The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. J. Struct. Biol., 160, 241-248. (Pubitemid 47539199)
-
(2007)
Journal of Structural Biology
, vol.160
, Issue.2
, pp. 241-248
-
-
Petrov, A.S.1
Boz, M.B.2
Harvey, S.C.3
-
8
-
-
21544474118
-
DNA knots reveal a chiral organization of DNA in phage capsids
-
DOI 10.1073/pnas.0409323102
-
Arsuaga, J., Vazquez, M., McGuirk, P., Trigueros, S., Sumners, D. and Roca, J. (2005) DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl Acad. Sci. USA, 102, 9165-9169. (Pubitemid 40923535)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.26
, pp. 9165-9169
-
-
Arsuaga, J.1
Vazquez, M.2
McGuirk, P.3
Trigueros, S.4
Sumners, D.W.5
Roca, J.6
-
9
-
-
77953811389
-
Mechanochemistry of a viral DNA packaging motor
-
Yu, J., Moffitt, J., Hetherington, C.L., Bustamante, C. and Oster, G. (2010) Mechanochemistry of a viral DNA packaging motor. J. Mol. Biol., 400, 186-203.
-
(2010)
J. Mol. Biol.
, vol.400
, pp. 186-203
-
-
Yu, J.1
Moffitt, J.2
Hetherington, C.L.3
Bustamante, C.4
Oster, G.5
-
10
-
-
0034642752
-
Twist in chiral interaction between biological helices
-
Kornyshev, A.A. and Leikin, S. (2000) Twist in chiral interaction between biological helices. Phys. Rev. Lett., 84, 2537-2540.
-
(2000)
Phys. Rev. Lett.
, vol.84
, pp. 2537-2540
-
-
Kornyshev, A.A.1
Leikin, S.2
-
11
-
-
0016168104
-
Location of DNA ends in P2 186, P4 and lambda bacteriophage heads
-
Chattoraj, D.K. and Inman, R.B. (1974) Location of DNA ends in P2, 186, P4 and lambda bacteriophage heads. J. Mol. Biol., 87, 11-22.
-
(1974)
J. Mol. Biol.
, vol.87
, pp. 11-22
-
-
Chattoraj, D.K.1
Inman, R.B.2
-
12
-
-
0015829833
-
On the sequence similarity of the cohesive ends of coliphage P4, P2, and 186 deoxyribonucleic acid
-
Wang, J.C., Martin, K.V. and Calendar, R. (1973) On the sequence similarity of the cohesive ends of coliphage P4, P2, and 186 deoxyribonucleic acid. Biochemistry, 12, 2119-2123.
-
(1973)
Biochemistry
, vol.12
, pp. 2119-2123
-
-
Wang, J.C.1
Martin, K.V.2
Calendar, R.3
-
13
-
-
0013511028
-
Knotted DNA from bacteriophage capsids
-
Liu, L.F., Perkocha, L., Calendar, R. and Wang, J.C. (1981) Knotted DNA from bacteriophage capsids. Proc. Natl Acad. Sci. USA, 78, 5498-5502. (Pubitemid 12245178)
-
(1981)
Proceedings of the National Academy of Sciences of the United States of America
, vol.78
, Issue.9
, pp. 5498-5502
-
-
Liu, L.F.1
Perkocha, L.2
Calendar, R.3
Wang, J.C.4
-
14
-
-
0032562742
-
Sedimentation and electrophoretic migration of DNA knots and catenanes
-
DOI 10.1006/jmbi.1998.1696
-
Vologodskii, A.V., Crisona, N.J., Laurie, B., Pieranski, P., Katritch, V., Dubochet, J. and Stasiak, A. (1998) Sedimentation and electrophoretic migration of DNA knots and catenanes. J. Mol. Biol., 278, 1-3. (Pubitemid 28196146)
-
(1998)
Journal of Molecular Biology
, vol.278
, Issue.1
, pp. 1-3
-
-
Vologodskii, A.V.1
Crisona, N.J.2
Laurie, B.3
Pieranski, P.4
Katritch, V.5
Dubochet, J.6
Stasiak, A.7
-
15
-
-
0035408589
-
Novel display of knotted DNA molecules by two-dimensional gel electrophoresis
-
Trigueros, S., Arsuaga, J., Vazquez, M.E., Sumners, D.W. and Roca, J. (2001) Novel display of knotted DNA molecules by two-dimensional gel electrophoresis. Nucleic Acids Res., 29, E67-E67.
-
(2001)
Nucleic Acids Res.
, vol.29
-
-
Trigueros, S.1
Arsuaga, J.2
Vazquez, M.E.3
Sumners, D.W.4
Roca, J.5
-
16
-
-
0037117517
-
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
-
DOI 10.1073/pnas.032095099
-
Arsuaga, J., Vazquez, M., Trigueros, S., Sumners, D. and Roca, J. (2002) Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc. Natl Acad. Sci. USA, 99, 5373-5377. (Pubitemid 34411555)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.8
, pp. 5373-5377
-
-
Arsuaga, J.1
Vazquez, M.2
Trigueros, S.3
Sumners, D.W.4
Roca, J.5
-
17
-
-
22244471562
-
Fractions of particular knots in Gaussian random polygons
-
Tsurusaki, K. and Deguchi, T. (1995) Fractions of particular knots in Gaussian random polygons. J. Phys. Soc. Jpn., 64, 1506-1518.
-
(1995)
J. Phys. Soc. Jpn.
, vol.64
, pp. 1506-1518
-
-
Tsurusaki, K.1
Deguchi, T.2
-
18
-
-
0034183593
-
Tightness of random knotting
-
Katritch, V., Olson, W.K., Vologodskii, A., Dubochet, J. and Stasiak, A. (2000) Tightness of random knotting. Phys. Rev. E. Stat. Phys., 61, 5545-5549.
-
(2000)
Phys. Rev. E. Stat. Phys.
, vol.61
, pp. 5545-5549
-
-
Katritch, V.1
Olson, W.K.2
Vologodskii, A.3
Dubochet, J.4
Stasiak, A.5
-
19
-
-
0027200062
-
Knotting of a DNA chain during ring closure
-
Shaw, S.Y. and Wang, J.C. (1993) Knotting of a DNA chain during ring closure. Science, 260, 533-536. (Pubitemid 23161616)
-
(1993)
Science
, vol.260
, Issue.5107
, pp. 533-536
-
-
Shaw, S.Y.1
Wang, J.C.2
-
20
-
-
0027279063
-
Probability of DNA knotting and the effective diameter of the DNA double helix
-
Rybenkov, V.V., Cozzarelli, N.R. and Vologodskii, A.V. (1993) Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl Acad. Sci. USA, 90, 5307-5311. (Pubitemid 23183027)
-
(1993)
Proceedings of the National Academy of Sciences of the United States of America
, vol.90
, Issue.11
, pp. 5307-5311
-
-
Rybenkov, V.V.1
Cozzarelli, N.R.2
Vologodskii, A.V.3
-
21
-
-
76149131390
-
DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting
-
Marenduzzo, D., Orlandini, E., Stasiak, A., Sumners de, W., Tubiana, L. and Micheletti, C. (2009) DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting. Proc. Natl Acad. Sci. USA, 106, 22269-22274.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 22269-22274
-
-
Marenduzzo, D.1
Orlandini, E.2
Stasiak, A.3
De, S.W.4
Tubiana, L.5
Micheletti, C.6
-
22
-
-
77955947433
-
Biopolymer organization upon confinement
-
Marenduzzo, D., Micheletti, C. and Orlandini, E. (2010) Biopolymer organization upon confinement. J. Phys. Condens. Matter, 22, 283102.
-
(2010)
J. Phys. Condens. Matter
, vol.22
, pp. 283102
-
-
Marenduzzo, D.1
Micheletti, C.2
Orlandini, E.3
-
23
-
-
25844439434
-
DNA cholesteric pitch as a function of density and ionic strength
-
DOI 10.1529/biophysj.105.064550
-
Stanley, C.B., Hong, H. and Strey, H.H. (2005) DNA cholesteric pitch as a function of density and ionic strength. Biophys. J., 89, 2552-2557. (Pubitemid 41401043)
-
(2005)
Biophysical Journal
, vol.89
, Issue.4
, pp. 2552-2557
-
-
Stanley, C.B.1
Hong, H.2
Strey, H.H.3
-
24
-
-
34249308788
-
Coarse-grained molecular dynamic simulations for lyotropic liquid-crystalline solutions of semiflexible rod-like molecules
-
DOI 10.1080/15421400701246309, PII 779017268
-
Lin, S., Numasawa, N., Nose, T. and Lin, J. (2007) Corse-grained molecular dynamic simulations for lyotropic liquid-crystalline solutions of semiflexible rod-like molecules. Mol. Cryst. Liq. Cryst., 466, 53-76. (Pubitemid 46806058)
-
(2007)
Molecular Crystals and Liquid Crystals
, vol.466
, Issue.1
, pp. 53-76
-
-
Lin, S.1
Numasawa, N.2
Nose, T.3
Lin, J.4
-
25
-
-
39749113170
-
Persistence lengths and structure factors of wormlike polymers under confinement
-
DOI 10.1021/jp076355n
-
Cifra, P., Benkova, Z. and Bleha, T. (2008) Persistence lengths and structure factors of wormlike polymers under confinement. J. Phys. Chem. B, 112, 1367-1375. (Pubitemid 351291639)
-
(2008)
Journal of Physical Chemistry B
, vol.112
, Issue.5
, pp. 1367-1375
-
-
Cifra, P.1
Benkova, Z.2
Bleha, T.3
-
26
-
-
77955714530
-
Shape transition of semi-flexible macromolecules confined in channel and cavity
-
Cifra, P. and Bleha, T. Shape transition of semi-flexible macromolecules confined in channel and cavity. Eur. Phys. J. E., 32, 273-279.
-
Eur. Phys. J. E.
, vol.32
, pp. 273-279
-
-
Cifra, P.1
Bleha, T.2
-
27
-
-
0002313994
-
A study of statistical globula-coil transition in macromolecules using the Monte-Carlo technique
-
Kron, A.K., Ptitsyn, O.B., Skvortsov, A.M. and Federov, A.K. (1967) A study of statistical globula-coil transition in macromolecules using the Monte-Carlo technique. Molek. Biol., 1, 576-582.
-
(1967)
Molek. Biol.
, vol.1
, pp. 576-582
-
-
Kron, A.K.1
Ptitsyn, O.B.2
Skvortsov, A.M.3
Federov, A.K.4
-
28
-
-
75749148281
-
Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states
-
Reith, D. and Virnau, P. (2010) Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states. Comput. Phys. Commun., 181, 800-805.
-
(2010)
Comput. Phys. Commun.
, vol.181
, pp. 800-805
-
-
Reith, D.1
Virnau, P.2
-
29
-
-
0028421135
-
Are there knots in proteins?
-
Mansfield, M.L. (1994) Are there knots in proteins? Nat. Struct. Biol., 1, 213-214.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 213-214
-
-
Mansfield, M.L.1
-
30
-
-
78651506437
-
Detection and visualization of physical knots in macromolecules
-
Virnau, P. (2010) Detection and visualization of physical knots in macromolecules. Phys. Procedia, 6, 117-125.
-
(2010)
Phys. Procedia
, vol.6
, pp. 117-125
-
-
Virnau, P.1
-
31
-
-
39749113170
-
Persistence lengths and structure factors of wormlike polymers under confinement
-
DOI 10.1021/jp076355n
-
Cifra, P., Benkova, Z. and Bleha, T. (2008) Persistence lengths and structure factors of wormlike polymers under confinement. J. Phys. Chem. B, 112, 1367-1375. (Pubitemid 351291639)
-
(2008)
Journal of Physical Chemistry B
, vol.112
, Issue.5
, pp. 1367-1375
-
-
Cifra, P.1
Benkova, Z.2
Bleha, T.3
-
32
-
-
38949099079
-
Production of highly knotted DNA by means of cosmid circularization inside phage capsids
-
Trigueros, S. and Roca, J. (2007) Production of highly knotted DNA by means of cosmid circularization inside phage capsids. BMC Biotechnol., 7, 94.
-
(2007)
BMC Biotechnol.
, vol.7
, pp. 94
-
-
Trigueros, S.1
Roca, J.2
-
34
-
-
0039051533
-
-
Mathematical Society, Providence, Rhode Island
-
Delbruck, M. (1962) Mathematical Problems in the Biological Sciences, Vol. 14. Mathematical Society, Providence, Rhode Island, pp. 55-63.
-
(1962)
Mathematical Problems in the Biological Sciences
, vol.14
, pp. 55-63
-
-
Delbruck, M.1
-
35
-
-
0016695375
-
Statistical mechanics and topology of polymer chains
-
Frank-Kamenetskii, M.D., Lukashin, A.V. and Vologodskii, A.V. (1975) Statistical mechanics and topology of polymer chains. Nature, 258, 398-402.
-
(1975)
Nature
, vol.258
, pp. 398-402
-
-
Frank-Kamenetskii, M.D.1
Lukashin, A.V.2
Vologodskii, A.V.3
-
36
-
-
61449215083
-
Knot-controlled ejection of a polymer from a virus capsid
-
Matthews, R., Louis, A.A. and Yeomans, J.M. (2009) Knot-controlled ejection of a polymer from a virus capsid. Phys. Rev. Lett., 102, 088101.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 088101
-
-
Matthews, R.1
Louis, A.A.2
Yeomans, J.M.3
-
37
-
-
34147122537
-
Size of knots in ring polymers
-
Marcone, B., Orlandini, E., Stella, A.L. and Zonta, F. (2007) Size of knots in ring polymers. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 75, 041105.
-
(2007)
Phys. Rev. e Stat. Nonlin. Soft Matter Phys.
, vol.75
, pp. 041105
-
-
Marcone, B.1
Orlandini, E.2
Stella, A.L.3
Zonta, F.4
-
38
-
-
27544511752
-
Knots in globule and coil phases of a model polyethylene
-
DOI 10.1021/ja052438a
-
Virnau, P., Kantor, Y. and Kardar, M. (2005) Knots in globule and coil phases of a model polyethylene. J. Am. Chem. Soc., 127, 15102-15106. (Pubitemid 41547376)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.43
, pp. 15102-15106
-
-
Virnau, P.1
Kantor, Y.2
Kardar, M.3
-
39
-
-
33749347406
-
Intricate knots in proteins: Function and evolution
-
Virnau, P., Mirny, L.A. and Kardar, M. (2006) Intricate knots in proteins: Function and evolution. PLoS Comput. Biol., 2, e122.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Virnau, P.1
Mirny, L.A.2
Kardar, M.3
-
40
-
-
2342443284
-
New developments in topological fluid mechanics: From Kelvin's vortex knots to magnetic knots
-
Stasiak, A., Katritch, V. and Kauffman, L.H. (eds) World Scientific, Singapore
-
Ricca, R.L. (1998) New developments in topological fluid mechanics: from Kelvin's vortex knots to magnetic knots. In: Stasiak, A., Katritch, V. and Kauffman, L.H. (eds), Ideal Knots, Vol. 19. World Scientific, Singapore, pp. 255-273.
-
(1998)
Ideal Knots
, vol.19
, pp. 255-273
-
-
Ricca, R.L.1
-
41
-
-
56049085375
-
Simulations of knotting in confined circular DNA
-
Micheletti, C., Marenduzzo, D., Orlandini, E. and Sumners, D.W. (2008) Simulations of knotting in confined circular DNA. Biophys. J., 95, 3591-3599.
-
(2008)
Biophys. J.
, vol.95
, pp. 3591-3599
-
-
Micheletti, C.1
Marenduzzo, D.2
Orlandini, E.3
Sumners, D.W.4
-
42
-
-
48549100410
-
DNA knotting in spooling like configurations in bacteriophages
-
Arsuaga, J. and Diao, Y. (2008) DNA knotting in spooling like configurations in bacteriophages. Comp. Math. Methods Med., 9, 303-316.
-
(2008)
Comp. Math. Methods Med.
, vol.9
, pp. 303-316
-
-
Arsuaga, J.1
Diao, Y.2
|