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Volumn 91, Issue 9, 2006, Pages 3135-3150

Extracting dwell time sequences from processive molecular motor data

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA TOPOISOMERASE; DYNEIN ADENOSINE TRIPHOSPHATASE; KINESIN; MOLECULAR MOTOR; MYOSIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RNA POLYMERASE;

EID: 33751238824     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.079517     Document Type: Article
Times cited : (27)

References (54)
  • 1
    • 0026512861 scopus 로고
    • The patch clamp technique
    • Neher, E., and B. Sakmann. 1992. The patch clamp technique. Sci. Am. 266:44-51.
    • (1992) Sci. Am. , vol.266 , pp. 44-51
    • Neher, E.1    Sakmann, B.2
  • 2
    • 0027453868 scopus 로고
    • Direct observation of kinesin stepping by optical trapping interferometry
    • Svoboda, K., C. F. Schmidt, B. J. Schnapp, and S. M. Block. 1993. Direct observation of kinesin stepping by optical trapping interferometry. Nature. 365:721-727.
    • (1993) Nature , vol.365 , pp. 721-727
    • Svoboda, K.1    Schmidt, C.F.2    Schnapp, B.J.3    Block, S.M.4
  • 3
    • 0029879228 scopus 로고    scopus 로고
    • Direct observation of single kinesin molecules moving along microtubules
    • Vale, R. D., T. Funatsu, D. W. Pierce, L. Romberg, Y. Harada, and T. Yanagida. 1996. Direct observation of single kinesin molecules moving along microtubules. Nature. 380:451-453.
    • (1996) Nature , vol.380 , pp. 451-453
    • Vale, R.D.1    Funatsu, T.2    Pierce, D.W.3    Romberg, L.4    Harada, Y.5    Yanagida, T.6
  • 5
    • 1342325553 scopus 로고    scopus 로고
    • Cytoplasmic dynein functions as a gear in response to load
    • Mallik, R., B. C. Carter, S. A. Lex, S. J. King, and S. P. Gross. 2004. Cytoplasmic dynein functions as a gear in response to load. Nature. 427:649-652.
    • (2004) Nature , vol.427 , pp. 649-652
    • Mallik, R.1    Carter, B.C.2    Lex, S.A.3    King, S.J.4    Gross, S.P.5
  • 6
    • 20344382542 scopus 로고    scopus 로고
    • Kinesin and dynein move a peroxisome in vivo: A tug-of-war or coordinated movement?
    • Kural, C., H. Kim, S. Syed, G. Goshima, V. I. Gelfand, and P. R. Selvin. 2005. Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated movement? Science. 308:1469-1472.
    • (2005) Science , vol.308 , pp. 1469-1472
    • Kural, C.1    Kim, H.2    Syed, S.3    Goshima, G.4    Gelfand, V.I.5    Selvin, P.R.6
  • 7
    • 0034111877 scopus 로고    scopus 로고
    • The mechanochemistry of molecular motors
    • Keller, D., and C. Bustamante. 2000. The mechanochemistry of molecular motors. Biophys. J. 78:541-556.
    • (2000) Biophys. J. , vol.78 , pp. 541-556
    • Keller, D.1    Bustamante, C.2
  • 8
    • 0037832404 scopus 로고    scopus 로고
    • Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5 nm localization
    • Yildiz, A., J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, and P. R. Selvin. 2003. Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5 nm localization. Science. 300:2061-2065.
    • (2003) Science , vol.300 , pp. 2061-2065
    • Yildiz, A.1    Forkey, J.N.2    McKinney, S.A.3    Ha, T.4    Goldman, Y.E.5    Selvin, P.R.6
  • 10
    • 33746831687 scopus 로고    scopus 로고
    • Maximum likelihood estimation of molecular motor kinetics from staircase dwell time sequences
    • Milescu, L. S., A. Yildiz, P. R. Selvin, and F. Sachs. 2006. Maximum likelihood estimation of molecular motor kinetics from staircase dwell time sequences. Biophys. J. 91:1156-1168.
    • (2006) Biophys. J. , vol.91 , pp. 1156-1168
    • Milescu, L.S.1    Yildiz, A.2    Selvin, P.R.3    Sachs, F.4
  • 11
    • 0000459587 scopus 로고
    • The distributions of the apparent open times and shut times in a single channel record when brief events cannot be detected
    • Hawkes, A. G., A. Jalali, and D. Colquhoun. 1990. The distributions of the apparent open times and shut times in a single channel record when brief events cannot be detected. Philos. Trans. R. Soc. Lond. B Biol. Sci. 332:511-538.
    • (1990) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.332 , pp. 511-538
    • Hawkes, A.G.1    Jalali, A.2    Colquhoun, D.3
  • 12
    • 0027128970 scopus 로고
    • Asymptotic distributions of apparent open times and shut times in a single channel record allowing for the omission of brief events
    • Hawkes, A. G., A. Jalali, and D. Colquhoun. 1992. Asymptotic distributions of apparent open times and shut times in a single channel record allowing for the omission of brief events. Philos. Trans. R. Soc. Lond. B Biol. Sci. 337:383-404.
    • (1992) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.337 , pp. 383-404
    • Hawkes, A.G.1    Jalali, A.2    Colquhoun, D.3
  • 13
    • 0002432817 scopus 로고
    • Generalised eigenproblems arising in aggregated Markov processes allowing for time interval omission
    • Jalali, A., and A. G. Hawkes. 1992. Generalised eigenproblems arising in aggregated Markov processes allowing for time interval omission. Adv. Appl. Probab. 24:302-321.
    • (1992) Adv. Appl. Probab. , vol.24 , pp. 302-321
    • Jalali, A.1    Hawkes, A.G.2
  • 14
    • 0030061670 scopus 로고    scopus 로고
    • Estimating single channel kinetic parameters from idealized patch-clamp data containing missed events
    • Qin, F., A. Auerbach, and F. Sachs. 1996. Estimating single channel kinetic parameters from idealized patch-clamp data containing missed events. Biophys. J. 70:264-280.
    • (1996) Biophys. J. , vol.70 , pp. 264-280
    • Qin, F.1    Auerbach, A.2    Sachs, F.3
  • 15
    • 0019143565 scopus 로고
    • Single Na1 channel currents observed in cultured rat muscle cells
    • Sigworth, F. J., and E. Neher. 1980. Single Na1 channel currents observed in cultured rat muscle cells. Nature. 287:447-449.
    • (1980) Nature , vol.287 , pp. 447-449
    • Sigworth, F.J.1    Neher, E.2
  • 16
  • 17
    • 0020490146 scopus 로고
    • On the stochastic properties of bursts of single ion channel openings and of clusters of bursts
    • Colquhoun, D., and A. G. Hawkes. 1982. On the stochastic properties of bursts of single ion channel openings and of clusters of bursts. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 300:1-59.
    • (1982) Philos. Trans. R. Soc. Lond. B. Biol. Sci. , vol.300 , pp. 1-59
    • Colquhoun, D.1    Hawkes, A.G.2
  • 18
    • 0025348901 scopus 로고
    • Stochastic properties of ion channel openings and bursts in a membrane patch that contains two channels: Evidence concerning the number of channels present when a record containing only single openings is observed
    • Colquhoun, D., and A. G. Hawkes. 1990. Stochastic properties of ion channel openings and bursts in a membrane patch that contains two channels: evidence concerning the number of channels present when a record containing only single openings is observed. Proc. R. Soc. Lond. B. Biol. Sci. 240:453-477.
    • (1990) Proc. R. Soc. Lond. B. Biol. Sci. , vol.240 , pp. 453-477
    • Colquhoun, D.1    Hawkes, A.G.2
  • 19
    • 0030956174 scopus 로고    scopus 로고
    • Maximum likelihood estimation of aggregated Markov processes
    • Qin, F., A. Auerbach, and F. Sachs. 1997. Maximum likelihood estimation of aggregated Markov processes. Proc. R. Soc. Lond. B Biol. Sci. 264:375-383.
    • (1997) Proc. R. Soc. Lond. B Biol. Sci. , vol.264 , pp. 375-383
    • Qin, F.1    Auerbach, A.2    Sachs, F.3
  • 20
    • 33751233128 scopus 로고    scopus 로고
    • A hybrid approach to hidden Markov modeling for single channel kinetics
    • Pos. (Abstr.)
    • Qin, F., A. Auerbach, and F. Sachs. 2000. A hybrid approach to hidden Markov modeling for single channel kinetics. Biophys. J. 78:1970Pos. (Abstr.)
    • (2000) Biophys. J. , vol.78 , pp. 1970
    • Qin, F.1    Auerbach, A.2    Sachs, F.3
  • 21
    • 0021797982 scopus 로고
    • Open channel noise. I. Noise in acetylcholine receptor currents suggests conformational fluctuations
    • Sigworth, F. J. 1985. Open channel noise. I. Noise in acetylcholine receptor currents suggests conformational fluctuations. Biophys. J. 47:709-720.
    • (1985) Biophys. J. , vol.47 , pp. 709-720
    • Sigworth, F.J.1
  • 22
    • 0022523172 scopus 로고
    • Open channel noise. II. A test for coupling between current fluctuations and conformational transitions in the acetylcholine receptor
    • Sigworth, F. J. 1986. Open channel noise. II. A test for coupling between current fluctuations and conformational transitions in the acetylcholine receptor. Biophys. J. 49:1041-1046.
    • (1986) Biophys. J. , vol.49 , pp. 1041-1046
    • Sigworth, F.J.1
  • 23
    • 0023492725 scopus 로고
    • Open channel noise. III. High-resolution recordings show rapid current fluctuations in gramicidin A and four chemical analogues
    • Sigworth, F. J., D. W. Urry, and K. U. Prasad. 1987. Open channel noise. III. High-resolution recordings show rapid current fluctuations in gramicidin A and four chemical analogues. Biophys. J. 52:1055-1064.
    • (1987) Biophys. J. , vol.52 , pp. 1055-1064
    • Sigworth, F.J.1    Urry, D.W.2    Prasad, K.U.3
  • 24
    • 0032124372 scopus 로고    scopus 로고
    • Identification of hidden Markov models for ion channel currents - Part II: State-dependent excess noise
    • Venkataramanan, L., R. Kuc, and F. J. Sigworth. 1998. Identification of hidden Markov models for ion channel currents - Part II: State-dependent excess noise. IEEE Trans. Signal Proc. 46:1916-1929.
    • (1998) IEEE Trans. Signal Proc. , vol.46 , pp. 1916-1929
    • Venkataramanan, L.1    Kuc, R.2    Sigworth, F.J.3
  • 25
    • 0032122144 scopus 로고    scopus 로고
    • Identification of hidden Markov models for ion channel currents - Part I: Colored background noise
    • Venkataramanan, L., J. L. Walsh, R. Kuc, and F. J. Sigworth. 1998. Identification of hidden Markov models for ion channel currents - Part I: Colored background noise. IEEE Trans. Signal Proc. 46:1901-1915.
    • (1998) IEEE Trans. Signal Proc. , vol.46 , pp. 1901-1915
    • Venkataramanan, L.1    Walsh, J.L.2    Kuc, R.3    Sigworth, F.J.4
  • 26
    • 0037444604 scopus 로고    scopus 로고
    • The quality of maximum likelihood estimates of ion channel rate constants
    • Colquhoun, D., C. J. Hatton, and A. G. Hawkes. 2003. The quality of maximum likelihood estimates of ion channel rate constants. J. Physiol. 547:699-728.
    • (2003) J. Physiol. , vol.547 , pp. 699-728
    • Colquhoun, D.1    Hatton, C.J.2    Hawkes, A.G.3
  • 27
    • 0025034113 scopus 로고
    • Yet another approach to the dwell-time omission problem of single-channel analysis
    • Crouzy, S. C., and F. J. Sigworth. 1990. Yet another approach to the dwell-time omission problem of single-channel analysis. Biophys. J. 58:731-743.
    • (1990) Biophys. J. , vol.58 , pp. 731-743
    • Crouzy, S.C.1    Sigworth, F.J.2
  • 28
    • 0027458539 scopus 로고
    • Fluctuations in ion channel gating currents. Analysis of nonstationary shot noise
    • Crouzy, S. C., and F. J. Sigworth. 1993. Fluctuations in ion channel gating currents. Analysis of nonstationary shot noise. Biophys. J. 64:68-76.
    • (1993) Biophys. J. , vol.64 , pp. 68-76
    • Crouzy, S.C.1    Sigworth, F.J.2
  • 29
    • 0001774017 scopus 로고
    • Fitting and statistical analysis of single-channel records
    • B. Sakmann and E. Neher, editors. Plenum Press, New York and London
    • Colquhoun, D., and F. J. Sigworth. 1983. Fitting and statistical analysis of single-channel records. In Single-Channel Recording. B. Sakmann and E. Neher, editors. Plenum Press, New York and London. 191.
    • (1983) Single-Channel Recording , pp. 191
    • Colquhoun, D.1    Sigworth, F.J.2
  • 30
    • 1542285356 scopus 로고    scopus 로고
    • Restoration of single-channel currents using the segmental k-means method based on hidden Markov modeling
    • Qin, F. 2004. Restoration of single-channel currents using the segmental k-means method based on hidden Markov modeling. Biophys. J. 86:1488-1501.
    • (2004) Biophys. J. , vol.86 , pp. 1488-1501
    • Qin, F.1
  • 31
    • 0000353178 scopus 로고
    • A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains
    • Baum, L. E., T. Petrie, G. Soules, and N. Weiss. 1970. A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat. 41:164-171.
    • (1970) Ann. Math. Stat. , vol.41 , pp. 164-171
    • Baum, L.E.1    Petrie, T.2    Soules, G.3    Weiss, N.4
  • 32
    • 85024423711 scopus 로고
    • New results in linear filtering and prediction theory
    • Kalman, R. E., and R. S. Bucy. 1961. New results in linear filtering and prediction theory. Trans. ASME, J. Basic Eng. 83D:95-108.
    • (1961) Trans. ASME, J. Basic Eng. , vol.83 D , pp. 95-108
    • Kalman, R.E.1    Bucy, R.S.2
  • 33
    • 0035912221 scopus 로고    scopus 로고
    • Resolution of distinct rotational substeps by submilisecond kinetic analysis of F1-ATPase
    • Yasuda, R., H. Noji, M. Yoshida, K. Kinosita, and H. Itoh. 2001. Resolution of distinct rotational substeps by submilisecond kinetic analysis of F1-ATPase. Nature. 410:898-904.
    • (2001) Nature , vol.410 , pp. 898-904
    • Yasuda, R.1    Noji, H.2    Yoshida, M.3    Kinosita, K.4    Itoh, H.5
  • 34
    • 0742270602 scopus 로고    scopus 로고
    • Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation
    • Nishizaka, T., K. Oiwa, H. Noji, S. Kimura, M. Yoshida, and K. Kinosita Jr. 2004. Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation. Nature. 11:142-148.
    • (2004) Nature , vol.11 , pp. 142-148
    • Nishizaka, T.1    Oiwa, K.2    Noji, H.3    Kimura, S.4    Yoshida, M.5    Kinosita Jr., K.6
  • 35
    • 0345047725 scopus 로고    scopus 로고
    • Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
    • Neuman, K. C., E. A. Abbondanzieri, R. Landick, J. Gelles, and S. M. Block. 2003. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell. 115:437-447.
    • (2003) Cell , vol.115 , pp. 437-447
    • Neuman, K.C.1    Abbondanzieri, E.A.2    Landick, R.3    Gelles, J.4    Block, S.M.5
  • 37
    • 18144410993 scopus 로고    scopus 로고
    • Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics
    • Bruno, W. J., J. Yang, and J. E. Pearson. 2005. Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics. Proc. Natl. Acad. Sci. USA. 102:6326-6331.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6326-6331
    • Bruno, W.J.1    Yang, J.2    Pearson, J.E.3
  • 38
    • 0026722956 scopus 로고
    • Dependency plots suggest the kinetic structure of ion channels
    • Magleby, K. L., and L. Song. 1992. Dependency plots suggest the kinetic structure of ion channels. Proc. R. Soc. Lond. B. Biol. Sci. 249:133-142.
    • (1992) Proc. R. Soc. Lond. B. Biol. Sci. , vol.249 , pp. 133-142
    • Magleby, K.L.1    Song, L.2
  • 39
    • 19644377414 scopus 로고    scopus 로고
    • Mechanics of the kinesin step
    • Carter, N. J., and R. A. Cross. 2005. Mechanics of the kinesin step. Nature. 435:308-312.
    • (2005) Nature , vol.435 , pp. 308-312
    • Carter, N.J.1    Cross, R.A.2
  • 40
    • 33746858803 scopus 로고    scopus 로고
    • Statistical analysis of kinesin kinetics by applying methods from single channel recordings
    • Pos. (Abstr.)
    • Jeney, S., F. Sachs, A. Pralle, E. L. Florin, and H. J. K. Horber. 2000. Statistical analysis of kinesin kinetics by applying methods from single channel recordings. Biophys. J. 78:717Pos. (Abstr.)
    • (2000) Biophys. J. , vol.78 , pp. 717
    • Jeney, S.1    Sachs, F.2    Pralle, A.3    Florin, E.L.4    Horber, H.J.K.5
  • 41
    • 85030594266 scopus 로고    scopus 로고
    • Buffalo, NY
    • QuB. www.qub.buffalo.edu, University at Buffalo, Buffalo, NY.
    • QuB
  • 42
    • 0029989974 scopus 로고    scopus 로고
    • Crystal structure of the kinesin motor domain reveals a structural similarity to myosin
    • Kull, F. J., E. P. Sablin, R. Lau, R. Fletterick, and R. D. Vale. 1996. Crystal structure of the kinesin motor domain reveals a structural similarity to myosin. Nature. 380:550-559.
    • (1996) Nature , vol.380 , pp. 550-559
    • Kull, F.J.1    Sablin, E.P.2    Lau, R.3    Fletterick, R.4    Vale, R.D.5
  • 44
    • 0033808511 scopus 로고    scopus 로고
    • A direct optimization approach to hidden Markov modeling for single channel kinetics
    • Qin, F., A. Auerbach, and F. Sachs. 2000. A direct optimization approach to hidden Markov modeling for single channel kinetics. Biophys. J. 79:1915-1927.
    • (2000) Biophys. J. , vol.79 , pp. 1915-1927
    • Qin, F.1    Auerbach, A.2    Sachs, F.3
  • 45
    • 0025716139 scopus 로고
    • Characterization of single channel currents using digital signal processing techniques based on Hidden Markov Models
    • Chung, S. H., J. B. Moore, L. G. Xia, L. S. Premkumar, and P. W. Gage. 1990. Characterization of single channel currents using digital signal processing techniques based on Hidden Markov Models. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 329:265-285.
    • (1990) Philos. Trans. R. Soc. Lond. B. Biol. Sci. , vol.329 , pp. 265-285
    • Chung, S.H.1    Moore, J.B.2    Xia, L.G.3    Premkumar, L.S.4    Gage, P.W.5
  • 46
    • 0015600423 scopus 로고
    • The Viterbi algorithm
    • Forney, G. D. 1973. The Viterbi algorithm. Proc. IEEE. 61:268-278.
    • (1973) Proc. IEEE , vol.61 , pp. 268-278
    • Forney, G.D.1
  • 47
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimal decoding algorithm
    • Viterbi, A. J. 1967. Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans. Inform. Theory. IT-13:260-269.
    • (1967) IEEE Trans. Inform. Theory , vol.IT-13 , pp. 260-269
    • Viterbi, A.J.1
  • 49
    • 0022712081 scopus 로고
    • A segmental K-means training procedure for connected word recognition
    • Rabiner, L. R., J. G. Wilpon, and B. Juang. 1986. A segmental K-means training procedure for connected word recognition. AT&T Tech. J. 64:21-40.
    • (1986) AT&T Tech. J. , vol.64 , pp. 21-40
    • Rabiner, L.R.1    Wilpon, J.G.2    Juang, B.3
  • 51
    • 0033556862 scopus 로고    scopus 로고
    • A unifying review of linearGaussian models
    • Roweis, S., and Z. Ghahramani. 1999. A unifying review of linearGaussian models. Neural Comput. 11:305-345.
    • (1999) Neural Comput. , vol.11 , pp. 305-345
    • Roweis, S.1    Ghahramani, Z.2
  • 52
    • 0037468838 scopus 로고    scopus 로고
    • Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization
    • Forkey, J. N., M. E. Quinlan, M. A. Shaw, J. E. Corrie, and Y. E. Goldman. 2003. Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization. Nature. 422:399-404.
    • (2003) Nature , vol.422 , pp. 399-404
    • Forkey, J.N.1    Quinlan, M.E.2    Shaw, M.A.3    Corrie, J.E.4    Goldman, Y.E.5
  • 53
    • 0033807604 scopus 로고    scopus 로고
    • Hidden Markov modeling for single channel kinetics with filtering and correlated noise
    • Qin, F., A. Auerbach, and F. Sachs. 2000. Hidden Markov modeling for single channel kinetics with filtering and correlated noise. Biophys. J. 79:1928-1944.
    • (2000) Biophys. J. , vol.79 , pp. 1928-1944
    • Qin, F.1    Auerbach, A.2    Sachs, F.3
  • 54
    • 0034757969 scopus 로고    scopus 로고
    • Hidden-Markov methods for the analysis of single-molecule actomyosin displacement data: The variance-hidden-Markov method
    • Smith, D. A., W. Steffen, R. M. Simmons, and J. Sleep. 2001. Hidden-Markov methods for the analysis of single-molecule actomyosin displacement data: the variance-hidden-Markov method. Biophys. J. 81:2795-2816.
    • (2001) Biophys. J. , vol.81 , pp. 2795-2816
    • Smith, D.A.1    Steffen, W.2    Simmons, R.M.3    Sleep, J.4


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