Open Problems on Information and Feedback Controlled Systems

Feedback or closed-loop control allows dynamical systems to increase their performance up to a limit imposed by the second law of thermodynamics. It is expected that within this limit, the system performance increases as the controller uses more information about the system. However, despite the relevant progresses made recently, a general and complete formal development to justify this statement using information theory is still lacking. We present here the state-of-the-art and the main open problems that include aspects of the redundancy of correlated operations of feedback control and the continuous operation of feedback control. Complete answers to these questions are required to firmly establish the thermodynamics of feedback controlled systems. Other relevant open questions concern the implications of the theoretical results for the limitations in the performance of feedback controlled flashing ratchets, and for the operation and performance of nanotechnology devices and biological systems.Comment: LaTeX, 10 pages, 2 figures. Improved version to appear in Entrop

Ecological Complex Systems

Main aim of this topical issue is to report recent advances in noisy nonequilibrium processes useful to describe the dynamics of ecological systems and to address the mechanisms of spatio-temporal pattern formation in ecology both from the experimental and theoretical points of view. This is in order to understand the dynamical behaviour of ecological complex systems through the interplay between nonlinearity, noise, random and periodic environmental interactions. Discovering the microscopic rules and the local interactions which lead to the emergence of specific global patterns or global dynamical behaviour and the noises role in the nonlinear dynamics is an important, key aspect to understand and then to model ecological complex systems.Comment: 13 pages, Editorial of a topical issue on Ecological Complex System to appear in EPJ B, Vol. 65 (2008

Dinámica estocástica en física y biología

Tesis de la Universidad Complutense de Madrid, Facultad de Ciencias Físicas, Departamento de Estructura de la Materia, Física Térmica y Electrónica, leída el 26-10-2018Stochastic processes are present in virtually any field of science. Actually, in general deterministic processes are no more than an approximation of more complex stochastic processes in some regime of validity. In the present thesis, we will study some systems that appear in Physics and Biology where the presence of these stochastic processes plays a major role. First, we will study the Brownian ratchet systems, which are able to generate a directed motion simply by rectifying the thermal fluctuations to which Brownian particles are subjected. These Brownian ratchets began to be studied in the field of Statistical Physics as a Gedanken experiment that apparently broke the Second Law of Thermodynamics. Later they were applied to study the operation of some molecular motors. In this thesis we will study different types of Brownian ratchets, characterizing the average flux, the efficiency, and the quality of the transport of particles they produce..En prácticamente cualquier rama de la ciencia están presentes los procesos estocásticos. De hecho, en general los procesos deterministas no son más que una aproximación de procesos estocásticos más complejos en algún régimen de validez. En la presente tesis, estudiaremos algunos sistemas que aparecen en Física y Biología donde la presencia de dichos procesos es crucial.Primero, estudiaremos los conocidos como trinquetes brownianos, que son capaces de generar movimiento dirigido simplemente a través de la rectificación de las fluctuaciones térmicas a las que se ven sometidas las partículas Brownianas. Estos trinquetes Brownianos se empezaron a estudiar en el campo de la Física Estadística como un experimento mental que aparentemente rompía la Segunda Ley de la Termodinámica. Sin embargo, más adelante se ha visto que pueden ser aplicados para estudiar el funcionamiento de algunos motores moleculares. En esta tesis estudiaremos distintos tipos de trinquetes Brownianos, caracterizando el flujo medio, la eficiencia, y la calidad del transporte de partículas que producen...Depto. de Estructura de la Materia, Física Térmica y ElectrónicaFac. de Ciencias FísicasTRUEunpu

Collective Dynamics of Kinesin-1.

Motor proteins are the engines of biology, converting chemical energy to mechanical work in cells. Kinesin-1 is a motor protein that transports vesicles towards the plus end of microtubules, widely believed to be responsible for anterograde transport of synaptic vesicles in neurons. Advances in single-molecule techniques have allowed the characterization of single kinesin motors in vitro at a range of loads and ATP concentrations. Single kinesin motors are capable of processive movement along the microtubule at a maximum velocity of approximately 1 μm/s. The velocity decreases roughly linearly in response to load until reaching stall at a load of approximately 6 pN. Several theoretical models have been proposed that describe the steady-state motion of single kinesin motors. However, growing evidence suggests that kinesin functions collectively in cells, whereby several motors work in a coordinated manner to transport a vesicle. A transient description is required to describe collective dynamics, as the interactions among coupled motors induce time-varying forces on each motor. Herein a mechanistic model of kinesin is proposed that is capable of accurately describing transient and steady-state dynamics. Each domain of the protein is modeled via a mechanical potential. The mechanical potentials are related explicitly to the chemical kinetics of each motor domain. The mechanistic model was used to simulate the collective behavior of coupled kinesin motors under varying loads, cargo linker stiffnesses, and numbers of motors. To analyze the simulations of coordinated transport, several metrics were developed that are specifically tailored to characterizing the synchronization of nonlinear, nonsmooth oscillators like kinesin. The model results suggest that, in the cell, coupled motors under low loads are loosely correlated. When the load is increased, such as when the cargo encounters an obstacle like another vesicle or the cytoskeleton, motors become more correlated in response to increased loads, allowing them to produce greater forces. Increasing the number of motors involved in the transport does not appreciably increase the dimensionality of the trajectory, implying large numbers of motors are able to work collectively, even without becoming fully synchronized.Ph.D.Mechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/60661/1/adhendri_1.pd

Simulating the kinesin walk : towards a definitive theory

Dementia is a set of incurable, fatal diseases characterised by irreversible degeneration of the brain. One theory of its cause is the failure of intracellular transport in the axons of the neurons that compose the brain. Kinesin is a key motor transporting vital cargo along the axon. We know that this motor is a bipedal engine stepping forward along a polypeptide track but it is too small and fast for this motion to be observed using current experimental techniques. The stepping detail is therefore open to debate. This study firstly addresses the question of how kinesin steps and secondly pilots a possible method for investigating transport disruption in silico. To investigate the detail of stepping, a program has been designed and built to simulate kinesin traversing its track along a section of axon. The motor is modelled as simple, interacting agents obeying rules abstracted from known chemical and binding properties of its components. The agent-based method has proven useful and efficient on the small scale and has potential for simulating the larger and more complex system of axonal transport. This would enable investigation of transport failure in the context of finding a cure for dementia. A new model of kinesin stepping has been formulated as a consequence of performing virtual experiments using the simulation. Analysis of in vivo and in vitro experimental studies shows that the model accounts for a wide range of published results, explaining many findings. New experiments are suggested to test the model based on its falsifiable predictions. The principal conclusion of this study is that kinesin stepping is rectified Brownian motion

Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase

[EN] During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive DNA replication. We determine the main kinetic parameters of the nucleotide incorporation cycle and their dependence on external load and nucleotide (dNTP) concentration. The data is inconsistent with power stroke models for translocation, instead supports a loose-coupling mechanism between chemical catalysis and mechanical translocation during DNA replication. According to this mechanism the DNA polymerase works by alternating between a dNTP/PPi-free state, which diffuses thermally between pre- and post-translocated states, and a dNTP/PPi-bound state where dNTP binding stabilizes the post-translocated state. We show how this thermal ratchet mechanism is used by the polymerase to generate work against large opposing loads (~50 pN).We thank Stephan Grill laboratory (MPI-CBG, Dresden) for help with data collection and E. Galburt, M. Manosas and M. De Vega for critical reading of the manuscript. Spanish Ministry of Economy and Competitiveness [BFU2011-29038 to J.L.C., BFU2013-44202 to J.M.V., BFU2011-23645 to M.S., FIS2010-17440, GR35/10-A920GR35/10-A-911 to F.J.C., MAT2013-49455-EXP to J.R.A.-G. and BFU2012-31825 to B.I.]; Regional Government of Madrid [S2009/MAT 1507 to J.L.C. and CDS2007-0015 to M.S.]; European Molecular Biology Organization [ASTF 276-2012 to J.M.L.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BFU2012-31825 to B.I.].Morin, J.; Cao, F.; Lázaro, J.; Arias-Gonzalez, JR.; Valpuesta, J.; Carrascosa, J.; Salas, M.... (2015). Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. Nucleic Acids Research. 43(7):3643-3652. https://doi.org/10.1093/nar/gkv204S36433652437Steitz, T. A., & Steitz, J. A. (1993). A general two-metal-ion mechanism for catalytic RNA. Proceedings of the National Academy of Sciences, 90(14), 6498-6502. doi:10.1073/pnas.90.14.6498Nakamura, T., Zhao, Y., Yamagata, Y., Hua, Y., & Yang, W. (2012). Watching DNA polymerase η make a phosphodiester bond. Nature, 487(7406), 196-201. doi:10.1038/nature11181Kohlstaedt, L., Wang, J., Friedman, J., Rice, P., & Steitz, T. (1992). Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science, 256(5065), 1783-1790. doi:10.1126/science.1377403Steitz, T. A. (2006). Visualizing polynucleotide polymerase machines at work. The EMBO Journal, 25(15), 3458-3468. doi:10.1038/sj.emboj.7601211Zhang, H., Cao, W., Zakharova, E., Konigsberg, W., & De La Cruz, E. M. (2007). Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates. Nucleic Acids Research, 35(18), 6052-6062. doi:10.1093/nar/gkm587Wang, W., Wu, E. Y., Hellinga, H. W., & Beese, L. S. (2012). Structural Factors That Determine Selectivity of a High Fidelity DNA Polymerase for Deoxy-, Dideoxy-, and Ribonucleotides. Journal of Biological Chemistry, 287(34), 28215-28226. doi:10.1074/jbc.m112.366609Berezhna, S. Y., Gill, J. P., Lamichhane, R., & Millar, D. P. (2012). Single-Molecule Förster Resonance Energy Transfer Reveals an Innate Fidelity Checkpoint in DNA Polymerase I. Journal of the American Chemical Society, 134(27), 11261-11268. doi:10.1021/ja3038273Hariharan, C., Bloom, L. B., Helquist, S. A., Kool, E. T., & Reha-Krantz, L. J. (2006). Dynamics of Nucleotide Incorporation:  Snapshots Revealed by 2-Aminopurine Fluorescence Studies†. Biochemistry, 45(9), 2836-2844. doi:10.1021/bi051644sJoyce, C. M., Potapova, O., DeLucia, A. M., Huang, X., Basu, V. P., & Grindley, N. D. F. (2008). Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase I (Klenow Fragment) and Their Role in Nucleotide Selectivity†. Biochemistry, 47(23), 6103-6116. doi:10.1021/bi7021848Vande Berg, B. J., Beard, W. A., & Wilson, S. H. (2000). DNA Structure and Aspartate 276 Influence Nucleotide Binding to Human DNA Polymerase β. Journal of Biological Chemistry, 276(5), 3408-3416. doi:10.1074/jbc.m002884200Showalter, A. K., & Tsai, M.-D. (2002). A Reexamination of the Nucleotide Incorporation Fidelity of DNA Polymerases†. Biochemistry, 41(34), 10571-10576. doi:10.1021/bi026021iShah, A. M., Li, S.-X., Anderson, K. S., & Sweasy, J. B. (2001). Y265H Mutator Mutant of DNA Polymerase β. Journal of Biological Chemistry, 276(14), 10824-10831. doi:10.1074/jbc.m008680200Rothwell, P. J., Mitaksov, V., & Waksman, G. (2005). Motions of the Fingers Subdomain of Klentaq1 Are Fast and Not Rate Limiting: Implications for the Molecular Basis of Fidelity in DNA Polymerases. Molecular Cell, 19(3), 345-355. doi:10.1016/j.molcel.2005.06.032Patel, S. S., Wong, I., & Johnson, K. A. (1991). Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry, 30(2), 511-525. doi:10.1021/bi00216a029Luo, G., Wang, M., Konigsberg, W. H., & Xie, X. S. (2007). Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase. Proceedings of the National Academy of Sciences, 104(31), 12610-12615. doi:10.1073/pnas.0700920104Joyce, C. M., & Benkovic, S. J. (2004). DNA Polymerase Fidelity:  Kinetics, Structure, and Checkpoints†. Biochemistry, 43(45), 14317-14324. doi:10.1021/bi048422zFiala, K. A., & Suo, Z. (2004). Mechanism of DNA Polymerization Catalyzed bySulfolobus solfataricusP2 DNA Polymerase IV†. Biochemistry, 43(7), 2116-2125. doi:10.1021/bi035746zCramer, J., & Restle, T. (2005). Pre-steady-state Kinetic Characterization of the DinB Homologue DNA Polymerase ofSulfolobus solfataricus. Journal of Biological Chemistry, 280(49), 40552-40558. doi:10.1074/jbc.m504481200Choi, J.-Y., & Guengerich, F. P. (2005). Adduct Size Limits Efficient and Error-free Bypass Across Bulky N2-Guanine DNA Lesions by Human DNA Polymerase η. Journal of Molecular Biology, 352(1), 72-90. doi:10.1016/j.jmb.2005.06.079Olsen, T. J., Choi, Y., Sims, P. C., Gul, O. T., Corso, B. L., Dong, C., … Weiss, G. A. (2013). Electronic Measurements of Single-Molecule Processing by DNA Polymerase I (Klenow Fragment). Journal of the American Chemical Society, 135(21), 7855-7860. doi:10.1021/ja311603rAllen, W. J., Rothwell, P. J., & Waksman, G. (2008). An intramolecular FRET system monitors fingers subdomain opening in Klentaq1. Protein Science, 17(3), 401-408. doi:10.1110/ps.073309208Johnson, S. J., & Beese, L. S. (2004). Structures of Mismatch Replication Errors Observed in a DNA Polymerase. Cell, 116(6), 803-816. doi:10.1016/s0092-8674(04)00252-1Yin, Y. W., & Steitz, T. A. (2004). The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase. Cell, 116(3), 393-404. doi:10.1016/s0092-8674(04)00120-5Golosov, A. A., Warren, J. J., Beese, L. S., & Karplus, M. (2010). The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis. Structure, 18(1), 83-93. doi:10.1016/j.str.2009.10.014Zhang, C., & Burton, Z. F. (2004). Transcription Factors IIF and IIS and Nucleoside Triphosphate Substrates as Dynamic Probes of the Human RNA Polymerase II Mechanism. Journal of Molecular Biology, 342(4), 1085-1099. doi:10.1016/j.jmb.2004.07.070Nedialkov, Y. A., Gong, X. Q., Hovde, S. L., Yamaguchi, Y., Handa, H., Geiger, J. H., … Burton, Z. F. (2003). NTP-driven Translocation by Human RNA Polymerase II. Journal of Biological Chemistry, 278(20), 18303-18312. doi:10.1074/jbc.m301103200Gong, X. Q., Zhang, C., Feig, M., & Burton, Z. F. (2005). Dynamic Error Correction and Regulation of Downstream Bubble Opening by Human RNA Polymerase II. Molecular Cell, 18(4), 461-470. doi:10.1016/j.molcel.2005.04.011Guajardo, R., & Sousa, R. (1997). A model for the mechanism of polymerase translocation 1 1Edited by A. R. Fersht. Journal of Molecular Biology, 265(1), 8-19. doi:10.1006/jmbi.1996.0707Thomen, P., Lopez, P. J., & Heslot, F. (2005). Unravelling the Mechanism of RNA-Polymerase Forward Motion by Using Mechanical Force. Physical Review Letters, 94(12). doi:10.1103/physrevlett.94.128102Larson, M. H., Zhou, J., Kaplan, C. D., Palangat, M., Kornberg, R. D., Landick, R., & Block, S. M. (2012). Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proceedings of the National Academy of Sciences, 109(17), 6555-6560. doi:10.1073/pnas.1200939109Bar-Nahum, G., Epshtein, V., Ruckenstein, A. E., Rafikov, R., Mustaev, A., & Nudler, E. (2005). A Ratchet Mechanism of Transcription Elongation and Its Control. Cell, 120(2), 183-193. doi:10.1016/j.cell.2004.11.045Bai, L., Fulbright, R. M., & Wang, M. D. (2007). Mechanochemical Kinetics of Transcription Elongation. Physical Review Letters, 98(6). doi:10.1103/physrevlett.98.068103Abbondanzieri, E. A., Greenleaf, W. J., Shaevitz, J. W., Landick, R., & Block, S. M. (2005). Direct observation of base-pair stepping by RNA polymerase. Nature, 438(7067), 460-465. doi:10.1038/nature04268Dangkulwanich, M., Ishibashi, T., Liu, S., Kireeva, M. L., Lubkowska, L., Kashlev, M., & Bustamante, C. J. (2013). Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife, 2. doi:10.7554/elife.00971Lieberman, K. R., Dahl, J. M., Mai, A. H., Cox, A., Akeson, M., & Wang, H. (2013). Kinetic Mechanism of Translocation and dNTP Binding in Individual DNA Polymerase Complexes. Journal of the American Chemical Society, 135(24), 9149-9155. doi:10.1021/ja403640bLieberman, K. R., Dahl, J. M., Mai, A. H., Akeson, M., & Wang, H. (2012). Dynamics of the Translocation Step Measured in Individual DNA Polymerase Complexes. Journal of the American Chemical Society, 134(45), 18816-18823. doi:10.1021/ja3090302Dahl, J. M., Mai, A. H., Cherf, G. M., Jetha, N. N., Garalde, D. R., Marziali, A., … Lieberman, K. R. (2012). Direct Observation of Translocation in Individual DNA Polymerase Complexes. Journal of Biological Chemistry, 287(16), 13407-13421. doi:10.1074/jbc.m111.338418Rodriguez, I., Lazaro, J. M., Blanco, L., Kamtekar, S., Berman, A. J., Wang, J., … de Vega, M. (2005). A specific subdomain in  29 DNA polymerase confers both processivity and strand-displacement capacity. Proceedings of the National Academy of Sciences, 102(18), 6407-6412. doi:10.1073/pnas.0500597102Morin, J. A., Cao, F. J., Valpuesta, J. M., Carrascosa, J. L., Salas, M., & Ibarra, B. (2012). Manipulation of single polymerase-DNA complexes: A mechanical view of DNA unwinding during replication. Cell Cycle, 11(16), 2967-2968. doi:10.4161/cc.21389Morin, J. A., Cao, F. J., Lazaro, J. M., Arias-Gonzalez, J. R., Valpuesta, J. M., Carrascosa, J. L., … Ibarra, B. (2012). Active DNA unwinding dynamics during processive DNA replication. Proceedings of the National Academy of Sciences, 109(21), 8115-8120. doi:10.1073/pnas.1204759109Ibarra, B., Chemla, Y. R., Plyasunov, S., Smith, S. B., Lázaro, J. M., Salas, M., & Bustamante, C. (2009). Proofreading dynamics of a processive DNA polymerase. The EMBO Journal, 28(18), 2794-2802. doi:10.1038/emboj.2009.219Bustamante, C., Chemla, Y. R., Forde, N. R., & Izhaky, D. (2004). Mechanical Processes in Biochemistry. Annual Review of Biochemistry, 73(1), 705-748. doi:10.1146/annurev.biochem.72.121801.161542Jahnel, M., Behrndt, M., Jannasch, A., Schäffer, E., & Grill, S. W. (2011). Measuring the complete force field of an optical trap. Optics Letters, 36(7), 1260. doi:10.1364/ol.36.001260Soengas, M. S., Esteban, J. A., Lázaro, J. M., Bernad, A., Blasco, M. A., Salas, M., & Blanco, L. (1992). Site-directed mutagenesis at the Exo III motif of phi 29 DNA polymerase; overlapping structural domains for the 3′-5′ exonuclease and strand-displacement activities. The EMBO Journal, 11(11), 4227-4237. doi:10.1002/j.1460-2075.1992.tb05517.xSoengas, M. S., Gutiérrez, C., & Salas, M. (1995). Helix-destabilizing Activity of φ29 Single-stranded DNA Binding Protein: Effect on the Elongation Rate During Strand Displacement DNA Replication. Journal of Molecular Biology, 253(4), 517-529. doi:10.1006/jmbi.1995.0570De Vega, M., Lazaro, J. M., Salas, M., & Blanco, L. (1996). Primer-terminus stabilization at the 3′-5′ exonuclease active site of phi29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases. The EMBO Journal, 15(5), 1182-1192. doi:10.1002/j.1460-2075.1996.tb00457.xVisscher, K., Schnitzer, M. J., & Block, S. M. (1999). Single kinesin molecules studied with a molecular force clamp. Nature, 400(6740), 184-189. doi:10.1038/22146Pandey, M., & Patel, S. S. (2014). Helicase and Polymerase Move Together Close to the Fork Junction and Copy DNA in One-Nucleotide Steps. Cell Reports, 6(6), 1129-1138. doi:10.1016/j.celrep.2014.02.025Truniger, V. (2002). A positively charged residue of phi29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide. Nucleic Acids Research, 30(7), 1483-1492. doi:10.1093/nar/30.7.1483Berman, A. J., Kamtekar, S., Goodman, J. L., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. A. (2007). Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. The EMBO Journal, 26(14), 3494-3505. doi:10.1038/sj.emboj.7601780Thomen, P., Lopez, P. J., Bockelmann, U., Guillerez, J., Dreyfus, M., & Heslot, F. (2008). T7 RNA Polymerase Studied by Force Measurements Varying Cofactor Concentration. Biophysical Journal, 95(5), 2423-2433. doi:10.1529/biophysj.107.125096Keller, D., & Bustamante, C. (2000). The Mechanochemistry of Molecular Motors. Biophysical Journal, 78(2), 541-556. doi:10.1016/s0006-3495(00)76615-xHerbert, K. M., Greenleaf, W. J., & Block, S. M. (2008). Single-Molecule Studies of RNA Polymerase: Motoring Along. Annual Review of Biochemistry, 77(1), 149-176. doi:10.1146/annurev.biochem.77.073106.100741Wong, I., Patel, S. S., & Johnson, K. A. (1991). An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry, 30(2), 526-537. doi:10.1021/bi00216a030Lowe, L. G., & Guengerich, F. P. (1996). Steady-State and Pre-Steady-State Kinetic Analysis of dNTP Insertion Opposite 8-Oxo-7,8-dihydroguanine byEscherichia coliPolymerases I exo-and II exo- †. Biochemistry, 35(30), 9840-9849. doi:10.1021/bi960485xKirmizialtin, S., Nguyen, V., Johnson, K. A., & Elber, R. (2012). How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations. Structure, 20(4), 618-627. doi:10.1016/j.str.2012.02.018Donlin, M. J., Patel, S. S., & Johnson, K. A. (1991). Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction. Biochemistry, 30(2), 538-546. doi:10.1021/bi00216a031Li, Y. (1998). Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. The EMBO Journal, 17(24), 7514-7525. doi:10.1093/emboj/17.24.7514Lieberman, K. R., Dahl, J. M., & Wang, H. (2014). Kinetic Mechanism at the Branchpoint between the DNA Synthesis and Editing Pathways in Individual DNA Polymerase Complexes. Journal of the American Chemical Society, 136(19), 7117-7131. doi:10.1021/ja5026408Subuddhi, U., Hogg, M., & Reha-Krantz, L. J. (2008). Use of 2-Aminopurine Fluorescence To Study the Role of the β Hairpin in the Proofreading Pathway Catalyzed by the Phage T4 and RB69 DNA Polymerases†. Biochemistry, 47(23), 6130-6137. doi:10.1021/bi800211fShamoo, Y., & Steitz, T. A. (1999). Building a Replisome from Interacting Pieces. Cell, 99(2), 155-166. doi:10.1016/s0092-8674(00)81647-5Lamichhane, R., Berezhna, S. Y., Gill, J. P., Van der Schans, E., & Millar, D. P. (2013). Dynamics of Site Switching in DNA Polymerase. Journal of the American Chemical Society, 135(12), 4735-4742. doi:10.1021/ja311641bKamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. A. (2004). Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell, 16(4), 609-618. doi:10.1016/j.molcel.2004.10.019Hogg, M., Wallace, S. S., & Doublié, S. (2004). Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. The EMBO Journal, 23(7), 1483-1493. doi:10.1038/sj.emboj.7600150Seifert, U. (2012). Stochastic thermodynamics, fluctuation theorems and molecular machines. Reports on Progress in Physics, 75(12), 126001. doi:10.1088/0034-4885/75/12/126001Cao, F. J., & Feito, M. (2009). Thermodynamics of feedback controlled systems. Physical Review E, 79(4). doi:10.1103/physreve.79.041118Cao, F. J., Dinis, L., & Parrondo, J. M. R. (2004). Feedback Control in a Collective Flashing Ratchet. Physical Review Letters, 93(4). doi:10.1103/physrevlett.93.040603Bier, M. (2007). The stepping motor protein as a feedback control ratchet. Biosystems, 88(3), 301-307. doi:10.1016/j.biosystems.2006.07.013Astumian, R. D. (1997). Thermodynamics and Kinetics of a Brownian Motor. Science, 276(5314), 917-922. doi:10.1126/science.276.5314.917Komissarova, N., & Kashlev, M. (1997). Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3’ end of the RNA intact and extruded. Proceedings of the National Academy of Sciences, 94(5), 1755-1760. doi:10.1073/pnas.94.5.1755Brueckner, F., & Cramer, P. (2008). Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation. Nature Structural & Molecular Biology, 15(8), 811-818. doi:10.1038/nsmb.145

A physical model describing the transport mechanisms of cytoplasmic dynein

Cytoplasmic dynein 1 is crucial for many cellular processes including endocytosis and cell division. Dynein malfunction can lead to neurodevelopmental and neurodegenerative disease, such as intellectual disability, Charcot-Marie-Tooth disease and spinal muscular atrophy with lower extremity predominance. We formulate, based on physical principles, a mechanical model to describe the stepping behaviour of cytoplasmic dynein walking on microtubules. Unlike previous studies on physical models of this nature, we base our formulation on the whole structure of dynein to include the temporal dynamics of the individual components such as the cargo (for example an endosome or bead), two rings of six ATPase domains associated with diverse cellular activities and the microtubule binding domains. This mathematical framework allows us to examine experimental observations across different species of dynein as well as being able to make predictions (not currently experimentally measured) on the temporal behaviour of the individual components of dynein. Initially, we examine a continuous model using plausible force functions to model the ATP force and binding affinity to the microtubule. Our results show hand-over-hand and shuffling stepping patterns in agreement with experimental observations. We are able to move from a hand-overhand to a shuffling stepping pattern by changing a single parameter. We also explore the effects of multiple motors. Next, we explore stochasticity within the model, modelling the binding of ATP as a random event. Our results reflect experimental observations that dynein walks using a predominantly shuffling stepping pattern. Furthermore, we study the effects of mutated dynein and extend the model to include variable step sizes, backward stepping and dwelling. Independent stepping is studied and the results show that coordinated stepping is needed in order to obtain experimental run lengths

Simulating the kinesin walk : towards a definitive theory

Dementia is a set of incurable, fatal diseases characterised by irreversible degeneration of the brain. One theory of its cause is the failure of intracellular transport in the axons of the neurons that compose the brain. Kinesin is a key motor transporting vital cargo along the axon. We know that this motor is a bipedal engine stepping forward along a polypeptide track but it is too small and fast for this motion to be observed using current experimental techniques. The stepping detail is therefore open to debate. This study firstly addresses the question of how kinesin steps and secondly pilots a possible method for investigating transport disruption in silico. To investigate the detail of stepping, a program has been designed and built to simulate kinesin traversing its track along a section of axon. The motor is modelled as simple, interacting agents obeying rules abstracted from known chemical and binding properties of its components. The agent-based method has proven useful and efficient on the small scale and has potential for simulating the larger and more complex system of axonal transport. This would enable investigation of transport failure in the context of finding a cure for dementia. A new model of kinesin stepping has been formulated as a consequence of performing virtual experiments using the simulation. Analysis of in vivo and in vitro experimental studies shows that the model accounts for a wide range of published results, explaining many findings. New experiments are suggested to test the model based on its falsifiable predictions. The principal conclusion of this study is that kinesin stepping is rectified Brownian motion.EThOS - Electronic Theses Online ServiceEngineering and Physical Sciences Research Council (EPSRC)GBUnited Kingdo