General Texts  | Quenched Flow  | Relaxations  | Surface Plasmon Resonance

Bagshaw, C.R.

Wegener, K.L., Basran, J., Bagshaw, C.R., Campbell, I.D., Roberts, G.C.K., Critchley, D.R. and Barsukov, I. (2008) Structural basis for the interaction between the cytoplasmic domain of the hyaluronate receptor layilin and the talin F3 sub-domain. J. Mol. Biol. 382, 112-126.

Gingras, A.R., Basran, J., Prescott, A., Kriajevska, M., Bagshaw, C.R. and Barsukov, I.L. (2008) Crystal structure of the Ca2+-form and Ca2+-binding kinetics of metastasis-associated protein, S100A4. FEBS Lett. 582, 1651-1656.

Bagshaw, C.R. and Cherny, D. (2006) Blinking fluorophores; what do they tell us about protein dynamics?  Biochem. Soc. Trans. 34, 979-982.

McAnaney, T.B., Zeng, W., Doe, C.E.F., Bhanji, N., Wakelin, S., Pearson, D.S., Abbyad, P., Shi, X., Boxer S.G. and Bagshaw, C.R. (2005) Protonation, photobleaching and photoactivation of Yellow Fluorescent Protein (YFP 10C): a unifying mechanism.  Biochemistry, 44, 5510-5524.

Conibear, P.B., Bagshaw, C.R., Fajer, P.G., Kovács. M. and Málnási-Csizmadia, A. (2003) Myosin cleft movement and its coupling to actomyosin dissociation. Nat. Struct. Biol. 10, 831-835.

Málnási-Csizmadia, A., Pearson, D.S., Kovács, M., Woolley, R. J., Geeves, M. A. & Bagshaw, C. R. (2001) Kinetic resolution of a conformational change and the ATP hydrolysis step using relaxation methods with a Dictyostelium myosin II mutant containing a single tryptophan residue. Biochemistry, 40, 12727-12737.

Conibear, P.B. and Bagshaw, C. R. (1996). Measurement of nucleotide exchange kinetics with isolated synthetic myosin filaments using flash photolysis. FEBS Lett., 380, 13-16.

Walmsley, A.R. and Bagshaw, C.R. (1989) A logarithmic timebase for stopped-flow data aquisition and analysis. Anal. Biochem. 176, 313-318.

Esters, H., Alexandrov, K., Iakovenko, A., Ivanova, T., Thoma, N., Rybin, V., Zerial, M., Scheidig, A.J. & Goody, R.S. (2001) Vps9, Rabex-5 and DSS4: proteins with weak but distinct nucleotide- exchange activities for Rab proteins. J. Mol. Biol. 310, 141-156.

Rensland, H., John, J., Linke, R., Simon, I., Schlichting, I., Wittinghofer, A. & Goody, R.S. (1995) Substrate and product structural requirements for binding of nucleotides to H-ras p21: the mechanism of discrimination between guanosine and adenosine nucleotides. Biochemistry 34, 593-599.

Rittinger, K., Divita, G. & Goody, R.S. (1995) Human immunodeficiency virus reverse transcriptase substrate-induced conformational changes and the mechanism of inhibition by nonnucleoside inhibitors. Proc. Natl. Acad. Sci. U.S.A. 92, 8046-8049.

John, J., Sohmen, R., Feuerstein, J., Linke, R., Wittinghofer, A. & Goody, R.S. (1990) Kinetics of interaction of nucleotides with nucleotide-free H-ras p21. Biochemistry 29, 6058-6065.

Nowak, E., Strzelecka-Golaszewska, H. & Goody, R.S. (1988) Kinetics of nucleotide and metal ion interaction with G-actin. Biochemistry 27, 1785-1792.

Konrad, M. & Goody, R.S. (1982) Kinetic and thermodynamic properties of the ternary complex between F-actin, myosin subfragment 1 and adenosine 5´-[b,g-imido]triphosphate. Eur. J. Biochem. 128, 547-555.

Guo, Z., Ahmadian, M.R., Goody, R.S. (2005) Guanine nucleotide exchange factors operate by a simple allosteric competitive mechanism. Biochemistry,  44, 15423-15429.

Jenkins, D.C., Pearson, D.S., Harvey, A., Sylvester, I.D., Geeves, M.A. & Pinheiro, T.J. (2009). Rapid folding of the prion protein captured by pressure-jump. Eur. Biophys. J. 38, 625-35.

Adamek, N., Coluccio, L.M. & Geeves, M.A. (2008). Calcium sensitivity of the cross-bridge cycle of Myo1c, the adaptation motor in the inner ear. Proc. Natl. Acad. Sci. USA 105, 5710-5.

Iorga, B., Adamek, N. & Geeves, M.A. (2007) The slow skeletal muscle isoform of myosin shows kinetic features common to smooth and non-muscle myosins. J. Biol. Chem.  282, 3559-3570.

Bloemink, M.J., Adamek, N., Reggiani, C. & Geeves, M.A. (2007) Kinetic Analysis of the Slow Skeletal Myosin MHC-1 Isoform from Bovine Masseter Muscle. J. Mol. Biol. 373, 1184-97.

Kintses, B., Gyimesi, M., Pearson, D.S., Geeves, M.A., Bagshaw, C.R. & Malnasi-Csizmadia, A. (2007) Reversible movement of switch 1 loop of myosin determines actin interaction.  EMBO J  26,  265-274.

Adio, S., Bloemink, M., Hartel, M., Leier, S., Geeves, M.A., Woehlke, G. (2006) Kinetic and mechanistic basis of the non-processive Kinesin-3 motor NcKin3. J. Biol. Chem. 281, 37782-93.

Varga, A., Lionne, C., Lallemand, P., Szabó, J., Adamek, N., Valentin, C., Vas, M., Barman, T., and Chaloin, L. (2009) Direct kinetic evidence that lysine 215 is involved in the phospho-transfer step of human 3-phosphoglycerate kinase. Biochemistry 48, 6998-7008.

Gondeau, C., Chaloin, L., Varga, A., Roy, B., Lallemand, L., Périgaud, C., Barman, T., Vas, M., and Lionne, C. (2008) Differences in the transient kinetics of the binding of D-ADP and its mirror image L-ADP to human 3-phosphoglycerate kinase revealed by the presence of 3-phosphoglycerate. Biochemistry 47, 3462-3473.

Gondeau, C., Chaloin, L., Lallemand, L., Roy, B., Périgaud, C., Barman, T., Vas, M., Lionne, C., and Arold, S. T. (2008) Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase. Nucleic Acids Res. 36, 3620-3629.

Agopian, A., Depollier, J., Lionne, C., and Divita, G. (2007) p66 Trp24 and Phe61 are essential for accurate association of HIV-1 reverse transcriptase with primer/template. J. Mol. Biol. 373, 127-140.

Barman, T., Bellamy, S. R. W., Gutfreund, H., Halford S. E., and Lionne, C. (2006) The identification of chemical intermediates in enzyme catalysis by the rapid quench-flow technique. Cell. Mol. Life Sci. 63, 2571-2583.

Geerlof, A., Travers, F., Barman, T., and Lionne, C. (2005) Perturbation of yeast 3-phosphoglycerate kinase reaction mixtures with ADP: transient kinetics of formation of ATP from bound 1,3-bisphosphoglycerate. Biochemistry 44, 14948-14955.

Stefan Weiss, Igor Chizhov and Michael A. Geeves. (2000) A flash photolysis fluorescence/light scattering apparatus for use with sub microgram quantities of muscle proteins. Journal of Muscle Research and Cell Motility 21: 423-432.

Chizhov I., Chernavskii, D.S., Engelhard, M., Müller, K.H., Zubov, B.V. and Hess, B. (1996) Spectrally silent transitions in the bacteriorhodopsin photocycle. Biophysical Journal 71:2329-2345.

Chernavskii D.S., Chizhov I.V., Lozier R.H., Murina T.M., Prokhorov, A.M., Zubov B.V. (1989) Kinetic model of bacteriorhodopsin photocycle: pathway from M state to bR. Photochem.Photobiol. 49:649-653.

Igor Chizhov, Georg Schmies, Ralf Seidel, Jens R. Sydor, Beate Lüttenberg and Martin Engelhard (1998) The photophobic receptor from Natronobacterium pharaonis: Temperature and pH-dependencies of the photocycle of sensory rhodopsin II. Biophysical Journal 75:999-1009

Igor Chizhov and Martin Engelhard. (2001) Temperature and Halide Dependence of the Photocycle of Halorhodopsin from Natronobacterium pharaonis. Biophysical Journal 81:1600–1612.

Porschke, D. (2002) Reaction coupling, acceptor pK, and diffusion control in light induced proton release of bacteriorhodopsin.  J. Phys. Chem. B 106, 10233-10241.

Wang, G. & Porschke, D. (2003) Dipole reversal in bacteriorhodopsin and separation of dipole components.  J. Phys. Chem. B 107, 4632-4638.

Porschke, D. (2003) Strong bending of purple membranes in the M-state.  J. Mol. Biol. 331, 667-679.

Porschke, D. (2004) Slow modes of polarization in purple membranes.  Phys. Chem. Chem. Phys. 6, 165-171.

Jose, D. & Porschke, D. (2004) Dynamics of the B-A transition of DNA double helices. Nucleic Acids Res. 32, 2251-2258.

Jose, D. & Porschke, D. (2005) The dynamics of the B-A transition of natural DNA double helices.  J. Amer. Chem. Soc. 127, 16120-16128.

Porschke, D. & Antosiewicz, J.M. (2005) Strong effect of hydrodynamic coupling on the electric dichroism of bent rods. J. Phys. Chem. 109, 1034-1038.

Porschke, D. & Antosiewicz, J.M. (2007) ‘Quantitative molecular electro-optics: Macromolecular structures and their dynamics in solution’, In Molecular and colloidal electro-optics  (Ed. Stoylov, S. P. and Stoimenova, M. V.), CRC, Boca Raton, Fla., pp. 55-107.

Porschke, D. (2007) The nature of “unusual” electro-optical transients observed for DNA.  Colloids Surf. B 56, 44-49.

Porschke, D. (2007) Unique physical signature of DNA curvature and its implications for structure and dynamics.  J. Phys. Chem. B 111, 12004-12011

Kastner, B., Fischer, N., Golas, M.M., Sander, B., Dube, P., Boehringer, D.,  Hartmuth, K., Deckert, J., Hauer, F., Wolf, E., Uchtenhagen, H., Urlaub, H., Herzog, F., Peters, J.M., Poerschke, D., Lührmann, R., Stark, H. (2008) GraFix: sample preparation for single particle electron cryomicroscopy.  Nature Methods 5, 53-55.

Antosiewicz, J.M. & Porschke, D. (2009) Effects of hydrodynamic coupling on electro-optical transients.  J. Phys. Chem. B 113, 13988-13992.

Roullier, V., Clarke, S., You, C., Pinaud, F., Gouzer, G. G., Schaible, D., Marchi-Artzner, V., Piehler, J. & Dahan, M. (2009). High-affinity labeling and tracking of individual histidine-tagged proteins in live cells using Ni2+ tris-nitrilotriacetic acid quantum dot conjugates.  Nano. Lett. 9, 1228-34.

Strunk, J. J., Gregor, I., Becker, Y., Li, Z., Gavutis, M., Jaks, E., Lamken, P., Walz, T., Enderlein, J. & Piehler, J. (2008). Ligand binding induces a conformational change in ifnar1 that Is propagated to its membrane-proximal domain.  J. Mol. Biol. 377, 725-739.

Lata, S., Schoehn, G., Jain, A., Pires, R., Piehler, J., Gottlinger, H. G. & Weissenhorn, W. (2008). Helical structures of ESCRT-III are disassembled by VPS4.  Science 321, 1354-7.

Reichel, A., Schaible, D., Al Furoukh, N., Cohen, M., Schreiber, G. & Piehler, J. (2007). Noncovalent, site-specific biotinylation of histidine-tagged proteins. Anal. Chem. 79, 8590-600.

Gavutis, M., Jaks, E., Lamken, P. & Piehler, J. (2006). Determination of the 2-dimensional interaction rate constants of a cytokine receptor complex. Biophys. J. 90, 3345-55.

Lata, S. & Piehler, J. (2005). Stable and functional immobilization of histidine-tagged proteins via multivalent chelator head-groups on a molecular poly(ethylene glycol) brush. Anal. Chem. 77, 1096 -1105.

Gavutis, M., Lata, S., Lamken, P., Müller, P. & Piehler, J. (2005). Lateral ligand-receptor interactions on membranes probed by simultaneous fluorescence-interference detection. Biophys. J. 88, 4289-302.

Lamken, P., Lata, S., Gavutis, M. & Piehler, J. (2004). Ligand-induced assembling of the type I interferon receptor on supported lipid bilayers. J. Mol. Biol. 341, 303-18.

General texts:

Gutfreund, H. (1995) Kinetics for the Life Sciences. Cambridge University Press.
ISBN: 0521480272

Gutfreund, H. (1972) Physical Principles (esp. Ch. 6 & 8) John Wiley.
ISBN: 0471337153

Fersht, A. (1985) Structure & Mechanism (esp. Ch. 4 & 6) W.H. Freeman.
ISBN: 0716716143

Roberts, D.V. (1977) Enzyme Kinetics (esp. Ch. 1 & 7) Cambridge University Press.
ISBN: 052121274

Hiromi, K. (1979) Kinetics of Fast Enzyme Reactions. Theory & Practice. John Wiley.
ISBN: 0470268662

Johnson, K.A. (2003) Kinetic Analysis of Macromolecules. Oxford University Press.
ISBN: 0198524943.

Eccleston, J.F., Hutchinson, J.P. & White, H.D. (2001) Stopped-flow techniques. In: Protein-Ligand Interactions: structure and spectroscopy (Ed. Harding, S.E. & Chowdhry, B.Z.). Oxford University Press.
ISBN: 019963747

Goodrich J. A. & Kugel, J. F. (2007)  Binding and kinetics for Molecular
Biologists, Cold Spring Harbor  Laboratory Press.
ISBN 0879697369

Quenched Flow:

Barman, T.E. & Travers, F. (1985) The rapid flow quench method in the study of fast reactions in biochemistry: Methods of Biochemical

Analysis 31, 1-59.

Relaxations:

Bernasconi, C.F. (1976) Relaxation Kinetics. Academic Press.
ISBN: 0120929503

Surface Plasmon Resonance:

Chaiken, I., Rose, S. & Karlsson (1992) Analytical Biochem. 201, 197.

Malmborg, A.C., Michaelson, A., Ohlin, M., Jansson, B. & Borrebasck, C.A. (1992) Scand. J. Immunol. 35, 643.