Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways.

@article{citeulike:2530783, abstract = {Dwell-time distributions, waiting-time distributions, and distributions of pause durations are widely reported for molecular motors based on single-molecule biophysical experiments. These distributions provide important information concerning the functional mechanisms of enzymes and their underlying kinetic and mechanical processes. We have extended the absorbing boundary method to simulate dwell-time distributions of complex kinetic schemes, which include cyclic, branching, and reverse transitions typically observed in molecular motors. This extended absorbing boundary method allows global fitting of dwell-time distributions for enzymes subject to different experimental conditions. We applied the extended absorbing boundary method to experimental dwell-time distributions of single-headed myosin V, and were able to use a single kinetic scheme to fit dwell-time distributions observed under different ligand concentrations and different directions of optical trap forces. The ability to use a single kinetic scheme to fit dwell-time distributions arising from a variety of experimental conditions is important for identifying a mechanochemical model of a molecular motor. This efficient method can be used to study dwell-time distributions for a broad class of molecular motors, including kinesin, RNA polymerase, helicase, F(1) ATPase, and to examine conformational dynamics of other enzymes such as ion channels.}, address = {Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.}, author = {Liao, J. C. and Spudich, J. A. and Parker, D. and Delp, S. L. }, citeulike-article-id = {2530783}, doi = {http://dx.doi.org/10.1073/pnas.0611519104}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {computation, molecular-motors, theory}, month = {February}, number = {9}, pages = {3171--3176}, posted-at = {2008-03-14 05:54:28}, priority = {2}, title = {Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways.}, url = {http://dx.doi.org/10.1073/pnas.0611519104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:2530783 L3 - citeulike-article-id:2530783 TI - Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways. JF - Proc Natl Acad Sci U S A VL - 104 IS - 9 SP - 3171 EP - 3176 AD - Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. SN - 0027-8424 N2 - Dwell-time distributions, waiting-time distributions, and distributions of pause durations are widely reported for molecular motors based on single-molecule biophysical experiments. These distributions provide important information concerning the functional mechanisms of enzymes and their underlying kinetic and mechanical processes. We have extended the absorbing boundary method to simulate dwell-time distributions of complex kinetic schemes, which include cyclic, branching, and reverse transitions typically observed in molecular motors. This extended absorbing boundary method allows global fitting of dwell-time distributions for enzymes subject to different experimental conditions. We applied the extended absorbing boundary method to experimental dwell-time distributions of single-headed myosin V, and were able to use a single kinetic scheme to fit dwell-time distributions observed under different ligand concentrations and different directions of optical trap forces. The ability to use a single kinetic scheme to fit dwell-time distributions arising from a variety of experimental conditions is important for identifying a mechanochemical model of a molecular motor. This efficient method can be used to study dwell-time distributions for a broad class of molecular motors, including kinesin, RNA polymerase, helicase, F(1) ATPase, and to examine conformational dynamics of other enzymes such as ion channels. KW - computation KW - molecular-motors KW - theory AU - Liao, JC AU - Spudich, JA AU - Parker, D AU - Delp, SL PY - 2007/02/27/ UR - http://dx.doi.org/10.1073/pnas.0611519104 ER -