Biomedical subjects

Lorin S Milescu

Publications and source records attributed to Lorin S Milescu.

4 recordsLinked to original sources

PubMed2006

Extracting dwell time sequences from processive molecular motor data.

Processive molecular motors, such as kinesin, myosin, or dynein, convert chemical energy into mechanical energy by hydrolyzing ATP. The mechanical energy is used for moving in discrete steps along the cytoskeleton and carrying a molecular load. Single-molecule recordings of motor position along a substrate polymer appear as a stochastic staircase. Recordings of other single molecules, such as F1-ATPase, RNA polymerase, or topoisomerase, have the same appearance. We present a maximum likelihood algorithm that extracts the dwell time sequence from noisy data, and estimates state transition probabilities and the distribution of the motor step size. The algorithm can handle models with uniform or alternating step sizes, and reversible or irreversible kinetics. A periodic Markov model describes the repetitive chemistry of the motor, and a Kalman filter allows one to include models with variable step size and to correct for baseline drift. The data are optimized recursively and globally over single or multiple data sets, making the results objective over the full scale of the data. Local binary algorithms, such as the t-test, do not represent the behavior of the whole data set. Our method is model-based, and allows rapid testing of different models by comparing the likelihood scores. From data obtained with current technology, steps as small as 8 nm can be resolved and analyzed with our method. The kinetic consequences of the extracted dwell sequence can be further analyzed in detail. We show results from analyzing simulated and experimental kinesin and myosin motor data. The algorithm is implemented in the free QuB software.

Adenosine Triphosphate↗

PubMed2006

Maximum likelihood estimation of molecular motor kinetics from staircase dwell-time sequences.

Molecular motors, such as kinesin, myosin, or dynein, convert chemical energy into mechanical energy by hydrolyzing ATP. The mechanical energy is used for moving in discrete steps along the cytoskeleton and carrying a molecular load. High resolution single molecule recordings of motor steps appear as a stochastic sequence of dwells, resembling a staircase. Staircase data can also be obtained from other molecular machines such as F1 -ATPase, RNA polymerase, or topoisomerase. We developed a maximum likelihood algorithm that estimates the rate constants between different conformational states of the protein, including motor steps. We model the motor with a periodic Markov model that reflects the repetitive chemistry of the motor step. We estimated the kinetics from the idealized dwell-sequence by numerical maximization of the likelihood function for discrete-time Markov models. This approach eliminates the need for missed event correction. The algorithm can fit kinetic models of arbitrary complexity, such as uniform or alternating step chemistry, reversible or irreversible kinetics, ATP concentration and mechanical force-dependent rates, etc. The method allows global fitting across stationary and nonstationary experimental conditions, and user-defined a priori constraints on rate constants. The algorithm was tested with simulated data, and implemented in the free QuB software.

Adenosine Triphosphate↗

PubMed2005

Activation of heteroliganded mouse muscle nicotinic receptors.

The activation of the mouse muscle-type nicotinic acetylcholine receptor was studied in the presence of carbachol, and in the simultaneous presence of carbachol and choline. The channel currents were recorded under steady-state conditions using cell-attached single-channel patch clamp, and during transient exposures to the agonists using a piezo-driven fast application system. The presence of choline resulted in inhibition of currents elicited by carbachol. The inhibitory effect of choline manifested as a reduction in the effective opening rate (increase in the mean intracluster closed time duration) in single-channel recordings. In the fast application experiments, the peak current amplitude was reduced and the current rise time increased when choline was co-applied with carbachol. The data were analysed according to a model in which receptor interactions with carbachol and choline resulted in three types of ligation: receptors occupied by two carbachol molecules, receptors occupied by two choline molecules, and receptors in which one agonist binding site was occupied by carbachol and the other by choline, i.e. heteroliganded receptors. All three agonist-bound receptor populations could open albeit with different efficacies. The affinity of the resting receptor to choline was estimated to be 1-2 mm, and heteroliganded receptors opened with an opening rate constant of approximately 3000 s(-1). The results of the analysis suggest that the presence of choline in the neuromuscular junction in vivo has little effect on the time course of synaptic currents. Nevertheless, the contribution of heteroliganded receptors should be taken into consideration when the receptor is exposed simultaneously to two or more agonists.

Animals↗

PubMed2005

Maximum likelihood estimation of ion channel kinetics from macroscopic currents.

We describe a maximum likelihood method for direct estimation of rate constants from macroscopic ion channel data for kinetic models of arbitrary size and topology. The number of channels in the preparation, and the mean and standard deviation of the unitary current can be estimated, and a priori constraints can be imposed on rate constants. The method allows for arbitrary stimulation protocols, including stimuli with finite rise time, trains of ligand or voltage steps, and global fitting across different experimental conditions. The initial state occupancies can be optimized from the fit kinetics. Utilizing arbitrary stimulation protocols and using the mean and the variance of the current reduce or eliminate problems of model identifiability (Kienker, 1989). The algorithm is faster than a recent method that uses the full autocovariance matrix (Celentano and Hawkes, 2004), in part due to the analytical calculation of the likelihood gradients. We tested the method with simulated data and with real macroscopic currents from acetylcholine receptors, elicited in response to brief pulses of carbachol. Given appropriate stimulation protocols, our method chose a reasonable model size and topology.

Algorithms↗