title: Analyzing complicated protein folding kinetics rapidly by analytical Laplace inversion using a Tikhonov regularization variant.
abstract: Kinetic experiments provide much information about protein folding mechanisms. Time-resolved signals are often best described by expressions with many exponential terms, but this hinders the extraction of rate constants by nonlinear least squares (NLS) fitting. Numerical inverse Laplace transformation, which converts a time-resolved dataset into a spectrum of amplitudes as a function of rate constant, allows easy estimation of the rate constants, amplitudes, and number of processes underlying the data. Here, we present a Tikhonov regularization-based method that converts a dataset into a rate spectrum, subject to regularization constraints, without requiring an iterative search of parameter space. This allows more rapid generation of rate spectra as well as analysis of datasets too noisy to process by existing iterative search algorithms. This method's simplicity also permits highly objective, largely automatic analysis with minimal human guidance. We show that this regularization method reproduces results previously obtained by NLS fitting and that it is effective for analyzing datasets too complex for traditional fitting methods. This method's reliability and speed, as well as its potential for objective, model-free analysis, make it extremely useful as a first step in analysis of complicated noisy datasets and an excellent guide for subsequent NLS analysis.
authors: Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5G 1L7. v.mulligan@utoronto.ca
authors: Vikram Khipple
authors: VK
authors: Mulligan
authors: Kevin Charles
authors: KC
authors: Hadley
authors: Avijit
authors: A
authors: Chakrabartty
mesh_terms: D000465:Algorithms; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D006801:Humans; D007700:Kinetics; D016018:Least-Squares Analysis; D017711:Nonlinear Dynamics; D011489:Protein Denaturation; D017510:Protein Folding; D013482:Superoxide Dismutase / Q000737:chemistry; D000072105:Superoxide Dismutase-1
chemical_list: C000606290:SOD1 protein, human; D013482:Superoxide Dismutase; D000072105:Superoxide Dismutase-1