The determination of pair-distance distribution by double electron-electron resonance: regularization by the length of distance discretization with Monte Carlo calculations.
Pulsed double electron-electron resonance technique (DEER, or PELDOR) is applied to study conformations and aggregation of peptides, proteins, nucleic acids, and other macromolecules. For a pair of spin labels, experimental data allows for the determination of their distance distribution function, P(r). P(r) is derived as a solution of a first-kind Fredholm integral equation, which is an ill-posed problem. Here, we suggest regularization by increasing the distance discretization length to its upper limit where numerical integration still provides agreement with experiment. This upper limit is found to be well above the lower limit for which the solution instability appears because of the ill-posed nature of the problem. For solving the integral equation, Monte Carlo trials of P(r) functions are employed; this method has an obvious advantage of the fulfillment of the non-negativity constraint for P(r). The regularization by the increasing of distance discretization length for the case of overlapping broad and narrow distributions may be employed selectively, with this length being different for different distance ranges. The approach is checked for model distance distributions and for experimental data taken from literature for doubly spin-labeled DNA and peptide antibiotics.
Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation. Electronic address: dzuba@kinetics.nsc.ru.
Sergei A
SA
Dzuba
D004578:Electron Spin Resonance Spectroscopy; D004583:Electrons; D009010:Monte Carlo Method; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D013113:Spin Labels
D009696:Nucleic Acids; D011506:Proteins; D013113:Spin Labels
DEER; DNA; Fredholm integral equation; PELDOR; Peptide antibiotics; Spin label