gfit | global analysis of experimental data

Models for gfit

gfit models are used for fitting data from many experiments at once (globally).

Here are some examples of models divided into sections according to the system type. Some of the datasets associated with models are from actual research projects. This list will continue to grow.

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A model can be written for many types of experiments as long as:

measured values are quantitative (numerical)
measured values are largely deterministic (not completely random)
there is some idea about the underlying mechanism

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Binding equilibrium

Simple binding
ID:	binding_eq_simple [view] [download] [versions] [download data]
System:	equilibrium binding E + L <=> EL
Simulate:	Signal proportional to [EL]

Lattice Binding
ID:	lattice_binding [view] [download] [versions] [download data]
System:	equilibrium binding of protein to linear lattice; binding is non-cooperative and sequence-independent
Simulate:	Signal proportional to concentration of bound protein
Note:	If lattice is long enough to bind 30 proteins or more, the model uses method from [Tsodikov2001]. Otherwise, method from [Epstein1978] is used. Model and data appeared in [Levin2002].

Fluorescence correlation spectroscopy (FCS)

FCS 3D diffusion
ID:	fcs_acf3D [view] [download] [versions] [download data]
System:	FCS experiment; fluorescent particles diffuse in 3 dimensions through Gaussian observation volume where particles are excited and the emitted light is captured
Simulate:	autocorrelation function of photons emitted by multiple groups of particles

FCS anomalous 3D diffusion
ID:	fcs_acf3D_anomal [view] [download] [versions]
System:	FCS experiment; fluorescent particles diffuse anomalously in 3 dimensions through Gaussian observation volume where particles are excited and the emitted light is captured
Simulate:	autocorrelation function of photons emitted by multiple groups of particles

Surface plasmon resonance (SPR)

SPR binding
ID:	spr_binding [view] [download] [versions]
System:	binding of analyte from solution to immobilized ligand with multiple binding sites measured by SPR; A + L <==> AL
Simulate:	SPR signal from binding of analyte at constant concentration followed by its release at zero concentration
Note:	uses analytical solution for binding ODEs; assumes homogenous analyte population and rapid mass-transport

SPR binding-conformational change
ID:	spr_bind_conf_change [view] [download] [versions] [download data]
System:	binding of analyte from solution to immobilized ligand with multiple binding site measured by SPR; analyte binding is followed by a conformational change; A + L <==> AL <==> B
Simulate:	SPR signal from binding of analyte at constant concentration followed by its release at zero concentration
Note:	uses analytical solution for binding-conformational change ODEs; assumes homogeneous reactant populations and rapid mass-transport

Kinetics

Helicase unwinding
ID:	unwinding [view] [download] [versions]
System:	unwinding of double-stranded nucleic acid by a helicase moving in uniform steps
Simulate:	amount of nucleic acid strand released after the intact duplex becomes shorter than critical
Note:	assumes homogeneous helicase population; this assumption was shown to be incorrect for some cases

References

[1] I. R. Epstein. “Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions.”. Biophys. Chem.. 8. 327–339. 1978.

[2] M. K Levin and S. S Patel. “Helicase from hepatitis C virus, energetics of DNA binding.”. J. Biol. Chem.. 277. 29377–29385. 2002.

[3] O. V. Tsodikov, J. A. Holbrook, I. A. Shkel, and M. T. Record. “Analytic binding isotherms describing competitive interactions of a protein ligand with specific and nonspecific sites on the same DNA oligomer.”. Biophys. J.. 81. 1960–1969. 2001.