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]. |
Multi-site binding – conformational change | |
| ID: | binding_unfolding_eq [view] [download] [versions] |
| System: |
Binding equilibrium of multiple ligands to a macromolecule followed by
unfolding. Each ligand binds independently. Binding of s1 ligands can
lead to unfolding and binding of additional s2 ligands
|
| Simulate: | signal proportional to the fraction of complexes that underwent conformational change |
| Note: | This revision of the model [view] and this dataset [download] were used in [Wieland2009]. |
|
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 |
|
Equilibrium titration by FCS | |
| ID: | fcs_binding [view] [download] [versions] [] |
| System: | Binding equilibrium of a fluorophore and a substrate measured by fluorescence correlation spectroscopy F + S <==> F*S |
| Simulate: | autocorrelation function of photons emitted by free and bound fluorophore |
| Note: | assume equilibrium conditions; assume binding slower than diffusion, 1/(kon+koff) << tD |
|
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 |
|
DNA unwinding by helicase | |
| 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. Model uses method described in [Lucius2003]. |
Helicase translocation | |
| ID: | translocation_02 [view] [download] [versions] |
| System: | translocation of a helicase on nucleic acid fueled by ATP hydrolysis |
| Simulate: | fluorescence change due to dissociation from the substrate (no re-bining), release of Pi, product of ATP hydrolysis |
| Note: | helicase occupies discrete positions on substrate; substrate is assumed to be in excess over helicase; requires rsys MEX-file library |
|
Polymerization | |
| System: | polymerization process with a certain number of intermediates; at each step polymerase can either synthesize the next intermediate or dissociate rendering the intermediate inactive |
| Simulate: | kinetics of polymerization products including all intermediates |
| ID: | polymerization_me [view] [download] [versions] |
| Note: | first order ODEs solved by matrix exponential |
| ID: | polymerization_ni [view] [download] [versions] |
| Note: | first order ODEs solved by numerical integration |
|
RFC clamp loader | |
| ID: | RFC_minimal_01 [view] [download] [versions] |
| System: | Loading a clamp protein onto DNA by RFC; kinetic steps include binding/release/hydrolysis of ATP and binding/release of DNA |
| Simulate: | signal due to RFC*DNA binding; signal due to Pi*PBP binding; fraction of ATP hydrolyzed |
| Note: |
RFC_minimal_01.m requires
rsys
MEX-file library for solving mass-action ODEs. This revision of the model [view] and this dataset [download] were used in [Chen2009]. |
[1] “ Cooperative and non-cooperative binding of large ligands to a finite one- dimensional lattice. A model for ligand-oligonucleotide interactions”. Biophys. Chem. 327–339. 1978.
[2] “ Helicase from hepatitis C virus, energetics of DNA binding”. J. Biol. Chem. 29377–29385. 2002.
[3] “ Analytic binding isotherms describing competitive interactions of a protein ligand with specific and nonspecific sites on the same DNA oligomer”. Biophys. J. 1960–1969. 2001. < /span>
