Binding of Ligands to an Infinite Linear Lattice: A Model for Non-Sequence-Selective Protein-DNA Interactions -- from Wolfram Library Archive

Title

Binding of Ligands to an Infinite Linear Lattice: A Model for Non-Sequence-Selective Protein-DNA Interactions

Author

Alan R. Wolfe

Organization:

Dept. of Biopharmaceutical Sciences, University of California at San Francisco

Old MathSource #

0206-031

Revision date

1999-03-10

Description

These notebooks calculate and graph Scatchard plots and other relevant data (conditional probabilities, ligand orientation, cluster length distributions) for the binding of ligands to an infinite linear lattice. The ligands may be symmetric or asymmetric, and the lattice may be isotropic or anisotropic. Binding site overlap and cooperative interactions between adjacent bound ligands are taken into account. This is a mathematical model for non-sequence-selective binding of proteins and other small molecules (ligands) to a linear macromolecule such as DNA (the lattice), and is a generalization of the work of McGhee & Von Hippel, who considered the symmetric ligand, isotropic lattice case. (Our treatment of the latter case allows for the presence two different types of ligand.) The method used is described in Wolfe, A. R. & Meehan, T. (1992) J. Mol. Biol. 223, 1063-1087.

Subjects

	Science > Chemistry
	Science > Medicine

Keywords

Chemistry, Life Sciences, biology, Applied Mathematics

Downloads

README.txt (15.3 KB) - Plain-text documentation for all notebooks.

2L-Ex&Th-Initialize.nb (66.3 KB) - Initialization notebook for the 2 types of symmetric ligand, isotropic lattice case, experimental versus theoretical.

2L-Ex&Th-Output.nb (43.2 KB) - Output notebook for the 2 types of symmetric ligand, isotropic lattice case, experimental versus theoretical.

2Lig-Initialize.nb (82.8 KB) - Initialization notebook for the 2 types of symmetric ligand, isotropic lattice case, theoretical only.

2Lig-Output.nb (29.3 KB) - Output notebook for the 2 types of symmetric ligand, isotropic lattice case, theoretical only.

Ani-Initialize.nb (215.6 KB) - Initialization notebook for the asymmetric ligand, anisotropic lattice case.

Ani-Output.nb (45.7 KB) - Output notebook for the asymmetric ligand, anisotropic lattice case.

Iso-Initialize.nb (95.5 KB) - Initialization notebook for the asymmetric ligand, isotropic lattice case.

Iso-Output.nb (37.6 KB) - Output notebook for the asymmetric ligand, isotropic lattice case.

README.nb (28.8 KB) - Mathematica notebook documentation for all notebooks.

Sym-Initialize.nb (49.4 KB) - Initialization notebook for the symmetric ligand case.

Sym-Output.nb (34.6 KB) - Output notebook for for the symmetric ligand case.

schema&derivation.nb (520.9 KB) - Mathematica notebook

Files specific to Mathematica 2.2 version:

README.txt (11.4 KB) - Plain-text documentation for all notebooks

2Lig-Initialize.ma (37.2 KB) - Initialization notebook for 2Lig-Output.ma

2Lig-Output.ma (14.9 KB) - Notebook for symmetric ligands of 2 types on an isotropic lattice

Ani-Initialize.ma (99.7 KB) - Initialization notebook for Ani-Output.ma

Ani-Output.ma (19.1 KB) - Notebook for asymmetric ligands on an anisotropic lattice

Iso-Initialize.ma (43.2 KB) - Initialization notebook for Iso-Output.ma

Iso-Output.ma (16 KB) - Notebook for asymmetric ligands on an isotropic lattice

README.ma (15.6 KB) - Mathematica notebook documentation for all notebooks

Sym-Initialize.ma (21 KB) - Initialization notebook for Sym-Output.ma

Sym-Output.ma (13.6 KB) - Notebook for symmetric ligands of 1 type