More detailed footprinting requires a smaller molecule that can

fit into the nooks and crannies of the DNA–protein complex and reveal more of the subtleties of the interaction. A favorite tool for this job is the methylating agent dimethyl sulfate (DMS).

TLS Online TPP Program

#Id: 8463

#Unit 1. Molecules and their Interaction Relevant to Biology

Interactions between amino acid residues at the ends of the helical segment and the electric dipole inherent to the  helix.

TLS Online TPP Program

#Id: 8464

#Unit 1. Molecules and their Interaction Relevant to Biology

The overall effect is a significant net dipole for the a helix that gives a partial positive charge at the amino end and a partial negative charge at the carboxy end of the a helix. 

TLS Online TPP Program

#Id: 8465

#Unit 1. Molecules and their Interaction Relevant to Biology

The magnitude of this dipole moment corresponds to about 0.5-0.7 unit charge at each end of the helix. These charges would be expected to attract ligands of opposite charge and negatively charged ligands, especially when they contain phosphate groups and frequently bind at the N-termini of a helices. In contrast, positively charged ligands rarely bind at the C-terminus

TLS Online TPP Program

#Id: 8466

#Unit 1. Molecules and their Interaction Relevant to Biology

Polyleucine and polyalanine readily form a-helical structures.

TLS Online TPP Program

#Id: 8467

#Unit 1. Molecules and their Interaction Relevant to Biology

polylysine is a random coil at pH values below about 11, where repulsion of positive charges prevents helix formation. At pH 12, where polylysine is a neutral peptide chain, it readily forms an a-helix.

TLS Online TPP Program

#Id: 8468

#Unit 1. Molecules and their Interaction Relevant to Biology

polyGlu is a random coil at pH values above about 5, where repulsion of negative charges prevents helix formation.