title: The interaction of amino acids, peptides, and proteins with DNA.
abstract: Amino acids that carry charges on their side groups can bind to double stranded DNA (dsDNA) and change the strength of the double helix. Measurement of the DNA melting temperature (Tm) confirmed that acidic amino acids (Glu, Asp) weaken the H-bonds between DNA strands, whereas basic amino acids (Arg, Lys) strengthen the interaction between the strands. A rank correlation exists between the amino acid isoelectric points and the observed changes in Tm. A similar dependence of the hyperchromic effect on the isoelectric point of a protein (pepsin, insulin, cortexin, and protamine) was observed for DNA-protein complexes at room temperature. Short peptides (KE, AEDG, and KEDP) containing a mixture of acidic and basic amino acid residues also affect Tm and the stability of the double helix. A model for binding Glu and Lys to dsDNA was explored by a docking simulation. The model shows that Glu, in an untwisted shape, binds to dsDNA in its major groove and disrupts three H-bonds between the strands, thereby destabilizing the double helix. Lys, in an untwisted shape, binds to the external side of the dsDNA and forms two bonds with O atoms of neighboring phosphodiester groups, thereby strengthening the DNA helix.
authors.affiliation: Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation.
authors.forename: Andrey Y
authors.initials: AY
authors.lastname: Solovyev
authors.affiliation: St. Petersburg State Polytechnical University, Polytekhnicheskaya ul. 29, St. Petersburg 195251, Russian Federation.
authors.forename: Svetlana I
authors.initials: SI
authors.lastname: Tarnovskaya
authors.affiliation: Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation.
authors.forename: Irina A
authors.initials: IA
authors.lastname: Chernova
authors.affiliation: Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation.
authors.forename: Larisa K
authors.initials: LK
authors.lastname: Shataeva
authors.affiliation: Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation; St. Petersburg State Chemical Pharmaceutical Academy, ul. Prof. Popova 14, St. Petersburg 197022, Russian Federation. Electronic address: yury_skorik@mail.ru.
authors.forename: Yury A
authors.initials: YA
authors.lastname: Skorik
mesh_terms: D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D044366:Transition Temperature
chemical_list: D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D004247:DNA
keywords: Amino acid; DNA binding; Melting temperature; Protein; Regulatory peptide