RESUMO
The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types of interactions occurring over different scales. This new two scale GMPC is applied in several specific cases to examine: The combined influence of stacking or antistacking and hydrogen bonding, or spatial restrictions on the length of helical segments, on the cooperativity and temperature interval of the helix-coil transition of duplex DNA. For the cases of stacking or antistacking in combination with hydrogen bonding the model reduces to the basic uniscale model with a redefined scaling parameter Delta. Antistacking increases the cooperativity, while stacking decreases it. In each case, explanations are given in terms of different lengths of helical segments. Restrictions on the length of helical regions result in the appearance of antiferromagnetic-type correlations where there is no apparent link between cooperativity and transition interval.
Assuntos
Físico-Química/métodos , DNA/química , Peptídeos/química , Algoritmos , Biofísica/métodos , Ligação de Hidrogênio , Magnetismo , Modelos Estatísticos , Modelos Teóricos , Conformação Molecular , Ácidos Nucleicos/química , Conformação Proteica , Software , Temperatura , TermodinâmicaRESUMO
A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heterogeneous blocks of various lengths. Within the framework of the GMPC the authors show that the inclusion of stacking interaction heterogeneity relative to homogeneous hydrogen bond interactions leads to an unexpected and quite remarkable increase in melting cooperativity for small blocks. In some cases this tendency persists for long blocks having sharp sequence heterogeneity.