Two scale generalized model of polypeptide chains.
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.
Badasyan
A V
AV
Department of Molecular Physics, Yerevan State University, A Manougian Str.1, 375025 Yerevan, Armenia.
Tonoyan
Sh A
ShA
Tsarukyan
A V
AV
Mamasakhlisov
Y Sh
YSh
Benight
A S
AS
Morozov
V F
VF
D000465:Algorithms; D001703:Biophysics / Q000379:methods; D002627:Chemistry, Physical / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008280:Magnetics; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009696:Nucleic Acids / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software; D013696:Temperature; D013816:Thermodynamics
D009696:Nucleic Acids; D010455:Peptides; D004247:DNA