Experimental thermodynamics of the helix-random coil transition. IV. Influence of the base composition of DNA on the transition enthalpy

Biopolymers ◽  
1971 ◽  
Vol 10 (3) ◽  
pp. 513-522 ◽  
Author(s):  
H. Klump ◽  
T. Ackermann
1978 ◽  
Vol 56 (11) ◽  
pp. 1569-1574
Author(s):  
Nga Ho-Duc

Theoretically we can determine the disordered or ordered structure of polypeptides and their dimensions in dilute solutions from hydrodynamic properties. We have presently a wealth of theories for random coil chains and a limited but sufficient number of theories for ordered chains for interpreting experimental results.Viscosity data for seven poly(γ-benzyl-L-glutamate) samples in 1,2-dichloroethane at 25 °C are analyzed and the length per monomeric residue (h) is calculated according to the equivalent ellipsoid approach. The degree of flexibility or rigidity is characterized by calculating Ns, the number of monomer units in a rigid segment or a Kuhn statistical segment; the determination of Ns is made by applying Yamakawa and Fujii's equation modified by Vitovskaya and Tsvetkov.Values obtained for h assuming the solute molecule to be a rigid, stiff chain, range between 1.3 to 2 Å. One notices that the h value close to 1.5 Å is found for the three following molecular weights: 1.8 × 105, 1.7 × 105, and 1.5 × 105. They are, in fact, the samples having a length in good quantitative agreement with that of the rigid segment determined by the method of Vitovskaya and Tsvetkov. This rigid segment corresponds to a sample of 700 ± 100 monomer units.The analysis of the experimental data of poly(γ-benzyl-L-glutamate) in dichloroacetic acid indicates that, in addition to the formation of hydrogen bonds, other interactions between the polypeptide and the solvent are present.In summary, we may conclude that the study of the helix–coil transition using hydrodynamic measurements is judged satisfactory but the determination of characteristic dimensions used to describe exactly the conformation of the macromolecule is somewhat ambiguous. One major problem is the degree of flexibility encountered with high molecular weight chains. However, to get around this difficulty, we propose, according to our results, a method which consists in determining the number of monomer units within a rigid segment from the different values found for h and then the dimensions from the samples for which the chain length is in good agreement with that of a rigid segment thus determined.


2006 ◽  
Vol 17 (02) ◽  
pp. 235-246 ◽  
Author(s):  
GÖKHAN GÖKOĞLU ◽  
TARIK ÇELİK

In order to provide insights into the misfolding mechanism and the subsequent aggregate formation which cause what are known as the neurodegenerative polyglutamine diseases, we have simulated a 10-residue polyglutamine (poly-Q) chain in vacuum and in solvent by multicanonical method, which enabled us to study the system in a wide temperature range and discuss thermodynamic properties. It is understood that the system in vacuum shows two phase transitions, first of them occur at high temperature that is the well-known helix-coil transition and the second one is a solid-solid transition. However, the poly-Q chain in solvent is in a random coil state at higher temperatures, goes through a conformational change at T = 200 K and assumes predominantly a mixture of anti-parallel β-sheet and α-helix structures at low temperatures. One-residue glutamine dipeptide is also simulated and low-energy stable conformations are identified.


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