Biomedical subjects

D M Soumpasis

Publications and source records attributed to D M Soumpasis.

24 records · Page 2Linked to original sources

PubMed1987

Relative stabilities and transitions of DNA conformations in 1:1 electrolytes: a theoretical study.

We use a recently developed formalism (1) to calculate the salt dependent part of the free energy determining DNA conformational stability in 1:1 electrolytes. The conformations studied are the A, B, C and alternating-B right-handed forms and the ZI, ZII left-handed forms of DNA. In the case of the B-ZI transition of d(G-C).d(G-C) helices in NaCl solution, the free energy contribution considered suffices to describe the transition in a quantitative manner. The theory also predicts the occurrence of salt-induced B-A transitions which have been recently observed with poly[d(n2 A-T)] and poly[d(G-C)]. In other cases, additional terms in the free energy balance, particularly due to hydration effects, must be at least as important as salt effects in determining conformational stability and structural transitions in solution. If diffuse ionic cloud electrostatic effects alone would dominate in all cases, the relative helical stabilities at 0.2 M monovalent salt would decrease in the order C greater than B greater than A greater than ZII greater than ZI greater than alternating-B. At high salt concentrations (2.0 M-5.0 M), the order would be alternating-B greater than ZI greater than A greater than ZII greater than B greater than C.

DNA↗

PubMed1985

Effects of monovalent cations on red cell shape and size.

Human erythrocytes were incubated in isotonic solutions of different monovalent cations. The apparent size of the red cells measured on scanning electron microscopic pictures decreases in the order Li+ greater than Na+ = K+ greater than Rb+. These differences in size are abolished after pretreatment with trypsin, which removes a large part of the charges associated with membrane glycoproteins. Shape alterations are also observed. Normal biconcave shapes are visible after Na+ or K+ incubation, whereas Li+ leads to flabby, flattened cells with a certain tendency to crenation, and Rb+ causes more pronounced biconcavity with a certain tendency to cupping. The overall effects of pretreatment with trypsin are similar to those of Li+. Our results provide evidence that the electrostatic repulsion of glycoproteins and other charged membrane components may play an essential role in maintaining red cell shape.

Cations, Monovalent↗

PubMed1985

Effects of DNA sequence and conformation on nucleosome formation.

A simple theoretical analysis of the free energy balance controlling nucleosome formation shows that the specific effects of different DNA sequences and/or conformations observed in vitro are mainly due to their different elastic properties. A calculation of the elastic free energy required to fold DNA on histone octamers yields quantitative results rationalizing the experimental findings provided that: (i) the average helical repeat of DNA on nucleosomes is greater than 10.2 bp per turn, and (ii) poly[dG.dC] adopts an A-type conformation.

Base Sequence↗

PubMed1984

Statistical mechanics of the B----Z transition of DNA: contribution of diffuse ionic interactions.

A theoretical framework is constructed to treat the effects of salt ions on polyionic structural transitions in the absence of specific ion binding. As an application, the salt concentration-dependent part of the free energy difference governing the B----ZI transition of [d(C-G) . d(C-G)]6 in 1:1 electrolytes is calculated; quantitative agreement with the experimental findings is obtained. The effects of temperature and multivalent cations are also discussed. Preliminary calculations indicate that the ZII conformation in solution is thermodynamically less favorable than ZI in the high-salt regime (2.0-5.0 M) but more favorable than ZI below 2.0 M salt.

DNA↗

PubMed1983

Theoretical analysis of fluorescence photobleaching recovery experiments.

We derive an exact closed formula for the fluorescence recovery curve measured in fluorescence photobleaching recovery experiments employing uniform circular laser beams. In contrast to the expression used currently, this result is very simple and free of mathematical drawbacks, thus facilitating the quantitative analysis of experimental data.

Mathematics↗

PubMedDate not supplied

Inclusion of ionic interactions in force field calculations of charged biomolecules--DNA structural transitions.

The potential of mean force (PMF) approach for treating polyion-diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA 81, 5116-5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER-PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C-G)6, and the B and heteronomous (H) conformations of dA12.dT12, as a function of salt concentration. In the case of d(C-G)6, the predicted B-ZI transition occurs at 2.4M and is essentially driven by the phosphate-diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B-DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl. In the range of 0.01-0.3M NaCl, the H form of dA12.dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence.

Biopolymers↗