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Biomedical subjects

F Gago

Publications and source records attributed to F Gago.

42 records · Page 3Linked to original sources
PubMed1990

Netropsin binding to poly[d(IC)].poly[IC)] and poly[d(GC].poly[d(GC)]: a computer simulation.

The thermodynamic cycle perturbation approach has been used to calculate the difference in the free energy of binding of netropsin to two different DNA molecules. In the computer simulations, all the inosine residues have been gradually 'mutated' into guanosine in a DNA dodecamer and in a complex of the same dodecamer with netropsin. The difference in binding free energy of about 4.3 kcal mol-1 agrees well with the experimentally determined value of 4.0 kcal mol-1. One structural determinant of the specificity seems to be the width of the minor groove in the two complexes.

Guanidines↗
PubMed1989

One left-handed strand in DNA-oligonucleotide complexes?

A single strand of oligonucleotide can bind to double helical DNA under certain conditions. This must involve some unwinding of the original double helix in a process leading to the formation of a three-stranded region. The free energy for such an entropically unlikely reaction may come from a change in the degree of supercoiling of the original DNA. The conformation of the triple strand is investigated here using computer graphics and molecular mechanics calculations. It is suggested that on binding the oligonucleotide (strand 3) to two paired strands (1 and 2) in a supercoiled DNA molecule, strand 2 might adopt a left-handed conformation whilst strand 1 and strand 3 pair in the normal Watson-Crick B-configuration.

Computer Simulation↗
PubMed1989

The binding of benzenesulfonamides to carbonic anhydrase enzyme. A molecular mechanics study and quantitative structure-activity relationships.

Molecular mechanics methods have been applied to study the interaction between a series of 20 deprotonated benzenesulfonamides and the enzyme carbonic anhydrase. The different contributions to the binding energy have been evaluated and correlated with experimental inhibition data and molecular orbital indices of the sulfonamides in their bound conformation. The results suggest that the discrimination shown by the enzyme toward these inhibitors is dominated by the short-range van der Waals forces.

Carbonic Anhydrase Inhibitors↗
PubMed1989

The binding of nonintercalative drugs to alternating DNA sequences.

Molecular mechanics methods have been applied to suggest possible models for netropsin and related compounds binding to two different sequences of DNA, namely poly[d(AT)].poly[d(AT)] and poly[d(GC)].poly[d(GC)], and to evaluate the different contributions to the binding affinities of these compounds in the ethidium displacement assay. The geometries found after energy refinement suggest that one of the reasons for the selectivity of binding of these agents to A + T-rich DNA regions could be the different widths of the minor groove of the double strand of DNA found in the complexes of these drugs with both DNA sequences.

Base Sequence↗