Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice.

Polymer-surfactant systems in bulk and at fluid interfaces.

Inhibition of human gingival gelatinases (MMP-2 and MMP-9) by metal salts.

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

Experimental studies related to the origin of the genetic code and the process of protein synthesis — A review

The binding of adenosine cyclic 3',5'-monophosphate (cAMP) and guanosine cyclic 3',5'-monophosphate (cGMP) to the adenosine cyclic 3',5'-monophosphate receptor protein (CRP) from Escherichia coli was investigated by equilibrium dialysis at pH 8.0 and 20 degrees C at different ionic strengths (0.05--0.60 M). Both cAMP and cGMP bind to CRP with a negative cooperativity that is progressively changed to positive as the ionic strength is increased. The binding data were analyzed with an interactive model for two identical sites and site/site interactions with the interaction free energy--RT ln alpha, and the intrinsic binding constant K and cooperativity parameter alpha were computed. Double-label experiments showed that cGMP is strictly competitive with cAMP, and its binding parameters K and alpha are not very different from that for cAMP. Since two binding sites exist for each of the cyclic nucleotides in dimeric CRP and no change in the quaternary structure of the protein is observed on binding the ligands, it is proposed that the cooperativity originates in ligand/ligand interactions. When bound to double-stranded deoxyribonucleic acid (dsDNA), CRP binds cAMP more efficiently, and the cooperativity is positive even in conditions of low ionic strength where it is negative for the free protein. By contrast, cGMP binding properties remained unperturbed in dsDNA-bound CRP. Neither the intrinsic binding constant K nor the cooperativity parameter alpha was found to be very sensitive to changes of pH between 6.0 and 8.0 at 0.2 M ionic strength and 20 degrees C. For these conditions, the intrinsic free energy and entropy of binding of cAMP are delta H degree = -1.7 kcal . mol-1 and delta S degree = 15.6 eu, respectively.

An equilibrium study of the cooperative binding of adenosine cyclic 3',5'-monophosphate and guanosine cyclic 3',5'-monophosphate to the adenosine cyclic 3',5'-monophosphate receptor protein from Escherichia coli.

The binding of nucleoside monophosphates by poly-L-arginine and guanosine monophosphate by poly-L-lysine at low ionic strength and pH 7 consists of two phases. At low values of r (number of bound nucleotides per amino acid residue) the binding behavior can be fitted to the Langmuir isotherm; at high r values the binding is cooperative and accompanied by precipitation of a polyamino acid-nucleotide complex. Three different mathematical approaches were used to describe the binding behavior of the cooperative phase. The results indicate that the magnitude of the parameters for nearest neighbor interaction of bound nucleotides parallels the tendency of self-association of the respective bases. A value of about 2 kcal/mole was determined for the nearest neighbor interaction energy of guanosine 5'-phosphate with poly-L-arginine at two different temperatures, and with poly-L-lysine. Two approaches yield intrinsic binding constants which, depending on the model chosen, correspond to binding by sites with free neighbor sites or to direct interaction of nucleotides with the polyamino acid. The intrinsic binding constants obtained with poly-L-arginine depend upon the nature of the nucleotide base and, as is shown in the case of guanosine 5'-phosphate, upon temperature. The corresponding value for guanosine monophosphate with poly-L-lysine is considerably smaller. It is pointed out that interaction of nucleotides with poly-L-arginine may be controlled by both the different stacking tendencies of the nucleotide bases and by the direct affinities between bases and polyamino acid.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1969.tb00683.x

K. G. Wagner

Papers

On the Interaction of Nucleotides with Basic Polyamino Acids. Cooperative Binding Behavior