This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.106.093419v1 92/5/1659    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Polydoridis, S. Articles by Archontis, G. Search for Related Content PubMed PubMed Citation Articles by Polydoridis, S. Articles by Archontis, G.

Recognition of Ribonuclease A by 3'–5'-Pyrophosphate-Linked Dinucleotide Inhibitors: A Molecular Dynamics/Continuum Electrostatics Analysis

Savvas Polydoridis ^*, Demetres D. Leonidas , Nikos G. Oikonomakos   and Georgios Archontis ^* 

^* Department of Physics, University of Cyprus, Nicosia, Cyprus; and Institute of Organic and Pharmaceutical Chemistry, Institute of Biological Research and Biotechnology, the National Hellenic Research Foundation, Athens, Greece

Correspondence: Address reprint requests to G. Archontis, E-mail: archonti{at}ucy.ac.cy.

The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic effect in pathological conditions associated with these proteins. The most potent low molecular weight inhibitor of RNase reported to date is the compound 5'-phospho-2'-deoxyuridine-3-pyrophosphate (P5)-adenosine-3-phosphate (pdUppA-3'-p). The 3',5'-pyrophosphate group of this compound increases its affinity and introduces structural features which seem to be unique in pyrophosphate-containing ligands bound to RNase A, such as the adoption of a syn conformation by the adenosine base at RNase subsite B₂ and the placement of the 5'-ß-phosphate of the adenylate (instead of the -phosphate) at subsite P₁ where the phosphodiester bond cleavage occurs. In this work, we study by multi-ns molecular dynamics simulations the structural properties of RNase A complexes with the ligand pdUppA-3'-p and the related weaker inhibitor dUppA, which lacks the 3' and 5' terminal phosphate groups of pdUppA-3'-p. The simulations show that the adenylate 5'-ß-phosphate binding position and the adenosine syn orientation constitute robust structural features in both complexes, stabilized by persistent interactions with specific active-site residues of subsites P₁ and B₂. The simulation structures are used in conjunction with a continuum-electrostatics (Poisson-Boltzmann) model, to evaluate the relative binding affinity of the two complexes. The computed relative affinity of pdUppA-3'-p varies between –7.9 kcal/mol and –2.8 kcal/mol for a range of protein/ligand dielectric constants (_p) 2–20, in good agreement with the experimental value (–3.6 kcal/mol); the agreement becomes exact with _p = 8. The success of the continuum-electrostatics model suggests that the differences in affinity of the two ligands originate mainly from electrostatic interactions. A residue decomposition of the electrostatic free energies shows that the terminal phosphate groups of pdUppA-3'-p make increased interactions with residues Lys⁷ and Lys⁶⁶ of the more remote sites P₂ and P₀, and His¹¹⁹ of site P₁.