Ribonucleotide Reductase (RNR) is an enzyme present in all cellular organisms in charge of reducing ribonucleotides diphosphates (NDP’s) to 2-deoxyribonucleotides (dNDP’s). Its function is to maintain balanced pools of deoxynucleotide triphosphates (dNTP) for proper DNA synthesis. It’s mainly active during the S phase of the cell, being involved in DNA replication and repair. Human ribonucleotide reductase (hRR) is a main mark in cancer therapies, drugs such as Gemcitabine used for treatment of pancreatic cancer are direct targets of this enzyme.<br/>hRR can catalyze four different reactions which are the reductions of ADP, UDP, CDP and GDP. To attain its goal, it has developed a very well-tuned allosteric regulation system. This system is managed from subunit R1 of the enzyme which contains three different sites; activity, allosteric and catalytic site. The allosteric site binds dNTP effectors such as ATP, dATP, dGTP and dTTP. Although, each effector presents activity for all four substrates, the level of activity within them can vary by Kcat/Km &gt;1000 fold. Therefore, each effector drives specificity for certain substrates and this will be a result of the interactions of the effector/substrate pair with loop 2. Loop 2 connects the catalytic site with the allosteric site and adopts different geometries according to the effector/substrate pair.<br/>Numerous experimental studies have been performed on this enzyme, nonetheless studying it at a computational level can help decipher the functional interactions and loop dynamics that gives place to the allosteric mechanism. In the Roitberg group we use AMBER 16 GPU package to perform molecular dynamics (MD) simulations and undergo a variety of computational studies. MD calculations performed to hRR with different effector/substrate pairs have demonstrated that loop 2 adopts different conformations with different substrates and the same effector. Additionally, the loop 2 conformation with only the effector is similar to the conformation with the effector/cognate substrate pair. Moreover, for dTTP/GDP and dGTP/ADP (both cognate substrates) loop 2 conformation is the same, regardless of the effector. The main differences between substrate interactions with loop 2 are given by the non-covalent interactions with the bases. However, an interesting interaction between R628 and the oxygen of the substrate phosphates has been only observed in the case of dTTP/GDP (cognate substrate).

Understanding allosteric regulation of human ribonucleotide reductase through computational studies

255th National Meeting (2018)

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