Keywords: Dimer, Enzyme, Ribonuclease A, Allosterism, Amino Terminal Sequence, Article, Carboxy Terminal Sequence, Cattle, Crystallography, Hydrogen Bond, Molecular Dynamics, Nonhuman, Pancreas, Protein Domain, Protein Structure, Site Directed Mutagenesis, Animals, Computer Simulation, Dimerization, Hydrogen Bonding, Macromolecular Substances, Models, Protein Conformation, Tertiary, Pancreatic, Bos Taurus, Bovinae,
Affiliations: *** IBB - CNR ***
Dipto. di Scienze Farmaceutiche, Università di Salerno, Fisciano, Italy
Dipartimento di Chimica, Univ. Studi Napoli Federico II, Naples, Italy
Ist. di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Naples, Italy
Dept. of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY, United States
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Dynamic properties of the N-terminal swapped dimer of ribonuclease
Bovine pancreatic ribonuclease (RNase A) forms two 3-dimensional domain-swapped dimers with different quaternary structures. One dimer is characterized by the swapping of the C-terminal region (C-Dimer) and presents a rather loose structure. The other dimer (N-Dimer) exhibits a very compact structure with exchange of the N-terminal helix. Here we report the results of a molecular dynamics/essential dynamics (MD/ED) study carried out on the N-Dimer. This investigation, which represents the first MD/ED analysis on a three-dimensional domain-swapped enzyme, provides information on the dynamic properties of the active site residues as well as on the global motions of the dinner subunits. In particular, the analysis of the flexibility of the active site residues agrees well with recent crystallographic and site-directed mutagenesis studies on monomeric RNase A, thus indicating that domain swapping does not affect the dynamics of the active sites. A slight but significant rearrangement of N-Dimer quaternary structure, favored by the formation of additional hydrogen bonds at subunit interface, has been observed during the MD simulation. The analysis of collective movements reveals that each subunit of the dimer retains the functional breathing motion observed for RNase A. Interestingly, the breathing motion of the two subunits is dynamically coupled, as they open and close in phase. These correlated motions indicate the presence of active site intercommunications in this dimer. On these bases, we propose a speculative mechanism that may explain negative cooperativity in systems preserving structural symmetry during the allosteric transitions.
Dynamic properties of the N-terminal swapped dimer of ribonuclease