Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.

ABSTRACT: Bovine pancreatic ribonuclease (RNase A) forms two three-dimensional (3D) domain swapped dimers. Crystallographic investigations have revealed that these dimers display completely different quaternary structures: one dimer (N-dimer), which presents the swapping of the N-terminal helix, is characterized by a compact structure, whereas the other (C-dimer), which is stabilized by the exchange of the C-terminal end, shows a rather loose assembly of the two subunits. The dynamic properties of monomeric RNase A and of the N-dimer have been extensively characterized. Here, we report a molecular dynamics investigation carried out on the C-dimer. This computational experiment indicates that the quaternary structure of the C-dimer undergoes large fluctuations. These motions do not perturb the proper

SUBMITTER: Merlino A 

PROVIDER: S-EPMC1305252 | biostudies-literature | 2005 Mar

REPOSITORIES: biostudies-literature