Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome

Abstract

We present a new method for the calculation of solvent accessible surface areas at the atomic and residue levels, which we call parameter optimized surfaces (POPS-A and POPS-R ). Atomic and residue areas (the latter simulated with a single sphere centered at the C(alpha)s atom for amino acids and at the P atom for nucleotides) have been optimized versus accurate all-atoms methods. We concentrated on an analytical formula for the approximation of solvent accessibilities. The formula is simple, easily derivable and fast to compute, therefore it is practical for use in molecular dynamics simulations as an approximation to the first solvation shell. The residue based approach POPS-R has been derived as a useful tool for the analysis of large macromolecular assemblies like the ribosome, and is especially suited for use in refinement of low resolution structures. The structures of the 70S, 50S and 30S ribosomes have been analyzed in detail and most of the interactions within the subunits and at their interfaces were clearly identified. Some interesting differences between 30S alone and within the 70S have been highlighted. Owing to the presence of the P-tRNA in the 70S ribosome, localized conformational rearrangements occur within the subunits, exposing Arg and Lys residues to negatively charged binding sites of P-tRNA. POPS-R also allows for estimates of the loss of free energy of solvation upon complex formation, particularly useful in designing new protein-RNA complexes and in suggesting more focused experimental work.

Figure 1

Percentual distribution of absolute atomic and residue SASAs errors with respect to NACS ones for POPS-A (A) and POPS-R (B). In (B) the NACS areas are calculated at atomic level and summed up to residues.

Figure 2

Naccess and POPS-R SASAs buried by the overlap between different components of 30S from the high resolution structure (10). Black and gray bars correspond to the Naccess hydrophobic and hydrophilic SASAs, respectively, while red and pink bars are the corresponding POPS-R SASAs. Cntrl, 3′-M and 3′-m indicate the central, 3′-major and 3′-minor domains, respectively.

Figure 3

Relative contribution of each amino acid of (A) S- and (B) L-proteins to: red bars, total SASA of the isolated amino acids of S- and L-proteins; green bars, total SASA of isolated S- and L-proteins; yellow bars, total SASA buried upon interaction of S- and L-proteins with 16S; blue bars, total SASA buried upon interaction of S- and L-proteins with 23S/5S.

Figure 4

Interface view of the 30S and 50S subunits from the 70S crystallographic structure (12). Yellow, orange and red spheres correspond to residues which, upon 30S and 50S association, bury <37.5 Ų, between 37.5 and 75 Ų, and >75 Ų of SASA, respectively. Green spheres correspond to residues that interact with the A-, E- and P-tRNAs.

Figure 5

Detailed view of the S9 P-tRNA interaction. Only the surface of the nucleotide stretch between G30 and A38 is reported for P-tRNA. Red, dark blue, light blue and yellow surfaces correspond to O, N, C and P atoms, respectively. The purple ribbon corresponds to the tail of S9 of 70S, while the green ribbon corresponds to the tail of 30S’s S9 after superposition with 70S’s S9. The sidechains of Arg128 and of Tyr125 of S9 of 30S are also reported. The purple and green spheres are centered at the C^α of Arg128.