Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose.
Cyanovirin-N (CVN) is a highly potent anti-HIV carbohydrate-binding agent that establishes its microbicide activity through interaction with mannose-rich glycoprotein gp120 on the virion surface. The m4-CVN and P51G-m4-CVN mutants represent simple models for studying the high-affinity binding site, B(M). A recently determined 1.35 A high-resolution structure of P51G-m4-CVN provided details on the di-mannose binding mechanism, and suggested that the Arg-76 and Glu-41 residues are critical components of high mannose specificity and affinity. We performed molecular-dynamics simulations in solution and a crystal environment to study the role of Arg-76. Network analysis and clustering were used to characterize the dynamics of Arg-76. The results of our explicit solvent solution and crystal simulations showed a significant correlation with conformations of Arg-76 proposed from x-ray crystallographic studies. However, the crystal simulation showed that the crystal environment strongly biases conformational sampling of the Arg-76 residue. The solution simulations demonstrated no conformational preferences for Arg-76, which would support its critical role as the residue that locks the ligand in the bound state. Instead, a comparative analysis of trajectories from >50 ns of simulation for two mutants revealed the existence of a very stable eight-hydrogen-bond network between the di-mannose ligand and predominantly main-chain atoms. This network may play a key role in the specific recognition and strong binding of mannose oligomers in CVN and its homologs.
Vorontsov
Ivan I
II
Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA.
Miyashita
Osamu
O
D019380:Anti-HIV Agents / Q000494:pharmacology; D001120:Arginine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics*; D001665:Binding Sites; D001703:Biophysics / Q000379:methods; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics*; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods*; D018698:Glutamic Acid / Q000737:chemistry; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D008358:Mannose / Q000737:chemistry*; D008958:Models, Molecular; D009154:Mutation; D011487:Protein Conformation
D019380:Anti-HIV Agents; D001426:Bacterial Proteins; D002352:Carrier Proteins; D015699:HIV Envelope Protein gp120; C107733:cyanovirin N; D018698:Glutamic Acid; D001120:Arginine; D008358:Mannose