The Trp-cage miniprotein with single-site mutations: Studies of stability and dynamics using molecular dynamics

Molecular dynamics combined with single-site mutations were used to study the stability and dynamics of the Trp-cage miniprotein. It was found that mutations W6G, L7G and P19G cause frequent conformational transitions and significant stability decreases. Their hydrophobic cores are fully hydrated and secondary and tertiary structures destroyed, especially in the case of W6G. Instead, only slight influences are induced by mutations N1G, L2G, Q5G, K8G, D9G, P12G and S20G. Albeit involved in the hydrophobic cluster, Pro12 is not so crucial as the three C-terminal prolines and supports that the Pro/Trp interaction is not essential for the core formation. The other seven mutations (Y3G, I4G, S13G, S14G, R16G, P17G and P18G) also exert observable influences, although not so great as W6G, L7G and P19G, to the Trp-cage stability. The hydrophobic and helix collapses are concomitant in the Trp-cage. Noticeable stability decreases are resulted by destroying the hydrophobic core, or Asp9/Arg16 salt bridge or buried H-bonding interactions. Nonetheless, the Asp9/Arg16 salt-bridge is intrinsic in the Trp-cage miniprotein and not readily affected, even with mutations (not including W6G, D9G and R16G). The roles of each residue (actually its sidechain) and their cooperative interactions were thus evaluated for the stability and dynamics of the Trp-cage miniprotein, which furthers our understanding towards the complex structure and stability of proteins.