Wu Xiaomin

Publications (10) View all

• Article: Identifying the Intermediates during the Folding/Unfolding of Protein GB1 with MD Simulations

  Xiaomin Wu, Gang Yang, Lijun Zhou
  Theoretical Chemistry Accounts 05/2012; 131(5):1299. · 2.16 Impact Factor
• Article: Molecular dynamics studies of β-hairpin folding with the presence of the sodium ion.

  Xiaomin Wu, Gang Yang, Yuangang Zu, Lijun Zhou
  [show abstract] [hide abstract]
  ABSTRACT: Metal ions are ubiquitous in protein systems and play a significant role during their folding processes. Nineteen independent structures were determined for the Na(+)/β-hairpin interacting systems, and their folding pathways are different. (i) For Na(S47), the turn is rapidly shaped with the help of Na(+) and acts as the folding nucleus for the rest regions. Two intermediate states are observed and the resulted structure is the most folded. (ii) For Na(B41), Na(B52), Na(B54), Na(S55) and Na(B56), the inclusive Na(+) ions are anchored by β-strands. The local structures around the Na(+) ions and the turn regions fold simultaneously and serve as two independent folding nuclei. (iii) The other systems have no folding nuclei and correspond to low-folded structures. Long-range electrostatic interactions contribute a lot to the folding, especially from the four negatively charged residues (Glu42, Asp46, Asp47 and Glu56). The initial positions of the Na(+) ions are largely responsible for the different folding behaviors. The interactions with sidechain- rather than backbone-O atoms generally lead to more compact structures. Another factor affecting the folding is whether the O atoms are associated with native H-bonds, and those involved show decreased affinities to metal ions. The addition of water solvent does not induce obvious folding and conformational transitions to the Na(+)/β-hairpin interacting systems.
  Computational biology and chemistry 03/2012; 38:1-9. · 1.37 Impact Factor
• Article: Molecular Dynamics Studies on the β-hairpin Folding with the Pressence of the Sodium Ion

  Xiaomin Wu, Gang Yang, Yuangang Zu, Yujie Fu, Lijun Zhou
  Comput. Biol. Chem. 03/2012;
• Article: Molecular Dynamics Characterizations of the Trp-cage Folding Mechanisms: In the Absence and Presence of Water Solvents

  Xiaomin Wu, Gang Yang, Yuangang Zu, Yujie Fu, Lijun Zhou, Xiaohui Yuan
  Mol. Simulat. 02/2012; 38(2):161-171.
• Article: The Trp-cage Miniprotein with Single-site Mutation: Studies of Stability and Dynamics Using Molecular Dynamics

  Xiaomin Wu, Gang Yang, Yuangang Zu, Yujie Fu, Xiaohui Yuan
  Comput. Theor. Chem. 10/2011; 973(1-3):1-8.