A 3D structural model of memapsin 2 protease generated from theoretical study
Abstract
Aim: To build a 3D structural model of memapsin 2 (M2) protease for theoretical study and drug design.
Methods: Structural alignment was performed based on multiple and pairwise sequence alignment of three templates. After the initial model was generated, energy minimization was completed by applying molecular mechanics method. Molecular dynamics (MD) technique was used to do further structural optimization.
Results: The 3D structural model of memapsin 2 was constructed. The model is reasonable according to several validation criteria. The active-site motifs of M2 are structurally supported by a beta-sheet rich domain and linked together with this domain through alpha helices. Tyr132 contained in beta-hairpin is a general characteristic of aspartic protease. The Calpha atom superimposing result is a direct verification that M2 is structurally unique but still belongs to the aspartic protease superfamily.
Conclusion: The 3D-structure model from our study is informative to guide future molecular biology study about M2 and drug design based on database searching.
Keywords:
Methods: Structural alignment was performed based on multiple and pairwise sequence alignment of three templates. After the initial model was generated, energy minimization was completed by applying molecular mechanics method. Molecular dynamics (MD) technique was used to do further structural optimization.
Results: The 3D structural model of memapsin 2 was constructed. The model is reasonable according to several validation criteria. The active-site motifs of M2 are structurally supported by a beta-sheet rich domain and linked together with this domain through alpha helices. Tyr132 contained in beta-hairpin is a general characteristic of aspartic protease. The Calpha atom superimposing result is a direct verification that M2 is structurally unique but still belongs to the aspartic protease superfamily.
Conclusion: The 3D-structure model from our study is informative to guide future molecular biology study about M2 and drug design based on database searching.