title: A 3D structural model of memapsin 2 protease generated from theoretical study.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  The 3D-structure model from our study is informative to guide future molecular biology study about M2 and drug design based on database searching.
authors.affiliation: Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: X Q
authors.initials: XQ
authors.lastname: Huang
authors.forename: H L
authors.initials: HL
authors.lastname: Jiang
authors.forename: X M
authors.initials: XM
authors.lastname: Luo
authors.forename: J K
authors.initials: JK
authors.lastname: Shen
authors.forename: K X
authors.initials: KX
authors.lastname: Chen
authors.forename: R Y
authors.initials: RY
authors.lastname: Ji
authors.forename: Y
authors.initials: Y
authors.lastname: Cao
authors.forename: H
authors.initials: H
authors.lastname: Xue
mesh_terms: D000595:Amino Acid Sequence; D053829:Amyloid Precursor Protein Secretases; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry*; D015195:Drug Design; D010450:Endopeptidases; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
chemical_list: D053829:Amyloid Precursor Protein Secretases; D010450:Endopeptidases; D016282:Aspartic Acid Endopeptidases