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    THẠC SĨ 3D domain swapping: Structural characterizations of domain-swapped dimer proteins FVE and rhodocetin

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  6. 3D domain swapping: Structural characterizations of domain-swapped dimer proteins FVE and rhodocetin

    TABLE OF CONTENTS



    CHAPTER 1: Introduction 1
    3D DOMAIN SWAPPING 2
    Background of 3D domain swapping 2
    3D domain swapping definition 4
    Helpful definitions 6
    History of 3D domain swapping Diphtheria toxin 6
    More than one domain swapping 7
    Examples of 3D domain swapping 9
    Single mutation induce 3D domain swapping 11
    Design of 3D domain-swapped molecule 19
    Human cystatin C dimerizes through 3D domain swapping 22
    Hinge loop role in 3D domain swapping 26
    PROTEIN X-RAY CRYSTALLOGRAPHY 28
    Protein crystallization 29
    Crystal systems and symmetry 29
    X-Ray diffraction and Bragg's Law 30
    Ewald construction 31
    The structure factor 31
    Fourier transform and phase problem 33
    Model building 35
    Refinement 35 AIM AND SCOPE OF THE THESIS 36
    CHAPTER 2: Structural characterizations of fungal immunomodulatory
    protein: Fve
    37
    MATERIALS AND METHODS 39
    Protein purification 39
    Protein crystallization and data collection 40
    Structure solution and refinement 40
    RESULTS AND DISCUSSION 43
    Overall fold 43
    Topology of FNIII fold in Fve 48
    Determinants of the Ig-like fold 51
    Structure-function relationships 56
    Dimerization by 3D domain swapping 57
    CHAPTER 3: Structural characterizations of venom of the Malayan pit
    viper: Rhodocetin
    67
    MATERIALS AND METHODS 69
    Protein purification 69
    Protein crystallization and data collection 69
    Structure solution and refinement 70
    RESULTS AND DISCUSSION 72
    Overall fold 72
    Structure comparison with C-type lectin 76
    Structure-function relationships 80 Dimerization by 3-D domain swapping 84
    CHAPTER 4: Conclusion 88
    Bibliography 93
    Appendix 112

















    SUMMARY

    Fve, a major fruiting body protein from Flammulina velutipes, a mushroom possessing
    immunomodulatory activity, stimulates lymphocyte mitogenesis, suppresses systemic
    anaphylaxis reactions and edema, enhances transcription of IL-2, IFN-γ and TNF-α, and
    hemagglutinates RBCs. It appears to be a lectin with specificity for complex cell surface
    carbohydrates. Fve is a non-covalently linked homodimer containing no Cys, His and Met.
    It shares sequence similarity only to the other Fungal Immunomodulatory Proteins (FIPs)
    LZ-8, Gts, Vvo and Vvl, all of unknown structure. The 1.7 Å structure of Fve solved by
    Single Anomalous Diffraction of NaBr-soaked crystals is novel: each monomer consists
    of an N-terminal α-helix followed by a fibronectin III (FNIII) fold. The FNIII fold is the
    first instance of “pseudo-h-type” topology – a transition between the seven β-stranded s-
    type and the eight β-stranded h-type topologies. The structure suggests that dimerization,
    critical for the activity of FIPs, occurs by 3-D domain swapping of the N-terminal helices
    and is stabilized predominantly by hydrophobic interactions. The structure of Fve is the
    first in this lectin family, and the first of an FNIII domain-containing protein of fungal
    origin.
    Rhodocetin is a unique heterodimer consisting of α and β subunits of 133 and 129
    residues respectively. The molecule, purified from the crude venom of the Malayan pit
    viper, Calloselasma rhodostoma, functions as an inhibitor of collagen induced platelet
    aggregation. Rhodocetin has been shown to have activity only when present as a dimer.
    The dimer is formed without an inter-subunit disulfide bridge as observed with all the other Ca
    2+
    - dependent lectin-like proteins (CLPs). The 1.9 Å resolution structure of
    rhodocetin is determined by molecular replacement. The structure reveals the inter-
    subunit interface which has compensatory interactions for forming the dimer in the
    absence of the disulfide bridge. This is the first structure of a CLP without a disulfide
    connecting the subunits and thus represents a novel molecule which can help to
    understand a new set of protein-protein interactions. Further, unlike other CLPs,
    rhodocetin does not require metal ions for its functional activity. However, like other
    CLPs, rhodocetin also forms the heterodimer by domain swapping, in which the central
    looped region is swapped.

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