On the Use of Strong Patterson Function Signals in Many-Body Molecular Replacement

Navaza, Jorge; Panepucci, Ezequiel; Martin, Carole

doi:10.1107/s0907444997019434

Cited by 19 publications

(15 citation statements)

References 6 publications

(7 reference statements)

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“…Crystals belonged to space group C222 1 with one molecule per asymmetric unit. Molecular replacement (AMORE program [71] ) using data in the 40 to 3.0 resolution range and the HDM2 coordinates from the HDM2/p53(15-29) crystal structure (pdb-code: 1YCR) yielded significant solutions. The correctly positioned search model was refined to 1.9 resolution with the program REFMAC.…”

Section: Methodsmentioning

confidence: 99%

Structure–Activity Studies in a Family of β‐Hairpin Protein Epitope Mimetic Inhibitors of the p53–HDM2 Protein–Protein Interaction

et al. 2006

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Inhibitors of the interaction between the p53 tumor-suppressor protein and its natural human inhibitor HDM2 are attractive as potential anticancer agents. In earlier work we explored designing beta-hairpin peptidomimetics of the alpha-helical epitope on p53 that would bind tightly to the p53-binding site on HDM2. The beta-hairpin is used as a scaffold to display energetically hot residues in an optimal array for interaction with HDM2. The initial lead beta-hairpin mimetic, with a weak inhibitory activity (IC(50)=125 microM), was optimized to afford cyclo-(L-Pro-Phe-Glu-6ClTrp-Leu-Asp-Trp-Glu-Phe-D-Pro) (where 6ClTrp=L-6-chlorotryptophan), which has an affinity almost 1,000 times higher (IC(50)=140 nM). In this work, insights into the origins of this affinity maturation based on structure-activity studies and an X-ray crystal structure of the inhibitor/HDM2(residues 17-125) complex at 1.4 A resolution are described. The crystal structure confirms the beta-hairpin conformation of the bound ligand, and also reveals that a significant component of the affinity increase arises through new aromatic/aromatic stacking interactions between side chains around the hairpin and groups on the surface of HDM2.

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Section: Methodsmentioning

confidence: 99%

Structure–Activity Studies in a Family of β‐Hairpin Protein Epitope Mimetic Inhibitors of the p53–HDM2 Protein–Protein Interaction

et al. 2006

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“…Initial phases for the Lb pro (residues 29–201) crystal form were obtained by molecular replacement with the sLb pro coordinates as a model. Rotation/translation parameters were calculated with 95% of data between 15 and 3.5 Å using the AMoRe package (Navaza, 1994), and the information about the presence of a translational symmetry derived from the strong peak found in the native Patterson at position u = 0.5, v = 0.5, w = 0.225 (Navaza et al ., 1998). Four independent solutions were found that generate the second four by translation.…”

Section: Methodsmentioning

confidence: 99%

Structure of the foot-and-mouth disease virus leader protease: a papain-like fold adapted for self-processing and eIF4G recognition

et al. 1998

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The leader protease of foot-and-mouth disease virus, as well as cleaving itself from the nascent viral polyprotein, disables host cell protein synthesis by specific proteolysis of a cellular protein: the eukaryotic initiation factor 4G (eIF4G). The crystal structure of the leader protease presented here comprises a globular catalytic domain reminiscent of that of cysteine proteases of the papain superfamily, and a flexible C-terminal extension found intruding into the substrate-binding site of an adjacent molecule. Nevertheless, the relative disposition of this extension and the globular domain to each other supports intramolecular self-processing. The different sequences of the two substrates cleaved during viral replication, the viral polyprotein (at LysLeuLys↓GlyAlaGly) and eIF4G (at AsnLeuGly↓ArgThrThr), appear to be recognized by distinct features in a narrow, negatively charged groove traversing the active centre. The structure illustrates how the prototype papain fold has been adapted to the requirements of an RNA virus. Thus, the protein scaffold has been reduced to a minimum core domain, with the active site being modified to increase specificity. Furthermore, surface features have been developed which enable C-terminal self-processing from the viral polyprotein.

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“…The structure of A. fumigatus MnSOD was solved by molecular replacement using the program AMORE (22). The structure of the human MnSOD dimer (PDB ID 1ABM) (4), which shares 45% sequence identity with A.fumigatus MnSOD, was used as a search model.…”

Section: Molecular Replacementmentioning

confidence: 99%

Comparison of the Crystal Structures of the Human Manganese Superoxide Dismutase and the Homologous Aspergillus fumigatus Allergen at 2-Å Resolution

Flückiger¹,

Mittl

Scapozza

et al. 2002

The Journal of Immunology

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Manganese superoxide dismutase (MnSOD) of Aspergillus fumigatus, a fungus involved in many pulmonary complications, has been identified as IgE-binding protein. It has been shown also that MnSODs from other organisms, including human, are recognized by IgE Abs from individuals sensitized to A. fumigatus MnSOD. Comparison of the fungal and the human crystal structure should allow the identification of structural similarities responsible for IgE-mediated cross-reactivity. The three-dimensional structure of A. fumigatus MnSOD has been determined at 2-Å resolution by x-ray diffraction analysis. Crystals belonged to space group P212121 with unit cell dimensions of a = 65.88 Å, b = 98.7 Å, and c = 139.28 Å. The structure was solved by molecular replacement using the structure of the human MnSOD as a search model. The final refined model included four chains of 199–200 amino acids, four manganese ions, and 745 water molecules, with a crystallographic R-factor of 19.4% and a free R-factor of 23.3%. Like MnSODs of other eukaryotic organisms, A. fumigatus MnSOD forms a homotetramer with the manganese ions coordinated by three histidines, one aspartic acid, and one water molecule. The fungal and the human MnSOD share high similarity on the level of both primary and tertiary structure. We identified conserved amino acids that are solvent exposed in the fungal and the human crystal structure and are therefore potentially involved in IgE-mediated cross-reactivity.

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On the Use of Strong Patterson Function Signals in Many-Body Molecular Replacement

Cited by 19 publications

References 6 publications

Structure–Activity Studies in a Family of β‐Hairpin Protein Epitope Mimetic Inhibitors of the p53–HDM2 Protein–Protein Interaction

Structure–Activity Studies in a Family of β‐Hairpin Protein Epitope Mimetic Inhibitors of the p53–HDM2 Protein–Protein Interaction

Structure of the foot-and-mouth disease virus leader protease: a papain-like fold adapted for self-processing and eIF4G recognition

Comparison of the Crystal Structures of the Human Manganese Superoxide Dismutase and the Homologous Aspergillus fumigatus Allergen at 2-Å Resolution

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