Browse by MODEL: Ab initio only

SASDM44 – LAF + P10 nanocomposite (NP added before fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 10 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 10 nm (hydrodynamic diameter) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 29
Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study Molecules 26(16):4864 (2021)
Schroer M, Hu P, Tomasovicova N, Batkova M, Zakutanska K, Wu P, Kopcansky P
RgGuinier 22.3 nm
Dmax 70.0 nm

SASDM54 – LAF + P30 nanocomposite (NP added before fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 30 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 30 nm (hydrodynamic diameter) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 29
Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study Molecules 26(16):4864 (2021)
Schroer M, Hu P, Tomasovicova N, Batkova M, Zakutanska K, Wu P, Kopcansky P
RgGuinier 22.5 nm
Dmax 95.0 nm

SASDM64 – LAF + P20 nanocomposite (NP added before fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 29
Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study Molecules 26(16):4864 (2021)
Schroer M, Hu P, Tomasovicova N, Batkova M, Zakutanska K, Wu P, Kopcansky P
RgGuinier 23.6 nm
Dmax 90.0 nm

SASDM74 – LAF + P20 nanocomposite (NP added after fibrilization)

lysozyme amyloid fibrilFe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) experimental SAS data
DAMMIN model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; nominal diameter 20 nm (hydrodynamic diameter) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Sep 2
Dependence of the Nanoscale Composite Morphology of Fe3O4 Nanoparticle-Infused Lysozyme Amyloid Fibrils on Timing of Infusion: A Combined SAXS and AFM Study Molecules 26(16):4864 (2021)
Schroer M, Hu P, Tomasovicova N, Batkova M, Zakutanska K, Wu P, Kopcansky P
RgGuinier 31.0 nm
Dmax 75.0 nm

SASDLR2 – PfMDH L-lactate dehydrogenase bound to inhibitor 2a

L-lactate dehydrogenase experimental SAS data
DAMMIF model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.4 nm
Dmax 10.5 nm
VolumePorod 244 nm3

SASDLS2 – PfMDH L-lactate dehydrogenase bound to inhibitor 6a

L-lactate dehydrogenase experimental SAS data
DAMMIF model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.6 nm
Dmax 11.4 nm
VolumePorod 223 nm3

SASDJW3 – YraP from Acinetobacter baumannii full-length, minus signal-peptide and acyl anchoring cysteine

BON domain protein experimental SAS data
DAMMIF model
Sample: BON domain protein decamer, 229 kDa Acinetobacter baumannii protein
Buffer: 20 mM Tris, 150 mM NaCl, 0.03 % NaN3, 5.0 % glycerol, pH: 7.8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Apr 11
BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function. mBio :e0148021 (2021)
Grinter R, Morris FC, Dunstan RA, Leung PM, Kropp A, Belousoff M, Gunasinghe SD, Scott NE, Beckham S, Peleg AY, Greening C, Li J, Heinz E, Lithgow T
RgGuinier 4.7 nm
Dmax 16.4 nm
VolumePorod 546 nm3

SASDJX3 – YraP from Acinetobacter baumannii full-length, minus signal-peptide and 27 N-terminal amino acids

BON domain protein experimental SAS data
DAMMIF model
Sample: BON domain protein monomer, 20 kDa Acinetobacter baumannii protein
Buffer: 20 mM Tris HCl, 150 nM NaCl, 0.02 % NaN3, 5% glycerol, pH: 7.8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Apr 11
BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function. mBio :e0148021 (2021)
Grinter R, Morris FC, Dunstan RA, Leung PM, Kropp A, Belousoff M, Gunasinghe SD, Scott NE, Beckham S, Peleg AY, Greening C, Li J, Heinz E, Lithgow T
RgGuinier 3.1 nm
Dmax 10.8 nm
VolumePorod 49 nm3

SASDKX6 – PSK, an antimicrobial peptide from Chrysomya megacephala

PSK, an antimicrobial peptide from Chrysomya megacephala experimental SAS data
DAMMIF model
Sample: PSK, an antimicrobial peptide from Chrysomya megacephala monomer, 10 kDa Chrysomya megacephala protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Dec 7
Crystal and solution structures of a novel antimicrobial peptide from Chrysomya megacephala. Acta Crystallogr D Struct Biol 77(Pt 7):894-903 (2021)
Xiao C, Xiao Z, Hu C, Lu J, Cui L, Zhang Y, Dai Y, Zhang Q, Wang S, Liu W
RgGuinier 1.6 nm
Dmax 5.0 nm
VolumePorod 18 nm3

SASDLB5 – CMT mutant i50del of human myelin protein P2

Myelin P2 disease mutant I50del experimental SAS data
DAMMIN model
Sample: Myelin P2 disease mutant I50del monomer, 15 kDa protein
Buffer: 20 mM HEPES, 300 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Jul 22
Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants. FEBS J (2021)
Uusitalo M, Klenow MB, Laulumaa S, Blakeley MP, Simonsen AC, Ruskamo S, Kursula P
RgGuinier 1.5 nm
Dmax 4.0 nm
VolumePorod 17 nm3