A new adaptive grid-size algorithm for the simulation of sedimentation velocity profiles in analytical ultracentrifugation

Brown, Patrick H.; Schuck, Peter

doi:10.1016/j.cpc.2007.08.012

Cited by 84 publications

(95 citation statements)

References 63 publications

(187 reference statements)

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“…The procedure reports, as a final result, the average distribution of all statistically indiscernible distributions. [26,31] The distribution of sedimentation coefficients c(s) is a robust result, which is over-determined because the apparent coefficient s* can be obtained from a single snapshot, in which diffusion is neglected. Details of the shape of the c(s) distribution can be deconvoluted from diffusion; that is, they are correlated with the frictional ratios.…”

Section: Introductionmentioning

confidence: 99%

“…The determination of the sedimentation, diffusion, and hydrodynamic frictional coefficients [26] in H 2 O and D 2 O enables the calculation of the anhydrous molar volume of the surfactant-encapsulated SWCNTs, which then allows the linear packing density of the surfactant on the nanotube surface to be determined. Based on these previous observations, the hydrodynamic properties of various SWCNT-surfactant systems have been compared in this study to aid the understanding of the interaction of SWCNTs and surfactant molecules in solution, which is of utmost importance for the design of novel, potent SWCNT dispersants.…”

Section: Introductionmentioning

confidence: 99%

“…The sedimentation coefficient, s, diffusion, D, and the hydrodynamic frictional coefficient, f (specifically the frictional ratio f/f 0 ) are obtained by fitting the experimental cA C H T U N G T R E N N U N G (r, t) profiles to the multicomponent Lamm equation by using appropriate programs such as SEDFIT [26,31,32] or Ultrascan.…”

Section: Introductionmentioning

confidence: 99%

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Determination of the Surfactant Density on SWCNTs by Analytical Ultracentrifugation

Backes

Karabudak

Schmidt

et al. 2010

Chemistry A European J

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We report on the extensive characterization of single-walled carbon nanotubes (SWCNTs) dispersed in a variety of surfactants, such as sodium dodecyl benzene sulfonate (SDBS), sodium cholate (SC), and three synthesized perylene-based surfactants, by using differential sedimentation in H(2)O and D(2)O. Multidimensional evaluation of the absorption profiles over radius, wavelength, and time allows the determination of the anhydrous specific volumes of the SWCNT-surfactant complexes as well as the concentration of the surfactant reservoir in free micelles with very slow sedimentation coefficients (<1 Svedberg). Among the perylene bisimide surfactants, the smallest derivative is densely adsorbed on the nanotube backbone with an anhydrous specific volume significantly above that of SC or SDBS. Bulky Newkome dendritic groups on one or both ends of the perylene moiety gradually reduce the adsorption density, in accord with the absolute adsorption between 0.66 and 1.7 mmol surfactant per gram SWCNTs. Furthermore, hydrodynamic analysis reveals that SDBS favors the "tails-on" configuration. The distribution of sedimentation coefficients of SWCNTs prepared by high-pressure carbon monoxide decomposition (HiPco) is broader and shifted to faster sedimentation than those prepared by using cobalt-molybdenum catalysis (CoMoCAT), which reflects the polydispersity in diameter and length.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Determination of the Surfactant Density on SWCNTs by Analytical Ultracentrifugation

Backes

Karabudak

Schmidt

et al. 2010

Chemistry A European J

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“…The structures were refined using REFMAC (36) and PHENIX (37) software packages. The AUC experiments were performed using a Beckman Coulter XL-A centrifuge, and the data were analyzed using SEDFIT and SEDPHAT software packages (38). Amyloid fibril formation of various SAA peptides and purified proteins was detected by thioflavin T fluorescence and Congo red absorption using a Synergy H1 hybrid reader (BioTek).…”

Section: Methodsmentioning

confidence: 99%

Structural mechanism of serum amyloid A-mediated inflammatory amyloidosis

Zhu

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

159

272

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Significance Serum amyloid A (SAA) is a major serum acute-phase protein and a cause of secondary amyloidosis, which impacts ∼1% of patients with chronic inflammation such as rheumatoid arthritis and neoplastic diseases. The lack of structural information has hampered our understanding of SAA-mediated amyloidosis and the development of effective therapies. Here we report a crystal structure of human SAA1.1 as a prototypic member of the family. SAA1.1 exists as a hexamer with subunits displaying a unique four-helix bundle fold. We further defined binding sites for heparin and high-density lipoprotein, identified major amyloidogenic epitopes, and visualized SAA-mediated protofibril formation using electron microscopy. These studies provide mechanistic insights into amyloidogenic conformational transition of SAA.

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“…The cells were scanned at 276 nm as frequently as possible, using a radial increment of 0.003 cm. At the end of the experiment, the data were analyzed by Sedfit (35).…”

Section: Analytical Ultracentrifugationmentioning

confidence: 99%

The Small Heat-Shock Proteins HSPB2 and HSPB3 Form Well-defined Heterooligomers in a Unique 3 to 1 Subunit Ratio

Engelsman

Boros

Dankers

et al. 2009

Journal of Molecular Biology

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Various mammalian small heat-shock proteins (sHSPs) can interact with one another to form large polydisperse assemblies. In muscle cells, HSPB2/MKBP (myotonic dystrophy protein kinase-binding protein) and HSPB3 have been shown to form an independent complex. To date, the biochemical properties of this complex have not been thoroughly characterized. In this study, we show that recombinant HSPB2 and HSPB3 can be successfully purified from E.coli cells co-expressing both proteins. Nanoelectrospray ionization mass spectrometry and sedimentation velocity analytical ultracentrifugation analysis showed that HSPB2/B3 forms a series of well defined hetero-oligomers, consisting of 4,8,12,16,20 and 24 subunits, each maintaining a strict 3:1 HSPB2:HSPB3 subunit ratio. These complexes are thermally stable up to 40 °C, as determined by far-UV circular dichroism spectroscopy. Surprisingly, HSPB2/B3 exerted a poor chaperone-like and thermoprotective activity, which is likely related to the low surface hydrophobicity, as revealed by its interaction with the hydrophobic probe 1-anilino-8-naphthalenesulfonic acid. Co-immunoprecipitation experiments demonstrated that the HSPB2/B3 oligomer cannot interact with HSP20, HSP27 or αB-crystallin, whereas the homomeric form of HSPB2, thus not in complex with HSPB3, could efficiently associate with HSP20. Taken altogether, this study brings evidence that despite the high sequence homology within the sHSP family, the biochemical properties of the HSPB2/B3 complex are distinctly different from other sHSPs, indicating that the HSPB2/B3 assembly likely possesses other cellular functions than its family members. Various mammalian small heat shock proteins (sHSPs) can interact with one another to form large polydisperse assemblies. In muscle cells, HSPB2/MKBP (myotonic dystrophy protein kinase-binding protein) and HSPB3 have been shown to form an independent complex. To date, the biochemical properties of this complex have not been thoroughly characterized. In this study, we show that recombinant HSPB2 and HSPB3 can be successfully purified from E.coli cells co-expressing both proteins. Nanoelectrospray ionization mass spectrometry and sedimentation velocity analytical ultracentrifugation analysis showed that HSPB2/B3 forms a series of well defined hetero-oligomers, consisting of 4, 8, 12, 16, 20 and 24 subunits, each maintains a strict 3:1 HSPB2:HSPB3 subunit ratio. Analyzing the thermal stability of the HSPB2/B3 assembly by far-UV circular dichroism spectroscopy revealed subtle structural changes, occurring slightly above 40 °C, and an unfolding curve with an inflection point at approximately 56 °C. Furthermore, HSPB2/B3 exerted poor chaperone-like and thermoprotective activity, which is likely related to the low surface hydrophobicity, as revealed by its interaction with the hydrophobic probe 1-anilino-8-naphthalenesulfonic acid. Finally, coimmunoprecipitation experiments demonstrated that the HSPB2/B3 oligomer does not interact with HSP20, HSP27 or αB-crystallin. However, HSPB2 that ...

show abstract

A new adaptive grid-size algorithm for the simulation of sedimentation velocity profiles in analytical ultracentrifugation

Cited by 84 publications

References 63 publications

Determination of the Surfactant Density on SWCNTs by Analytical Ultracentrifugation

Determination of the Surfactant Density on SWCNTs by Analytical Ultracentrifugation

Structural mechanism of serum amyloid A-mediated inflammatory amyloidosis

The Small Heat-Shock Proteins HSPB2 and HSPB3 Form Well-defined Heterooligomers in a Unique 3 to 1 Subunit Ratio

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