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Analytical Ultracentrifugation:

Analytical Ultracentrifugation Mücke N et al.: Molecular and Biophysical Characterization of Assembly-Starter Units of Human Vimentin. J Mol Biol . 2004 Jun 25;340(1):97-114.

Outline:

21.01.2008 Cindy Horwedel 2 Outline Analytical Ultracentrifugation Applications Design and principles of an analytical ultracentrifuge Sedimentation velocity vs. sedimentation equilibrium experiments Fundamental mathematics Data analyses Vimentin Characterization of Assembly-Starter Units of Human Vimentin References

Analytical Ultracentrifugation – Applications:

21.01.2008 Cindy Horwedel 3 Analytical Ultracentrifugation – Applications determine sample purity characterize assembly and disassembly mechanisms of biomolecular complexes determine subunit stoichiometries detect and characterize macromolecular conformational changes measure equilibrium constants and thermodynamic parameters for self- and hetero-associating systems  characterize the solution-state behavior of macromolecules under various conditions

Analytical Ultracentrifugation – Applications:

21.01.2008 Cindy Horwedel 4 Analytical Ultracentrifugation – Applications determine sample purity characterize assembly and disassembly mechanisms of biomolecular complexes determine subunit stoichiometries detect and characterize macromolecular conformational changes measure equilibrium constants and thermodynamic parameters for self- and hetero-associating systems  thermodynamic and hydrodynamic information

Analytical Ultracentrifugation – Design:

21.01.2008 Cindy Horwedel 5 Analytical Ultracentrifugation – Design analytical ultracentrifuge = preparative ultracentrifuge + optical detection system  measure sample concentration inside the centrifuge cell during or after sedimentation centrifugation parameters and data acquisition under computer control  experiments lasting many days performed with minimal operator intervention

Analytical Ultracentrifugation – Design:

21.01.2008 Cindy Horwedel 6 Analytical Ultracentrifugation – Design http://www-bioc.rice.edu/bios576/AU/AU%20Page_files/image022.jpg

Analytical Ultracentrifugation – Design: Optical systems:

21.01.2008 Cindy Horwedel 7 Analytical Ultracentrifugation – Design: Optical systems Absorbance optical system:  measurement of sample concentration at wavelengths from 200 to 800 nm  detection of macromolecules containing strong chromophores Rayleigh interference optical system:  measurement of sample concentration based on refractive index changes  analyze macromolecules lacking intense chromophores (eg, polysaccharides) and samples that contain strongly absorbing buffer components (eg, ATP/GTP, DTToxidized)

Analytical Ultracentrifugation – Sedimentation velocity experiments:

21.01.2008 Cindy Horwedel 8 Analytical Ultracentrifugation – Sedimentation velocity experiments Meniscus of solvent Sedimentation front Meniscus of solution Plateau conc. Cell radius Concentration of solute Modified from http://www.kolloidanalytik.de/uz/sed/uzsedhr.gif

Analytical Ultracentrifugation – Sedimentation velocity experiments:

21.01.2008 Cindy Horwedel 9 Spherical particle with radius R moves with constant velocity v in a centrifuge at the radial distance r: Analytical Ultracentrifugation – Sedimentation velocity experiments

Analytical Ultracentrifugation – Sedimentation velocity experiments:

21.01.2008 Cindy Horwedel 10 Spherical particle moves with constant velocity v in a centrifuge at the radial distance r:  Possibility to determine molecular mass of a spherical molecule Possibility to determine shape of a molecule using the friction factor of an idealized spherical particle compared to the measured friction factor  axial ratio of oblate or prolate elipsoide Analytical Ultracentrifugation – Sedimentation velocity experiments

Analytical Ultracentrifugation – Sedimentation velocity experiments:

21.01.2008 Cindy Horwedel 11 Analytical Ultracentrifugation – Sedimentation velocity experiments Svedberg equation:  influenced by density and viscosity of solvent  standard solvent (water, 20°C): s 20,w Boundary spreading: Flux J

Analytical Ultracentrifugation – Sedimentation velocity experiments:

21.01.2008 Cindy Horwedel 12 Analytical Ultracentrifugation – Sedimentation velocity experiments Hydrodynamic information Experimentally determined parameters: Sedimentation coefficient s Diffusion constant D or friction factor f Molecular mass M Estimation of the molecule’s shape in solution High rotor speeds  sedimentation dominates diffusion

Analytical Ultracentrifugation – Data analyses: sedimentation velocity:

21.01.2008 Cindy Horwedel 13 Analytical Ultracentrifugation – Data analyses: sedimentation velocity plot natural logarithm of boundary midpoint versus time  single-point boundary analyses  slope of straight line yields sedimentation coefficient s time derivative (DCDT) method (Stafford)  subtract different scans  convert the boundaries into apparent differential distribution of s , g( s *) and plot g( s *) versus s *

Analytical Ultracentrifugation – Data analyses: sedimentation velocity:

21.01.2008 Cindy Horwedel 14 Analytical Ultracentrifugation – Data analyses: sedimentation velocity time derivative (DCDT) method (Stafford)  subtract different scans http://www.bbri.org/faculty/stafford/dcdt/dcdt.html

Analytical Ultracentrifugation – Data analyses: sedimentation velocity:

21.01.2008 Cindy Horwedel 15 Analytical Ultracentrifugation – Data analyses: sedimentation velocity time derivative (DCDT) method  convert boundaries into distribution of s http://www.bbri.org/faculty/stafford/dcdt/dcdt.html

Analytical Ultracentrifugation – Data analyses: sedimentation velocity:

21.01.2008 Cindy Horwedel 16 Analytical Ultracentrifugation – Data analyses: sedimentation velocity time derivative (DCDT) method  recalculate to obtain g( s *)  area under the peak equals plateau concentration http://www.bbri.org/faculty/stafford/dcdt/dcdt.html

Analytical Ultracentrifugation – Sedimentation equilibrium experiments:

21.01.2008 Cindy Horwedel 17 Cell radius Intensity Diffusion Sedimentation Analytical Ultracentrifugation – Sedimentation equilibrium experiments Slower rotor speeds  balance between sedimentation and diffusion forces  no net transport  no influence of shape factors Determination of M: http://www.kolloidanalytik.de/uz/equil/hequil.pdf

Analytical Ultracentrifugation – Sedimentation equilibrium experiments:

21.01.2008 Cindy Horwedel 18 Analytical Ultracentrifugation – Sedimentation equilibrium experiments Thermodynamic information Experimentally determined parameters: Molecular mass M Solution assembly state Thermodynamic parameters like the equilibrium constant K  calculation of the free energy of the association reaction Other thermodynamic parameters

Analytical Ultracentrifugation – Data analyses: sedimentation equilibrium:

21.01.2008 Cindy Horwedel 19 Analytical Ultracentrifugation – Data analyses: sedimentation equilibrium Graphical data analysis methods Plot ln(c) versus r 2  straight line with slope proportional to M: Alternative for more complex systems:  direct fitting of sedimentation equilibrium concentration gradients to mathematical functions

Analytical Ultracentrifugation – Examples of Applications:

21.01.2008 Cindy Horwedel 20 Analytical Ultracentrifugation – Examples of Applications Sedimentation velocity Biomolecular Shape Biomolecular Conformational Changes Assembly and Disassembly of Biomolecular Complexes Molecular Mass and Subunit Stoichiometry Equilibrium Constants for Self-Associating Systems Sedimentation equilibrium Molecular Mass and Subunit Stoichiometry Equilibrium Constants for Hetero-associating Systems Equilibrium Constants for Self-Associating System

Vimentin:

21.01.2008 Cindy Horwedel 21 Vimentin Intermediate filament of eukaryotic cells Structure: - monomer with central α-helical domain, capped with non-helical head/tail  two monemers: coiled-coil dimer  further oligomerisation - α-helical sequences with "hydrophobic seal" on the surface of the helix  allows coiling - homopolymeric filaments

Vimentin:

21.01.2008 Cindy Horwedel 22 Vimentin Intermediate filament of eukaryotic cells Function: anchoring the position of organelles in the cytosole important for the flexibility of cells and cell integrity stabilization of cytoskeletal interaction transport of LDL inside the cell no enzymatic activity (unlike actin and tubulin)

Vimentin:

21.01.2008 Cindy Horwedel 23 Vimentin Structure of a dimer of human vimentin: Formation of tetramers in vitro Head Rod Tail Herrmann H, Nat Rev Mol Cell Biol, 2007

Characterization of Assembly-Starter Units of Human Vimentin:

21.01.2008 Cindy Horwedel 24 Characterization of Assembly-Starter Units of Human Vimentin Structure of a dimer of human wt vimentin: Study of the assembly of wt, headless, tailless vimentin and vimentin rod Head Rod Tail Herrmann H, Nat Rev Mol Cell Biol, 2007

Characterization of Assembly-Starter Units of Human Vimentin: Aims and Questions:

21.01.2008 Cindy Horwedel 25 Characterization of Assembly-Starter Units of Human Vimentin: Aims and Questions Investigation of complex assembly of wt vimentin in low salt and physiological buffer  Investigation of the homogeneity of the vimentin complexes Quantify influence of truncation of the non- α -helical head and tail domains  Determination of the association constants of wt and headless vimentin  Determination of s-values  Modeling of the shape of different vimentins

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 26 Characterization of Assembly-Starter Units of Human Vimentin: Results Investigation of complex assembly of wt vimentin in low salt and physiological buffer  analytical ultracentrifugation Mücke N, J Mol Biol . 2004

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 27 Characterization of Assembly-Starter Units of Human Vimentin: Results Investigation of complex assembly of wt vimentin in low salt and physiological buffer  by sedimentation equilibrium runs  concentration dependent deviation  non-ideal sedimentation behavior caused by rod domain rather than by the head  extrapolation of values for molecular mass to zero concentration Mücke N, J Mol Biol . 2004

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 28 Characterization of Assembly-Starter Units of Human Vimentin: Results Investigation of complex assembly of wt vimentin in low salt and physiological buffer  extrapolation of values for molecular mass to zero concentration Mücke N, J Mol Biol . 2004

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 29 Characterization of Assembly-Starter Units of Human Vimentin: Results Investigation of complex assembly of vimentin in low salt and physiological buffer  extrapolation of values for molecular mass to zero concentration  wt vimentin: 2.1x10 5  tetrameric complex  headless vimentin: 1.0x10 5  dimeric complex  at higher ionic strength: tetramers Results confirmed using a non-linear global fit program

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 30 Characterization of Assembly-Starter Units of Human Vimentin: Results Determination of the association constants of wt and headless vimentin  increase in the ionic strength results in a shift of the equilibrium towards higher oligomers of wt vimentin  association of tetramers to octamers  small effect of salt addition of headless vimentin  association of dimers to tetramers

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 31 Characterization of Assembly-Starter Units of Human Vimentin: Results Determination of s-values  by sedimentation velocity runs using low protein concentrations (avoid non-ideality)  pH dependent sedimentation coefficients of wt and tailless vimentin  pH dependent changes in molecule size, shape or stiffness  wt: good agreement with data obtained from sedimentation equilibrium runs  tailless: second species with higher s value (<10%)  headless vimentin and vimentin rod: sedimentation as homogenous species

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 32 Characterization of Assembly-Starter Units of Human Vimentin: Results Determination of s-values  pH dependent sedimentation coefficients of wt and tailless vimentin  wt: homogenous species  tailless: second species with higher s value (<10%)  headless vimentin and vimentin rod: sedimentation as homogenous species Mücke N, J Mol Biol . 2004

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 33 Characterization of Assembly-Starter Units of Human Vimentin: Results Modeling of the shape of different vimentins  using SEDNTERP  electron microscopy: elongated, rod-like shape  modeling as prolate ellipsoids  wt: 73 nm length, 3.3 nm width  tailless: 53 nm length  rod (dimeric): 49 nm length  headless (dimeric): 59 nm length Herrmann H, Nat Rev Mol Cell Biol, 2007

Characterization of Assembly-Starter Units of Human Vimentin: Results:

21.01.2008 Cindy Horwedel 34 Characterization of Assembly-Starter Units of Human Vimentin: Results Modeling of the shape of different vimentins  at higher pH values: increasing lengths  correlation with lower s values  description of vimentin oligomers as prolate ellipsoids Results obtained from analytical ultracentrifugation and other methods  similar complex sizes determined

References:

21.01.2008 Cindy Horwedel 35 References Mücke N et al.: Molecular and Biophysical Characterization of Assembly-Starter Units of Human Vimentin. J Mol Biol . 2004 Jun 25;340(1):97-114. Cole JL, Hansen JC: Analytical Ultracentrifugation as a Contemporary Biomolecular Research Tool. J Biomol Tech. 1999 Dec; 10(4) (Epub) Lebowitz J et al.: Modern analytical ultracentrifugation in protein science: a tutorial review. Protein Sci. 2002 Sep;11(9):2067-79. Goldman RD et al.: The function of intermediate filaments in cell shape and cytoskeletal integrity. J Cell Biol 1996; 134(4):pp. 971-83. http://128.220.22.46/Research/fuge.html http://www.bbri.org/faculty/stafford/dcdt/dcdt.html http://www.beckmancoulter.com/resourcecenter/labresources/sia/ ds820.asp http://www.nature.com/nrm/journal/v8/n7/images/nrm2197-f2.jpg Herrmann H et al.: Intermediate filaments: from cell architecture to nanomechanics. Nat Rev Mol Cell Biol 2007 Jul; 8(7): 562-573

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