Physical Methods to Characterize Proteins. Molecular weight Physical properties of key interest...
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Transcript of Physical Methods to Characterize Proteins. Molecular weight Physical properties of key interest...
Physical Methods to Characterize Proteins
Molecular weight
Physical properties of key interest
Oligomerization state
Structure
Interactors
Transport Processes
1. Transport in an electric field (electrophoresis)
2. Transport in a gravitational field (centrifugation)
3. Transport by partitioning between mobile and stationary phases (gel exclusion chromatography)
Requires a matrix (either agarose or polyacrylamide) to minimize convective effects due to heating and Brownian motion. Mobility is also affected by partioning with the stationary phase (matrix). Provides relative molecular weights determined by comparison to standards.
Requires a centrifuge to generate the large gravitational forces required for protein transport. Provides an absolute molecular weight and informs on the oligomerization state for stable complexes.
Requires a suitably-sized partitioning matrix for the solid phase. Provides relative molecular weights determined by comparison to standards.
Gel Electrophoresis
u = A(q/f)
Electrophoretic mobility (u) is proportional to its net charge (q), specifically the ratio of its net surface charge to accessible surface area, and inversely proportional to its frictional coefficient (f), a function of solvent viscosity and protein geometry. The constant of proportionality (A) is unique to each protein.
Mobility can be measured to the cathode or anode depending on protein charge and pH.
Free radicals are provided by ammonium persulfate. TEMED (tetramethylenediamine) is included to stabilize the free radicals resulting from decomposition of the ammonium persulfate. Ratio of acrylamide to bisacrylamide is held constant. Pore size is expressed as percent (w/v) acrylamide and designated %T.
Disc (Discontinuous) Gel Electrophoresis
Leading anion: Cl-
Trailing ion: glycine
Changes in electrophoretic mobility in the focusing zone
SDS PAGE
SDS: Sodium Dodecyl Sulfate (Lauryl sulfate)
SDS binds protein with a constant ratio of 1.4 gm SDS/gm protein.
Calibration plot for a series of molecular weight standards vs. %T
Gel Filtration/Size Exclusion Chromatography
Comparison of size resolution by gel filtration (left) and PAGE (right)
Band spreading as a function of elution position
Calibration plots for molecular weight standards resolved on different media
Mass Spectrometry
Basic mass spectrometer design
Detection methods
Time of Flight (TOF)- Accuracy to 0.1%
Quadrupole mass analyzers- Accuracy to 0.01%
FT ion cyclotron- Accuracy to 0.001%
Ionization methods
Matrix-assisted Laser desorption/ionization (MALDI)
Electrospray ionization (ESI)
Mass determination of intact proteins
Tandem mass spectrometry
Tandem mass spectrometry analysis by collision-induced dissociation (CID)
Types of MS Data
SILAC-Stable Isotope Labeling by Amino Acids