FOUR MODELS OF HUMAN FACTOR H DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING
SOLUTION SCATTERING
Solution Scattering Data Acquistion
1
2
3
4
Scattering Type
x-ray
neutron
neutron
modelling
Radiation/Neutron Source
SRS BEAMLINE 2.1
ILL
ISIS
Synchrotron
Y
N
N
Beamline Type
PULSED NEUTRON
Detector Type
500-CHANNEL QUADRANT
AREA
AREA (TIME-OF-FLIGHT)
Detector Manufacturer Details
Temperature (K)
288
pH
Numer of Time Frames Used
10
Protein Concentration Range (mg/mL)
0.7 - 14
0.4 - 9.6
3.7, 6.1
Sample Buffer
TRIS
PBS IN 99.9% D2O
PBS IN 99.9% D2O
Data Reduction Software
OTOKO
DETEC, RNILS, SPOLLY
COLLETTE
Guiner Mean Radius Of Gyration (nm)
11.1
11.3
11.7
Sigma Mean Radius Of Gyration
0.4
0.4
0.5
R(XS-1) Mean Cross Sectional Radii (nm)
4.4
3.9
R(XS-1) Sigma Mean Cross Sectional Radii
0.2
0.2
R(XS-2) Mean Cross Sectional Radii (nm)
1.7
1.51
R(XS-2) Sigma Mean Cross Sectional Radii
0.1
0.06
P(R) Protein Length (nm)
40
37 - 39
40
Solution Scattering Data Analysis and Model Fitting
Method
Software
Software Authors
Starting Model
Conformers, Number Calculated
Conformers, Number Submitted
Conformers, Selection Criteria
Best Representative Conformer
Other Details
CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, SCTPL5, GNOM
MSI
PDB CODE 1HFI, 1HCC, 1HFH, 1VCC
2010
4
THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND RXS-2 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 1.4 NM-1.
1
HOMOLOGY MODELS WERE BUILT FOR THE 17 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. TRIANTENNARY CO ...
HOMOLOGY MODELS WERE BUILT FOR THE 17 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. TRIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES (MAN3GLCNAC6GAL3FUC3NEUNAC1) WERE ADDED TO EACH OF THE N-LINKED GLYCOSYLATION SITES. A LIBRARY OF LINKER PEPTIDE CONFORMATIONS WAS USED IN DOMAIN MODELLING CONSTRAINED BY THE SOLUTION SCATTERING FITS. MODELLING WITH THE SCATTERING DATA WAS ALSO CARRIED OUT BY ROTATIONAL SEARCH METHODS. THE X-RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED MODELS.
