MODEL OF HUMAN IGA1 DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING
SOLUTION SCATTERING
Solution Scattering Data Acquistion
1
2
Scattering Type
x-ray
neutron
Radiation/Neutron Source
SRS DARESBURY
ISIS RUTHERFORD
Synchrotron
Y
Y
Beamline Type
2.1
LOQ
Detector Type
QUADRANT DETECTOR
HE-3 ORDELA DETECTOR
Detector Manufacturer Details
Temperature (K)
pH
Numer of Time Frames Used
1
1
Protein Concentration Range (mg/mL)
Sample Buffer
Data Reduction Software
OTOKO
COLETTE
Guiner Mean Radius Of Gyration (nm)
Sigma Mean Radius Of Gyration
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)
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
SCATTERING FITTING, ENERGY MINIMIZATION
INSIGHT II, DISCOVERY 2.9.7, BIOSYM
1
1
THE MODEL OF HUMAN IGA1 WAS BASED
ON SEVERAL IMMUNOGLOBULIN CRYSTAL STRUCTURES FROM THE
PDB. AN IGA1 MONOMER CONTAINS TWEL ...
THE MODEL OF HUMAN IGA1 WAS BASED
ON SEVERAL IMMUNOGLOBULIN CRYSTAL STRUCTURES FROM THE
PDB. AN IGA1 MONOMER CONTAINS TWELVE DOMAINS ON TWO
FOUR-DOMAIN HEAVY CHAINS AND TWO TWO-DOMAIN LIGHT CHAINS.
THE CHAINS ASSOCIATE TO FORM TWO FOUR-DOMAIN FAB
FRAGMENTS AND ONE FOUR-DOMAIN FC FRAGMENT. EACH FAB
FRAGMENT IS JOINED TO THE FC FRAGMENT BY A 23-RESIDUE
PEPTIDE LINKER. THERE ARE SIX DOMAIN TYPES IN IGA1
(VH, CH1, CH2, CH3, VL AND CL), AND A MONOMER CONTAINS
TWO COPIES OF EACH DOMAIN-TYPE. THE SEQUENCES OF THE CH1,
CH2 AND CH3 DOMAINS ARE SPECIFIC TO IGA1.
REFINEMENT WAS CARRIED OUT USING DISCOVER 2.9.7, BIOSYM.
ALSO USED ENERGY MINIMISATION.
THE IGA1 CH1 DOMAIN WAS MODELLED USING THE
CORRESPONDING DOMAIN FROM THE THE MOUSE IGA J539 FAB
STRUCTURE (CODE: 2FBJ) AND THE HUMAN IGG1 TR1.9 FAB
STRUCTURE (CODE: 1VGE) AS TEMPLATES. THE IGA1 CH2 AND CH3
DOMAINS WERE MODELLED USING THE CORRESPONDING
DOMAINS FROM THE HUMAN IGG1 FC STRUCTURE (CODE: 1FC1)
AS TEMPLATES. THE REMAINING DOMAINS IN THE IGA1 MODEL
(VL, CL AND VH) USED THE APPROPRIATE DOMAINS FROM THE
TR1.9 FAB STRUCTURE DIRECTLY. EACH FAB FRAGMENT CONTAINS
A SINGLE COPY OF THE VH, CH1, VL AND CL DOMAINS, AND
THEIR ARRANGEMENT WAS BASED DIRECTLY ON THE TR1.9 FAB
STRUCTURE. IN THE FC STRUCTURE, TWO COPIES OF THE CH2 AND
CH3 DOMAINS WERE USED. THEIR ARRANGEMENT WAS BASED ON
THAT IN THE HUMAN IGG1 FC STRUCTURE (CODE 1FC1) EXCEPT
THAT THE TWO CH2 DOMAINS WERE REORIENTATED AND REMODELLED
SLIGHTLY TO ACCOMMODATE A PROPOSED DISULPHIDE BRIDGING
PATTERN.
THE POSITIONS OF THE FAB FRAGMENTS RELATIVE TO
THE FC FRAGMENT WERE DETERMINED BY AN APPROACH THAT
COMBINED RANDOM HINGE PEPTIDE STRUCTURES PRODUCED BY
MOLECULAR DYNAMICS SIMULATIONS WITH CURVE-FITTING TO
EXPERIMENTAL SOLUTION SCATTERING DATA. A SINGLE
ARRANGEMENT OF THE FAB FRAGMENTS IS PRESENTED, WHICH IS
REPRESENTATIVE OF A FAMILY OF STRUCTURES THAT FIT THE
SCATTERING DATA. IN ADDITION, IGA1 CONTAINS AN 18-RESIDUE
TAILPIECE PEPTIDE AT THE C-TERMINAL OF EACH CH3 DOMAIN.
THE TAILPIECE STRUCTURE PRODUCED BY MOLECULAR DYNAMICS
SIMULATIONS THAT BEST-FITTED THE EXPERIMENTAL DATA IS
SHOWN ON EACH MODEL. MORE DETAILS ON THE MODELLING
STRATEGY ARE CONTAINED IN THE PRIMARY REFERENCE.