Table S1. Theoretical and apparent molecular weights of the proteins and protein complexes used for ITC analysis
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1 Table S1. Theoretical and apparent molecular weights of the proteins and protein complexes used for ITC analysis Sample Theoretical molecular weight (without glycosylation) Apparent molecular weight R-2 ECD/VEGF complex 199 kda 212 kda R-2 ECD 84 kda 98 kda R-2 D23/VEGF complex 79 kda 86 kda R-2 D23 24 kda 22 kda VEGF 31 kda 33 kda
2 Table S2. X-ray data collection and refinement statistics VEGF-A/VEGFR-2 D23 VEGF-E/VEGFR-2 D23 Data collection Radiation source SLS Villigen (CH), beamline PX06SA Wavelength (Å) Detector PILATUS Space group P P Cell dimensions a, b, c (Å) 81.0, 81.0, , 79.9, 340.0,, 90, 90, , 90, 120 Resolution range (Å) ( )* ( )* R merge (%) 5.7 (76.0) 9.4 (78.0) I/ 10.4 (1.3) 11.3 (2.2) Completeness (%) 95.9 (94.1) 99.3 (97.7) Redundancy Refinement Resolution (Å) No. reflections R work /R free 0.244/ /0.276 No. atoms Average B factors (Å 2 ) Rms deviations from ideal values Bond lengths (Å) Angles ( ) Ramachandran plot Favoured regions 87.9% 91.6% Outliers 0.7% (2 residues) 1.5% (4 residues) * Values in parentheses correspond to the highest resolution shell.
3 Absorption (280nm) SEC profiles kda 500 MWS 400 VEGF 300 R-2 D R-2 D23/VEGF 100 R-2 ECD 0 R-2 ECD/VEGF Elution volume (ml) Figure S1. Molecular weight determination of VEGF and VEGFR-2 proteins and protein complexes by Superdex S200 size exclusion chromatography A calibration curve with molecular weight standards (MWS) was recorded and the molecular weights of the proteins and protein complexes was determined from the retention times (see Supplemental Table 1). The VEGFR-2 constructs VEGFR-2 D23 (R-2 D23) and VEGFR-2 ECD (R-2 ECD) eluted as monomeric proteins whereas the molecular weights of the complexes corresponded to two receptor molecules and one covalent VEGF dimer.
4 Figure S2A. Thermodynamic profiles of VEGFR-2 D23 (R-2 D23) with VEGF In all cases the interaction of VEGF with VEGFR-2 D23 is accompanied with a large unfavourable change in enthalpy. Binding is strongly dominated by entropic contribution which overcompensates the enthalpic contribution.
5 Figure S2B. Thermodynamic profiles of the full length VEGFR-2 ECD (R-2 ECD) with with VEGF. In all cases the interaction of VEGF with the VEGFR-2 ECD was accompanied with a large unfavourable change in enthalpy. Binding is strongly dominated by entropic contribution which overcompensates the enthalpic contribution.
6 Figure S2C. Changes in the thermodynamic profile of VEGF binding to either VEGFR-2 D23 or the full length VEGFR-2 ECD
7 Figure S3. Interfaces in VEGF-A/VEGFR-2 D23 complex interface VEGF-A: (7.3%) VEGFR-2: (4.3%) total (100.0%) (100.0%) 1 A:TYR 21[ OH ] 3.45 R:GLY 196[ O ] 2 A:TYR 25[ OH ] 3.61 R:TYR 165[ O ] 3 A:ASN 62[ ND2] 3.36 R:TYR 165[ O ] 4 A:ASN 62[ ND2] 2.80 R:TYR 194[ O ] 5 A:GLU 64[ N ] 3.30 R:ASN 253[ OD1] 6 A:GLU 64[ OE1] 3.67 R:ASN 253[ N ] 7 A:ASP 63[ OD1] 2.90 R:ASN 253[ ND2] 8 A:GLU 64[ OE1] 2.67 R:LYS 286[ NZ ] Salt bridges 1 A:GLU 64[ OE2] 3.71 R:LYS 286[ NZ ] 2 A:GLU 64[ OE1] 2.67 R:LYS 286[ NZ ] interface VEGF-A: (10.7%) VEGFR-2: (5.8%) total (100.0%) (100.0%) 1 A:ILE 43[ O ] 2.82 R:ILE 256[ N ] 2 A:GLN 89[ OE1] 3.62 R:TYR 137[ OH ] No salt bridges found Summary: Interface: = 1120 Å 2 in total Buried surface area Site 1 = 930 Å 2 Buried surface area Site 2 = 1310 Å 2 Solvent-accessible area at the interfaces: = 927 Å 2 in total = 1312 Å 2 in total VEGF-A = 1189 Å 2 in total VEGFR = 1051 Å 2 in total and salt bridges: = 11 in total
8 Interfaces in VEGF-E/VEGFR-2 D23 complex interface VEGF-E: (9.5%) VEGFR-2: (4.7%) total (100.0%) (100.0%) 1 R:ASN 253[ ND2] 2.78 A:ASP 63[ OD1] 2 R:LYS 286[ NZ ] 2.82 A:GLU 64[ OE1] 3 R:SER 193[ O ] 3.44 A:ASP 63[ N ] 4 R:TYR 194[ O ] 2.90 A:ASN 62[ N ] 5 R:ALA 195[ O ] 2.82 A:ASN 62[ ND2] 6 R:VAL 216[ O ] 3.12 A:ASN 62[ ND2] 7 R:ASN 253[ OD1] 3.27 A:GLU 64[ N ] Salt bridges 1 R:LYS 286[ NZ ] 2.82 A:GLU 64[ OE1] 2 R:LYS 286[ NZ ] 3.48 A:GLU 64[ OE2] interface VEGF-E: (9.7%) VEGFR-2: (5.0%) total (100.0%) (100.0%) 1 R:ILE 256[ N ] 3.41 A:THR 43[ O ] 2 R:TYR 137[ OH ] 2.52 A:ASN 89[ OD1] 3 R:ILE 256[ O ] 3.02 A:THR 43[ OG1] 4 R:ASN 253[ OD1] 3.09 A:ARG 46[ NH2] 5 R:GLY 196[ O ] 3.15 A:ASN 48[ ND2] 6 R:VAL 216[ O ] 2.89 A:ASN 48[ ND2] No salt bridges found Summary: Interface: = 1388 Å 2 Buried surface area Site 1 = 1110 Å 2 Buried surface area Site 2 = 1160 Å 2 Solvent-accessible area at the interfaces: = 1110 Å 2 in total = 1162 Å 2 in total VEGF-E = 1216 Å 2 in total VEGFR = 1056 Å 2 in total and salt bridges: = 14 in total
9 Interfaces in VEGF-C/VEGFR-2 D23 complex (2X1X.pdb) interface VEGF-C: (10.8%) VEGFR-2: (6.3%) total (100.0%) (100.0%) 1 R:TYR 165[ OH ] 2.95 E:ASP 123[ OD1] 2 R:ARG 164[ NH1] 2.56 E:ASP 123[ OD2] 3 R:ASN 253[ ND2] 2.97 E:SER 168[ OG ] 4 R:ASN 253[ ND2] 3.12 E:GLU 169[ O ] 5 R:GLN 132[ OE1] 3.72 E:THR 116[ OG1] 6 R:TYR 194[ O ] 2.71 E:ASN 167[ ND2] 7 R:ASN 253[ OD1] 3.18 E:GLU 169[ N ] Salt bridges 1 R:ARG 164[ NH1] 3.88 E:ASP 123[ OD1] 2 R:ARG 164[ NE ] 3.97 E:ASP 123[ OD2] 3 R:ARG 164[ NH1] 2.56 E:ASP 123[ OD2] 4 R:LYS 286[ NZ ] 3.77 E:GLU 169[ OE1] 5 R:LYS 286[ NZ ] 3.59 E:GLU 169[ OE2] interface VEGF-C: (9.1%) VEGFR-2: (5.0%) total (100.0%) (100.0%) 1 R:ILE 256[ N ] 2.88 E:THR 148[ O ] 2 R:ILE 256[ O ] 2.64 E:THR 148[ OG1] No salt bridges found Summary: Interface area: = 1388 Å 2 Buried surface area Site 1 = 1530 Å 2 Buried surface area Site 2 = 1250 Å 2 Solvent-accessible area at the interfaces: = 1526 Å 2 in total = 1249 Å 2 in total VEGF-C = 1449 Å 2 in total VEGFR = 1326 Å 2 in total and salt bridges: = 13 in total
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