App Note I May 17, 2017

List of protein hydrodynamic diameters DH

ProteinMolecular weightDH measured with
switchSENSE® (i)
Dh calculated from
PDB file (ii)
PDB codeStructure
anti-human Fab fragment050 kDa06.6 nm07.2 nm3WD5

anti-human IgG150 kDa12.7 nm11.2 nm1IGT

anti-IgG Affibody®014 kDa03.9 nm03.9 nm2B88

anhydrase I
029 kDa04.9 nm04.9 nm2CAB

CD64031 kDa06.7 nm05.7 nm4ZNE

EGFR071 kDa07.1 nm07.8 nm1NQL

Erythropoetin021 kDa04.7 nm04.6 nm1BUY

GFP-Trap® (nanobody)013 kDa03.9 nm03.9 nm3OGO

Glutathion-S-Transferase026 kDa04.7 nm04.8 nm1B8X

Glycosylceramidase056 kDa06.4 nm06.2 nm3RIL

Her2 (Met1-Thr652)070 kDa07.6 nm07.7 nm1N8Z

HIV Env protein500 kDa11.0 nm11.5 nm4NCO

Human serum albumin069 kDa04.2 nm-1AO6

Neutravidin060 kDa07.4 nm06.1 nm1VYO

p38 kinase041.5 kDa05.0 nm05.8 nm1W84

Pim-1031.5 kDa05.2 nm05.2 nm3C4E

Protein kinase A040 kDa05.5 nm05.6 nm1Q8U

Pyruvate kinase M2058 kDa06.9 nm06.4 nm1T5A

Sting dimer056 kDa06.5 nm06.6 nm4F5D

Sting monomer028 kDa05.1 nm04.9 nm4F5E

TNFα017.5 kDa04.4 nm04.4 nm3WD5

Ubiquitin008.5 kDa03.2 nm03.4 nm1UBQ

(i) Experimental protein diameters are analyzed from switching dynamics measurements with standard 48 bp DNA nanolevers (length = 16 nm) using the drift-diffusion ‘Lollipop’ model described in J. Phys. Chem. B 118, 597 (2014).

(ii) Theoretical calculations of protein diameters from PDB files are performed with the HydroPro algorithm [Garcia de la Torre et al. Biophys. J. 78:179, (2000)], that calculates an effective hydrodynamic diameter from atomic coordinates using a hydrodynamic bead-shell model. Note that crystal structures may not always reflect the native protein structure in solution (especially for large proteins with several domains connected by flexible linkers).