Biochemical and biophysical characterization of natural polyreactivity in antibodies

. Author manuscript; available in PMC: 2024 Feb 10.

Published in final edited form as: Cell Rep. 2023 Oct 5;42(10):113190. doi: 10.1016/j.celrep.2023.113190

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains

E. coli BL21(DE3)pLysS	Laboratory of E.J. Adams	N/A
E. coli DH5α	Laboratory of E.J. Adams	N/A

Chemicals, peptides, and recombinant proteins

StockOptions Salt Kit	Hampton Research	Cat# HR2-245
StockOptions pH	Hampton Research	Cat# HR2-941
NeXtal Stock PEG 3,000	Molecular Dimensions (previously QIAGEN)	Cat# MD2-100-8
NeXtal Stock PEG 3,350	Molecular Dimensions (previously QIAGEN)	Cat# MD2-100-9
NeXtal Stock PEG 4,000	Molecular Dimensions (previously QIAGEN)	Cat# MD2-100-11
NeXtal Stock PEG 5,000MME	Molecular Dimensions (previously QIAGEN)	Cat# MD2-100-19
Sf-900 II SFM	GIBCO	Cat# 10902104
Ultra-low IgG FBS	Invitrogen	Cat# 16250078
FBS Superior	MERCK, Biochrom	Cat# S 0615
Insect-XPRESS Protein-free Insect Cell Medium with L-Gln	Lonza	Cat# 12-730F
E. coli biotin ligase BirA	Laboratory of E.J. Adams	N/A
Expi Expression System Kit	Thermo Fisher	Cat# A14635
Biotin	SIGMA-ALDRICH	Cat# B4501
Calf thymus DNA	Life Technologies	Cat# 15633019
Human insulin	Fitzgerald	Cat# 30AI51
LPS from E.coli	Millipore-Sigma	Cat# L2630
Flagellin from S. typhiumurium	InvivoGen	Cat# TLRL-STFLA
Cardiolipin	Millipore-Sigma	Cat# C0563
Albumin from human serum, low endotoxin	Millipore-Sigma	Cat# A5843
KLH, endotoxin-free	Millipore-Sigma	Cat# H8283
Lysozyme from chicken egg white	Millipore-Sigma	Cat# SAE0152
50nt ssDNA	IDT	ATACCTTGCAGAAATCGAGGCCGT TCGTTAATTCCTGTTGCATTCGTACC
Biotinylated 25 nt s DNA	IDT	ATACCTTGCAGAAATCGAGGCCGTT
Goat anti-human IgG HRP	Southern Biotech	Cat# 2040-05; RRID: AB_2795644
Super AquaBlue ELISA Substrate	Thermo Fisher (eBioscience)	Cat# 00-4203-56

Critical commercial assays

Nickel-nitrilotriacetic acid (Ni-NTA) resin	QIAGEN	Cat# 30250
Superdex S200	(GE Healthcare)	Cat# 17517501
Blitz Biolayer Interferometry instrument (Forte Bio and Octet K2)	PALL ForteBio	N/A
Streptavidin biosensor tips	PALL ForteBio	Cat# 18-5020
Amicon Ultra-4 Centrifugal Filter Units	Millipore Sigma	Cat# UFC803024
ELISA plate washer	BioTek	N/A
ELISA plate reader	BioTek	N/A

Deposited data

338E6 Fab structure	This paper	PDB ID: 8FZO
43G10 Fab structure	This paper	PDB ID: 8FZP
2G02 Fab structure	This paper	PDB ID: 8G1B
3B03 Fab structure	This paper	PDB ID: 8G1C
4C05 Fab structure	This paper	PDB ID: 8G19

Experimental models: Cell lines

S. frugiperda: Sf9 cell line	Laboratory of E.J. Adams	CLS Cat# 604328/p700_Sf9, RRID: CVCL_0549
T. ni: High Five cell line	Laboratory of E.J. Adams	CCLV Cat# CCLV-RIE 0350, RRID: CVCL_C190
Expi293	Thermo Fisher	Cat# A14635

Recombinant DNA

All mouse Fab clones	Laboratory of A. Bendelac	N/A
All human Fab clones	Laboratory of P. Wilson	N/A
Humanized Fab scaffold	Laboratory of A. Kossiakoff	N/A
Insect cell expression vector pACgp67A	Laboratory of E.J. Adams	N/A
E. coli expression vector pET28a	Laboratory of E.J. Adams	N/A
BestBac 2.0 Δ v-cath/chiA Linearized Baculovirus DNA	Expression Systems	Cat# 91-002
Human ubiquitin	Laboratory of R. Keenan	N/A

Software and algorithms

Prism (v5)	GraphPad	http://www.graphpad.com
CCP4 (v7.0.032)	Winn et al., 2011	http://www.ccp4.ac.uk
Phenix (v1.11.1-2575)	Adams et al., 2010	http://www.phenix-online.org
Coot (v0.8.7, part of CCP4 package)	Emsley and Cowtan, 2004	http://www.ccp4.ac.uk
Pymol (v1.7.6.6)	PyMOL	https://www.pymol.org
Phaser (part of CCP4 package)	McCoy et al., 2007	www.ccp4.ac.uk/html/phaser.html
PDBePISA	Krissinel & Henrick 2007⁴⁷	http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver
iMosflm (7.2.2)	Battyeetal. 2011⁴⁸	https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver740/introduction.html
BLItzPro (1.1.0.25)	PALL ForteBio	N/A
VMD (1.9.3)	Humphrey et al., 1996⁴⁹	www.ks.uiuc.edu/Research/vmd/
MDtraj (1.9.4)	McGibbon et al., 2015⁵⁰	https://www.mdtraj.org/
PyEmma (2.5.7)	Scherer et al., 2015⁵¹	http://emma-project.org/