Micro-Nano Technology for Genomics and Proteomics BioMEMs - Ozkan

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

245

Screening Molecule

Library

Technology

Reference

anti-FVIII mab ESH8

ESH8 binding peptides identified by

SPOT

[567]

phage display; peptide scan of the

C2 domain of blood coagulation

factor VIII

anti-CD30 mabs Ber-H2, Ki-2, Ki-4,

peptide scans of the extracellular

SPOT

[114]

R4-4

domain of CD30 and substitutional

analyses of selected antibody

binding peptides

Antibody Paratope Mapping

thyroglobulin; lysozyme; angiotensin

peptide scans of the variable regions of

SPOT

[290]

II

the anti-thyroglobulin mab Tg10,

anti-lysozyme antibody HyHEL-5,

and anti-angiotensin II mab 4D8

hen egg-white lysozyme; anti-idiotypic

peptide scan of the variable regions of

SPOT

[291]

mab AI-10 (anti-thyroglobulin mab

anti-lysozyme antibody HyHEL-5

Tg10)

and anti-thyroglobulin mab Tg10

CD4

peptide scan of the variable regions of

SPOT

[374]

anti-CD4 mab ST40

anti-idiotypic mab AI-10

peptide scan of the variable regions of

SPOT

[292]

(anti-thyroglobulin mab Tg10)

anti-thyroglobulin mab Tg10

CD4

alanine scans of 3 peptides derived

SPOT

[432]

from the CDRs of anti-CD4 mab

ST40

angiotensin II

peptide scan of the variable domain of

SPOT

[90]

anti-angiotensin II mab 4D8

Review article describing the application of peptide arrays to identify critical

SPOT

[293]

paratope residues for antigen binding and the identification of antigen binding

peptides thereof

CD4

alanine substitution scan of peptides

SPOT

[38]

from the anti-CD4 Fab 13B8.2

paratope

Protein-Protein Interactions

Protein-Protein Interactions in General

procine transferrin (3 different

peptide scan of TfbA of Actinobacillus

SPOT

[531]

detection methods: (i)

pleuropneumoniae

immunologically, (ii) 59Fe-loaded

transferring, (iii) biotinylated

transferrin and streptavidin-alkaline

phosphatase)

35S-Met-labeled protein extract from

peptide scans of the TNFR-R55

SPOT

[2]

Jurkat cells containing the novel

cytoplasmic domain

WD-repeat protein FAN

calmodulin

peptide scans of the cytoplasmic

SPOT

[125]

domains of C-CAM1 and C-CAM2

(rat) and BGP (mouse) and Bgp

(man)

anti-IL-10 mab; anti-TNFα mabs;

peptide scans of IL-10, TNFα, 55-kDa

SPOT

[444]

TNFα

TNFα receptor

S100C (EF-hand-type Ca2+ binding

peptide scan of the N-terminal region

SPOT

[505]

protein)

of annexin I

246

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

soluble interleukin 6 receptor

peptide scans of IL-6 and IL-6R;

SPOT

[582]

(sIL-6R); interleukin 6 (IL-6)

substitutional analyses of IL-6

derived peptides

human transferrin (huTf)

peptide scan of the

SPOT

[461]

transferrin-binding protein B

(TbpB) from Neisseria

meningitidis (strain M982)

125I-calmodulin

phosphorylated and

SPOT

[126]

unphosphorylated peptides derived

from cell-cell adhesion molecule

(C-CAM) isoforms S and L and

single site substitution analogs

porcine protein kinase C β and

partial peptide scans of the C-CAM

γ 32P-ATP

isoforms S and L

32P-labeled CaBP1 and CaBP2;

peptide scan of the erd2 receptor

SPOT

[234]

peptides LEKDEL and

CYDDQKAVKDEL as

competitors

dimeric hepatitis B virus (HBV) core

partial peptide scan of the HBV core

SPOT

[266]

protein variants c1-149 and c1-124

protein 1–161

plasma-derived factor VIII (FVIII)

partial peptide scan of von

SPOT

[379]

and recombinant FVIII

Willebrand factor (vWF)

interleukin 10 (IL-10); interleukin 10

peptide scans of IL-10 and IL-10Rα

SPOT

[446]

receptor a (IL-10Rα); 3 anti-IL-10

mabs; 1 anti-IL-10Rα mab

cytosolic domains of the translocase

peptide scans of the cytochrome c

SPOT

[62]

of the outer mitochondrial

oxidase subunit IV (CoxIV) and

membrane (Tom) 20, 22, and 70 (S.

phosphate carrier (Pi C) preproteins

cerevisiae)

(S. cerevisiae)

α−actinin

peptide scan of zyxin

SPOT

[120]

p24 (HIV-1)

peptide scan of p24 (HIV-1)

SPOT

[205]

tubulin; γ -tubulin

peptide scans of α-, β-, and γ -tubulin

SPOT

[331]

125I vascular endothelial growth

peptide scans of VEGF receptor II;

SPOT

[417]

factor (VEGF)

substitutional analysis of a selected

α−actinin

peptide

peptide scan of zyxin

SPOT

[460]

N-lobe, C-lobe, and complete

peptide scans of human transferrin

SPOT

[463]

transferrin binding protein B

(hTf)

(TbpB) from Neisseria

meningitidis; TbpB from

Moraxella catarrhalis

CD4; anti-gp17 polyclonal antibody

peptide scan of gp17; alanine walks

SPOT

[28]

of selected peptides

cytoplasmic and core domain of

peptide scan of the phosphate carrier

SPOT

[63]

mitochondrial import receptor

protein

Tom70 from Saccaromyces

cerevisiae

cardiac troponin C

scans of cardiac troponin I

SPOT

[146]

α2−macroglobulin

peptide scan of β2-microglobulin

SPOT

[181]

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

247

Screening Molecule

Library

Technology

Reference

secretory immunogobulin A (SIgA)

peptide scans of the SIgA and SC

SPOT

[194]

and scretory component (SC)

binding domain of Streptococcus

pneumoniae surface protein SpsA;

truncation analyses of selected

peptides

ActA (L. monocytogenes) and

peptide scans of p21-Arc and ActA

SPOT

[423]

p21-Arc

125I-PHF43 fragment of τ protein

partial peptide scan of τ protein

SPOT

[574]

calmodulin

partial peptide scan of human

SPOT

[55]

Ca2+ -calmodulin-dependent

protein kinase II β chain (CaM

kinase II); peptide scan of the rat

N-STOP protein

anti-α-bungarotoxin scFv C12;

peptide scan of α-bungarotoxin

SPOT

[58]

nicotinic acetylcholine receptor

nAchR

cpSRP, cpSRP54 and cpSRP43 from

peptide scans of cpSRP54 and

SPOT

[185]

Arabidopsis thaliana (cpSRP =

preLhcb1 from pea

chloroplast signal recognition

particle)

8 kDa dynein light chain (LC8)

(partial) peptide scans of cellular

SPOT

[478]

(nNOS, Kid-1 renal transcription

factor, Bim, DNA cytosine methyl

transferase,

microtubule-associated protein,

dynein heavy chain, Drosophila

swallow, GKAP) and viral target

proteins from Mokola virus,

rabies virus and ASF virus; N-

and C-terminal extensions of the

consensus binding motif KSTQT

Lyn

partial peptide scan of the

SPOT

[543]

erythropoietin receptor (EPOR)

Practical protocols for the mapping of protein-protein interactions using

SPOT

[184]

peptide arrays prepared by SPOT synthesis

Puumala virus nucleocapsid protein

partial peptide scan of the

SPOT

[315]

(PUUV-N)

C-terminal 243 amino acids of the

human apoptosis enhancer Daxx

human islet amyloid polypeptide

peptide scan of hIAPP

SPOT

[358]

(hIAPP) fused with maltose

binding protein (MBP)

human fibrinogen

alanine substitution scan and

SPOT

[499]

complete L-amino acid

248

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

regulatory subunit RII from protein

partial peptide scans of 10 different A

SPOT

[10]

kinase A

kinase anchoring proteins (AKAPs);

complete L-amino acid

substitutional analysis of an

AKAP-specific “position-dependent

scoring matrix” (PDSM) consensus

sequence derived from the AKAP

peptide scans

human plasminogen

peptide scan of pneumococcal

SPOT

[35]

α-enolase (Eno) and length analysis

of the human plasminogen biding

sequence

regulatory subunits RIα and RIIα of

L-substitutional analysis of a 27-mer

SPOT

[68]

protein kinase A

peptide derived from the dual

specific A kinase anchoring protein

2 (D-AKAP2)

E. coli YoeB-GST fusion protein

peptide scans of E. coli YefM and

SPOT

[81]

single site substitution analogs of a

selected peptide

PSK (a protein-bound polysaccharide

peptide scan of chicken gizzard

SPOT

[165]

from Basidiomycetes)

regulatory light chain (RLC) of

smooth muscle myosin

125I-human soluble urokinase-type

peptide scan of uPAR

SPOT

[317]

plasminogen activator receptor

suPAR

Cdc42-maltose binding protein (MBP)

peptide scan of the C-terminal half of

SPOT

[353]

fusion protein in the presence of a

IQGAP1

non-hydrlyzable GTP analog

(GMPPMP)

125I vascular endothelial growth factor

complete D-amino acid substitutional

SPOT

[418]

(VEGF)

analyses of VEGF receptor

II-derived peptides

N-terminal clathrin domain

partial peptide scans of auxilin

SPOT

[491]

(clathrin-TD); α-ear domain of

AP-2

soluble cytosolic domains of Tom20,

peptide scan of the inner membrane

SPOT

[524]

Tom22, Tom70

mitochondrial protein BCS1

αMI-domain of integrin αMβ2

partial peptide scans of the P2 peptide

SPOT

[556]

of the γC domain of fibrinogen

Tim9/Tim10 comlex

peptide scans of Tim17, Tim22,

SPOT

[564]

Tim23, Sc AAC2, FLX1, Hs UCP1,

and 11 control peptides

Protein Domain—Ligand Interactions

γ 32P-labeled GST-WW-domain of

substitutional analysis (including

SPOT

[79]

human YAP

phospho amino acids) of WBP-1

derived peptide GTPPPPYTVG

WW domain of human Yes-Associated

substitutional analysis of a peptide

SPOT

[323]

Protein (hYAP)

derived from the WW binding

protein WBP

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

249

Screening Molecule

Library

Technology

Reference

vasodilator-stimulated phosphoprotein

peptide scans of ActA (Listeria

SPOT

[382]

(VASP) and Mena (mammalian

monocytogenes) and truncation and

homolog of Drosophila Ena) both

substitutional analyses of selected

containing EVH1 domains

peptides; a library of proline-rich

(Ena-VASP homology domain 1)

sequences from cytoskeletal

proteins; a library of SH3 and

WW/WWP ligands

syntrophin PDZ domain

combinatorial library of the type

SPOT

[501]

XXB1B2SXV; substitutional

analysis of a peptide ligand for the

syntrophin PDZ domain

SH3 domains of amphiphysin 1 and

peptide scan of synaptojanin and

SPOT

[73]

endophilin 2

substitutional analyses of selected

peptides; peptides derived from

dynamins from Drosophila, rat,

32−

humans

peptide scan of zyxin

SPOT

[120]

α actinin

P-labeled GST-hYAP WW1 and

PPPPXPAAAA and 19 L-amino acid

SPOT

[138]

FE65 WW domain; several mutated

substitutions at position X

WW domains to switch the

specificity between hYAPWW1 and

FE65

syntrophin PDZ domain

library of C-terminal peptides from all

SPOT

[211]

known human proteins (3514 spots);

substitutional analysis of a selected

peptide

phospho-tyrosine –binding domain

amyloid precursor protein (APP)

SPOT

[220]

(PTB) of Dab1

derived peptides and known ligands

of PTB domains; substitutional

analyses of selected peptides

tumor necrois factor receptor

L- and D-amino acid substitutional

SPOT

[434]

associated factors (TRAFs) 1, 2, 3,

analyses of peptides derived from

and 6

the cytoplasmatic portion of CD40

vasodilator-stimulated phosphoprotein

substitutional analysis of an ActA

SPOT

[19]

(VASP) EVH1 domain

(Listeria monocytogenes) derived

peptide

STAT5a and a mutant STAT5a (STAT:

peptide scan of the intracellular

SPOT

[44]

signal transducer and activator of

domain of erythropoietin receptor

transcription)

(EPOR)

32P-labeled GST, GST- RSP5-WW1,

truncation analyses, alanine

SPOT

[75]

GST- RSP5-WW2, GST-

substitution scans, and phospho

RSP5-WW3; (RSP = reversion pf

amino acid analogs of

Spt phenotype, Saccharomyces

carboxy-terminal domain (CTD)

cerevisiae)

derived peptides of the RNA

polymerase II large subunit

Mena (mammalian homolog of

peptide scan of zyxin and Phe-Ala

SPOT

[121]

Drosophila Enabled (Ena) protein)

substitution analogs of selected

peptides

vasodilator-stimulated phosphoprotein

peptide scans of Fyb/SLAP1 and 2

SPOT

[277]

(VASP)

(Fynand SLP-76-associated

protein