Micro-Nano Technology for Genomics and Proteomics BioMEMs - Ozkan

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

233

Screening Molecule

Library

Technology

Reference

8 anti-sIL-6R mabs

partial peptide scans of the IL-6

SPOT

[192]

receptor extracellular domain

anti-dynorphin B mab D32.39 and goat

deletions and truncations of

LDPS

[213]

anti-mouse IgG-FITC conjugate or

FLRRQFKVVT (1024 peptides)

mab D32.39-FITC conjugate

anti-transforming growth factor α

combinatorial clustered hexapeptide

SPOT

[271]

(TGFα) mab Tab2

library and deconvolution libraries

6 mabs against phosphoprotein

peptide scans of the P-proteins of

SPOT

[348]

(P-protein) of morbillivirus strains

morbillivirus strains PDV and CDV

PDV and CDV

anti-protein-S of transmissible

4450 randomly generated 12-mer

MPC

[516]

gastroenteritis virus (TGEV) mabs

peptides; all 8000 tripeptides based

6A.A6 and 57.9; anti-EGF-like

on the genetically encoded amino

domain of surface protein pfs25 of

acids

Plasmodium falciparum mab 32F81

anti-gp41 (HIV-1) mab 3D6

complete L- and D amino acid

SPOT

[528]

substitutional analyses of the linear

epitope

6 anti-listeriolysin (Listeria

peptide scans of listriolysin

SPOT

[98]

monocytogenes) mabs

anti-porcine tubulin-tyrosine ligase

peptide scan of porcine

SPOT

[158]

(TTL) mab 1D3

tubulin-tyrosine ligase (TTL),

substitutional and truncation

analysis of a selected peptide,

combinatorial library (XXB1B2XX)

anti-porcine tubulin-tyrosine ligase

substitutional and truncation analysis

SPOT

[159]

(TTL) mab 1D3

of a TTL-derived peptide;

combinatorial library (XXB1B2XX)

and deconvolution libraries

streptavidin-alkaline phosphatase

combinatorial library (XXB1B2XX)

and deconvolution libraries

cAMP-dependent protein kinase

combinatorial library (XXB1B2XX)

and deconvolution libraries

5 polyclonal anti-U1 small nuclear

peptide scans of U1 snRNP-C

SPOT

[193]

ribonucleoprotein complex (U1

snRNP-C) antibodies (rabbit); 5 sera

from patients with mixed connective

tissue disease (MCTD) or systemic

lupus erythematosus (SLE)

rabbit serum against a peptide derived

partial peptide scan of the β-antigen of

SPOT

[239]

from the β-antigen of the c protein

the c protein complex of group B

complex of group B streptococci

streptococci and truncation analysis

of a selected peptide

12 sera from patients with

peptide scans of intestinal alkaline

SPOT

[264]

autoantibodies against intestinal

phosphatase (IAP)

alkaline phosphatase (IAP)

anti-gp41 (HIV-1) mab 2F5

complete L-amino acid substitutional

SPOT

[436]

analysis of the epitope peptide

234

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

anti-transforming growth factor α

substitutional analyses; combinatorial

SPOT

[494]

(TGFα) mab Tab2; anti-p24

library of the type

(HIV-1) mab CB4-1

XXXXB1B2B3XXXX; positional

scanning combinatorial library

lead(II); calcium(II); iron(III);

combinatorial libraries of the type

silver(I); nickel(II); technetium-99m

XB1XB2XX; deconvolution

libraries; positional scanning library

2 anti-presenilin 1 (PS1) polyclonal

partial peptide scans of presenilin 1

SPOT

[542]

rabbit antisera

human antiserum against pertussis

peptide scan of pertussis toxin

SPOT

[575]

toxin

3 anti-FcRIIb2 mabs

peptide scans of FcRIIb2

SPOT

[586]

pooled sera from 10 latex-sensitized

peptide scan of the latex allergy

SPOT

[20]

health care workers; pooled sera

associated allergen prohevin

from 10 patients with spina bifida

pooled sera from latex-allergic

peptide scans of prohevein

SPOT

[29]

patients; serum from a single latex

allergic patient; high IgE control

sera; pooled anti-latex rabbit sera

anti-RhopH3 (Plasmodium

partial peptide scan (aa 816-836) of

SPOT

[119]

falciparum) mouse mabs 84, 85, 87,

RhopH3

and 91

serum from a juvenile rheumatoid

partial peptide scan of the nucleosomal

SPOT

[248]

arthritis (JRA) patient

high mobility group protein 2

(HMG-2) and a glycine walk of a

selected peptide

anti-p24 (HIV-1) mab CB4-1

positional scanning combinatorial L-

SPOT

[272]

and D-amino acid libraries,

deconvolution libraries,

substitutional analyses

2 mabs against the heavy chain of

peptide scans of two regions of

SPOT

[279]

botulinum type E neurotoxin

botulinum type E neurotoxin

9 sera from patients with

peptide scan of the C-terminal

SPOT

[312]

Goodpasture’s disease

noncollagenous domain of the α3

chain of type VI collagen

anti-profilin mab 2H11

peptide scan of bovine profiling I

SPOT

[357]

anti-human thyroglobulin (hTg) mouse

partial peptide scan of the central part

SPOT

[372]

mabs Tg2 and Tg8

of human thyroglobulin (hTg)

mAb 3E7 and goat anti-mouse

endorphin epitope derived peptides up

LDPS

[422]

IgG-FITC conjugate

to 16-mers (65536 peptides)

anti-troponin I mabs

peptide scans of sceletal troponin I

SPOT

[440]

HIV-1 positive sera

peptide scans of the gp120 (HIV-1) V3

SPOT

[497]

loop

anti-protein-S of transmissible

4450 randomly generated 12-mer

MPC

[517]

gastroenteritis virus (TGEV) mabs

peptides; all 8000 tripeptides based

6A.A6; anti-FLAG mab M2

on the genetically encoded amino

acids

mab 755 against the α-chain of C3

peptide of the C-terminal region of the

SPOT

[569]

C3 α-chain

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

235

Screening Molecule

Library

Technology

Reference

10 antibodies against ras proteins

peptide scans of the human oncogene

SPOT

[579]

products Ha-ras, K-ras, and N-ras;

truncation analyses and complete

L-amino acid substitutional analyses

of selected peptides

anti-elongation factor TU (EF-TU)

peptide scan of EF-TU, truncation and

SPOT

[18]

mab

substitutional analysis of a selected

peptide

2 anti-centrosome scleroderma

peptide scans of the immunogenic

SPOT

[23]

autoimmune sera

regions of the centrosome autoantigen

PCM-1

anti-lipoprotein lipase (LPL) mab

peptide scan of LPL and substitutional

SPOT

[74]

(discontinuos epitope possible)

analyses of selected peptides

anti-glucoamylase

partial peptide scan of glucoamylase

SPOT

[123]

(thermoanaerobacterium

thermosaccharolyticum) polyclonal

antibody

anti-M2 acetylcholine receptor mab

partial peptide scan of M2 acetylcholine

SPOT

[131]

receptor

anti-cardiac troponin I monoclonal and

peptide scans of cardiac troponin I

SPOT

[145]

polyclonal antibodies

28 anti-cardiac troponin I (cTnI) mabs

peptide scans of cTnI

SPOT

[150]

IgG fractions from 2 patients with

partial peptide scan of the C-terminal

SPOT

[152]

erythema multiforme major,

part of desmoplakin

polyclonal serum from a rabbit

immunized containing the epitope

YSYSYS

3 anti-C3aR scFvs

peptide scans of the second extracellular

SPOT

[198]

loop of C3aR

anti-alanine dehydrogenase (AlaDH)

peptide scan of AlaDH

SPOT

[224]

of Mycobacterium tubercolosis mab

HBT-10

anti-transforming growth factor α

peptide scan of TGFα, substitutional

SPOT

[273]

(TGFα) mab Tab2

analysis of a selectd peptide,

combinatorial library (XXB1B2XX)

anti-cholera toxin mab TE33; anti-p24

D-amino acid substitutional analyses for

SPOT

[274]

(HIV-1) mab CB4-1

the transformation of linear

wt-epitopes into all-D peptide analogs

anti-cardiac troponin I monoclonal and

peptide scans of cardiac troponin I

SPOT

[289]

polyclonal antibodies

anti-β2 adrenergic receptor mabs

peptide scans of the β2 adrenergic

SPOT

[297]

receptor and alanine scans of selected

peptides

5 anti-glycoprotein G of HSV-2 (gG-2)

peptide scans of gG-2

SPOT

[321]

mabs; 8 anti-gG-2 antibodies

purified from patients sera

biotinylated antibodies directed against

pyrrole peptides (18–39) and (11–24) of

CPPP

[328]

ACTH derived peptides and

ACTH

strepavidin-phycoerythrin conjugate

236

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

8 anti-gliadin polyclonal rabbit sera; 6

peptides identified by phage display

SPOT

[389]

human sera positive for gliadin

(panning against anti-gliadin rabbit

antibodies

sera)

anti-eukaryotic initiation factor 4E

peptide scans of eIF4E

SPOT

[431]

(eIF4E) mabs

7 rabbit sera against coxsackievirus A9

peptide scans of the capsid proteins

SPOT

[435]

and B3 and against echovirus 11

VP1, VP2 and VP3 from

coxsackievirus A9

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

sera from insulin-dependent diabetes

peptide scans of glutamic acid

SPOT

[468]

mellitus (IDDM) patients

decarboxylase 65 (GAD65) and

alanine scans of selected peptides

15 sera from systemic lupus

peptide scans of the SLE autoantigen

SPOT

[469]

erythematosus (SLE) patients

SmD1

anti-interferon regulatory factor 1

peptide scan of interferon regulatory

SPOT

[487]

(IRF-1) polyclonal antibody

factor 1 (IRF-1)

sera from patients with allergic

peptide scan of a major allergen (Asp f

SPOT

[21]

bronchopulmonary aspergillosis

2) of Aspergillus fumigatus;

(ABPA)

truncation scans of selected peptides

sera from latex allergic patients and

peptide scans of the latex protein Hev

SPOT

[30]

sera of rabbits immunized with latex

b 5 from Hevea brasiliensis

proteins

several sera from patients with primary

partial peptide scans of the nuclear

SPOT

[47]

biliary cirrhosis containing

protein sp100

autoantibodies against nuclear

protein sp100

68 murine IgG mabs recognizing linear

peptide scans, length analyses,

SPOT

[113]

epitopes

L-substitutional analyses

13 sera from multiple sclerosis patients

peptide scans of TAL-H

SPOT

[142]

positive for human transaldolase

(TAL-H); 2 anti-TAL-H polyclonal

rabbit antibodies

anti-pneumolysin mab PLY-5

peptide scan of pneumolysin (PLY)

SPOT

[231]

sera from parvovirus B19 infected

peptide scans of the VP1 and VP2

SPOT

[250]

patients

parvovirus B19 capsid proteins;

truncation analyses; alanine and

glycine walks of selected peptides

3 mouse mabs and a polyclonal rabbit

peptide scans of pVIII; truncation

SPOT

[259]

serum against pVIII of filamenteous

analyses and glycine walks of

bacteriophage fd

selected peptides

anti-pre-S1 and pre-S2 (hepatitis B

peptide scan of the pre-S domain,

SPOT

[281]

virus) mabs 1F6 and MA 18/7

substitutional analyses of selected

peptides

anti-RNA polymerase II (Drosophila

substitutional analysis of the RNA

SPOT

[326]

melanogaster) scFv215

polymerase II derived epitope

2 anti-interleukin 10 (IL-10) mabs

peptide scans of IL-10 and

SPOT

[449]

substitutional analyses of selected

peptides

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

237

Screening Molecule

Library

Technology

Reference

anti-midsize neurofilament NF-M

peptide scan of neurofilament NF-M

SPOT

[500]

mab 155

anti-colera toxin mab TE33

substitutional analyses of mab TE33

SPOT

[529]

binding peptides

sera from patients receiving

peptide scans of streptokinase

SPOT

[552]

streptokinase (SK) therapy

polyclonal serum against

peptide scans of the bacteriophage

SPOT

[559]

bacteriophage φ29 connector

φ29 connector protein (p10)

protein

polyclonal serum against

peptide scans of the bacteriophage

SPOT

[560]

bacteriophage φ29 connector

φ29 connector protein (p10)

protein

anti-β-amyloid (Aβ) polyclonal

peptide scan of apolipoprotein E

SPOT

[594]

antibody

(apoE) each peptide being flanked

by randomized positions

(hybritope scan)

sera from latex-sensitized health care

peptide scan of the latex allergy

SPOT

[22]

workers; sera from patients with

associated proteins Hev b 1 and

spina bifida

Hev b 3

CD4; anti-gp17 polyclonal antibody

peptide scan of gp17; alanine walks

SPOT

[28]

of selected peptides

sera from patients with

partial peptide scan of the

SPOT

[48]

polymyositis-scleroderma overlap

polymyositis-scleroderma overlap

syndrome

syndrome antigen PM/Scl-100;

length analysis, glycine-walk and

complete substitutional analysis of

a selected positive peptide from the

peptide scan

mab 2E11 against a peptide 38 from

truncation analysis of peptide 38

SPOT

[52]

the variable region of the Vb 6.2

T-cell receptor

mab 3E12 against Kx blood group

overlapping peptides derived from

SPOT

[72]

antigen and spectrin β-chain

epitope regions in Kx blood group

antigen and spectrin β-chain

2 anti-tubulin-tyrosine ligase (TTL)

peptide scan of pig TTL

SPOT

[135]

mabs

anti-cardiac troponin I mab 11E12

alanine walks of mab 11E12 binding

SPOT

[147]

peptides

10 sera from patients with malaria

peptide scan of block 17 of merozoite

SPOT

[164]

surface glycoprotein-1 (MSP1) of

Plasmodium falciparum

anti-p24 (HIV-1) mab CB4-1

libraries with all possible single step

SPOT

[212]

transition pathways between 3

sequentially and structually

unrelated mab CB4-1 binding

peptides; substitutional analyses of

peptides from selected transition

pathways

35S-labeled calmodulin

mastpoparan

SPOT

[223]

(Ac-INLKALAALAKKIL) and

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

239

Screening Molecule

Library

Technology

Reference

phosphorylation specific anti-human

peptide scan of phosphorylated and

SPOT

[551]

tau protein mab AD2

unphosphorylated tau protein and

alanine walks of selected peptides

anti-glycoprotein G-1 (gG-1)

peptide scans of gG-1 (HSV-1)

SPOT

[554]

antibodies purified from herpes

simplex virus 1 (HSV-1) patients

anti-p24 (HIV-1) scFv CB4-1 and 2

substitutional analyses of the

SPOT

[595]

mutants thereof

p24-derived wt epitope and a

mimotope

mouse sera against peptides from Der

alanine walks of peptides derived from

SPOT

[599]

p2 (house dust mite

Der p2

Dermatophogoides pteronyssinus)

anti-plastidic phosphorylase (Pho 1a)

peptide scan of Pho 1a; complete

SPOT

[9]

from Solanum tuberosum L. mab

substitutional analysis of the Pho

1a-derived epitope peptide

anti-α-bungarotoxin scFv C12;

peptide scan of α-bungarotoxin

SPOT

[58]

nicotinic acetylcholine receptor

nAchR

sera from cow’s milk allergy patients

peptide scans of αs1-casein

SPOT

[77]

(IgG and IgE antibody detection)

polyclonal sera from mice, rabbits and

peptide scans of TsNTxP and alanine

SPOT

[78]

horses against a non-toxic protein

substitution scans of selected

from the venom of the noxious

peptides; peptide scans of active

scorpion Tityus serrulatus (TsNTxP)

toxins from the venom of Tityus

serrulatus

anti-tobacco mosaic virus protein

partial peptide scan of tobacco mosaic

SPOT

[86]

(TMVP) Fab 57P

virus protein (TMVP); substitutional

analysis, truncation analysis and

alanine walk of a selected peptide

anti-vascular endothelial cadherin

peptide scans of the extracellular

SPOT

[93]

(VE-cadherin) mabs BV6 and Cad 5

domain of vascular endothelial

p60c-src protein tyrosine kinase and

cadherin (VE-cadherin)

Ttds-EEIYGEFF

DIPP

[143]

γ 32P-ATP

strepavidin-Cy3 conjugate; avidin-Cy5

biotin, HPYPP and WSHPQFEK

conjugate

anti-human insulin mab HB125 and

biotin, wGeyidvk, pqrGstG,

anti-mouse IgG-Cy5 conjugate

WSHPQFEK and YGGFL

WEHI-231 cells and negative control

wGeyidvk

cells

anti-genome-derived Ag 33 (GNA33)

peptide scans of genome-derived Ag

SPOT

[182]

mab 25; anti-loop 4 of porin A mab

33 (GNA33) of Neisseria

P1.2

meningitidis and loop 4 of porin A

anti-transforming growth factor α

5 substitutional analyses of linear and

SPOT

[191]

(TGFα) mab Tab2

cyclic (disulfide cyclization and

amide cyclization from the N-α to

the C-terminal glutamic acid side

chain) analogs of the epitope

scFv-phage library; anti-C3a receptor

peptide scans of the 2e loop of C3a

SPOT

[199]

2e loop scFvs E10 and E6

receptor

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

241

Screening Molecule

Library

Technology

Reference

Practical protocols to optimize the mapping of antibody epitopes and

SPOT

[59]

protein-protein interactions with respect to protein concentrations, blocking

conditions, detection systems, and the efficiency of the regeneration procedures

sera from 13 cow’s milk allergic

peptide scan of αs2-casein

SPOT

[69]

children

anti-E6 oncoprotein (papillomvirus

partial E6 peptide scan; truncation

SPOT

[87]

type 16) mabs 1F1, 6F4, and scFv

analyses, alanine substitution scans,

1F4

and complete L- amino acid

substitutional analses of selected

peptides

mixture of anti-phosphotyrosine

phosphotyrosine-containing peptides

SPOT

[140]

antibodies, POD-conjugated

derived from human insulin

anti-mouse antibody

receptor; degenerate SPOT library of

general structure AABX1ZX2BAA

(Z = phosphotyrosine, B = mixture

of 20 natural amino acids, X defined

amino acids) and peptides derived

from human STAT 5A containing

both phosphotyrosine and

phosphothreonine residues

sera from older patients with persistent

25 peptides representing epitopes on

SPOT

[236]

cow’s milk allergy; sera from

cow’s milk proteins: 5 epitopes on

younger children with decreasing

αs1-casein, 5 on αs2-casein, 9 on

milk-specific IgE antibodies

κ-casein, 1 on α-lactalbumin, and 5

on β-lactoglobulin)

Practical protocols for mapping monoclonal and polyclonal antibody epitopes

SPOT

[261]

using peptide scans, length analyses, amino acid substitution scans and

complete substitutional analyses

anti-p53 mAb DO-1

peptides SDLHKL, DSLGKL, and

LDPS

[265]

fluorescence shift following Pb2+ or

SGLHKL

As3+ binding

dns (dansyl)-ECEE, dns-CCCC,

dns-GGGG, EEEE

5 murine mabs against glycoprotein

peptide scans of gG-2 of HSV-2

SPOT

[322]

G-2 (gG-2) of herpes simplex virus

type 2 (HSV-2)

Practical protocols for (a) affinity purification of subfractions from polyclonal

SPOT

[342]

sera that are specific for a defined linear epitope and (b) competition assays on

peptide arrays

12 sera from a patient with systemic

peptide scans of centromeric protein A

SPOT

[343]

sclerosis

(CENP-A) as well as several

mimotopes from potential

autoantigens

sera from HCV and EBV patients and

peptides from HCV core and NS4 and

DIPP

[361]

negative control sera

EBV capsid, negative control

peptide

anti-SA-Le (tetrasaccharide) mab

L-substitutional analysis of the NS19-9

SPOT

[386]

NS19-9

epitope DLWDWVVGKPAG

anti-p53 antibody (PAb240)

substitutional analysis of the PAb240

LDPS

[406]

peptide epitope including

proteinogenic amino acids and

unnatural building blocks; length

analysis of the epitope

242

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

anti-IL-10 mab CB/RS/13;

5520-membered library of randomly

SPOT

[458]

anti-transforming growth factor α

generated 15-mer L-peptides; 8

(TGFα) mab Tab2; anti-p24

substitutional analyses of selected

(HIV-1) mab CB4-1

antibody-binding peptides

different pooled sera from autoimmune

immunodominant peptides from

DIPP

[472]

patients; 2 sera from single systemic

snRNP proteins, Sm proteins,

lupus erythematodes (SLE) patients;

myelin basic protein (MBP), poly A

negative control sera;

ribose polymerase (PARP), and

histones H1, H2A, H2B, H3, and H4

sera from mice immunized with

selected peptides derived from myelin

DIPP

[475]

myelin oligodendrocyte

basis protein (MBP), proteolipid

glycoprotein (MOG) p35–55,

protein (PLP), myelin

proteolipid protein (PLP) p139–151,

oligodendrocyte glycoprotein

and negative control serum

(MOG), oligodendrocyte-specific

protein (OSP), αb crystalline and

other unspecified myelin proteins

incubation with blood sera followed by

peptide scan through major peanut

DIPP

[511]

incubation with biotinylated

allergens Ara h1, Ara h2 and Ara h3

anti-human IgE Ab and avidin-Cy3

(210 peptides)

conjugate

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-FLAG mab M2

FLAG epitope; 3 single site alanine

DIPP

[581]

substitutions of the FLAG epitope;

HA epitope

pooled sera from Parietaria judaica

peptide scans of the Par j 1 and 2

SPOT

[17]

allergic patients

allergens from Parietaria judaica

pollen

sera from peanut allergy patients and

8 peptides representing the

SPOT

[39]

nonatopic control sera (detection of

immunodominant epitopes of the

IgE antibodies)

peanut allergens Ara h 1, Ara h 2,

and Ara h 3

individual and pooled sea from cow’s

truncation libraries and alanine

SPOT

[89]

milk allergy (CMA) patients

substitution scans of peptides from

the αs1-casein allergen

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

FITC-labeled anti-RHSVV pAb240

multiple substitutional analysis of

LDPS

[172]

RHSVV epitop using 28 different

amino acids (2304 peptides)

individual and pooled sera form

peptide scan of the peach allergen

SPOT

[173]

patients with peach allergy

Pru p 3 and alanine substituted

analogs of selected peptides

anti-transforming growth factor α

randomly generated library of 8000

SPOT

[202]

(TGFα) mab Tab2

hexapeptoids and -peptomers