Micro-Nano Technology for Genomics and Proteomics BioMEMs - Ozkan

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

253

Screening Molecule

Library

Technology

Reference

streptavidin-alkaline phosphatase

combinatorial library (XXB1B2XX)

and deconvolution libraries

cAMP-dependent protein kinase

combinatorial library (XXB1B2XX)

and deconvolution libraries

casein kinase I (CKI) or II (CKII)

peptides derived from the

SPOT

[549]

protein kinase C (PKC) catalytic

phosphorylation sites RRASVA,

subunit of protein kinase A (PKA)

QKRPSQRAKYL,

and γ 32P-ATP

DDDDEESITRR,

DDDSDDDAAAA

potato acid phosphatase

RRASS*VA, QKRPS*QRAKYL,

DDDDEES*ITRR,

DDDS*DDDAAAA (S* =

phospho-serine)

protein kinase A (PKA), protein kinase

panel of human phosphorylation sites

SPOT

[550]

C (PKC), casein kinase I (CKI),

casein kinase II (CKII) and

γ 32P-ATP

125I-calmodulin

phosphorylated and unphosphorylated

SPOT

[126]

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

androgen receptor protein kinase and

panel of kinase substrates known from

SPOT

[370]

γ 32P-ATP

literature

enzyme I of bacterial sugar

combinatorial library of the type

SPOT

[376]

phosphotransferase system and

XXXXXO1HO2XXXXX and

32P-phosphoenolpyruvate

iterative deconvolution libraries

catalytic subunit of protein kinase A or

combinatorial libraries of the type

SPOT

[540]

cGMP activated protein kinase G

XXXO1O2XXX and

and γ 32P-ATP

XXXRRO1O2X

catalytic subunit of protein kinase A or

combinatorial libraries of the type

SPOT

[115]

cGMP activated protein kinase G

O1KARKKSNO2,

and γ 32P-ATP

O1O2TQAKRKKSLA,

O1O2KATQAKRKKSLA,

TQAKRKKSLAO1O2, and

TQAKRKKSLAMAO1O2

catalytic subunit of protein kinase A or

combinatorial library of the type

SPOT

[116]

cGMP activated protein kinase G

XXXO1O2XXX and deconvolution

and γ 32P-ATP

libraries: XXXRKO1O2X,

XRKKKO1O2X, O1RKKKKKO2,

LRKKKKKHO1O2, and

O1O2LRKKKKKH

GST-Dyrk1A- (500–763) and

partial substitutional analysis of

SPOT

[207]

γ 32P-ATP

RRRFRPASPLRGPPK

maize Ca2+ -dependent protein kinase

partial substitutional analysis of

SPOT

[334]

(CDPK-1) and γ 32P-ATP

LARLHSVRER

protein kinase A (PKA), casein kinase

kinase substrates Kemptide and Elk1;

CLPP

[338]

II (CKII), p42-MAP kinase (Erk2)

protein kinase inhibitor 2

and γ 32P-ATP

254

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

p60c-src protein tyrosine kinase and

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

Practical protocols to measure phosphorylation of peptides on peptide arrays

SPOT

[50]

prepared by SPOT synthesis exemplified by the kinase CKII

cyclic GMP-dependent protein kinase

XXXRKB1B2X (deconvolution

SPOT

[117]

(phosphorylation γ 32P-ATP)

libraries described but data not

shown)

32P-labeled cyclic GMP-dependent

B1RKKKKKB2 (preceding libraries

protein kinase (binding)

described but data not shown)

GST-protein tyrosine phosphatase 1B;

15-mer phospho-tyrosine-containing

SPOT

[140]

mixture of anti-phospho-tyrosine

peptides derived from human insulin

antibodies, POD-conjugated

receptor; degenerate SPOT library of

anti-mouse antibody

general structure AABX1ZX2BAA

(Z = phospho-tyrosine, B =

mixture of 20 natural amino acids,

X defined amino acids) and peptides

derived from human STAT 5A

containing both phospho-tyrosine

and phospho-threonine residues

GST-protein tyrosine phosphatase ß;

15-mer phospho-tyrosine-containing

mixture of anti-phospho-tyrosine

peptides derived from human Tie2

antibodies, POD-conjugated

receptor containing additional

anti-mouse antibody

phospho-serine or

phospho-threonine residues

GST-fusion protein of substrate

15-mer phospho-tyrosine-containing

trapping mutant of protein tyrosine

peptides derived from human insulin

phosphatase 1B (D181A),

receptor; degenerate SPOT library

radioactively labeled by incubation

of general structure

kinase A in the

AABX1ZX2BAAA (Z =

with protein

32

P-ATP

presence of γ

phospho-tyrosine, B = mixture of

20 natural amino acids, X defined

amino acids), progressive alanine

substitution of

MTRDIYETDYZRKGG ( Z =

phospho-tyrosine), alanine scan of

TRDIYETDYZRKGGKGL,

substitutional analysis for X in

MTRDIYETDXZRKGG ( Z =

phospho-tyrosine)

panel of known kinase substrates

DIPP

[218]

c-Src substrate

DIPP

[219]

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

255

Screening Molecule

Library

Technology

Reference

p60 and FITC-labeled

YIYGSFK, ALRRASLG,

DIPP

[310]

anti-phospho-tyrosine antibody

KGTGYIKTG and

monophosphorylated derivatives

PKA or p60 and FITC-labeled

YIYGSFK, ALRRASLG, YIYGSFK

DIPP

[311]

anti-phospho-tyrosine or

and monophosphorylated

anti-phospho-serine antibody

derivatives

NEK6 kinase and γ 32P-ATP

human annotated phosphorylation

DIPP

[330]

sites and mutational analysis of

GLAKSFGSPNRAY

Protein tyrosine kinase ABL and

collection of 720 peptides (13-mers)

DIPP

[443]

γ 32P-ATP or FITC-labeled

derived from human annotated

anti-phospho-tyrosine antibody

phosphorylation sites (databases

SwissProt and Phosphobase)

GST-ERK-2 or GST-MEK-EE,

double peptide synthesis of

SPOT

[141]

anti-phospho-Elk-1 antibody, POD

ELK1-substrate peptide

labeled anti-rabbit antibody

FWSTLSPIAPR, D-loop peptide

KGRKPRDLELP and control

peptide MNGGAANGRIL

GST-fusion protein-protein tyrosine

double peptide synthesized SPOTs

phosphatase 1B;

containing the PTP-1B substrate

anti-phospho-tyrosine antibody,

IYETDYZRKGG (Z =

POD-conjugated anti-mouse

phospho-tyrosine) and on the

antibody

second site a scan of 11-mers

overlapping peptides derived from

the cytoplasmic domain of insulin

receptor

GST-fusion protein of substrate

double peptide synthesis of insulin

trapping mutant of protein tyrosine

receptor derived substrate peptide

phosphatase 1B (D181A),

IYETDYZRKGG (Z =

radioactively labeled by incubation

phospho-tyrosine) and binding

with protein kinase A in the

motif for YAP WW1 domain and

presence of γ 32P-ATP

p53 binding protein-2, respectively

(YPPYPPPPYPS)

PKA and Abl; Pro-Q Diamong

Kemptide, p60 c-src (521-533), delta

DIPP

[350]

phospho-specific stain or

sleep inducing peptide (DSIP),

FITC-labeled

phosphoDSIP, CamKII peptide

anti-phospho-tyrosine antibody for

(GS1-10), different proteins

detection

GST-proteins of substrate trapping

7 peptides (14-mers) derived from

SPOT

[397]

mutants of tyrosine phosphatases

human GHR together with the

(PTP-H1, SAP-1, TC-PTP,

appropriate

PTP-1B) radioactively labeled by

phospho-tyrosine-containing

incubation with protein kinase A in

derivatives

the presence of γ 32P-ATP

tyrosine kinase p60 c-scr and

deletion, alanine scanning, positional

DIPP

[558]

FITC-labeled

scanningand full combinatorial

anti-phospho-tyrosine antibody

mixture libraries of

CGG-YIYGSFK (p60 c-src

256

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology Reference

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

257

Screening Molecule

Library

Technology

Reference

caspase-3

substitutional analysis of a known

SPOT

[457]

substrate; protein sequence derived,

combinatorial, positional scanning,

and randomly generated peptide

libraries (data not shown) for

substrate identification

cathepsin C and cathepsin L

peptidic cathepsin inhibitors tethered to

DIPP

[596]

fluorescence-labeled peptide nucleic

acids

elastase, cathepsin G

partial peptide scan and substitution

SPOT

[254]

analogs of the transferrin receptor

stalk

trypsin, granzyme B and thrombin

Ac-LGPL-U, Ac-Nle-TPK-U,

DIPP

[486]

Ac-IEPD-U and 361 variants of

Ac-AOOK-U (Cys omitted); U =

alkoxyamino-substituted coumarin

derivative

caspase 3, granzyme B, Jurkat cell

peptide derivatives tethered to

DIPP

[597]

lysates and granzyme B activated

fluoresceine-labeled peptide nucleic

apoptotic Jurkat cell lysates

acids

lysyl-endopeptidase (LEP),

3 substrate peptides with LEP,

[258]

chymotrypsin, V8 protease; BSA

chymotrypsin or V8 protease

and ConA as negative controls;

specificity

TLCK and Boc-glu as inhibitors

Isomerases

human peptidyl-prolyl cis/trans

peptide scan of human Cdc25C

SPOT

[336]

isomerase Pin1, sequential

including phosphorylated S/T-P

electo-blotting to

moieties

PVDF-membranes, incubation of

PVDV-membranes with anti-Pin1

antibody followed by secondary

antibody

Triggerfactor (TF) (Escherichia coli)

peptide scans of E. coli proteins: EF-Tu

SPOT

[399]

and TF-fragments

(elongation factor Tu), MetE

(methionine biosynthesis enzyme),

ICDH (isocitrate dehydrogenase),

GlnRS (glutamine-tRNA-

258

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

Trigger Factor and DnaK from E. coli

peptides derived from Trigger Factor

SPOT

[112]

and DnaK substrate proteins

Diverse Enzymes

pertussis toxin (Bordetella pertussis)

5 to 25-mer C-terminal peptides of the

SPOT

[576]

and ATP + 32P-NAD: ADP

G-Protein α-subunits of Gi3, Gi, Gs,

ribosylation

Go1, Go2, GoX1, Trod, Gz, Gq/11 and

Gh, partial substitutional analysis of

the 16-mer C-terminal peptide of the

Gi 3α-subunit

peptide detection by MALDI-TOF MS

Ac-IYAAPKKKC-NH2

DIPP

[532]

concanavalin A (lectin binding)

α-mannose

β-1,4-galactosyltransferase

N -acetylglucosamine

galactosidase

N -acetyllactosamine

Rhodococcus rhodochrous epoxide

5 substrates for the 4 hydrolases

DIPP

[616]

hydrolase, Electrophorus electricus

among them being 2 peptidic

acetylcholine esterase, bovine

substrates for trypsin and caspases

pancreas trypsin, bovine intestinal

mucosa alkaline phosphatase

Applications of Peptide Arrays: Miscellaneous

DNA Binding Peptides

oligonucleotide with an endonuclease

peptide scan of EcoRII and

SPOT

[465]

EcoRII specific recgnition site

substitutional analyses of selected

peptides

Practical protocols for the analysis of DNA-protein and DNA-peptide interactions

SPOT

[466]

Metal Ion Binding Peptides

anti-transforming growth factor (TGF)

combinatorial libraries of the type

SPOT

[269]

mab Tab2; silver(I); dsDNA

XXB1B2XX and XB1XB2XX

technetium–99m; nickel(II);

combinatorial with 2 defined positions

SPOT

[270]

anti-transforming growth factor α

(linear, cyclic, L- and D- amino

(TGFα) mab Tab2

acids) and deconvolution libraries

technetium–99m

combinatorial hexapeptide library

SPOT

[346]

B1XB2XB3X (8000 peptide

mixtures) and deconvolution

libraries

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

anti-p53 mAb DO-1

peptides SDLHKL, DSLGKL, and

LDPS

[265]

SGLHKL

fluorescence shift following Pb2+ or

dns(dansyl)-ECEE, dns-CCCC,

As3+ binding

dns-GGGG, dns-EEEE

fluorescence shift following

dns(dansyl)-ECEE, dns-CCCC,

LDPS

[172]

Pb2+ binding

dns-GGGG, dns-EEEE

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

259

Screening Molecule

Library

Technology

Reference

Arrays of 4 α-Helix Bundle Mini-Proteins

FeIII-protoporphyrin IX

libraries of antiparallel 4-α-helix

SPOT

[441]

bundle hemoproteins

copper(II), cobalt(II)

libraries of antiparallel 4-α-helix

SPOT

[495]

bundle metalloproteins

Identification, Characterization, and Optimization of Peptidic Ligands

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

streptavidin

substitution analogs of Strep-tag II

SPOT

[493]

amyloid β-peptide (Aβ)

peptide scan of amyloid β-peptide

SPOT

[544]

(Aβ); truncation analysis and

alanine scan of a selected peptide

amyloid β-peptide (Aβ); Aβ-derived

peptide scans of amyloid β-peptide

SPOT

[545]

peptide LBMP1620

(Aβ) and truncation analyses of

selected peptides

anti-cholera toxin mab TE33; anti-p24

D-amino acid substitutional analyses

SPOT

[274]

(HIV-1) mab CB4-1

for the transformation of linear

wt-epitopes into all-D peptide

analogs

strepavidin-FITC conjugate

2888 O1O2-P/L-Q/F-F/L derived

SODA

[298]

peptides bound to functionalized

teflon membranes

plasma-derived factor VIII (pdFVIII),

dual position scanning library with the

SPOT

[12]

recombinant factor VIII (rFVIII)

sublibraries O1O2XXXXXX,

XXO1O2XXXX, XXXXO1O2XX,

XXXXXXO1O2; combination

library of hits from the dual position

sublibraries

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

truncation and deletion analogs

pIII phage display library of

mastpoparan

calmodulin variants

(Ac-INLKALAALAKKIL) and

truncation and deletion analogs

260

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

pIII phage display scFv library

partial peptide scan of the extracellular

presenting the antibody repertoire of

domain of the C3a receptor

a mouse immunized with the

recombinant extracellular domain of

the C3a receptor

FeIII-meso-tetrakis(4-

alanine walk, partial substitutional

SPOT

[535]

carboxyphenyl)porphyrin

anlaysis, and truncation analysis of

(FeIII-TCPP)

an anti-porphyrin mab CDR-derived

peptide

biotinylated α-bungarotoxin (snake

combinatorial 14-mer peptide library

SPOT

[57]

neurotoxin)

with 5 invariant, 4 partially variant

and 5 totally variant positions

plasma-derived factor VIII (pdFVIII),

complete substitutional analyses of the

[409]

recombinant factor VIII (rFVIII)

factor VIII binding peptide

EYKSWEYC

125I vascular endothelial growth factor

complete D-amino acid substitutional

SPOT

[418]

(VEGF)

analyses of VEGF receptor

II-derived peptides

α-thrombin

peptide scans of clones T10-11 and

SPOT

[439]

T10-39 identified by mRNA display

with α-thrombin as target;

L-substitutional analyses of T10-11

and T10-39

Chemical Transformations

Dpab-Ala-O-FM = Methyl Red

combinatorial libraries of all possible

SPOT

[538]

(2{[4-(dimethylamino)phanyl]azo}

dipeptide combinations

benzoic acid)-labeled alanine

α-formylmethyl (FM) ester

aldehydes for the evaluation of

amide chemical ligation strategies

combinatorial dipeptide libraries were used to elucidate the reactivity of the

SPOT

[377]

amino termini and amino acid side chains to be non-enzymatically modified by

reducing sugars leading to advanced glycation end products (AGEs) or

crosslinked by BSA-AGE

Cell Binding to Peptide Arrays

p60c-src protein tyrosine kinase and

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

3T3 fibroblasts

Gly-Arg-Gly-Asp-Ser

DIPP

[609]

Review for therapeutic cancer targeting peptides including a short peptide

DIPP

[8]

microarray section and experimental data of an array with 42 different peptides

that was probed with Jurkat T-lymphoma cells

PEPTIDE ARRAYS IN PROTEOMICS AND DRUG DISCOVERY

261

Screening Molecule

Library

Technology

Reference

T-cell Epitope Mapping

HLA-DR1 and HLA-DR4 molecules,

partial peptide scans of the merozoite

SPOT

[163]

HLA-DR4 binding self peptide as

surface glycoprotein 1 (MSP1) of

competitor, malaria-infected human

plasmodium falciparum

serum

9C5.D8-H T-cell hybridoma

peptide scan of rabies virus

SPOT

[394]

nucleoprotein

Peptidomimetics

synthesis of peptide nucleic acid (PNA) oligomer arrays on polymer membranes

SPOT

[583]

and their hybridisation with DNA probes

simutaneous synthesis of peptides, peptomers and peptoids on continuous

SPOT

[16]

surfaces; amino funtionalization of cellulose membranes with epibromohydrin

and 4,7,10-trioxa-1,13-tridecanediamine

fluorescent-labeled model DNA

peptide nucleic acid (PNA) oligomer

SPOT

[355]

oligonucletide

arrays on cellulose, polypropylene

and PTFE membranes with different

spacer molecules

anti-transforming growth factor α

amino and amino-oxy-substituted

SPOT

[488]

(TGFα) mab Tab2

1,3,5-triazine arrays (detailed

synthesis protocols

Synthesis of 1,3,5-triazines on continuous surfaces

SPOT

[489]

synthesis of 1,3,5-trisubstituted hydantoin arrays on cellulose membranes

SPOT

[201]

anti-transforming growth factor α

peptoidic building block substitutional

SPOT

[456]

(TGFα) mab Tab2

analyses of the mab Tab2 peptide

epitope VVSHFND and of

peptomers and peptoids derived

thereof

Synthesis of macrocyclic peptidomimetics which incorporate heteroaromatic

SPOT

[490]

building blocks such as 2,4,6-trichloro-[1,3,5]triazine,

2,4,6-trichloropyrimidine, 4,6-dichloro-5-nitropyrimidine,

2,6,8-tricloro-7-methylpurine

anti-transforming growth factor α

randomly generated library of 8000

SPOT

[202]

(TGFα) mab Tab2

hexapeptoids and -peptomers

262

ULRICH REINEKE, JENS SCHNEIDER-MERGENER AND MIKE SCHUTKOWSKI

Screening Molecule

Library

Technology

Reference

VASP-EVH1 domain GST fusion

peptoid building block substitutional

SPOT

[617]

protein

analysis of a VASP-EVH1 peptide

ligand; combinatorial peptoid

building block library of two

positions within a VASP-EVH1

peptide ligand

Review Articles

Description of the SPOT method in the context of other combinatorial library

SPOT

[157]

techniques: practical approaches, library types, binding assays with

anti-porcine tubulin-tyrosine ligase (TTL) mab 1D3

Different types of combinatorial peptide libraries are described: XB1XB2XX

SPOT

[494]

(400 spots), XXXXB1B2B3XXXX (8.000 spots) and a positional scanning

combinatorial library XXXX(3B3X)XXXX (68.000 spots) as well as

deconvolution libraries and substitutional analyses. These libraries were

applied for the identification of linear antibody epitopes (anti-TGFα mab Tab2

and anti-p24 (HIV-1) mab CB4-1) and metal ion binding peptides.

Review describing the technology and applications of peptides on pins,

Diff.

[422]

macroscopic DNA arrays, light-directed synthesis (DNA and peptides),

peptides on paper (SPOTmethod), and inorganic combinatorial libraries

Solid-Phase synthesis on planar supports including synthesis on glass, cellulose,

Diff.

[298]

cotton, and teflon membrane supports)

Personal comments on “classical” papers in combinatorial chemistry (e.g., R.

Diff.

[299]

Frank on SPOT synthesis)

Describes the mapping of linear and discontinuous interactions of

SPOT

[447]

antibody/antigen and protein/protein complexes using sequence-derived

peptide scans, substitutional analyses and combinatorial libraries prepared by

SPOT synthesis

Mapping of linear epitopes of 2 anti-interleukin-10 (IL-10) mabs with peptide

scans and substitutional analyses, mapping of the IL-10/IL-10R interaction

with peptide scans, identification of the anti-TGFα mab Tab2 by combinatorial

hexapeptide libraries, identification of the anti-p24 (HIV-1) mab CB4-1 with a

positional scanning combinatorial library

Summary of the SPOT synthesis technique particularly addressing small

SPOT

[53]

molecule and peptidomimetic arrays

Review article describing peptide and protein arrays

Diff.

[133]

Synthesis and application of peptide and peptidomimetic/small molecule arrays

SPOT

[179]

prepared by SPOT synthesis; brief description of peptide library types

Extensive review describing polymeric solid supports for SPOT synthesis

SPOT

[592]

(cellulose and polypropylene) amino functionalization of membrane suports,

linker systems

peptide synthesis on solid supports, examples for product quality,

compatibility of polymer membranes for peptide-antibody binding assays (p24

(HIV-1) mab CB4-1 and anti-interleukin-10 mab CB/RS/3),

biological screening (types of peptide libraries, mapping of antibody epitopes and

protein-protein interactions, enzymatic modification of cellulose-bound

peptides, DNA and metal binding peptides, T-cell epitope mapping, and

cellular assays)

Detailed experimental assay protocols for the mapping of linear and

SPOT

[453]

discontinuous antibody epitopes and protein-protein interactions