Purification of Peptides in High-Complexity Arrays: A New Method for the Specific Surface Exchange and Purification of Entire Peptide Libraries

138 Pages·2013·6.32 MB·English

by  Christopher Schirwitz (auth.)

Springer Theses
Recognizing Outstanding Ph.D. Research
Christopher Schirwitz

Purification of
Peptides in High-
Complexity Arrays
A New Method for the Specific
Surface Exchange and Purification
of Entire Peptide Libraries
Springer Theses
Recognizing Outstanding Ph.D. Research
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Christopher Schirwitz
Purification of Peptides in
High-Complexity Arrays
A New Method for the Specific
Surface Exchange and Purification
of Entire Peptide Libraries
Doctoral Thesis accepted by
the University of Heidelberg and the German Cancer
Research Center (DKFZ), Germany
123
Author Supervisor
Dr. ChristopherSchirwitz Prof.(apl.) Dr. Reiner Dahint
FunctionalGenome Analysis/ AppliedPhysical Chemistry
Chip-based Peptide Libraries Universityof Heidelberg
GermanCancer Research Center Heidelberg
Heidelberg Germany
Germany
ISSN 2190-5053 ISSN 2190-5061 (electronic)
ISBN 978-3-319-00806-6 ISBN 978-3-319-00807-3 (eBook)
DOI 10.1007/978-3-319-00807-3
SpringerChamHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2013942482
(cid:2)SpringerInternationalPublishingSwitzerland2013
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Parts of this thesis have been published in:
C. Schirwitz, F. F. Löffler, T. Felgenhauer, V. Stadler, A. Nesterov-Müller,
R. Dahint, F. Breitling, and F. R. Bischoff, Purification of High-complexity
Peptide Microarrays by Spatially Resolved Array Transfer to Gold-coated
Membranes, Advanced Materials 2013, 25, 1598–1602.
Supervisor’s Foreword
Comparedtothehumangenomewhichisformedbyapproximately25,000genes,
the human proteome with over a million functional proteins represents a much
higher diversity. Although genetic research provides valuable information on the
proteins which can be translated, a great task in the future will be the exploration
of the entire protein interaction network. Understanding the set of protein inter-
actions will greatly help to identify the mechanisms behind fatal diseases such as
cancer, AIDS, or tuberculosis and, hopefully, provide new cures. Hence, micro
arrayscontainingproteinsorsmallproteinfragmentsintheformofpeptideshave
become of great interest in proteomic research. Using these microarrays, a large
numberof potential target molecules can be screened for interaction with aprobe
in a short time frame.
However, protein and peptide micro arrays are still lacking behind oligonu-
cleotide arrays in terms of density, quality, and manufacturing costs. A new
approachdevelopedattheGermanCancerResearchCenter(DKFZ)hassolvedthe
problems in synthesizing high-density peptide arrays. The current technology is
capableofproducingarrayswithupto40,000differentpeptidespercm2bymeans
ofamicroparticle-basedsolid-phasepeptidesynthesis.SimilartoRonaldFrank’s
Spot synthesis, the peptides are combinatorially synthesized directly on a solid
support, whereby the exact location of each peptide is known.
However, the in situ synthesis bears a conceptual disadvantage: The quality of
the peptides is dependent on the efficiency of the synthesis so that peptide frag-
ments are present in the resulting array among the desired full length peptides. In
peptide–proteininteractionstudiessuchpeptidefragmentscan,forexample,cause
unwanted side reactions and display false binding events. In his Ph.D. thesis,
Christopher Schirwitz presents an innovative approach to improve the quality of
insitusynthesizedhigh-complexitypeptidemicroarrays.Thecentralachievement
isanewmethodallowingforthefastone-steppurificationofentirearrayswithout
loss of resolution or spatial information.
Meanwhile,effortisputintothedevelopmentoflabel-freedetectiontechniques
to screen for interactions in such purified peptide arrays without the need of
fluorescenct labels. As current biosensors allow for the label-free readout of
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viii Supervisor’sForeword
binding events with high sensitivity and lateral resolution, substantial progress is
expected towards the development of a fully integrated, easy-to-use detection
system for insituhigh-throughputscreeningofbiomolecular interactions inhigh-
density peptide arrays. Most likely, other interesting applications will follow.
Heidelberg, June 2013 Prof. Dr. Dahint Reiner
Acknowledgments
I would like to thank PD Dr. F. Ralf Bischoff (DKFZ), Prof. (apl.) Dr. Reiner
Dahint, and Prof. Michael Grunze (Applied Physical Chemistry, University of
Heidelberg) for supervising and supporting my work as my Thesis Advisory
Committee (TAC) in the International Ph.D. Program of the DKFZ. This thesis
would not have been possible without funding and support by the DKFZ, the
Helmholtz International School for Cancer Research, the Max-Buchner research
foundation, the Baden–Württemberg Stiftung, and the federal state of Baden–
Württemberg. I am obliged to my colleagues in the group Chip-based Peptide
Libraries at the DKFZ, the spin-off company PEPperPRINT GmbH, and the
‘‘new’’ department of Peptide Arrays and Antibody Libraries at the Karlsruhe
InstituteforTechnology(KIT),whobroughttheprojectintobeingandcontributed
to its success. Namely: PD Dr. Frank Breitling, PD Dr. F. Ralf Bischoff,
Dr.VolkerStadler,PDDr.AlexanderNesterov-Müller,Dr.ThomasFelgenhauer,
Dr. Felix Löffler, Jürgen Kretschmer, Daniela Rambow, Klaus Leibe, Jochen
Stortz, Michelle Leuenberger, Frieder Märkle, Sebastian Schillo, Jakob Striffler,
Bastian Münster, Yun–Chien Cheng, Lothar Hahn and Fanny Liu. I would also
liketothankouralumni,firstandforemostDr.MarioBeyer,Dr.SimonFernandez,
Dr. Kai König and Dr. Ines Block.
Fortheexcellentcollaborationandscientific supportIam trulythankfultomy
groupatthedepartmentofAppliedPhysicalChemistry,UniversityofHeidelberg:
Prof. (apl.) Dr. Reiner Dahint, Anna Grab, Franziska Schenk, Dr. Noha Waly,
Dr.AndreaSeehuber,HacıOsmanGüvenç,andMustafaSayin.Iwouldalsoliketo
showmygratitudetothegroupsofProf.(apl.)Dr.MichaelZharnikov(inparticular
Dr.NikolausMeyerbrökerformaintainingtheMAX200),Prof.Dr.AxelRosenhahn
andallothercolleaguesatthedepartmentofAppliedPhysicalChemistryunderthe
direction of Prof. Dr. Michael Grunze for their support and valuable scientific
discussions.
Furthermore,IamobligedtomanyofmycolleaguesattheDKFZ,particularly
the groups of PD Dr. Stefan Wiemann (DKFZ) and Prof. Dr. Holger Sültmann,
first and foremostJohanna Sonntag, Christian Schmidt, and Mark Laible. I would
alsoliketothankthegroupofProf.Dr.JoachimSpatz(UniversityofHeidelberg),
in particular Dr. Nadine Perschmann, Theresa Pohl, and Dr. Marcus Abel, for
ix
x Acknowledgments
technical and scientific support. I owe sincere and earnest thankfulness to our
collaboration partners: PD Dr. Peter Findeisen and Dr. Diego Yepes (Institute for
Clinical Chemistry, University of Mannheim). Moreover, it is a great pleasure to
thank everyone who helped me write my dissertation successfully, first and
foremost Hacı Osman Güvenc and Michelle Leuenberger.
I am truly indebted and thankful to my wife, my parents, my sister, my grand
parents, and the rest of my family for inspiring and supporting me in every
situation.