AnAlysis of Coiled Coil oligomerizAtion -A multidisCiplinAry ApproACh Inaugural-Dissertationto obtain the academic degreeDoctor rerum naturalium (Dr. rer. nat.)submitted to the Department of Biology, Chemistry and Pharmacyof Freie Universität Berlin by Dipl. Biol. CARSTEN C. MAHRENHOLZ, MBAborn in Wiesbaden Berlin, September 2010Research for this thesis was conducted from 2007 to 2010, supervised by Dr. Rudolf Volkmerat the Molecular Libraries Group, Charité Berlin.st1 Reviewer: Prof. Dr. Hans-Dieter Volk, Institute of Medical Immunology, Charité Berlinnd2 Reviewer: Prof. Dr. Beate Koksch, Institute for Chemistry and Biochemistry, Freie Universität Berlin date of defence ____________This work was generously funded by the Manchot Foundation (Henkel KGaA) and sup-ported by scholar- and fellowships from the Federation of the Societies of Biochemistry and Molecular Biology, the Charité Medical School, and GlaxoSmithKline.molecular librariesand recognition groupThis work would not have been possible without the kind support of: Rudolf Volkmer, Christiane Landgraf, Ines Kretzschmar, Victor Tapia, and all group members of the Molecular Libraries, Charité, Berlin; Ulrich Bodenhofer, Sepp Hochreiter, Johannes Kepler University, Linz.
Prisca Boisguérin, and icole ittenbring contributed aluable
comments on the manuscript.
y special thans go to Ingrid bfalter for moral support and many
fruitful and stimulating discussions that influenced this or.
is or as generously funded by the
Manchot Foundation enel Gaand sup-
ported by scholar- and felloships from the
Federation of the ocieties of Biochemistry and
Molecular Biology, theCharité Medical chool,
andGlaomithline.
relatiodingthednretsnaenuaceeiotseneetrpnihsnebpreathegoftoneisuterrtcudnsinenci.gyloiobnisegnellahchetascofehetibutiusuoliocedcoilmotif,srtcuuteradnoccurrence hae been described in etensie detail, it might stand to reason that e hae a clearly dran picture of coiled coils. oeer, the rules for oligomeric formation, and thus the ey to biological function, are poorly understood.
is or inestigates the oligomeriation of coiled coils by means of a multidisciplinary approach that combines biochemistry, biophysics, and bioinformatics to shed ne light on the formation of to- and three-stranded coiled coils
Based on comprehensie peptide libraries of C and other coiled coil mutants, the influence of amino acid substitutions on their associa -tion is eamined. Furthermore, this or uses a machine learning ap -proach to tacle coiled coil oligomeriation and identify its underlying rules in the form of eighted amino acid patterns. ese rules form the basis of the highly reliable classification tool PrCoil, hich also isualies the contribution of each indiidual amino acid to the oerall oligomeric tendency of a gien coiled coil seuence.
us, for the first time, a complete netor of seuence parameters that influence oligomeriation is established, and the underlying rules of coiled-coil formation are presented.
is or is rounded off by a methodical contribution. In order for a method to proide a basis for draing sound conclusions, it must be reieed carefully. In the case of peptide libraries, little is non about the cross-reactiity beteen peptides and detection agents. systematic reie and appraisal of the potential of three common read-out systems – ()-, FIC, and biotinstreptaidin-PD – to cross-react ith indiidual amino acids in a peptide seuence is therefore presented.
I
Dasänsterruttu-endunietonenorrPnBeiehudnisderehneugnicsigutherdengeunmI.eigoloiBnegrodereineistdrresuofeareßn Falle des eit erbreiteten Coiled-Coil-otis sind speiell trutur und orommen detailliert beschrie -ben. s ist also naheliegend, on einer ollständig aufgelärten trutur ausugehen. m so erstaunlicher ist aber, dass die Coiled-Coil-ligo -merisierung – entrales riterium für die biologische Funtion dieser Proteine – naheu unerstanden ist.
In dieser rbeit ird das Phänomen der Coiled-Coil-ligomerisierung anhand eines multidisiplinären nsates untersucht. rst die ombi -nation aus Biochemie, Biophysi und Bioinformati erlaubt es, die For -mation on ei- und dreisträngigen Coiled-Coils u erlären
u diesem ec ird auf Basis on umfangreichen Peptidbibliothe -en on C und anderen Coiled-Coil-utanten der influss on minosäure-ubstitutionen auf das ssoiationserhalten untersucht. eiterhin beschäftigt sich die orliegende rbeit mit der ntersuchung des ligomerisierungserhaltens on Coiled-Coils. Basierend auf einer neuen eorie und unter uhilfenahme on upport ector aschi -nen erden die der ligomerisierung ugrundeliegenden egeln prä -sentiert. Diese egeln, in Form on geichteten Beiehungen ischen minosäuren, bilden die rundlage eines neuartigen lassifiations-ools. PrCoil ist in der age, die töchiometrie on Coiled-Coils mit außergeöhnlicher enauigeit orherusagen und den Beitrag einelner minosäuren dau u isualisieren. In Form eines eters on euenparametern ird hier erstmalig ein odell eingeführt, das in der age ist, die Coiled-Coil ligomerisierung u erlären. us methodischer icht feit die nendung einer tandard-ethode nicht or ritischer efleion. nabdingbar für eine uerlässige Inter -pretation on Peptidbibliotheen ist das issen um potenielle reu -reatiität on membrangebundenen Peptiden mit den acheisrea -genien des nalyten. Daher beinhaltet diese rbeit als dritten Focus eine Begutachtung und Beertung on drei in diesem usammenhang häufig genutten acheissystemen. ()-, FIC und Biotin treptaidin-PD erden auf ihre reureatiität mit einelnen mi -nosäuren in Peptidseuenen hin untersucht.
C . n Icetinoi.la.P,ccgemoPsualbinntgihaeuhlinfirCric,bidethtsdserceeaetrpsatlor.thteftnbdooraetuuc,ttoFpycileaaedfoeoeampllriCoc.lcaicil.eh-C. a structural motif, being commonly described as consisting of beteen to and seenaof the proteins in the Protein-helices. lmost Data Ban (PDB) Bernsteinet al., contain coiled coil regions adleyet al.of hich more than sho dimeric or tri -, , meric interactions. Due to their ability to oligomerie, coiled coils per -form, either on their on or as part of larger protein complees, a ariety of important cellular functions Burhardet al., . eir ubi-uity and the stable interactions of their helices mae coiled coils ideal building blocs for designing noel proteins. Furthermore, coiled coil interactions hae recently attracted attention as promising drug targets trausset al.successful inhibition of membrane fu -, . eir use in sion proteins of iruses such as I Bianchiet al., and aian in-fluena ussellet al.supports the concept of rational drug design, based on coiled coil proteins cFarlaneet al., . oadays, coiled coils are used etensiely and successfully to rationally design multi-stranded structures for applications including basic research, biotechnol -ogy, nanotechnology, material science, and medicine. e ide range of applications and the important functions these structures play in almost all biological processes highlight the need for a detailed understanding of the factors that control coiled-coil folding and oligomeriation. page
Figure 1 | Schematic representation and struc -ture of the parallel dimeric coiled-coil mo -tif. (A) elical heel diagram looing don the helical ais from the - to the C-terminus. eptad positions are labeleda–g anda–g res-pectiely. Positionsa,d,e, andgare color-coded. (B)In the side ie, the helical bacbones are represented by cylinders, the side chains by n -obs, and the path of the polypeptide chain is indicated by a line rapped around the cylin -ders. For simplicity, the supercoiling of the he -lices is not shon. hile residues at positionsa(purple) andd(blue) mae up the hydrophobic interface, residues at positionse (orange) andg(red) pac against the hydrophobic core. ey can participate in interhelical electrostatic in -teractions beteen residue i (g of one position) heli and residue i of the other heli (e po-sition in the net heptad), as indicated by the hatched bars. lso indicated is the corea posi-tion (green), hich is often occupied by polar residues mediating strand-pairing specificity. (Figure adapted from asonet al.)
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oday, a plethora of information about coiled coils is aailable, including their prealence, seuence characteristics, and struc -tures. s illustrated inFigure 1, they hae in common a peri -odically recurrent seuence called a heptad repeat of the form (abcdefg)n. sually, the positionsaanddin these repeats are occupied by hydrophobic amino acids located at the hydrophobic core crucial for tertiary structure, hile positionseandgtypically are charged residues ’heaet al., .
A
B
ese obious regularities are used to predict coiled coil segments in amino acid seuences upaset al., Deloreniet al., c-Donnellet al., . ence, one might epect our understanding of coiled coils to be complete. ost remarably, hoeer, the hidden and more comple rules for oligomeric formation, and thus the ey to bi -ological function, are poorly understood. first but crude indicator of hether the oligomeric state of a coiled coil is dimeric (Figure 2) or trimeric (Figure 3) may be its intra etra-cellular prealence and -upaset al., , but it clearly does not proide any information about the seuence features that goern oligomeriation.
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Figure 2 | Eamples and helical heel diagram of dimeric coiled coils. are both the Displayed complete proteins and details of the a-helices of (A) and tropomyosin() the D-bound c-unc-un P dimer. ropomyosin mediates the interactions beteen the troponin comple and actin so as to regulate muscle contraction eis et al., . e c-un oncoprotein is a maor component of the transcription factor comple P-, hich regulates the epression of multiple genes essential for cell proliferation, differentiati -on, and apoptosis artlet al., .(B)elical heel diagram of a dimer looing don the he -lical ais from the - to the C-terminus. eptad positions are labeled from a to g. rros repre -sent the interhelical electrostatic interactions.
Despite etensie eperimental and computational efforts such as mutation analysis, , -ray crystallography, and statistics upaset al., Portichet al., ingraset al., heriffet al., uet al., , our noledge of hich oligomer a specific coiled coil forms has, until no, been limited to describing the phenomenon on the basis of a small number of protein samples.
B A
B A
Figure 3 | Eamples and helical heel diagram of trimeric coiled coils.Displayed are both the complete proteins and details of thea-helices of(A) the surface transmembrane glycoprotein (P) of the ebola irus and()mannose-bin-ding lectin (B). P is responsible for bin -ding to target cells and subseuent fusion of the iral and host-cell membranes alasheichet al., . B is a calcium-dependent serum protein that plays a role in the innate immune response by binding to carbohydrates on the sur -face of a ide range of pathogens urner, . ll figures ere created using Py (httppy -mol.sourceforge.net)(B)elical heel diagram of a trimer looing don the helical ais from the - to the C-terminus. eptad positions are labe -led from a to g. rros represent the interhelical electrostatic interactions.
o, as the amount of aailable post-genomic seuence data is groing rapidly, the challenge is to eplain coiled coil oligomeriation by etract -ing an actual set of rules from this data.