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university of tampere: faculty of medicine and life sciences: research: markku kulomaa - molecular biotechnology:
Lääketieteen ja biotieteiden tiedekuntaUniversity of TampereLääketieteen ja biotieteiden tiedekunta
Markku Kulomaa - Molecular Biotechnology

Previous publications

Agrawal N, Määttä JAE, Kulomaa MS, Hytönen VP, Johnson MS, Airenne TT
Structural characterization of core-bradavidin in complex with biotin.
PLoS One ;12(4)e0176086, 2017
PMID

Lehtonen SI, Tullila A, Agrawal N, Kukkurainen S, Kähkönen N, Koskinen M, Nevanen TK, Johnson MS, Airenne TT, Kulomaa MS, Riihimäki TA, Hytönen VP
Artificial Avidin-Based Receptors for a Panel of Small Molecules.
ACS Chem Biol ;11(1)211-21, 2016
PMID

Koho T, Ihalainen TO, Stark M, Uusi-Kerttula H, Wieneke R, Rahikainen R, Blazevic V, Marjomäki V, Tampé R, Kulomaa MS, Hytönen VP
His-tagged norovirus-like particles: A versatile platform for cellular delivery and surface display.
Eur J Pharm Biopharm ;2015
PMID

Lehtonen SI, Taskinen B, Ojala E, Kukkurainen S, Rahikainen R, Riihimäki TA, Laitinen OH, Kulomaa MS, Hytönen VP
Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning.
Protein Eng Des Sel ;28(1)23-8, 2015
PMID

Taskinen B, Zauner D, Lehtonen SI, Koskinen M, Thomson C, Kähkönen N, Kukkurainen S, Määttä JA, Ihalainen TO, Kulomaa MS, Gruber HJ, Hytönen VP
Switchavidin: reversible biotin-avidin-biotin bridges with high affinity and specificity.
Bioconjug Chem ;25(12)2233-43, 2014
PMID

Kurppa K, Hytönen VP, Nakari-Setälä T, Kulomaa MS, Linder MB
Molecular engineering of avidin and hydrophobin for functional self-assembling interfaces.
Colloids Surf B Biointerfaces ;2014
PMID

Tossavainen H, Kukkurainen S, Määttä JA, Kähkönen N, Pihlajamaa T, Hytönen VP, Kulomaa MS, Permi P
Chimeric Avidin--NMR structure and dynamics of a 56 kDa homotetrameric thermostable protein.
PLoS One ;9(6)e100564, 2014
PMID

Taskinen B, Airenne TT, Jänis J, Rahikainen R, Johnson MS, Kulomaa MS, Hytönen VP
A novel chimeric avidin with increased thermal stability using DNA shuffling.
PLoS One ;9(3)e92058, 2014
PMID

Koho T, Koivunen MR, Oikarinen S, Kummola L, Mäkinen S, Mähönen AJ, Sioofy-Khojine A, Marjomäki V, Kazmertsuk A, Junttila I, Kulomaa MS, Hyöty H, Hytönen VP, Laitinen OH
Coxsackievirus B3 VLPs purified by ion exchange chromatography elicit strong immune responses in mice.
Antiviral Res ;2014
PMID

Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP
Zebavidin - an avidin-like protein from zebrafish.
PLoS One 2013 ;8(10)e77207
PMID

Leppiniemi J, Meir A, Kähkönen N, Kukkurainen S, Määttä JA, Ojanen M, Jänis J, Kulomaa MS, Livnah O, Hytönen VP
The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins.
Protein Sci 2013 ;22(7)980-94
PMID

Tossavainen H, Helppolainen SH, Määttä JA, Pihlajamaa T, Hytönen VP, Kulomaa MS, Permi P
Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms.
Biomol NMR Assign 2013 ;7(1)35-8
PMID

Leppiniemi J, Grönroos T, Määttä JA, Johnson MS, Kulomaa MS, Hytönen VP, Airenne TT
Structure of bradavidin-C-terminal residues act as intrinsic ligands.
PLoS One 2012 ;7(5)e35962
PMID

Koho T, Mäntylä T, Laurinmäki P, Huhti L, Butcher SJ, Vesikari T, Kulomaa MS, Hytönen VP
Purification of norovirus-like particles (VLPs) by ion exchange chromatography.
J Virol Methods 2012 ;181(1)6-11
PMID

Niederhauser B, Siivonen J, Määttä JA, Jänis J, Kulomaa MS, Hytönen VP
DNA family shuffling within the chicken avidin protein family - A shortcut to more powerful protein tools.
J Biotechnol 2012 ;157(1)38-49
PMID

Koho T, Huhti L, Blazevic V, Nurminen K, Butcher SJ, Laurinmäki P, Kalkkinen N, Rönnholm G, Vesikari T, Hytönen VP, Kulomaa MS
Production and characterization of virus-like particles and the P domain protein of GII.4 norovirus.
J Virol Methods 2012 ;179(1)1-7
PMID

Heikkinen JJ, Kivimäki L, Määttä JA, Mäkelä I, Hakalahti L, Takkinen K, Kulomaa MS, Hytönen VP, Hormi OE
Versatile bio-ink for covalent immobilization of chimeric avidin on sol-gel substrates.
Colloids Surf B Biointerfaces 2011 ;87(2)409-14
PMID

Riihimäki TA, Hiltunen S, Rangl M, Nordlund HR, Määttä JA, Ebner A, Hinterdorfer P, Kulomaa MS, Takkinen K, Hytönen VP
Modification of the loops in the ligand-binding site turns avidin into a steroid-binding protein.
BMC Biotechnol 2011 ;1164
PMID

Riihimäki TA, Kukkurainen S, Varjonen S, Hörhä J, Nyholm TK, Kulomaa MS, Hytönen VP
Construction of chimeric dual-chain avidin by tandem fusion of the related avidins.
PLoS One 2011 ;6(5)e20535
PMID

Heikkinen JJ, Riihimäki TA, Määttä JA, Suomela SE, Kantomaa J, Kulomaa MS, Hytönen VP, Hormi OE
Covalent biofunctionalization of cellulose acetate with thermostable chimeric avidin.
ACS Appl Mater Interfaces 2011 ;3(7)2240-5
PMID

Leppiniemi J, Määttä JA, Hammaren H, Soikkeli M, Laitaoja M, Jänis J, Kulomaa MS, Hytönen VP
Bifunctional avidin with covalently modifiable ligand binding site.
PLoS One 2011 ;6(1)e16576
PMID

Määttä JA, Eisenberg-Domovich Y, Nordlund HR, Hayouka R, Kulomaa MS, Livnah O, Hytönen VP
Chimeric avidin shows stability against harsh chemical conditions--biochemical analysis and 3D structure.
Biotechnol Bioeng 2011 ;108(3)481-90
PMID

Määttä JA, Helppolainen SH, Hytönen VP, Johnson MS, Kulomaa MS, Airenne TT, Nordlund HR
Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis.
BMC Struct Biol 2009 ;963
PMID

Hilvo M, Salzano AM, Innocenti A, Kulomaa MS, Scozzafava A, Scaloni A, Parkkila S, Supuran CT
Cloning, expression, post-translational modifications and inhibition studies on the latest mammalian carbonic anhydrase isoform, CA XV.
J Med Chem 2009 ;52(3)646-54
PMID

Meir A, Helppolainen SH, Podoly E, Nordlund HR, Hytönen VP, Määttä JA, Wilchek M, Bayer EA, Kulomaa MS, Livnah O
Crystal structure of rhizavidin: insights into the enigmatic high-affinity interaction of an innate biotin-binding protein dimer.
J Mol Biol 2009 ;386(2)379-90
PMID

Hilvo M, Baranauskiene L, Salzano AM, Scaloni A, Matulis D, Innocenti A, Scozzafava A, Monti SM, Di Fiore A, De Simone G, Lindfors M, Jänis J, Valjakka J, Pastoreková S, Pastorek J, Kulomaa MS, Nordlund HR, Supuran CT, Parkkila S
Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes.
J Biol Chem ;283(41)27799-809, 2008
PMID

Hayouka R, Eisenberg-Domovich Y, Hytönen VP, Määttä JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O
Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.
Acta Crystallogr D Biol Crystallogr ;64(Pt 3)302-8, 2008
PMID

Laakkonen JP, Kaikkonen MU, Ronkainen PH, Ihalainen TO, Niskanen EA, Häkkinen M, Salminen M, Kulomaa MS, Ylä-Herttuala S, Airenne KJ, Vihinen-Ranta M
Baculovirus-mediated immediate-early gene expression and nuclear reorganization in human cells.
Cell Microbiol ;10(3)667-81, 2008
PMID

Määttä JA, Airenne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS, Hytönen VP
Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis.
Chembiochem ;9(7)1124-35, 2008
PMID

Innocenti A, Hilvo M, Scozzafava A, Lindfors M, Nordlund HR, Kulomaa MS, Parkkila S, Supuran CT
Carbonic anhydrase inhibitors: the very weak inhibitors dithiothreitol, beta-mercaptoethanol, tris(carboxyethyl)phosphine and threitol interfere with the binding of sulfonamides to isozymes II and IX.
Bioorg Med Chem Lett ;18(6)1898-903, 2008
PMID

Helppolainen SH, Nurminen KP, Määttä JA, Halling KK, Slotte JP, Huhtala T, Liimatainen T, Ylä-Herttuala S, Airenne KJ, Närvänen A, Jänis J, Vainiotalo P, Valjakka J, Kulomaa MS, Nordlund HR
Rhizavidin from Rhizobium etli: the first natural dimer in the avidin protein family.
Biochem J 2007 ;405(3)397-405
PMID

Laitinen OH, Nordlund HR, Hytönen VP, Kulomaa MS
Brave new (strept)avidins in biotechnology.
Trends Biotechnol 2007 ;25(6)269-77
PMID

Hytönen VP, Määttä JA, Niskanen EA, Huuskonen J, Helttunen KJ, Halling KK, Nordlund HR, Rissanen K, Johnson MS, Salminen TA, Kulomaa MS, Laitinen OH, Airenne TT
Structure and characterization of a novel chicken biotin-binding protein A (BBP-A).
BMC Struct Biol 2007 ;78
PMID

Kallistova AY, Kevbrina MV, Nekrasova VK, Shnyrev NA, Einola JK, Kulomaa MS, Rintala JA, Nozhevnikova AN
Enumeration of methanotrophic bacteria in the cover soil of an aged municipal landfill.
Microb Ecol 2007 ;54(4)637-45
PMID

Rinne J, Albarran B, Jylhävä J, Ihalainen TO, Kankaanpää P, Hytönen VP, Stayton PS, Kulomaa MS, Vihinen-Ranta M
Internalization of novel non-viral vector TAT-streptavidin into human cells.
BMC Biotechnol 2007 ;71
PMID

Laitinen OH, Hytönen VP, Nordlund HR, Kulomaa MS
Genetically engineered avidins and streptavidins.
Cell Mol Life Sci 2006 ;63(24)2992-3017
PMID

Repo S, Paldanius TA, Hytönen VP, Nyholm TK, Halling KK, Huuskonen J, Pentikäinen OT, Rissanen K, Slotte JP, Airenne TT, Salminen TA, Kulomaa MS, Johnson MS
Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4.
Chem Biol 2006 ;13(10)1029-39
PMID

Hytönen VP, Hörhä J, Airenne TT, Niskanen EA, Helttunen KJ, Johnson MS, Salminen TA, Kulomaa MS, Nordlund HR
Controlling quaternary structure assembly: subunit interface engineering and crystal structure of dual chain avidin.
J Mol Biol 2006 ;359(5)1352-63
PMID

Prizant M, Eisenberg-Domovich Y, Hytönen VP, Kulomaa MS, Wilchek M, Bayer EA, Livnah O
Factors dictating the pseudocatalytic efficiency of avidins.
J Mol Biol 2006 ;358(3)754-63
PMID

Hytönen VP, Määttä JA, Kidron H, Halling KK, Hörhä J, Kulomaa T, Nyholm TK, Johnson MS, Salminen TA, Kulomaa MS, Airenne TT
Avidin related protein 2 shows unique structural and functional features among the avidin protein family.
BMC Biotechnol 2005 ;528
PMID

Hytönen VP, Nordlund HR, Hörhä J, Nyholm TK, Hyre DE, Kulomaa T, Porkka EJ, Marttila AT, Stayton PS, Laitinen OH, Kulomaa MS
Dual-affinity avidin molecules.
Proteins 2005 ;61(3)597-607
PMID

Nordlund HR, Laitinen OH, Uotila ST, Kulmala M, Kalkkinen N, Kulomaa MS
Production of Hev b5 as a fluorescent biotin-binding tripartite fusion protein in insect cells.
Biochem Biophys Res Commun 2005 ;336(1)232-8
PMID

Nordlund HR, Hytönen VP, Hörhä J, Määttä JA, White DJ, Halling K, Porkka EJ, Slotte JP, Laitinen OH, Kulomaa MS
Tetravalent single-chain avidin: from subunits to protein domains via circularly permuted avidins.
Biochem J 2005 ;392(Pt 3)485-91
PMID

Eisenberg-Domovich Y, Hytönen VP, Wilchek M, Bayer EA, Kulomaa MS, Livnah O
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
Acta Crystallogr D Biol Crystallogr 2005 ;61(Pt 5)528-38
PMID

Niskanen EA, Hytönen VP, Grapputo A, Nordlund HR, Kulomaa MS, Laitinen OH
Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family.
BMC Genomics 2005 ;6(1)41
PMID

Karisola P, Kotovuori A, Poikonen S, Niskanen E, Kalkkinen N, Turjanmaa K, Palosuo T, Reunala T, Alenius H, Kulomaa MS
Isolated hevein-like domains, but not 31-kd endochitinases, are responsible for IgE-mediated in vitro and in vivo reactions in latex-fruit syndrome.
J Allergy Clin Immunol 2005 ;115(3)598-605
PMID

Laitinen OH, Airenne KJ, Hytönen VP, Peltomaa E, Mähönen AJ, Wirth T, Lind MM, Mäkelä KA, Toivanen PI, Schenkwein D, Heikura T, Nordlund HR, Kulomaa MS, Ylä-Herttuala S
A multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and expression in vivo.
Nucleic Acids Res 2005 ;33(4)e42
PMID

Salminen M, Airenne KJ, Rinnankoski R, Reimari J, Välilehto O, Rinne J, Suikkanen S, Kukkonen S, Ylä-Herttuala S, Kulomaa MS, Vihinen-Ranta M
Improvement in nuclear entry and transgene expression of baculoviruses by disintegration of microtubules in human hepatocytes.
J Virol 2005 ;79(5)2720-8
PMID

Nordlund HR, Hytönen VP, Laitinen OH, Kulomaa MS
Novel avidin-like protein from a root nodule symbiotic bacterium, Bradyrhizobium japonicum.
J Biol Chem 2005 ;280(14)13250-5
PMID

Hytönen VP, Määttä JA, Nyholm TK, Livnah O, Eisenberg-Domovich Y, Hyre D, Nordlund HR, Hörhä J, Niskanen EA, Paldanius T, Kulomaa T, Porkka EJ, Stayton PS, Laitinen OH, Kulomaa MS
Design and construction of highly stable, protease-resistant chimeric avidins.
J Biol Chem 2005 ;280(11)10228-33
PMID

Hytönen VP, Laitinen OH, Airenne TT, Kidron H, Meltola NJ, Porkka EJ, Hörhä J, Paldanius T, Määttä JA, Nordlund HR, Johnson MS, Salminen TA, Airenne KJ, Ylä-Herttuala S, Kulomaa MS
Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli.
Biochem J 2004 ;384(Pt 2)385-90
PMID

Nordlund HR, Laitinen OH, Hytönen VP, Uotila ST, Porkka E, Kulomaa MS
Construction of a dual chain pseudotetrameric chicken avidin by combining two circularly permuted avidins.
J Biol Chem 2004 ;279(35)36715-9
PMID

Karisola P, Mikkola J, Kalkkinen N, Airenne KJ, Laitinen OH, Repo S, Pentikäinen OT, Reunala T, Turjanmaa K, Johnson MS, Palosuo T, Kulomaa MS, Alenius H
Construction of hevein (Hev b 6.02) with reduced allergenicity for immunotherapy of latex allergy by comutation of six amino acid residues on the conformational IgE epitopes.
J Immunol 2004 ;172(4)2621-8
PMID

Räty JK, Airenne KJ, Marttila AT, Marjomäki V, Hytönen VP, Lehtolainen P, Laitinen OH, Mähönen AJ, Kulomaa MS, Ylä-Herttuala S
Enhanced gene delivery by avidin-displaying baculovirus.
Mol Ther 2004 ;9(2)282-91
PMID

Hytönen VP, Nyholm TK, Pentikäinen OT, Vaarno J, Porkka EJ, Nordlund HR, Johnson MS, Slotte JP, Laitinen OH, Kulomaa MS
Chicken avidin-related protein 4/5 shows superior thermal stability when compared with avidin while retaining high affinity to biotin.
J Biol Chem 2004 ;279(10)9337-43
PMID

Nordlund HR, Hytönen VP, Laitinen OH, Uotila ST, Niskanen EA, Savolainen J, Porkka E, Kulomaa MS
Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding.
FEBS Lett 2003 ;555(3)449-54
PMID

Kukkonen SP, Airenne KJ, Marjomäki V, Laitinen OH, Lehtolainen P, Kankaanpää P, Mähönen AJ, Räty JK, Nordlund HR, Oker-Blom C, Kulomaa MS, Ylä-Herttuala S
Baculovirus capsid display: a novel tool for transduction imaging.
Mol Ther 2003 ;8(5)853-62
PMID

Lehtolainen P, Wirth T, Taskinen AK, Lehenkari P, Leppänen O, Lappalainen M, Pulkkanen K, Marttila A, Marjomäki V, Airenne KJ, Horton M, Kulomaa MS, Ylä-Herttuala S
Targeting of biotinylated compounds to its target tissue using a low-density lipoprotein receptor-avidin fusion protein.
Gene Ther 2003 ;10(25)2090-7
PMID

Pazy Y, Eisenberg-Domovich Y, Laitinen OH, Kulomaa MS, Bayer EA, Wilchek M, Livnah O
Dimer-tetramer transition between solution and crystalline states of streptavidin and avidin mutants.
J Bacteriol 2003 ;185(14)4050-6
PMID

Tiirola MA, Suvilampi JE, Kulomaa MS, Rintala JA
Microbial diversity in a thermophilic aerobic biofilm process: analysis by length heterogeneity PCR (LH-PCR).
Water Res 2003 ;37(10)2259-68
PMID

Hytönen VP, Laitinen OH, Grapputo A, Kettunen A, Savolainen J, Kalkkinen N, Marttila AT, Nordlund HR, Nyholm TK, Paganelli G, Kulomaa MS
Characterization of poultry egg-white avidins and their potential as a tool in pretargeting cancer treatment.
Biochem J 2003 ;372(Pt 1)219-25
PMID

Laitinen OH, Nordlund HR, Hytönen VP, Uotila ST, Marttila AT, Savolainen J, Airenne KJ, Livnah O, Bayer EA, Wilchek M, Kulomaa MS
Rational design of an active avidin monomer.
J Biol Chem 2003 ;278(6)4010-4
PMID

Nordlund HR, Laitinen OH, Uotila ST, Nyholm T, Hytönen VP, Slotte JP, Kulomaa MS
Enhancing the thermal stability of avidin. Introduction of disulfide bridges between subunit interfaces.
J Biol Chem 2003 ;278(4)2479-83
PMID

Marttila AT, Hytönen VP, Laitinen OH, Bayer EA, Wilchek M, Kulomaa MS
Mutation of the important Tyr-33 residue of chicken avidin: functional and structural consequences.
Biochem J 2003 ;369(Pt 2)249-54
PMID

Wang H, Marjomäki V, Ovod V, Kulomaa MS
Subcellular localization of pentachlorophenol 4-monooxygenase in Sphingobium chlorophenolicum ATCC 39723.
Biochem Biophys Res Commun 2002 ;299(5)703-9
PMID

Tiirola M, Valtonen ET, Rintamäki-Kinnunen P, Kulomaa MS
Diagnosis of flavobacteriosis by direct amplification of rRNA genes.
Dis Aquat Organ 2002 ;51(2)93-100
PMID

Tiirola MA, Wang H, Paulin L, Kulomaa MS
Evidence for natural horizontal transfer of the pcpB gene in the evolution of polychlorophenol-degrading sphingomonads.
Appl Environ Microbiol 2002 ;68(9)4495-501
PMID

Laitinen OH, Hytönen VP, Ahlroth MK, Pentikäinen OT, Gallagher C, Nordlund HR, Ovod V, Marttila AT, Porkka E, Heino S, Johnson MS, Airenne KJ, Kulomaa MS
Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin.
Biochem J 2002 ;363(Pt 3)609-17
PMID

Karisola P, Alenius H, Mikkola J, Kalkkinen N, Helin J, Pentikäinen OT, Repo S, Reunala T, Turjanmaa K, Johnson MS, Palosuo T, Kulomaa MS
The major conformational IgE-binding epitopes of hevein (Hev b6.02) are identified by a novel chimera-based allergen epitope mapping strategy.
J Biol Chem 2002 ;277(25)22656-61
PMID

Tiirola MA, Männistö MK, Puhakka JA, Kulomaa MS
Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system.
Appl Environ Microbiol 2002 ;68(1)173-80
PMID

Lehtolainen P, Taskinen A, Laukkanen J, Airenne KJ, Heino S, Lappalainen M, Ojala K, Marjomäki V, Martin JF, Kulomaa MS, Ylä-Herttuala S
Cloning and characterization of Scavidin, a fusion protein for the targeted delivery of biotinylated molecules.
J Biol Chem 2002 ;277(10)8545-50
PMID

Pazy Y, Laitinen OH, Ravoy B, Kulomaa MS, Wilchek M, Bayer EA, Livnah O
Crystallization and preliminary X-ray analysis of W120K mutant of streptavidin.
Acta Crystallogr D Biol Crystallogr 2001 ;57(Pt 12)1885-6
PMID

Wang H, Tiirola MA, Puhakka JA, Kulomaa MS
Production and characterization of the recombinant Sphingomonas chlorophenolica pentachlorophenol 4-monooxygenase.
Biochem Biophys Res Commun 2001 ;289(1)161-6
PMID

Ahlroth MK, Ahlroth P, Kulomaa MS
Copy-number fluctuation by unequal crossing-over in the chicken avidin gene family.
Biochem Biophys Res Commun 2001 ;288(2)400-6
PMID

Ahlroth MK, Grapputo A, Laitinen OH, Kulomaa MS
Sequence features and evolutionary mechanisms in the chicken avidin gene family.
Biochem Biophys Res Commun 2001 ;285(3)734-41
PMID

Laitinen OH, Marttila AT, Airenne KJ, Kulik T, Livnah O, Bayer EA, Wilchek M, Kulomaa MS
Biotin induces tetramerization of a recombinant monomeric avidin. A model for protein-protein interactions.
J Biol Chem 2001 ;276(11)8219-24
PMID

 
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