Tieteelliset julkaisut
Protein discovery
(Please scroll to Protein engineering below)
Enzymatically and chemically oxidized lignin nanoparticles for biomaterial applications.
Mattinen M-L, Valle-Delgado JJ, Leskinen T, Anttila T, Riviere G, Sipponen M, Paananen A, Lintinen K, Kostiainen M and Österberg M.
Enzyme Microb. Technol. 2018, 111, 48–56. DOI: 10.1016/j.enzmictec.2018.01.005
Simple process for lignin nanoparticle preparation.
Lievonen M, Valle-Delgado JJ, Mattinen M-L, Hult E-L, Lintinen K, Kostiainen MA, Paananen A, Szilvay GR, Setälä H and Österberg M.
Green Chem., 2016, 18, 1416–1422. http://dx.doi.org/10.1039/c5gc01436k
Keratin-reinforced cellulose filaments from ionic liquid solutions.
Kammiovirta K, Jääskeläinen A-S, Kuutti L, Holopainen-Mantila U, Paananen A, Suurnäkki A and Orelma H.
RSC Adv., 2016, 6, 88797-88806. http://dx.doi.org/10.1039/C6RA20204G
Swollenin from Trichoderma reesei exhibits hydrolytic activity against cellulosic substrates with features of both endoglucanases and cellobiohydrolases.
Andberg M, Penttilä M, Saloheimo M.
Bioresour Technol. 2015 Apr;181:105-13. http://www.ncbi.nlm.nih.gov/pubmed/25643956
Interaction of transglutaminase with adsorbed and spread films of β-casein and к-casein.
Ridout MJ, Paananen A, Mamode A, Linder MB, Wilde PJ.
Colloids Surf B Biointerfaces. 2015 Apr 1;128:254-60. http://www.ncbi.nlm.nih.gov/pubmed/25686794
Adsorption of oat proteins to air-water interface in relation to their colloidal state.
Ercili-Cura D, Miyamoto A, Paananen A, Yoshii H, Poutanen K and Partanen R.
Food Hydrocolloids (2015) 44, 183–190.
Heterotrophic communities supplied by ancient organic carbon predominate in deep fennoscandian bedrock fluids.
Purkamo L, Bomberg M, Nyyssönen M, Kukkonen I, Ahonen L, Itävaara M.
Microb Ecol. 2015 Feb;69(2):319-32. http://www.ncbi.nlm.nih.gov/pubmed/25260922
Rapid reactivation of deep subsurface microbes in the presence of C-1 compounds.
Rajala P, Bomberg M, Kietäväinen R, Kukkonen I, Ahonen L, Nyyssönen M, Itävaara M.
Microorganisms (2015) 3, 17-33, doi:10.3390/microorganisms3010017, Open access, Microorganisms. ISSN 2076-2607, www.mdpi.com/journal/microorganisms.
Purification, crystallization and preliminary X-ray diffraction analysis of a novel keto-deoxy-D-galactarate (KDG) dehydratase from Agrobacterium tumefaciens.
Taberman H, Andberg M, Parkkinen T, Richard P, Hakulinen N, Koivula A, Rouvinen J.
Acta Crystallogr F Struct Biol Commun. 2014 Jan;70(Pt 1):49-52. http://www.ncbi.nlm.nih.gov/pubmed/24419616
Single-molecule imaging analysis of elementary reaction steps of Trichoderma reesei cellobiohydrolase I (Cel7A) hydrolyzing crystalline cellulose Iα and IIII.
Shibafuji Y, Nakamura A, Uchihashi T, Sugimoto N, Fukuda S, Watanabe H, Samejima M, Ando T, Noji H, Koivula A, Igarashi K, Iino R.
J Biol Chem. 2014 May 16;289(20):14056-65. http://www.ncbi.nlm.nih.gov/pubmed/24692563
L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae.
Aro-Kärkkäinen N, Toivari M, Maaheimo H, Ylilauri M, Pentikäinen OT, Andberg M, Oja M, Penttilä M, Wiebe MG, Ruohonen L, Koivula A.
Appl Microbiol Biotechnol. 2014 Dec;98(23):9653-65. http://www.ncbi.nlm.nih.gov/pubmed/25236800
Structure and function of a decarboxylating Agrobacterium tumefaciens keto-deoxy-d-galactarate dehydratase.
Taberman H, Andberg M, Parkkinen T, Jänis J, Penttilä M, Hakulinen N, Koivula A, Rouvinen J.
Biochemistry. 2014 Dec 30;53(51):8052-60. http://www.ncbi.nlm.nih.gov/pubmed/25454257
Micelle formation of coenzyme Q10 with dipotassium glycyrrhizate using inclusion complex of coenzyme Q10 with γ-cyclodextrin.
Uekaji Y, Onishi M, Nakata D, Terao K, Paananen A, Partanen R, Yoshii H.
J Phys Chem B. 2014 Oct 2;118(39):11480-6. http://www.ncbi.nlm.nih.gov/pubmed/25187379
Hydrophobin film structure for HFBI and HFBII and mechanism for accelerated film formation.
Magarkar A, Mele N, Abdel-Rahman N, Butcher S, Torkkeli M, Serimaa R, Paananen A, Linder M, Bunker A.
PLoS Comput Biol. 2014 Jul 31;10(7):e1003745. http://www.ncbi.nlm.nih.gov/pubmed/25079355
Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield.
Nyyssönen M, Hultman J, Ahonen L, Kukkonen I, Paulin L, Laine P, Itävaara M, Auvinen P.
ISME J. 2014 Jan;8(1):126-38. http://www.ncbi.nlm.nih.gov/pubmed/23949662
A spectroscopic characterization of a phenolic natural mediator in the laccase biocatalytic reaction.
Martorana A, Sorace L, Boer H, Vazquez-Duhalt R, Basosi R.
Journal of Molecular Catalysis B: Enzymatic (2013) 97: 203–208
Effect of temperature on lignin-derived inhibition studied with three structurally different cellobiohydrolases.
Rahikainen JL, Moilanen U, Nurmi-Rantala S, Lappas A, Koivula A, Viikari L, Kruus K.
Bioresour Technol. 2013 Oct;146:118-25. http://www.ncbi.nlm.nih.gov/pubmed/23920120
Novel Penicillium cellulases for total hydrolysis of lignocellulosics.
Marjamaa K, Toth K, Bromann PA, Szakacs G, Kruus K.
Enzyme Microb Technol. 2013 May 10;52(6-7):358-69. http://www.ncbi.nlm.nih.gov/pubmed/23608505
Swollenin aids in the amorphogenesis step during the enzymatic hydrolysis of pretreated biomass.
Gourlay K, Hu J, Arantes V, Andberg M, Saloheimo M, Penttilä M, Saddler J.
Bioresour Technol. 2013 Aug;142:498-503. http://www.ncbi.nlm.nih.gov/pubmed/23759433
Cellulase-lignin interactions-the role of carbohydrate-binding module and pH in non-productive binding.
Rahikainen JL, Evans JD, Mikander S, Kalliola A, Puranen T, Tamminen T, Marjamaa K, Kruus K.
Enzyme Microb Technol. 2013 Oct 10;53(5):315-21. http://www.ncbi.nlm.nih.gov/pubmed/24034430
Preferential adsorption and activity of monocomponent cellulases on lignocellulose thin films with varying lignin content.
Martín-Sampedro R, Rahikainen JL, Johansson LS, Marjamaa K, Laine J, Kruus K, Rojas OJ.
Biomacromolecules. 2013 Apr 8;14(4):1231-9. http://www.ncbi.nlm.nih.gov/pubmed/23484974
Inhibitory effect of lignin during cellulose bioconversion: the effect of lignin chemistry on non-productive enzyme adsorption.
Rahikainen JL, Martin-Sampedro R, Heikkinen H, Rovio S, Marjamaa K, Tamminen T, Rojas OJ, Kruus K.
Bioresour Technol. 2013 Apr;133:270-8. http://www.ncbi.nlm.nih.gov/pubmed/23428824
Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones.
Purkamo L, Bomberg M, Nyyssönen M, Kukkonen I, Ahonen L, Kietäväinen R, Itävaara M.
FEMS Microbiol Ecol. 2013 Aug;85(2):324-37. http://www.ncbi.nlm.nih.gov/pubmed/23560597
Visualization of cellobiohydrolase I from Trichoderma reesei moving on crystalline cellulose using high-speed atomic force microscopy.
Igarashi K, Uchihashi T, Koivula A, Wada M, Kimura S, Penttilä M, Ando T, Samejima M.
Methods Enzymol. 2012;510:169-82. http://www.ncbi.nlm.nih.gov/pubmed/22608726
Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate.
Andberg M, Maaheimo H, Boer H, Penttilä M, Koivula A, Richard P.
J Biol Chem. 2012 May 18;287(21):17662-71. http://www.ncbi.nlm.nih.gov/pubmed/22493433
Transglutaminase catalyzed cross-linking of sodium caseinate improves oxidative stability of flaxseed oil emulsion.
Ma H, Forssell P, Kylli P, Lampi AM, Buchert J, Boer H, Partanen R.
J Agric Food Chem. 2012 Jun 20;60(24):6223-9. http://www.ncbi.nlm.nih.gov/pubmed/22655797
Methanogenic and sulphate-reducing microbial communities in deep groundwater of crystalline rock fractures in Olkiluoto, Finland.
Nyyssönen M, Bomberg M, Kapanen A, Nousiainen A, Pitkänen P, Itävaara M.
Geomicrobiology Journal (2012) 29, 863–878, 2012, doi-link: 10.1080/01490451.2011.635759
Microbes in bentonite.
Rättö M and Itävaara M.
VTT Technology: (2012) 20, 30 pages, ISBN 978-951-38-7833-7
Self-assembly of class II hydrophobins on polar surfaces.
Grunér MS, Szilvay GR, Berglin M, Lienemann M, Laaksonen P, Linder MB.
Langmuir. 2012 Mar 6;28(9):4293-300. http://www.ncbi.nlm.nih.gov/pubmed/22315927
Direct Electron Transfer of Trametes Hirsuta Laccase in a Dual-Layer-Architecture of Poly(3,4-Ethylenedioxythiophene) Films.
Wang X, Latonen R-M, Sjöberg-Eerola P, Eriksson J-E, Bobacka J, Boer H, Bergelin M.
J. Phys. Chem. (2011) 115, 5919–5929
Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens.
Parkkinen T, Boer H, Jänis J, Andberg M, Penttilä M, Koivula A, Rouvinen J.
J Biol Chem. 2011 Aug 5;286(31):27294-300. http://www.ncbi.nlm.nih.gov/pubmed/21676870
Crystal structure of an ascomycete fungal laccase from Thielavia arenaria--common structural features of asco-laccases.
Kallio JP, Gasparetti C, Andberg M, Boer H, Koivula A, Kruus K, Rouvinen J, Hakulinen N.
FEBS J. 2011 Jul;278(13):2283-95. http://www.ncbi.nlm.nih.gov/pubmed/21535408
Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface.
Igarashi K, Uchihashi T, Koivula A, Wada M, Kimura S, Okamoto T, Penttilä M, Ando T, Samejima M.
Science. 2011 Sep 2;333(6047):1279-82. http://www.ncbi.nlm.nih.gov/pubmed/21885779
Inhibition of enzymatic hydrolysis by residual lignins from softwood--study of enzyme binding and inactivation on lignin-rich surface.
Rahikainen J, Mikander S, Marjamaa K, Tamminen T, Lappas A, Viikari L, Kruus K.
Biotechnol Bioeng. 2011 Dec;108(12):2823-34. http://www.ncbi.nlm.nih.gov/pubmed/21702025
Adsorption of monocomponent enzymes in enzyme mixture analyzed quantitatively during hydrolysis of lignocellulose substrates.
Várnai A, Viikari L, Marjamaa K, Siika-aho M.
Bioresour Technol. 2011 Jan;102(2):1220-7. http://www.ncbi.nlm.nih.gov/pubmed/20736135
Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield.
Itävaara M, Nyyssönen M, Kapanen A, Nousiainen A, Ahonen L, Kukkonen I.
FEMS Microbiol Ecol. 2011 Aug;77(2):295-309. http://www.ncbi.nlm.nih.gov/pubmed/21488910
Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene.
Boer H, Maaheimo H, Koivula A, Penttilä M, Richard P.
Appl Microbiol Biotechnol. 2010 Apr;86(3):901-9. http://www.ncbi.nlm.nih.gov/pubmed/19921179
Bio-electrochemical characterisation of high and low redox potential laccases from fungal and bacterial origin.
Frasconi M, Favero G, Boer H, Koivula A and Mazzei F.
BBA (2010) 1804, 899–908.
Cell wall lignin is polymerised by class III secretable plant peroxidases in Norway spruce.
Fagerstedt KV, Kukkola EM, Koistinen VV, Takahashi J, Marjamaa K.
J Integr Plant Biol. 2010 Feb;52(2):186-94. http://www.ncbi.nlm.nih.gov/pubmed/20377680
Protein engineering
Single-Molecule Force Spectroscopy Reveals Self-Assembly Enhanced Surface Binding of Hydrophobins.
Li B, Wang X, Li Y, Paananen A, Szilvay GR, Qin M, Wang W and Cao Y.
Accepted to Chem. Eur. J. 2018, 10.1002/chem.201801730
Single-molecule force spectroscopy study on modular resilin fusion protein.
Griffo A, Hähl H, Grandthyll S, Muller F, Paananen A, Ilmén M, Szilvay GR, Landowski CP, Penttilä M, Jacobs K, and Laaksonen P.
ACS Omega, 2017, 2 (10), 6906-6915. DOI: 10.1021/acsomega.7b01133
Pure protein bilayers and vesicles from native fungal hydrophobins
Hähl, H., Vargas, J. N., Griffo, A., Laaksonen, P., Szilvay, G., Lienemann, M., Jacobs, K., Seemann, R., Fleury, J.-B.,
Advanced Materials, 2017, 29, 1602888, https://doi.org/10.1002/adma.201602888
Elastic and pH responsive hybrid interfaces created with engineered resilin and nanocellulose.
Fang W, Paananen A, Vitikainen M, Koskela S, Westerholm-Parvinen A, Joensuu J, Landowski C, Penttilä M, Linder MB and Laaksonen P.
Biomacromolecules, 2017, 18(6), 1866-1873. http://dx.doi.org/10.1021/acs.biomac.7b00294
The Dynamics of Multimer Formation of the Amphiphilic Hydrophobin Protein HFBII.
Grunér MS, Paananen A, Szilvay GR and Linder MB.
Colloids Surf. B., 2017, 155, 111–117. http://dx.doi.org/10.1016/j.colsurfb.2017.03.057
Molecular Structure of Hydrophobins Studied with Site-Directed Mutagenesis and Vibrational Sum-Frequency Generation Spectroscopy.
Meister K, Paananen A, Speet B, Lienemann M and Bakker HJ.
J. Phys. Chem., 2017, 121(40), 9398-9402. DOI: 10.1021/acs.jpcb.7b08865
Observation of PH-Induced Protein Reorientation at the Water Surface.
Meister K, Roeters S, Paananen A, Woutersen S, Versluis J, Szilvay GR and Bakker H.
J. Phys. Chem. Lett., 2017, 8, 1772−1776. http://dx.doi.org/10.1021/acs.jpclett.7b00394
Identification of the response of protein N–H vibrations in vibrational sum-frequency generation spectroscopy of aqueous protein films.
Meister K, Paananen A and Bakker HJ.
Phys. Chem. Chem. Phys., 2017, 19(17), 10804-10807. DOI: 10.1039/c6cp08325k
Graphene Biosensor Programming with Genetically Engineered Fusion Protein Monolayers.
Soikkeli M, Kurppa K, Kainlauri M, Arpiainen S, Paananen A, Gunnarsson D, Joensuu JJ, Laaksonen P, Prunnila M, Linder M. and Ahopelto J.
ACS Appl. Mater. Interfaces, 2016, 8, 8257–8264. http://dx.doi.org/10.1021/acsami.6b00123
Self-Assembly of Hydrophobin Classes at the Air-Water Interface.
Meister K, Bäumer A, Szilvay GR, Paananen A and Bakker HJ.
J. Phys. Chem. Lett., 2016, 7, 4067–4071. http://dx.doi.org/10.1021/acs.jpclett.6b01917
Modular architecture of protein binding units for designing properties of cellulose nanomaterials
Malho, J-M., Arola, S., Laaksonen, P., Szilvay, G. R., Ikkala, O., Linder, M. B.,
Angewandte Chemie International Edition, 2015, 54, 12025 – 12028
Hydrophobin as a nanolayer primer that enables the fluorinated coating of poorly reactive polymer surfaces.
Gazzera L, Corti C, Pirrie L, Paananen A, Monfredini A, Cavallo G, Bettini S, Giancane G, Valli L, Linder MB, Resnati G, Milani R and Metrangolo P.
Adv. Mater. Interfaces 2015, 2, article number 1500170. https://doi.org/10.1002/admi.201500170
Charge-Based Engineering of Hydrophobin HFBI: Effect on Interfacial Assembly and Interactions.
Lienemann M, Grunér MS, Paananen A, Siika-Aho M, Linder MB.
Biomacromolecules. 2015 Apr 13;16(4):1283-92. http://www.ncbi.nlm.nih.gov/pubmed/25724119
A synthetically modified hydrophobin showing enhanced fluorous affinity.
Milani R, Pirrie L, Gazzera L, Paananen A, Baldrighi M, Monogioudi E, Cavallo G, Linder M, Resnati G, Metrangolo P.
J Colloid Interface Sci. 2015 Jun 15;448:140-7. http://www.ncbi.nlm.nih.gov/pubmed/25725398
The effect of hydrophobin protein on conductive properties of carbon nanotube field-effect transistors: first study on sensing mechanism
Yotprayoonsak, P., Szilvay, G.R., Laaksonen, P., Linder, M.B., Ahlskog, M.,
Journal of Nanoscience and Nanotechnology, 2015, 15, 2079 – 2087.
Engineering of the function of diamond-like carbon binding peptides through structural design.
Gabryelczyk B, Szilvay GR, Singh VK, Mikkilä J, Kostiainen MA, Koskinen J, Linder MB.
Biomacromolecules. 2015 Feb 9;16(2):476-82. http://www.ncbi.nlm.nih.gov/pubmed/25522202
Engineering chimeric thermostable GH7 cellobiohydrolases in Saccharomyces cerevisiae.
Voutilainen SP, Nurmi-Rantala S, Penttilä M, Koivula A.
Appl Microbiol Biotechnol. 2014 Apr;98(7):2991-3001. http://www.ncbi.nlm.nih.gov/pubmed/23974371
Formation of ceramophilic chitin and biohybrid materials enabled by a genetically engineered bifunctional protein.
Malho JM, Heinonen H, Kontro I, Mushi NE, Serimaa R, Hentze HP, Linder MB, Szilvay GR.
Chem Commun (Camb). 2014 Jul 14;50(55):7348-51. http://www.ncbi.nlm.nih.gov/pubmed/24871427
The tryptophan residue at the active site tunnel entrance of Trichoderma reesei cellobiohydrolase Cel7A is important for initiation of degradation of crystalline cellulose.
Nakamura A, Tsukada T, Auer S, Furuta T, Wada M, Koivula A, Igarashi K, Samejima M.
J Biol Chem. 2013 May 10;288(19):13503-10. http://www.ncbi.nlm.nih.gov/pubmed/23532843
A His-tagged Melanocarpus albomyces laccase and its electrochemistry upon immobilisation on NTA-modified electrodes and in conducting polymer films.
Sosna M, Boer H, Bartlett PN.
Chemphyschem. 2013 Jul 22;14(10):2225-31. http://www.ncbi.nlm.nih.gov/pubmed/23757174
Impact of hydrothermal pre-treatment to chemical composition, enzymatic digestibility and spatial distribution of cell wall polymers.
Holopainen-Mantila U, Marjamaa K, Merali Z, Käsper A, de Bot P, Jääskeläinen AS, Waldron K, Kruus K, Tamminen T.
Bioresour Technol. 2013 Jun;138:156-62. http://www.ncbi.nlm.nih.gov/pubmed/23612175
Directing enzymatic cross-linking activity to the air-water interface by a fusion protein approach.
Paananen A, Ercili-Cura D, Saloheimo M, Lantto R & Linder M.
Soft Matter (2013) 9, 1612 – 1619.
Engineering chitinases for the synthesis of chitin oligosaccharides: catalytic aminoacid mutations convert the GH-18 family glycoside hydrolases into transglycosylases.
Andres E, Boer H, Koivula A, Samain E, Driguez H, Armand S, and Cottaz S.
Journal of Molecular Catalysis B: Enzymatic (2012), 74: 89-96
Metabolic engineering of Saccharomyces cerevisiae for bioconversion of D-xylose to D-xylonate.
Toivari M, Nygård Y, Kumpula EP, Vehkomäki ML, Benčina M, Valkonen M, Maaheimo H, Andberg M, Koivula A, Ruohonen L, Penttilä M, Wiebe MG.
Metab Eng. 2012 Jul;14(4):427-36. http://www.ncbi.nlm.nih.gov/pubmed/22709678
Lignocellulosic ethanol: from science to industry.
Viikari L, Vehmaanperä J and Koivula A.
Biomass and Bioenergy (2012) 46, 13-24.
Genetic engineering in biomimetic composites.
Laaksonen P, Szilvay GR, Linder MB.
Trends Biotechnol. 2012 Apr;30(4):191-7. http://www.ncbi.nlm.nih.gov/pubmed/22310297
High level secretion of cellobiohydrolases by Saccharomyces cerevisiae.
Ilmén M, den Haan R, Brevnova E, McBride J, Wiswall E, Froehlich A, Koivula A, Voutilainen SP, Siika-Aho M, la Grange DC, Thorngren N, Ahlgren S, Mellon M, Deleault K, Rajgarhia V, van Zyl WH, Penttilä M.
Biotechnol Biofuels. 2011 Sep 12;4:30. http://www.ncbi.nlm.nih.gov/pubmed/21910902
Self-assembly of cellulose nanofibrils by genetically engineered fusion proteins.
Varjonen S, Laaksonen P, Paananen A, Valo H, Hähl H, Laaksonen T & Linder M.
Soft Matter (2011) 7, 2402 – 2411.
Engineering of a redox protein for DNA-directed assembly.
Szilvay GR, Brocato S, Ivnitski D, Li C, De La Iglesia P, Lau C, Chi E, Werner-Washburne M, Banta S, Atanassov P.
Chem Commun (Camb). 2011 Jul 14;47(26):7464-6. http://www.ncbi.nlm.nih.gov/pubmed/21541425
Expression of Talaromyces emersonii cellobiohydrolase Cel7A in Saccharomyces cerevisiae and rational mutagenesis to improve its thermostability and activity.
Voutilainen S, Murray P, Tuohy M and Koivula A.
PEDS (2010), 23, 69–79.
Electrochemical evaluation of electron transfer kinetics of high and low redox potential laccases on gold electrode.
Frasconi M, Boer H, Koivula A and Mazzei F.
Electrochimica Acta (2010) 56, 817–82
Performance of a printable enzymatic fuel cell - study on mediated ThL laccase cathode.
Tuurala S, Smolander M, Uotila J, Kaukoniemi O-V, Boer H, Valkiainen M, Vaari A, Koivula A and Jenkins P.
ECS Transactions (2010) 25, 1-10.
Hydrophobins: the protein-amphiphiles of filamentous fungi.
Linder MB, Szilvay GR, Nakari-Setälä T, Penttilä ME.
FEMS Microbiol Rev. 2005 Nov;29(5):877-96. http://www.ncbi.nlm.nih.gov/pubmed/16219510
