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Proteiinien kehitys ja muokkaus

Parempia proteiineja ainutlaatuisilla ominaisuuksilla

​Tutkimme ja kehitämme proteiineja moniin sovellutuksiin: uusia ja parempia entsyymejä sekä nanomateriaaleja ainutlaatuisilla ominaisuuksilla.

Ota meihin yhteyttä, jos haluat parantaa proteiiniesi suorituskykyä ja taloudellisuutta tai haluat kehittää uusia proteiineja sovellutuksiisi.

Olemme tehneet useita kehitysprojekteja asiakkaillemme. Olemme esimerkiksi kehittäneet Mascoma Corporationille hiivan bioetanolin valmistukseen. Sen avulla valmistusprosessiin lisättävän entsyymin määrää on pystytty vähentämään 50 %:lla, mikä tuo huomattavia kustannussäästöjä. 

Entsyymien ja muiden proteiinien kehitystä eri sovellutuksiin

Kehitämme uusia entsyymejä ja muokkaamme niitä eri sovellutuksiin asiakkaan tarpeiden mukaan. Etsimme ja kehitämme uusia aktiivisuuksia, karakterisoimme reaktiomekanismeja ja parannamme entsyymien ominaisuuksia moderneilla proteiininmuokkaustekniikoilla.

Tutkimme ja kehitämme myös uusia biomolekyylejä nanomateriaalisovellutuksiin. Rakennamme toiminnallisia laitteita ja materiaaleja käyttämällä hyväksi proteiinien ja nanomateriaalien välisiä vuorovaikutuksia. Erityisiä fokusalueitamme ovat proteiinien muokkaus, pintatekniikat, vuorovaikutusten karakterisointi, itse-järjestäytyminen ja mikroskopia.

Nykyiset aktiviteettimme ovat fokusoituneet metaboliareittien entsyymien muokkaukseen ja materiaalien funktionalisointiin proteiinien avulla.

Vankkaa osaamista nykyaikaisilla välineillä

Vuosikymmenien kokemuksen lisäksi meillä on erinomaiset tilat ja välineet proteiinien tutkimukseen ja kehitykseen. Klassisten skriinausmenetelmien lisäksi käytämme moderneja genomi- ja metagenomidataan perustuvia tekniikoita. Pystymme analysoimaan suuria määriä näytteitä robotiikan avulla. Käytössämme on laaja kirjo erilaisia spektrometrisia- ja kuvantamislaitteita proteiinien karakterisointiin ja ominaisuuksien tutkimiseen.

Useimmat projekteistamme ovat liittyneet biokemikaaleihin ja -polttoaineisiin sekä nanomateriaaleihin ja elintarvikesovellutuksiin. Osaamisemme on kuitenkin sovellettavissa missä tahansa proteiinikehitystä ja -muokkausta tarvitaan.

 

​Tieteelliset julkaisut

 

Protein discovery

(Please scroll to Protein engineering below) 

 

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

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

 

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