Markus Alahuhta

2024

Cell-Free Systems Biology: Characterizing Central Metabolism of Clostridium thermocellum with a Three-Enzyme Cascade Reaction

Jilani, S. B., Alahuhta, M., Bomble, Y. & Olson, D., 2024, In: ACS Synthetic Biology. 13, 11, p. 3587-3599 13 p.

Research output: Contribution to journal › Article › peer-review

Long-Term Stability of Nicotinamide Cofactors in Common Aqueous Buffers: Implications for Cell-Free Biocatalysis: Article No. 5453

Wolfe, K., Alahuhta, M., Himmel, M., Bomble, Y., Jennings, G. K. & Cliffel, D., 2024, In: Molecules. 29, 22, 11 p.

Research output: Contribution to journal › Article › peer-review

Streamlining Heterologous Expression of Top Carbonic Anhydrases in Escherichia coli: Bioinformatic and Experimental Approaches: Article No. 190

Wei, H., Lunin, V., Alahuhta, M., Himmel, M., Huang, S., Bomble, Y. & Zhang, M., 2024, In: Microbial Cell Factories.

Research output: Contribution to journal › Article › peer-review

2022

Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus

Hengge, N., Mallinson, S., Pason, P., Lunin, V., Alahuhta, M., Chung, D., Himmel, M., Westpheling, J. & Bomble, Y., 2022, In: International Journal of Molecular Sciences. 23, 11, 13 p., 6070.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus Citations

2021

Chimeric Cellobiohydrolase I Expression, Activity, and Biochemical Properties in Three Oleaginous Yeast

Alahuhta, P., Xu, Q., Knoshaug, E., Wang, W., Wei, H., Amore, A., Baker, J., VanderWall, T., Himmel, M. & Zhang, M., 2021, In: Biotechnology for Biofuels. 14, 1, 11 p., 6.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus Citations

Self-Assembling Metabolon Enables the Cell Free Conversion of Glycerol to 1,3-Propanediol

Xu, Q., Alahuhta, M., Hewitt, P., Sarai, N., Wei, H., Hengge, N., Mittal, A., Himmel, M. & Bomble, Y., 2021, In: Frontiers in Energy Research. 9, 10 p., 680313.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus Citations

Target Highlights in CASP14: Analysis of Models by Structure Providers

Alexander, L., Lepore, R., Kryshtafovych, A., Adamopoulos, A., Alahuhta, M., Arvin, A., Bomble, Y., Bottcher, B., Breyton, C., Chiarini, V., Chinnam, N. B., Chiu, W., Fidelis, K., Grinter, R., Gupta, G., Hartmann, M., Hayes, C., Heidebrecht, T., Ilari, A. & Joachimiak, A. & 18 others, Kim, Y., Linares, R., Lovering, A., Lunin, V., Lupas, A., Makbul, C., Michalska, K., Moult, J., Mukherjee, P., Nutt, W., Oliver, S., Perrakis, A., Stols, L., Tainer, J., Topf, M., Tsutakawa, S., Valdivia-Delgado, M. & Schwede, T., 2021, In: Proteins: Structure, Function and Bioinformatics. 89, 12, p. 1647-1672 26 p.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus Citations

2020

Chapter 10: Crystallography of Metabolic Enzymes

Alahuhta, M., Himmel, M., Bomble, Y. & Lunin, V., 2020, Methods in Molecular Biology: Methods in Molecular Biology, Volume 2096. Himmel, M. E. & Bomble, Y. J. (eds.). Humana Press Inc., p. 125-139 15 p. (Methods in Molecular Biology; vol. 2096).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis Xylan O-acetyltransferase XOAT1

Lunin, V., Wang, H.-T., Bharadwaj, V., Alahuhta, M., Pena, M., Yang, J.-Y., Archer-Hartmann, S., Azadi, P., Himmel, M., Moremen, K., York, W., Bomble, Y. & Urbanowicz, B., Jul 2020, In: Plant Cell. 32, 7, p. 2367-2382 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

40 Scopus Citations

Phylogenetics-Based Identification and Characterization of a Superior 2,3-Butanediol Dehydrogenase for Zymomonas mobilis Expression

Subramanian, V., Lunin, V., Farmer, S., Alahuhta, P., Moore, K., Ho, A., Chaudhari, Y., Zhang, M., Himmel, M. & Decker, S., 2020, In: Biotechnology for Biofuels. 13, 1, 20 p., 186.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus Citations

2019

Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely Thermophilic Caldicellulosiruptor Species

Lunin, V., Alahuhta, P., Bomble, Y., Himmel, M., Lee, L., Hart, W., Blumer-Schuette, S., Adams, M. & Kelly, R., 1 Feb 2019, In: Applied and Environmental Microbiology. 85, 3, 13 p., e01983-18.

Research output: Contribution to journal › Article › peer-review

Open Access

13 Scopus Citations

Target Highlights in CASP13: Experimental Target Structures Through the Eyes of Their Authors

Lepore, R., Kryshtafovych, A., Alahuhta, M., Veraszto, H. A., Bomble, Y. J., Bufton, J. C., Bullock, A. N., Caba, C., Cao, H., Davies, O. R., Desfosses, A., Dunne, M., Fidelis, K., Goulding, C. W., Gurusaran, M., Gutsche, I., Harding, C. J., Hartmann, M. D., Hayes, C. S. & Joachimiak, A. & 15 others, Leiman, P. G., Loppnau, P., Lovering, A. L., Lunin, V. V., Michalska, K., Mir-Sanchis, I., Mitra, A. K., Moult, J., Phillips, G. N., Pinkas, D. M., Rice, P. A., Tong, Y., Topf, M., Walton, J. D. & Schwede, T., 2019, In: Proteins: Structure, Function and Bioinformatics. 87, 12, p. 1037-1057 21 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus Citations

2018

An Iterative Computational Design Approach to Increase the Thermal Endurance of a Mesophilic Enzyme

Sammond, D., Donohoe, B., Alahuhta, P., Lunin, V., Chung, D., Mittal, A., Himmel, M., Bomble, Y., Kastelowitz, N., Yin, H., Guss, A. & Sarai, N., 2018, In: Biotechnology for Biofuels. 11, 1, 13 p., 189.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus Citations

Engineering Enhanced Cellobiohydrolase Activity

Decker, S., Knott, B., Alahuhta, P., Linger, J., Lunin, V., Subramanian, V., Xu, Q., VanderWall, T., Crowley, M., Himmel, M., Beckham, G., Taylor II, L., Hobdey, S., Podkaminer, K., Schuster, L., Chaudhari, Y., Adney, W., Baker, J. & Amore, A., 1 Dec 2018, In: Nature Communications. 9, 1, 10 p., 1186.

Research output: Contribution to journal › Article › peer-review

Open Access

75 Scopus Citations

Expression and Characterization of Chimeric CBHI in Yeasts and the Effects of CBHI Fusion to EGII

Alahuhta, P., Xu, Q., Knoshaug, E., Wei, H., Wang, W., VanderWall, T., Himmel, M., Zhang, M., Amore, A. & Baker, J., 2018

Research output: NREL › Poster

Expression of an Endoglucanase-Cellobiohydrolase Fusion Protein in Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi

Alahuhta, P., Xu, Q., Wei, H., Knoshaug, E., Wang, W., VanderWall, T., Himmel, M., Zhang, M. & Baker, J., 2018, In: Biotechnology for Biofuels. 11, 1, 15 p., 322.

Research output: Contribution to journal › Article › peer-review

Open Access

15 Scopus Citations

Novel Multidomain, Multifunctional Glycoside Hydrolases from Highly Lignocellulolytic Caldicellulosiruptor Species

Lunin, V., Alahuhta, P., Himmel, M., Bomble, Y., Conway, J., Crosby, J., Hren, A., Southerland, R., Lee, L., Adams, M. & Kelly, R., 2018, In: AIChE Journal. 64, 12, p. 4218-4228 11 p.

Research output: Contribution to journal › Article › peer-review

21 Scopus Citations

2017

Expression and Secretion of Fungal Endoglucanase II and Chimeric Cellobiohydrolase I in the Oleaginous Yeast Lipomyces starkeyi

Wei, H., Xu, Q., Knoshaug, E., Wang, W., Alahuhta, P., VanderWall, T., Decker, S., Himmel, M., Zhang, M., Baker, J. & Yang, S., 2017, In: Microbial Cell Factories. 16, 1, 16 p., 126.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Scopus Citations

Natural Diversity of Glycoside Hydrolase Family 48 Exoglucanases: Insights from Structure

Bomble, Y., Brunecky, R., Alahuhta, P., Xu, Q., Himmel, M., Lunin, V., Chen, M., Wilson, D., Brady, J. & Sammond, D., 2017, In: Biotechnology for Biofuels. 10, 1, 9 p., 274.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus Citations

Structural, Mutagenic and In Silico Studies of Xyloglucan Fucosylation in Arabidopsis thaliana Suggest a Water-Mediated Mechanism

Crowley, M., Alahuhta, P., Lunin, V., Bomble, Y., Himmel, M., Bharadwaj, V., Urbanowicz, B., Pena, M., Wang, S., Yang, J.-Y., Tuomivaara, S., Moremen, K. & York, W., Sep 2017, In: Plant Journal. 91, 6, p. 931-949 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

53 Scopus Citations

Structure of a Thermobifida fusca Lytic Polysaccharide Monooxygenase and Mutagenesis of Key Residues

Bomble, Y., Alahuhta, P., Lunin, V., Himmel, M., Kruer-Zerhusen, N. & Wilson, D., 2017, In: Biotechnology for Biofuels. 10, 1, 12 p., 243.

Research output: Contribution to journal › Article › peer-review

Open Access

45 Scopus Citations

2016

Crystal Structure and Biochemical Characterization of Chlamydomonas FDX2 Reveal Two Residues that, When Mutated, Partially Confer FDX2 the Redox Potential and Catalytic Properties of FDX1

Boehm, M., Alahuhta, M., Mulder, D. W., Peden, E. A., Long, H., Brunecky, R., Lunin, V. V., King, P. W., Ghirardi, M. L. & Dubini, A., Apr 2016, In: Photosynthesis Research. 128, 1, p. 45-57 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

23 Scopus Citations

Prospect for Developing a Consolidated Bioprocessing (CBP) Strain Using Xylan as the Substrate: the Case Study of Yarrowia lipolytica

Wang, W., Wei, H., Alahuhta, P., Zhang, M. & Himmel, M., 2016

Research output: NREL › Poster

Strategies to Reduce End-Product Inhibition in Family 48 Glycoside Hydrolases

Bomble, Y., Alahuhta, P., Bu, L., Brunecky, R., Xu, Q., Lunin, V., Crowley, M., Himmel, M., Chen, M. & Brady, J., 2016, In: Proteins: Structure, Function and Bioinformatics. 84, 3, p. 295-304 10 p.

Research output: Contribution to journal › Article › peer-review

11 Scopus Citations

2015

Discrete and Structurally Unique Proteins (Tapirins) Mediate Attachment of Extremely Thermophilic Caldicellulosiruptor Species to Cellulose

Blumer-Schuette, S. E., Alahuhta, M., Conway, J. M., Lee, L. L., Zurawski, J. V., Giannone, R. J., Hettich, R. L., Lunin, V. V., Himmel, M. E. & Kelly, R. M., 24 Apr 2015, In: Journal of Biological Chemistry. 290, 17, p. 10645-10656 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

23 Scopus Citations

Expressing Heterologous Cellulases in Oleaginous Yeast Yarrowia lipolytica: Bottlenecks and Opportunities

Wei, H., Wang, W., Alahuhta, P., VanderWall, T., Decker, S., Zhang, M., Himmel, M., Baker, J. & Taylor, L., 2015

Research output: NREL › Poster

The Catalytic Mechanism and Unique Low pH Optimum of Caldicellulosiruptor bescii Family 3 Pectate Lyase

Alahuhta, P., Brunecky, R., Michener, W., Himmel, M., Bomble, Y., Lunin, V., Adams, M., Taylor, L. & Sammond, D., 1 Sep 2015, In: Acta Crystallographica Section D: Biological Crystallography. 71, 9, p. 1946-1954 9 p.

Research output: Contribution to journal › Article › peer-review

11 Scopus Citations

2014

Cel48A from Thermobifida fusca: Structure and Site Directed Mutagenesis of Key Residues

Alahuhta, P., Lunin, V., Brunecky, R., Himmel, M., M., K., M., C., J., B. & D.B., W., 2014, In: Biotechnology and Bioengineering. 111, 4, p. 664-673 10 p.

Research output: Contribution to journal › Article › peer-review

37 Scopus Citations

Engineering Towards a Complete Heterologous Cellulase Secretome in Yarrowia lipolytica Reveals its Potential for Consolidated Bioprocessing

Wei, H., Wang, W., Alahuhta, P., VanderWall, T., Decker, S., Himmel, M., Zhang, M., Baker, J. & Taylor, L., 2014, In: Biotechnology for Biofuels. 7, 10, 14 p., 148.

Research output: Contribution to journal › Article › peer-review

Open Access

42 Scopus Citations

Heterologous Expression of Xylanase Enzymes in Lipogenic Yeast Yarrowia lipolytica

Wang, W., Wei, H., Alahuhta, M., Chen, X., Hyman, D., Johnson, D. K., Zhang, M. & Himmel, M. E., 2014, In: PLoS ONE. 9, 12, 16 p., e111443.

Research output: Contribution to journal › Article › peer-review

Open Access

33 Scopus Citations

Response to Comment on 'Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA'

Brunecky, R., Alahuhta, M., Xu, Q., Donohoe, B. S., Crowley, M. F., Kataeva, I. A., Yang, S. J., Resch, M. G., Adams, M. W. W., Lunin, V. V., Himmel, M. E. & Bomble, Y. J., 2014, In: Science. 344, 6184, 2 p., 578-b.

Research output: Contribution to journal › Article › peer-review

1 Scopus Citations

Structural Studies of Biomass Degrading Enzyme Systems

Lunin, V., Alahuhta, P., Brunecky, R., Donohoe, B., Xu, Q., Bomble, Y. & Himmel, M., 2014

Research output: NREL › Poster

2013

Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA

Brunecky, R., Alahuhta, P., Xu, Q., Donohoe, B., Crowley, M., Resch, M., Lunin, V., Himmel, M., Bomble, Y., Kataeva, I., Yang, S.-J. & Adams, M., 2013, In: Science. 342, 6165, p. 1513-1516 4 p.

Research output: Contribution to journal › Article › peer-review

250 Scopus Citations

Structure of Acidothermus cellulolyticus Family 74 Glycoside Hydrolase at 1.82 Angstrom Resolution

Alahuhta, P., Lunin, V., Himmel, M. & Adney, W., Dec 2013, In: Acta Crystallographica Section F:Structural Biology Communications. 69, 12, p. 1335-1338 4 p.

Research output: Contribution to journal › Article › peer-review

9 Scopus Citations

The Structure and Mode of Action of Caldicellulosiruptor Bescii Family 3 Pectate Lyase in Biomass Deconstruction

Alahuhta, M., Brunecky, R., Chandrayan, P., Kataeva, I., Adams, M. W. W., Himmel, M. E. & Lunin, V. V., Apr 2013, In: Acta Crystallographica Section D: Biological Crystallography. 69, 4, p. 534-539 6 p.

Research output: Contribution to journal › Article › peer-review

7 Scopus Citations

2012

Sequence, Structure, and Evolution of Cellulases in Glycoside Hydrolase Family 48

Sukharnikov, L. O., Alahuhta, M., Brunecky, R., Upadhyay, A., Himmel, M. E., Lunin, V. V. & Zhulin, I. B., 30 Nov 2012, In: Journal of Biological Chemistry. 287, 49, p. 41068-41077 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access