Publications
2021
Scholarly publications
le Paige, U. B., Xiang, S., Hendrix, M. M. R. M.
, Zhang, Y., Folkers, G. E., Weingarth, M., Bonvin, A. M. J. J., Kutateladze, T. G., Voets, I. K.
, Baldus, M., & van Ingen, H. (2021).
Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy.
Magnetic Resonance,
2(1), 187-202.
https://doi.org/10.5194/mr-2-187-2021 Narasimhan, S., Pinto, C., Lucini Paioni, A., van der Zwan, J., Folkers, G. E., & Baldus, M. (2021).
Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy.
Nature protocols,
16, 893-918.
https://doi.org/10.1038/s41596-020-00439-4 2020
Scholarly publications
Narasimhan, S., Folkers, G. E., & Baldus, M. (2020).
When Small becomes Too Big: Expanding the Use of In-Cell Solid-State NMR Spectroscopy.
ChemPlusChem,
85(4), 760-768.
https://doi.org/10.1002/cplu.202000167 2019
Scholarly publications
Narasimhan, S., Scherpe, S.
, Lucini Paioni, A., van der Zwan, J., Folkers, G. E., Ovaa, H.
, & Baldus, M. (2019).
Back Cover: DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells (Angew. Chem. Int. Ed. 37/2019).
Angewandte Chemie-International Edition,
58(37), 13162.
https://doi.org/10.1002/anie.201908849 Narasimhan, S., Scherpe, S.
, Lucini Paioni, A., van der Zwan, J., Folkers, G. E., Ovaa, H.
, & Baldus, M. (2019).
DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells.
Angewandte Chemie,
131(37), 13103-13107.
https://doi.org/10.1002/ange.201903246 Narasimhan, S., Scherpe, S.
, Lucini Paioni, A., van der Zwan, J., Folkers, G. E., Ovaa, H.
, & Baldus, M. (2019).
DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells.
Angewandte Chemie - International Edition,
58(37), 12969-12973.
https://doi.org/10.1002/anie.201903246 Geng, C., Vangone, A., Folkers, G. E., Xue, L. C., & Bonvin, A. M. J. J. (2019).
iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations.
Proteins: Structure, Function and Genetics,
87(2), 110-119.
https://doi.org/10.1002/prot.25630 2018
Scholarly publications
2017
Scholarly publications
Das, D., Faridounnia, M., Kovacic, L., Kaptein, R., Boelens, R., & Folkers, G. E. (2017).
Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex.
Journal of Biological Chemistry,
292(7), 2842-2853.
https://doi.org/10.1074/jbc.M116.747857 Cloin, B. M. C., De Zitter, E.
, Salas Pastene, D., Gielen, V.
, Folkers, G. E., Mikhaylova, M., Bergeler, M., Krajnik, B., Harvey, J.
, Hoogenraad, C. C., Van Meervelt, L., Dedecker, P.
, & Kapitein, L. C. (2017).
Efficient switching of mCherry fluorescence using chemical caging.
Proceedings of the National Academy of Sciences of the United States of America,
114(27), 7013-7018.
https://doi.org/10.1073/pnas.1617280114 2016
Scholarly publications
Kaplan, M., Narasimhan, S., de Heus, C., Mance, D., van Doorn, S., Houben, K., Popov-Celeketic, D., Damman, R., Katrukha, E. A., Jain, P., Geerts, W. J. C., Heck, A. J. R., Folkers, G. E., Kapitein, L. C., Lemeer, S., van Bergen En Henegouwen, P. M. P., & Baldus, M. (2016).
EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR.
Cell,
167(5), 1241-1251.e11.
https://doi.org/10.1016/j.cell.2016.10.038 Dongre, R., Folkers, G. E., Gualerzi, C. O.
, Boelens, R., & Wienk, H. (2016).
A model for the interaction of the G3-subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit.
Protein Science,
25(9), 1722-33.
https://doi.org/10.1002/pro.2977 2015
Scholarly publications
Baker, L. A., Daniëls, M., Van Der Cruijsen, E. A. W., Folkers, G. E., & Baldus, M. (2015).
Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling.
Journal of Biomolecular NMR,
62(2), 199-208.
https://doi.org/10.1007/s10858-015-9936-5 Kaplan, M., Cukkemane, A., Van Zundert, G. C. P., Narasimhan, S., Daniëls, M., Mance, D., Waksman, G.
, Bonvin, A. M. J. J., Fronzes, R.
, Folkers, G. E., & Baldus, M. (2015).
Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR.
Nature Methods,
12(7), 649-652.
https://doi.org/10.1038/nmeth.3406 Faridounnia, M., Wienk, H., Kovacic, L., Folkers, G. E., Jaspers, N. G. J.
, Kaptein, R., Hoeijmakers, J. H. J.
, & Boelens, R. (2015).
The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex.
Journal of Biological Chemistry,
290(33), 20541-20555.
https://doi.org/10.1074/jbc.M114.635169 Baker, L. A., Folkers, G. E., Sinnige, T., Houben, K., Kaplan, M., van der Cruijsen, E. A. W., & Baldus, M. (2015).
Magic-Angle-Spinning Solid-State NMR of Membrane Proteins.
Methods in Enzymology,
557, 307-328.
https://doi.org/10.1016/bs.mie.2014.12.023 2014
Scholarly publications
Khan, F., Daniëls, M. A., Folkers, G. E., Boelens, R., Saqlan Naqvi, S. M.
, & Van Ingen, H. (2014).
Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: Implications for its RNA chaperone function.
Nucleic Acids Research,
42(13), 8705-8718.
https://doi.org/10.1093/nar/gku468 Kastritis, P. L., Garcia Lopes Maia Rodrigues, J., Folkers, G. E., Boelens, R., & Bonvin, A. M. J. J. (2014).
Proteins feel more than they see: Fine-tuning of binding affinity by properties of the non-interacting surface.
Journal of Molecular Biology,
426(14), 2632-2652.
https://doi.org/10.1016/j.jmb.2014.04.017 2013
Scholarly publications
Wienk, H., Slootweg, J. C., Speerstra, S., Kaptein, R., Boelens, R., & Folkers, G. E. (2013). Solution structure of the helix hairpin helix domain of FAAP24 reveals that substrate specificity depends on an evolutionary conserved domain. Nucleic Acids Research, 41, 6739-6749.
Wienk, H. L. J., Slootweg, J. C., Speerstra, S.
, Kaptein, R., Boelens, R., & Folkers, G. E. (2013).
The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition.
Nucleic Acids Research,
41(13), 6739-6749.
https://doi.org/10.1093/nar/gkt354 2012
Scholarly publications
Das, D., Folkers, G. E., van Dijk, M., Jaspers, N. G. J., Hoeijmakers, J. H. J.
, Kaptein, R., & Boelens, R. (2012).
The Structure of the XPF-ssDNA Complex Underscores the Distinct Roles of the XPF and ERCC1 Helix- Hairpin-Helix Domains in ss/ds DNA Recognition.
Structure,
20(4), 667-675.
https://doi.org/10.1016/j.str.2012.02.009 Wienk, H. L. J., Tishchenko, E., Belardinelli, R., Tomaselli, S.
, Dongre, R., Spurio, R.
, Folkers, G. E., Gualerzi, C. O.
, & Boelens, R. (2012).
Structural Dynamics of Bacterial Translation Initiation Factor IF2.
Journal of Biological Chemistry,
287(14), 10922-10932.
https://doi.org/10.1074/jbc.M111.333393 2011
Scholarly publications
Busso, D., Peleg, Y.
, Folkers, G. E., & Celie, P. H. N. (2011).
Expression of potein complexes using multiple E. coli protein co-expression systems: a benchmarking study.
Journal of Structural Biology,
175, 159-170.
https://doi.org/10.1016/j.jsb.2011.03.004Berger, I., Blanco, A. G.
, Boelens, R., Cavarelli, J., Coll, M.
, Folkers, G. E., Nie, Y., Pogenberg, V., Schultz, P., Wilmanns, M., Moras, D., & Poterszman, A. (2011).
Structural insights into transcription complexes.
Journal of Structural Biology,
175(2), 135-146.
https://dspace.library.uu.nl/bitstream/handle/1874/213119/1304-main.pdf?sequence=12010
Scholarly publications
Bird, L. E., Ren, J., Nettleship, J. E.
, Folkers, G. E., Owens, RJ., & Stammers, D. K. (2010).
Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains.
BMC Structural Biology,
10(13), 1-15.
https://dspace.library.uu.nl/bitstream/handle/1874/202650/1472-6807-10-13.pdf?sequence=12009
Scholarly publications
Dadvar, P., Kovanich, D., Folkers, G. E., Rumpel, K., Raijmakers, R., & Heck, A. J. R. (2009). Phosphatidylethanolamine-binding proteins, including RKIP, exhibit affinity for phosphodiesterase-5 inhibitors. ChemBioChem, (10), 2654-2662.
Romanuka, J., Folkers, G. E., Biris, N., Tishchenko, E.
, Wienk, H. L. J., Bonvin, A. M. J. J., Kaptein, R., & Boelens, R. (2009).
Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein–DNA complexes.
Journal of Molecular Biology,
390(3), 478-489.
https://doi.org/10.1016/j.jmb.2009.05.022 Romanuka, J., van den Bulke, H., Kaptein, R., Boelens, R., & Folkers, G. E. (2009). Novel strategies to overcome expression problems encountered with toxic proteins: application to the production of Lac repressor proteins for NMR studies. Protein Expression and Purification, 67(2), 104-112.
Wienk, H. L. J., Lammers, I., Hotze, A. C. G., Wu, J., Wechselberger, R. W., Owens, R., Stammers, D. K., Stuart, D., Kaptein, R., & Folkers, G. E. (2009). The tandem zinc-finger region of human ZHX adopts a novel C2H2 zinc finger structure with a C-terminal extension. Biochemistry, 48(21), 4431-4439.
2008
Scholarly publications
Diercks, T., AB, E., Daniels, M. A.
, de Jong, R. N., Besseling, R.
, Kaptein, R., & Folkers, G. E. (2008).
Solution structure and characterization of the DNA-binding activity of the B3BP–Smr domain.
Journal of Molecular Biology,
383(5), 1156-1170.
https://dspace.library.uu.nl/bitstream/handle/1874/33233/543Supplementary%2520material.pdf?sequence=1 de Jong, R. N., Truffault, V. P. M.
, Diercks, T., AB, E., Daniels, M. A.
, Kaptein, R., & Folkers, G. E. (2008).
Structure and DNA binding of the human Rtf1 Plus3 domain.
Structure,
16(1), 149-159.
https://dspace.library.uu.nl/bitstream/handle/1874/33204/531.pdf?sequence=1 Das, D., Tripsianes, K., Jaspers, N. G. J., Hoeijmakers, J. H. J., Kaptein, R., Boelens, R., & Folkers, G. E. (2008). The HhH domain of the human DNA repair protein XPF forms stable homodimers. Proteins: Structure function and bioinformatics, 70(4), 1551-1563.
2007
Scholarly publications
Kamphuis, M. B., Monti, M. C.
, van den Heuvel, R. H. H., Santos-Sierra, S.
, Folkers, G. E., Lemonnier, M., Diaz-Orejas, R.
, Heck, A. J. R., & Boelens, R. (2007).
Interactions between the toxin kid of the bacterial parD system and the antitoxins Kis and MazE.
Proteins: Structure function and bioinformatics,
67, 219-231.
https://dspace.library.uu.nl/bitstream/handle/1874/26116/524.pdf?sequence=1Tripsianes, K., Folkers, G. E., Zheng, C.
, Das, D., Grinstead, J. S., Kaptein, R., & Boelens, R. (2007).
Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization.
Nucleic Acids Research,
17, 5789-5798.
https://dspace.library.uu.nl/bitstream/handle/1874/26828/528.pdf?sequence=1 2006
Scholarly publications
AB, E., Atkinson, A. R., Banci, L., Bertini, I., Ciofi-Baffoni, S., Brunner, K.
, Diercks, T., Doetsch, V., Engelke, F.
, Folkers, G. E., Griesinger, C., Gronwald, W., Gunther, U., Habeck, M.
, de Jong, R. N., Kalbitzer, H. R., Kieffer, B.
, Leeflang, B. R., Loss, S.
, ... Kaptein, R. (2006).
NMR in the SPINE Structural Proteomics project.
Acta crystallographica. Section D, biological crystallography,
D62, 1150-1161.
https://dspace.library.uu.nl/bitstream/handle/1874/20122/514.pdf?sequence=1Grenha, R., Rzechorzek, N. J., Brannigan, J. A.
, de Jong, R. N., AB, E.
, Diercks, T., Truffault, V. P. M., Ladds, J. C., Fogg, M. J., Bongiorni, C., Perego, M.
, Kaptein, R., Wilson, K. S.
, Folkers, G. E., & Wilkinson, A. J. (2006).
Structural Characterization of Spo0E-like Protein-aspartic Acid Phosphatases That Regulate Sporulation in Bacilli.
Journal of Biological Chemistry,
281(49), 37993-38003.
https://dspace.library.uu.nl/bitstream/handle/1874/20124/516.pdf?sequence=1Jonker, H. R. A., Wechselberger, R. W., Boelens, R., Kaptein, R., & Folkers, G. E. (2006). The intrinsically unstructured domain of PC4 modulates the activity of the structured core through inter- and intramolecular interactions. Biochemistry, 45(15), 5067-5081.
Jonker, H. R. A.
, Wechselberger, R. W., Pinkse, M. W. H., Kaptein, R., & Folkers, G. E. (2006).
Gradual phosphorylation regulates PC4 coactivator function.
The FEBS journal,
273, 1430-1444.
https://dspace.library.uu.nl/bitstream/handle/1874/19762/508.pdf?sequence=1de Jong, R. N., AB, E.
, Diercks, T., Truffault, V. P. M., Daniels, M. A.
, Kaptein, R., & Folkers, G. E. (2006).
Solution Structure of the Human Ubiquitin-specific Protease 15 DUSP Domain.
Journal of Biological Chemistry,
281(8), 5026-5031.
https://dspace.library.uu.nl/bitstream/handle/1874/20094/499.pdf?sequence=1 Milon, P., Tischenko, E. V., Tomsic, J., Caserta, E., Folkers, G. E., La Teana, A., Rodnina, M. V., Pon, C. L., Boelens, R., & Gualerzi, C. O. (2006). The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proceedings of the National Academy of Sciences of the United States of America, 103(38), 13962-13967.
2005
Scholarly publications
Salinas, R. K.
, Folkers, G. E., Bonvin, A. M. J. J., Das, D., Boelens, R., & Kaptein, R. (2005).
Altered specificity in DNA binding by the lac repressor: A mutant lac headpiece that mimics the gal repressor.
ChemBioChem,
6(9), 1628-1637.
https://doi.org/10.1002/cbic.200500049Jonker, H. R. A.
, Wechselberger, R. W., Folkers, G. E., & Kaptein, R. (2005).
Structural properties of the promiscuous VP16 activation domain.
Biochemistry,
44(3), 827-839.
https://doi.org/10.1021/bi0482912Tripsianes, K., Folkers, G. E., AB, E.
, Das, D., Odijk, H., Jaspers, N. G. J., Hoeijmakers, J. H. J.
, Kaptein, R., & Boelens, R. (2005).
The Structure of the Human ERCC1/XPF Interaction Domains Reveals a Complementary Role for the Two Proteins in Nucleotide Excision Repair.
Structure,
13, 1849-1858.
https://dspace.library.uu.nl/bitstream/handle/1874/14818/493.pdf?sequence=1 Patterson, H. M., Brannigan, J. A., Cutting, S. M., Wilson, K. S., Wilkinson, A. J., AB, E.
, Diercks, T., de Jong, R. N., Truffault, V. P. M.
, Folkers, G. E., & Kaptein, R. (2005).
The Structure of Bypass of Forespore C, an Intercompartmental Signaling Factor during Sporulation in Bacillus.
Journal of Biological Chemistry,
280, 36214-36220.
https://dspace.library.uu.nl/bitstream/handle/1874/14817/492.pdf?sequence=12004
Scholarly publications
Dominguez, C., Folkers, G. E., & Boelens, R. (2004). RING domain proteins. In A. Messerschmidt (Ed.), Handbook of metalloproteins. Vol. 3 (pp. 338-350). Wiley.
Folkers, G. E., van Buuren, B. N. M., & Kaptein, R. (2004). Expression screening, protein purification and NMR analysis of human protein domains for structural genomics. Journal of Structural and Functional Genomics, 5(1-2), 119-131.
2002
Scholarly publications
Singh, S.
, Folkers, G. E., Bonvin, A. M. J. J., Boelens, R., Wechselberger, R. W., Niztayev, A.
, & Kaptein, R. (2002).
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
EMBO Journal,
21(22), 6257-6266.
https://doi.org/10.1093/emboj/cdf627https://dspace.library.uu.nl/bitstream/handle/1874/42772/7594843a.pdf?sequence=12001
Scholarly publications
Kalodimos, C.
, Folkers, G. E., Boelens, R., & Kaptein, R. (2001).
Strong DNA binding by covalently linked dimeric Lac headpiece: Evidence for the crucial role of the hinge helices.
Proceedings of the National Academy of Sciences of the United States of America,
98(11), 6039-6044.
http://www.pnas.org/Folkers, G. E., Hanzawa, H., & Boelens, R. (2001). Zinc finger proteins. In Handbook on Metalloproteins (pp. 961-1000). Marcel Dether inc.
2000
Scholarly publications
Nooren, I. M.
, Folkers, G. E., Kaptein, R., Sauer, R. T.
, & Boelens, R. (2000).
Structure and dynamics of the tetrameric mnt repressor and a model for its DNA complex.
Journal of Biomolecular Structure and Dynamics,
17 Suppl 1, 113-22.
https://doi.org/10.1080/07391102.2000.10506611Van Tilborg, P. J. A., Czisch, M., Mulder, F. A. A.
, Folkers, G. E., Bonvin, A. M. J. J., Nair, M.
, Boelens, R., & Kaptein, R. (2000).
Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site.
Biochemistry,
39(30), 8747-8757.
https://doi.org/10.1021/bi991550g1999
Scholarly publications
Spronk, C. A.
, Folkers, G. E., Noordman, A. M.
, Wechselberger, R., van den Brink, N.
, Boelens, R., & Kaptein, R. (1999).
Hinge-helix formation and DNA bending in various lac repressor-operator complexes.
EMBO Journal,
18(22), 6472-80.
https://doi.org/10.1093/emboj/18.22.6472van Tilborg, PJA., Mulder, FAA., de Backer, MME., Nair, M., van Heerde, EC., Folkers, G., van der Saag, PT., Karimi-Nejad, Y., Boelens, R., & Kaptein, R. (1999). Millisecond to microsecond time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation. Biochemistry, 38(7), 1951-1956.
van Eijk, M. J., van Rooijen, M. A., Modina, S., Scesi, L., Folkers, G., van Tol, H. T., Bevers, M. M., Fisher, S. R., Lewin, H. A., Rakacolli, D., Galli, C., de Vaureix, C., Trounson, A. O., Mummery, C. L., & Gandolfi, F. (1999). Molecular cloning, genetic mapping, and developmental expression of bovine POU5F1. Biology of Reproduction, 60(5), 1093-103.