Publications from the Hansen Lab

 

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Vaibhav Kumar Shukla, Gabriella T Heller, D Flemming Hansen. "Biomolecular NMR spectroscopy in the era of artificial intelligence"

Structure (2023) doi: 10.1016/j.str.2023.09.011

 

Vaibhav Kumar Shukla, Lucas Siemons, D Flemming Hansen. "Intrinsic structural dynamics dictate enzymatic activity and inhibition"

Proceedings of the National Academy of Sciences, 120 (41) (2023):e2310910120 doi: 10.1073/pnas.2310910120

 

Gogulan Karunanithy, Vaibhav Kumar Shukla, D Flemming Hansen. "Solution State Methyl NMR Spectroscopy of Large Non-Deuterated Proteins Enabled by Deep Neural Networks"

bioRxiv 2023.09.15.557823 (2023) doi: 10.1101/2023.09.15.557823

 

Gabriella T. Heller, Vaibhav Kumar Shukla, Angelo M. Figueiredo, D Flemming Hansen. "Small-molecule binding to an intrinsically disordered protein revealed by experimental NMR 19F transverse spin-relaxation"

bioRxiv 2023.05.03.539297 (2023) doi: 10.1101/2023.05.03.539297

 

Nicolas Bolik-Coulon, Alexander IM Sever, Robert W Harkness, James M Aramini, Yuki Toyama, D Flemming Hansen, Lewis E Kay. "Less is more: A simple methyl-TROSY based pulse scheme offers improved sensitivity in applications to high molecular weight complexes"

Journal of Magnetic Resonance 346 (2023):107326. doi: 10.1016/j.jmr.2022.107326

 

Nicolas Bolik-Coulon, D. Flemming Hansen, Lewis E. Kay. "Optimizing frequency sampling in CEST experiments"

Journal of biomolecular NMR 76 (2022):167-193. doi: 10.1007/s10858-022-00403-2

 

Gabriella T Heller, Lefan Yu, D Flemming Hansen. "Characterising Intrinsically Disordered Proteins Using NMR Spectroscopy and MD Simulations"

NMR Spectroscopy for Probing Functional Dynamics at Biological Interfaces, edited by Anirban Bhunia, Hanudatta S Atreya, Neeraj Sinha (2022):383-410. doi: 10.1039/9781839165702-00383

 

Gogulan Karunanithy, Tairan Yuwen, Lewis E Kay, D Flemming Hansen. "Towards autonomous analysis of Chemical Exchange Saturation Transfer experiments using Deep Neural Networks"

Journal of biomolecular NMR 76 (2022):75-86. doi: 10.1007/s10858-022-00395-z

 

Zoja Soloviev, Joshua MA Bullock, Juliette MB James, Andrea C Sauerwein, Joanne E Nettleship, Raymond J Owens, D Flemming Hansen, Maya Topf, Konstantinos Thalassinos. "Structural mass spectrometry decodes domain interaction and dynamics of the full-length Human Histone Deacetylase 2"

Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics (2022):140759.  doi: 10.1016/j.bbapap.2022.140759

 

Gogulan Karunanithy, Tairan Yuwen, Lewis E Kay, D Flemming Hansen. "Towards autonomous analysis of Chemical Exchange Saturation Transfer experiments using Deep Neural Networks"

ChemRxiv (2021) doi: 10.26434/chemrxiv-2021-r1cmw

 

Tim A Mollner, Patrick G Isenegger, Brian Josephson, Charles Buchanan, Lukas Lercher, Daniel Oehlrich, D Flemming Hansen, Shabaz Mohammed, Andrew J Baldwin, Véronique Gouverneur, Benjamin G Davis. "Post-translational insertion of boron in proteins to probe and modulate function"

Nature chemical biology 12 (2021):1245-1261. doi: 10.1038/s41589-021-00883-7

 

Yulia Pustovalova, Frank Delaglio, D Levi Craft, Haribabu Arthanari, Ad Bax, Martin Billeter, Mark J Bostock, Hesam Dashti, D Flemming Hansen, Sven G Hyberts, Bruce A Johnson, Krzysztof Kazimierczuk, Hengfa Lu, Mark Maciejewski, Tomas M Miljenović, Mehdi Mobli, Daniel Nietlispach, Vladislav Orekhov, Robert Powers, Xiaobo Qu, Scott Anthony Robson, David Rovnyak, Gerhard Wagner, Jinfa Ying, Matthew Zambrello, Jeffrey C Hoch, David L Donoho, Adam D Schuyler. "NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR"

Magnetic Resonance (2021):843-861. doi: 10.5194/mr-2-843-2021

 

Gogulan Karunanithy, Harold W Mackenzie, D Flemming Hansen. "Virtual Homonuclear Decoupling in Direct Detection Nuclear Magnetic Resonance Experiments Using Deep Neural Networks"

Journal of the American Chemical Society 41 (2021):16935-16942. doi: 10.1021/jacs.1c04010

 

Gogulan Karunanithy, Vaibhav Kumar Shukla, D Flemming Hansen. "Methodological advancements for characterising protein side chains by NMR spectroscopy"

Current opinion in structural biology 70 (2021):61-69. doi: 10.1016/j.sbi.2021.04.002

 

Rita Puglisi, Gogulan Karunanithy, D Flemming Hansen, Annalisa Pastore, Piero Andrea Temussi. "The anatomy of unfolding of Yfh1 is revealed by site-specific fold stability analysis measured by 2D NMR spectroscopy"

Communications Chemistry 4 (2021):1-9. doi: 10.1038/s42004-021-00566-3

 

Vaibhav Kumar Shukla, Lucas Siemons, Francesco L Gervasio, D Flemming Hansen. "Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8"

Chemical Science 12 (2021):9318. doi: 10.1039/D1SC01929E

 

Gogulan Karunanithy, Harold W Mackenzie, D Flemming Hansen. "Virtual Homonuclear Decoupling in Direct Detection NMR Experiments using Deep Neural Networks"

chemRxiv (2021). doi: 10.26434/chemrxiv.14269463

 

Gogulan Karunanithy, D Flemming Hansen. "FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling"

Journal of Biomolecular NMR (2021). doi: 10.1007/s10858-021-00366-w

 

Nicolas D Werbeck, Vaibhav Kumar Shukla, Micha B A Kunze, Havva Yalinca, Ruth B Pritchard, Lucas Siemons, Somnath Mondal, Simon O R Greenwood, John Kirkpatrick, Charles M Marson, D Flemming Hansen. "A distal regulatory region of a class I human histone deacetylase"

Nature Communications 11 (2020):3841. doi: 10.1038/s41467-020-17610-w

 

Gogulan Karunanithy, Jochen Reinstein, D Flemming Hansen. "Multiquantum Chemical Exchange Saturation Transfer NMR to Quantify Symmetrical Exchange: Application to Rotational Dynamics of the Guanidinium Group in Arginine Side Chains"

Journal of Physical Chemistry Letters 11 (2020):5649-5654 doi: 10.1021/acs.jpclett.0c01322

 

Yun Song, Lisbeth Dagil, Louise Fairall, Naomi Robertson, Mingxuan Wu, T. J. Ragan, Christos G. Savva, Almutasem Saleh, Nobuhiro Morone, Micha B.A. Kunze, Andrew G. Jamieson, Philip A. Cole, D. Flemming Hansen, John W.R.Schwabe. "Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex"

Cell Reports 30 (2020): 2699-2711 doi: 10.1016/j.celrep.2020.01.091

 

Simon O.R.Greenwood, A.W. Edith Chan, D. Flemming Hansen, Charles M. Marson. "Potent non-hydroxamate inhibitors of histone deacetylase-8: Role and scope of an isoindolin-2-yl linker with an α-amino amide as the zinc-binding unit"

Bioorganic & Medicinal Chemistry Letters (2020) doi: 10.1016/j.bmcl.2019.126926

 

Lucas Siemons, Harold W Mackenzie, Vaibhav Kumar Shukla, D. Flemming Hansen. "Intra-residue methyl-methyl correlations for valine and leucine residues in large proteins from a 3D-HMBC-HMQC experiment"

Journal of Biomolecular NMR (2019) doi: 10.1007/s10858-019-00287-9

 

Lucas Siemons, Boran Uluca-Yazgi, Ruth B. Pritchard, Stephen McCarthy, Henrike Heise, D. Flemming Hansen. "Determining isoleucine side-chain rotamer-sampling in proteins from 13C chemical shift"

Chemical Communications (2019) doi: 10.1039/c9cc06496f

 

Rachael Dickman, Emma Danelius, Serena A. Mitchell, D. Flemming Hansen, Máté Erdélyi, Alethea B. Tabor. "A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1–12): Synthesis and NMR Ensemble Analysis of Nisin(1–12) and Analogues"

Chemistry - A European Journal (2019) doi: 10.1002/chem.201902814

 

Rachael Dickman, Serena A. Mitchell, Angelo M. Figueiredo, D. Flemming Hansen, Alethea B. Tabor. "Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B"

Journal of Organic Chemistry 84 (2019): 11493-11512 doi: 10.1021/acs.joc.9b01253

 

D. Flemming Hansen. "Using Deep Neural Networks to Reconstruct Non-uniformly Sampled NMR Spectra"

Journal of Biomolecular NMR 73 (2019): 577-585 doi: 10.1007/s10858-019-00265-1

 

Lisbeth Dagil, Kathrin S. Troelsen, Gert Bolt, Lars Thim, Bo Wu, Xin Zhao, Edward G.D. Tuddenham, Thomas E. Nielsen, David A. Tanner, Johan H. Faber, Jens Breinholt, Jakob E. Rasmussen, D. Flemming Hansen. "Interaction between the a3 region of Factor VIII and the TIL'E' domains of the von Willebrand Factor"

Biophysical Journal 117 (2019): 479-489 doi: 10.1016/j.bpj.2019.07.007

 

Ruth B. Pritchard, D. Flemming Hansen. "Characterising side chains in large proteins by protonless 13C-detected NMR spectroscopy"

Nature Communications 10 (2019):1747 doi: 10.1038/s41467-019-09743-4

 

Antonija Kuzmanic, Ruth B. Pritchard, D. Flemming Hansen, Francesco Luigi Gervasio. "Importance of the Force-Field Choice in Capturing Functionally Relevant Dynamics in Von Willebrand Factor"

Journal of Physical Chemistry Letters 10 (2019): 1928-1934 doi: 10.1021/acs.jpclett.9b00517

 

Harold W Mackenzie, D. Flemming Hansen. "Arginine Side-Chain Hydrogen Exchange: Quantifying Arginine Side-Chain Interactions in Solution"

Chemphyschem. 20 (2019): 252-259 doi: 10.1002/cphc.201800598  Front Cover  Editorial Comment

 

Anusha B. Gopalan, D. Flemming Hansen, Pramodh Vallurupalli. "CPMG Experiments for Protein Minor Conformer Structure Determination"

Methods Mol Biol. 1688 (2018): 223-242 doi: 10.1007/978-1-4939-7386-6_11

 

Harold W Mackenzie, D. Flemming Hansen. "A 13C-detected 15N double-quantum NMR experiment to probe arginine side-chain guanidinium 15Nh chemical shifts"

Journal of Biomolecular NMR 69 (2017): 123-132 doi:10.1007/s10858-017-0137-2

 

Karola Gerecht, Angelo Miguel Figueireda, D. Flemming Hansen. "Determining rotational dynamics of the guanidino group of arginine side chains in proteins by carbon-detected NMR"

Chemical Communications 53 (2017): 10065-10068  doi:10.1039/C7CC04821A

 

Anatoly Malevanets, P. Andrew Chong, D. Flemming Hansen, Paul Rizk, Yulong Sun, Hong Lin, Ranjith Muhandiram, Avi Chakrabartty, Lewis E. Kay, Julie D. Forman-Kay, Shoshana J. Wodak. "Interplay of buried histidine protonation and protein stability in prion misfolding"

Scientific Reports 7 (2017): 882 doi:10.1038/s41598-017-00954-7

 

D. Flemming Hansen. "Measurement of 15N Longitudinal Relaxation Rates in 15NH4+ Spin Systems to Characterise Rotational Correlation Times and Chemical Exchange" J

ournal of Magnetic Resonance 279 (2017): 91-98.  doi:10.1016/j.jmr.2017.01.015 Front Cover

 

Cathleen Zeymer, Nicolas D Werbeck, Sabine Zimmermann, Jochen Reinstein, D. Flemming Hansen. "Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Ezymatic Phosphoryl Transfer Reaction"

Angewandte Chemie International Edition 55 (2016): 11533-11537. Angewandte Chemie

 

Mechael A Juen, Christoph H. Wunderlich, Felix Nussbaumer, Martin Tollinger, Georg Kontaxis, Robert Konrat, D Flemming Hansen, Christoph Kreut. "Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR spectroscopy" Angewandte Chemie International Edition 55 (2016): 12008-12012. Angewandte Chemie

 

Andrea Sauerwein, D. Flemming Hansen. "Relaxation Dispersion NMR spectroscopy"

Protein NMR, Biological Magnetic Resonance 32 (2015): 75-132. Springer

 

Robert Schneider, Damien Maurin, Guillaume Communie, Jake Krageli, D. Flemming Hansen, Rob W.H. Ruigrok, Malene Ringkjobing Jensen, Martin Blackledge. "Visualizing the Molecular Recognition Trajectory of an Intrinsically Disordered Protein Using Multinuclear Relaxation Dispersion NMR."

Journal of the American Chemical Society 137 (2015): 1220-1229. PMID: 25551399

 

Nicolas D Werbeck, D Flemming Hansen "Heteronuclear transverse and longitudinal relaxation in AX4 spin systems: application to (15)N relaxations in (15)NH4(+)."

Journal of Magnetic Resonance 246 (2014): 136-148 doi:10.1016/j.jmr.2014.06.010

 

Nuha Shiltagh, John Kirkpatrick, Lisa D Cabrita, Tom A McKinnon, Kostas Thalassinos, Edward G Tuddenham, D Flemming Hansen. "Solution structure of the major factor VIII binding region on von Willebrand factor"

Blood 123 (2014): 4143-4151 doi:10.1182/blood-2013-07-517086. Front Cover

 

Nicolas D Werbeck, John Kirkpatrick, Jochen Reinstein, and D Flemming Hansen. "Using (15) N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy."

ChemBioChem 15 (2014): 543-548 doi:10.1002/cbic.201300700

 

Micha B A Kunze, David W Wright, Nicolas D Werbeck, John Kirkpatrick, Peter V Coveney, and D Flemming Hansen. "Loop Interactions and Dynamics Tune the Enzymatic Activity of the Human Histone Deacetylase 8."

Journal of the American Chemical Society 135,  47 (2013): 17862–17868. doi:10.1021/ja408184x

 

Nicolas D Werbeck, John Kirkpatrick, and D Flemming Hansen. "Probing Arginine Side-Chains and Their Dynamics with Carbon-Detected NMR Spectroscopy: Application to the 42 kDa Human Histone Deacetylase 8 at High pH."

Angewandte Chemie International Edition 52, 11 (2013): 3145–3147. doi:10.1002/anie.201209385

 

D Flemming Hansen, William M Westler, Micha B A Kunze, John L Markley, Frank Weinhold, and Jens J Led. "Accurate Structure and Dynamics of the Metal-Site of Paramagnetic Metalloproteins from NMR Parameters Using Natural Bond Orbitals."

Journal of the American Chemical Society 134, 10 (2012): 4670–82. doi:10.1021/ja209348p

 

D Flemming Hansen and Lewis E Kay. "Determining Valine Side-Chain Rotamer Conformations in Proteins from Methyl 13C Chemical Shifts: Application to the 360 kDa Half-Proteasome."

Journal of the American Chemical Society 133, 21 (2011): 8272–81. doi:10.1021/ja2014532