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Publications of Prof. Dr. Petra Imhof

[49] Haltenhof, T., Kotte, A., de Bortoli, F., Schiefer, S., Meinke, S., Emmerichs. A.-K., Petermann, K.K.,  Timmermann, B.,  Franz, A., Wahl, M.C., Imhof, P., Preußner, M., Heyd, F. A conserved kinase-based body temperature sensor globally controls alternative splicing and gene expression Mol. Cell, (2020) in press

[48] Bagherpoor Helabad, M., Volkenandt, S., and Imhof, P. .
Molecular Dynamics Simulations of a Chimeric Androgen Receptor Protein (SPARKI) Confirm the Importance of the Dimerization Domain on DNA Binding Specificity .
Frontiers in Molecular Bioscience 7 (2020) 4

[47] Robalo, J.R., Streacker, L.M.,  Mendes de Oliveira, D., Imhof, P., Ben-Amotz, D. Vila Verde, A. Hydrophobic but Water-Friendly: Favorable Water–Perfluoromethyl Interactions Promote Hydration Shell Defects J. Am. Chem. Soc. 141 (2019) 15856-15868

[46] Krachtus, D., Smith, J.C., and Imhof, P. Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase Molecules 23 (2018) 3342

[45] Reidelbach, M., Weber, M., and Imhof, P. Prediction of perturbed proton transfer networks Plos ONE.13 (2018) e0207718

[44] Kanaan, N. and Imhof, P. Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with cognate and non-cognate DNA Biochemistry 57 (2018) 5654–5665

[43] Hassan, I., Donati, L., Stensitzki, T., Keller, B.G., Heyne, K., and Imhof, P. The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculations Chem. Phys. Lett. 698  (2018) 227-223

[42] Ghane, T., Gorriz, R.F., Wrzalek, S., Volkenandt, S., Delatieh, F. Reidelbach, M., and Imhof, P. Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase The Journal of Membrane Biology 251 (2018), 299-314

[41] Batebi, H., Dragelj, J. and Imhof, P. Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA comples Proteins:Structure, Function, and Bioinformatics 86 (2018) 439-453

[40] Bagherpoor Helabad, M., Ghane, T., Reidelbach, M., Woelke, A. L., Knapp, E. W., and Imhof, P. Protonation-state dependent communication in Cytochrome c Oxidase Biophysical J. 113 (2017) 817-828 (Corrected version of this paper)

[39] Batebi, H. and Imhof, P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor. Chem. Acc. 135 (2016) 262

[38] Schöne, S., Jurk, M., Bagherpoor Helabad, M., Dror, I., Lebars, I., Kieffer, B., Imhof, P., Rohs, R., Vingron, M., Thomas-Chollier, M., and Meijsing, S. Sequences flanking the core binding site modulate glucocorticoid receptor structure and activity Nat. Commun. 7 (2016) 12621

[37] Reidelbach, M., Betz, F., Mäusle, R. M., and Imhof, P. Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states Chem. Phys. Lett. 659 (2016) 169-175

[36] Imhof,P. A Networks Approach to Modeling Enzymatic Reactions
in Methods in Enzymology: Computational approaches for studying Enzyme Mechanism, (ed. G. A. Voth), 578 (2016) chapter 11, p.249-271

[35] Kanaan, N., Crehuet, R., and Imhof,P. Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations J. Phys. Chem. B 119 (2015) 12365-12380

[34] Bagherpoor Helabad, M., Kanaan, N., and Imhof, P. Base Flip in DNA Studied by Molecular Dynamics Simulations of Differently-Oxidized Forms of Methyl-Cytosine   Int. J. Mol. Sci 15 (2014) 11799-11816

[33] Ivchenko, O., Bachert, P., and Imhof, P. Umbrella sampling of proton transfer in a creatine-water system Chem. Phys. Lett 600 (2014) 51-55

[32] Ivchenko, O., Whittleston, C.S., Carr, J.M., Imhof, P., Goerke, S., Bachert, P. and Wales, D.J. Proton Transfer Pathways, Energy Landscape, and Kinetics in Creatine–Water Systems J. Phys. Chem. B 118 (2014) 1969–1975

[31] Vasu, K., Nagamalleswar, E., Zahran, M., Imhof, P., Xu, S.-Y., Zhu, Z., Chan, S.-H. and Nagaraja, V. Increasing cleavage specificity and activity of restriction endonuclease KpnI Nucl. Acid. Res. 41 (2013) 9812-9824

[30] Imhof, P. and Zahran, M. The effect of a G:T mispair on the dynamics of DNA Plos ONE 8 (2013) e53305

[29] Imhof, P. A computational study of the absorption spectra of the photoconvertible fluorescent protein EosFP in different protonation states J. Chem. Theory Comput. 8 (2012) 4828-4836

[28] Held. M, Imhof, P., Keller, B. and Noe, F. Modulation of a Ligand’s Energy Landscape and Kinetics by the Chemical Environment J. Phys. Chem. B 116 (2012) 13597-13607

[27] Berezniak, T., Jäschke, A. and Smith, J. C and Imhof, P. Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study J. Comp. Chem. 33 (2012) 1603-1614

[26] Zahran, M., Berezniak, T., Imhof, P. and Smith, J. C. Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease, FEBS Letters 585 (2011) 2739-2743

[25] Parks, J. M., Imhof, P. and Smith, J. C. Modelling Enzyme Catalysis by Computer Simulations Istvan T. Horvath (ed.), Encyclopedia of Catalysis, John Wiley & Sons Ltd.

[24] Berezniak, T., Zahran, M., Imhof, P., Jäschke, A. and Smith, J. C. Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme J. Am. Chem. Soc, 132 (2010) 12587-12596

[23] Zahran, M., Daidone, I., Smith, J. C., and Imhof, P. Mechanism of DNA recognition by the Restriction Enzyme EcoRV J. Mol. Biol., 401 (2010) 415-432

[22] Imhof, P., Fischer, S. and Smith, J. C. Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis Biochemistry, 48 (2009) 9061-9075

[21] Zahran, M., Imhof, P., and Smith, J. C. Sequence specific DNA recognition by EcoRV in Hansmann, U. H., Meinke, J. H., Mohanty, S., Nadler, W., and Zimmermann, O. (eds.), From Computational Biophysics to Systems Biology 2008 (CBSB08), Jülich, vol. 40, (2008) pp. 417–420, Proceedings, NIC Series Juelich

[20] Imhof, P., Noé, F., Fischer, S., and Smith, J. C. AM1/d parameters for magnesium in metalloenzymes J. Chem. Theory Comput., 2 (2006) 1050–1056

[19] Jagoda, M., Warzeska, S., Pritzkow, H., Wadepohl, H., Imhof, P., Smith, J. C., and Krämer, R. Catalytic transesterification of dialkyl phosphates by a bioinspired dicopper(II) macrocyclic complex J. Am. Chem. Soc, 127 (2005) 15061–15070

[18] Imhof, P., Fischer, S., Krämer, R., and Smith, J. C. Density functional theory analysis of dimethylphosphate hydrolysis: effect of solvation and nucleophile variation J. Mol. Struct. (Theochem), 713 (2005) 1–5

[17] Imhof, P., Krügler, D., Brause, R., and Kleinermanns, K. Geometry change of simple aromatics upon electronic excitation obtained from Franck-Condon fits of dispersed fluorescence spectra J. Chem. Phys., 121 (2004) 2598–2610

[16] Bühl, M., Schurhammer, R., and Imhof, P. Peroxovanadate imidazole complexes as catalysts for olefin epoxidation: Density functional study of dynamics, 51V NMR chemical shifts, and mechanism J. Am. Chem. Soc., 126 (2004) 3310–3320

[15] Bühl, M., Imhof, P., and Repisky, M. Rovibrational corrections to transition metal NMR shielding constants Chem Phys Chem, 5 (2004) 410–414

[14] Spangenberg, D., Imhof, P., and Kleinermanns, K. The S1 state geometry of phenol determined by simultaneous Franck Condon and rotational constants fits Phys. Chem. Chem. Phys., 5 (2003) 2505–2514

[13] Imhof, P., Brause, R., and Kleinermanns, K. Determination of ground state vibrational frequencies of jet-cooled resorcinol by means of dispersed fluorescence spectroscopy and ab Initio calculations J. Mol. Spec., 201 (2002) 65–70

[12] Imhof, P. and Kleinermanns, K. Dispersed fluorescence spectroscopy of pchlorophenol Phys. Chem. Chem. Phys., 4 (2002) 264–170

[11] Nir, E., Janzen, C., Imhof, P., Kleinermanns, K., and de Vries, M. S. Pairing of the nucleobases guanine and cytosine in the gas phase studied by IR–UV doubleresonance spectroscopy and ab initio calculations Phys. Chem. Chem. Phys., 4 (2002) 732–739

[10] Nir, E., Janzen, C., Imhof, P., Kleinermanns, K., and de Vries, M. S. Pairing of the nucleobase guanine studied by IR–UV double-resonance spectroscopy and ab initio calculations Phys. Chem. Chem. Phys., 4 (2002) 740–750.

[9] Nir, E., Janzen, C., Imhof, P., Kleinermanns, K., and de Vries, M. S. Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy J. Chem. Phys., 115 (2001) 4604–4611

[8] Imhof, P. and Kleinermanns, K. Dispersed fluorescence spectra and ab initio calculations of o-Cyanophenol J. Phys. Chem. A, 105 (2001) 8922–8925

[7] Imhof, P. and Kleinermanns, K. Dispersed fluorescence spectra of chlorobenzene Chem. Phys., 270 (2001) 227–236

[6] Roth, W., Imhof, P., and Kleinermanns, K. Laser induced dispersed fluorescence spectroscopy and ab initio calculations of p-cyanophenol Phys. Chem. Chem. Phys., 3 (2001) 1806

[5] Nir, E., Imhof, P., Kleinermanns, K., and deVries, M. S. REMPI spectroscopy of laser desorbed guanosines J. Am. Chem. Soc., 122 (2000) 8091–809

[4] Roth, W., Imhof, P., Gerhards, M., Schumm, S., and Kleinermanns, K. Reassignment of ground and first excited state vibrations in phenol Chem. Phys., 252 (2000) 247–256

[3] Spangenberg, D., Imhof, P., Roth, W., Janzen, C., and Kleinermanns, K. Phenol-(ethanol)1 isomers studied by double-resonance spectroscopy and ab initio calculations J. Phys. Chem.A, 103 (1999) 5918–5924

[2] Imhof, P., Roth, W., Janzen, C., Spangenberg, D., and Kleinermanns, K. Hydrogen-bonded phenol-acid clusters studied by vibrational resolved laser spectroscopy and ab initio calculations – I. Formic acid Chem. Phys., 242 (1999) 141–151

[1] Imhof, P., Roth, W., Janzen, C., Spangenberg, D., and Kleinermanns, K. Hydrogen-bonded phenol-acid clusters studied by vibrational resolved laser spectroscopy and ab initio calculations – II. Acetic acid Chem. Phys., 242 (1999) 153–159