Publications
Publications of Prof. Dr. Petra Imhof
2024
Effects of Ring Functionalization in Anthracene-Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA
In: Chemistry - A European Journal (2024)
ISSN: 0947-6539
DOI: 10.1002/chem.202402106 , , , , , :
In Silico Study of Camptothecin-Based Pro-Drugs Binding to Human Carboxylesterase 2
In: Biomolecules 14 (2024), Article No.: 153
ISSN: 2218-273X
DOI: 10.3390/biom14020153 , , , , :
A concept of dual-responsive prodrugs based on oligomerization-controlled reactivity of ester groups: an improvement of cancer cells versus neutrophils selectivity of camptothecin
In: RSC Medicinal Chemistry (2024)
ISSN: 2632-8682
DOI: 10.1039/d3md00609c , , , , , , , , , , , , , , , , , , :
2023
Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase
In: International Journal of Molecular Sciences 24 (2023), Article No.: 10464
ISSN: 1422-0067
DOI: 10.3390/ijms241310464 , , :
Structural analysis of DNA molecule in a confined shell
In: Physica A-Statistical Mechanics and Its Applications 609 (2023)
ISSN: 0378-4371
DOI: 10.1016/j.physa.2022.128382 , , , :
Comparison of Empirical Zn2+ Models in Protein–DNA Complexes
In: Biophysica 3 (2023), p. 214-230
ISSN: 2673-4125
DOI: 10.3390/biophysica3010014 , :
2022
Oxidation Enhances Binding of Extrahelical 5-Methyl-Cytosines by Thymine DNA Glycosylase
In: Journal of Physical Chemistry B 126 (2022), p. 1188-1201
ISSN: 1520-6106
DOI: 10.1021/acs.jpcb.1c09896 , , :
Interplay of Hydration and Protonation Dynamics in the K-Channel of Cytochrome c Oxidase
In: Biomolecules 12 (2022), Article No.: 1615
ISSN: 2218-273X
DOI: 10.3390/biom12111615 , :
Effect of a U:G mispair on the water around DNA
In: Biophysical Chemistry 283 (2022), Article No.: 106779
ISSN: 0301-4622
DOI: 10.1016/j.bpc.2022.106779 , , , , , :
2021
Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2
In: Journal of Biological Chemistry 297 (2021)
ISSN: 0021-9258
DOI: 10.1016/j.jbc.2021.100829 , , , , , , , , :
Structural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine
In: Journal of Biomolecular Structure & Dynamics (2021)
ISSN: 0739-1102
DOI: 10.1080/07391102.2021.1968499 , , , , , , :
Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide
In: Molecules 26 (2021)
ISSN: 1420-3049
DOI: 10.3390/molecules26082148 , , :
Tacrine-sugar mimetic conjugates as enhanced cholinesterase inhibitors
In: Organic & Biomolecular Chemistry 19 (2021), p. 2322-2337
ISSN: 1477-0520
DOI: 10.1039/d0ob02588g , , , , , , , :
Editorial: Computational and Experimental Insights in Redox-Coupled Proton Pumping in Proteins
In: Frontiers in Chemistry 9 (2021), Article No.: 762612
ISSN: 2296-2646
DOI: 10.3389/fchem.2021.762612 , , :
Protonation dynamics in the K-channel of cytochrome C oxidase estimated from molecular dynamics simulations
In: Processes 9 (2021), p. 1-24
ISSN: 2227-9717
DOI: 10.3390/pr9020265 , , :
Interaction of thymine dna glycosylase with oxidised 5-methyl-cytosines in their amino-and imino-forms
In: Molecules 26 (2021), Article No.: 5728
ISSN: 1420-3049
DOI: 10.3390/molecules26195728 , , :
2020
A Conserved Kinase-Based Body-Temperature Sensor Globally Controls Alternative Splicing and Gene Expression
In: Molecular Cell 78 (2020), p. 57-69.e4
ISSN: 1097-2765
DOI: 10.1016/j.molcel.2020.01.028 , , , , , , , , , , , , , :
Molecular Dynamics Simulations of a Chimeric Androgen Receptor Protein (SPARKI) Confirm the Importance of the Dimerization Domain on DNA Binding Specificity
In: Frontiers in Bioscience 7 (2020), Article No.: ARTN 4
ISSN: 1093-9946
DOI: 10.3389/fmolb.2020.00004 , , :
Proton transfer in the D-channel of cytochrome c oxidase modeled by a transition network approach
In: Biochimica Et Biophysica Acta-General Subjects 1864 (2020), Article No.: 129614
ISSN: 0304-4165
DOI: 10.1016/j.bbagen.2020.129614 , :
Quantifying how step-wise fluorination tunes local solute hydrophobicity, hydration shell thermodynamics and the quantum mechanical contributions of solute-water interactions
In: Physical Chemistry Chemical Physics 22 (2020), p. 22997-23008
ISSN: 1463-9076
DOI: 10.1039/d0cp04205f , , , , :
2019
Hydrophobic but Water-Friendly: Favorable Water-Perfluoromethyl Interactions Promote Hydration Shell Defects
In: Journal of the American Chemical Society 141 (2019)
ISSN: 1520-5126
DOI: 10.1021/jacs.9b06862 , , , , , :
2018
Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA complex
In: Proteins-Structure Function and Bioinformatics 86 (2018), p. 439-453
ISSN: 0887-3585
DOI: 10.1002/prot.25460 , , :
Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase
In: Journal of Membrane Biology 251 (2018), p. 299-314
ISSN: 0022-2631
DOI: 10.1007/s00232-018-0019-x , , , , , , :
The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations
In: Chemical Physics Letters 698 (2018), p. 227-233
ISSN: 0009-2614
DOI: 10.1016/j.cplett.2018.03.026 , , , , , :
Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with Cognate and Noncognate DNA
In: Biochemistry 57 (2018), p. 5654-5665
ISSN: 0006-2960
DOI: 10.1021/acs.biochem.8b00409 , :
Quantum mechanical/molecular mechanical analysis of the catalytic mechanism of phosphoserine phosphatase
In: Molecules 23 (2018), Article No.: 3342
ISSN: 1420-3049
DOI: 10.3390/molecules23123342 , , :
Prediction of perturbed proton transfer networks
In: PLoS ONE 13 (2018), Article No.: e0207718
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0207718 , , :
2017
Protonation-State-Dependent Communication in Cytochrome c Oxidase
In: Biophysical Journal 113 (2017), p. 817-828
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2017.07.005 , , , , , :
Retraction Notice to: Protonation State-Dependent Communication in Cytochrome c Oxidase
In: Biophysical Journal 113 (2017), p. 223-
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2017.06.036 , , , , , :
2016
Phosphodiester hydrolysis computed for cluster models of enzymatic active sites
In: Theoretical Chemistry Accounts 135 (2016), Article No.: 262
ISSN: 1432-881X
DOI: 10.1007/s00214-016-2020-8 , :
A Networks Approach to Modeling Enzymatic Reactions
In: Methods in Enzymology, Academic Press Inc., 2016, p. 249-271 (Methods in Enzymology, Vol.578)
DOI: 10.1016/bs.mie.2016.05.025 :
Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states
In: Chemical Physics Letters 659 (2016), p. 169-175
ISSN: 0009-2614
DOI: 10.1016/j.cplett.2016.07.021 , , , :
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity
In: Nature Communications 7 (2016), Article No.: 12621
ISSN: 2041-1723
DOI: 10.1038/ncomms12621 , , , , , , , , , , :
2015
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
In: Journal of Physical Chemistry B 119 (2015), p. 12365-12380
ISSN: 1520-6106
DOI: 10.1021/acs.jpcb.5b05496 , , :
2014
Base flip in DNA studied by molecular dynamics simulations of differently-oxidized forms of methyl-cytosine
In: International Journal of Molecular Sciences 15 (2014), p. 11799-11816
ISSN: 1422-0067
DOI: 10.3390/ijms150711799 , , :
Umbrella sampling of proton transfer in a creatine-water system
In: Chemical Physics Letters 600 (2014), p. 51-55
ISSN: 0009-2614
DOI: 10.1016/j.cplett.2014.03.045 , , :
Proton transfer pathways, energy landscape, and kinetics in creatine-water systems
In: Journal of Physical Chemistry B 118 (2014), p. 1969-1975
ISSN: 1520-6106
DOI: 10.1021/jp410172k , , , , , , :
2013
The Effect of a G:T Mispair on the Dynamics of DNA
In: PLoS ONE 8 (2013), Article No.: e53305
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0053305 , :
Increasing cleavage specificity and activity of restriction endonuclease KpnI
In: Nucleic Acids Research 41 (2013), p. 9812-9824
ISSN: 0305-1048
DOI: 10.1093/nar/gkt734 , , , , , , , :
2012
Stereoselection in the diels-alderase ribozyme: A molecular dynamics study
In: Journal of Computational Chemistry 33 (2012), p. 1603-1614
ISSN: 0192-8651
DOI: 10.1002/jcc.22993 , , , :
Modulation of a ligand's energy landscape and kinetics by the chemical environment
In: Journal of Physical Chemistry B 116 (2012), p. 13597-13607
ISSN: 1520-6106
DOI: 10.1021/jp3006684 , , , :
Computational study of absorption spectra of the photoconvertible fluorescent protein EosFP in different protonation states
In: Journal of Chemical Theory and Computation 8 (2012), p. 4828-4836
ISSN: 1549-9618
DOI: 10.1021/ct300706r :
2011
Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease
In: FEBS letters 585 (2011), p. 2739-2743
ISSN: 1873-3468
DOI: 10.1016/j.febslet.2011.07.036 , , , :
2010
Magnesium-dependent active-site conformational selection in the Diels-Alderase ribozyme
In: Journal of the American Chemical Society 132 (2010), p. 12587-12596
ISSN: 1520-5126
DOI: 10.1021/ja101370e , , , , :
Mechanism of DNA recognition by the restriction enzyme EcoRV
In: Journal of Molecular Biology 401 (2010), p. 415-432
ISSN: 0022-2836
DOI: 10.1016/j.jmb.2010.06.026 , , , :
2009
Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: A quantum mechanical/molecular mechanical analysis
In: Biochemistry 48 (2009), p. 9061-9075
ISSN: 0006-2960
DOI: 10.1021/bi900585m , , :
[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
[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
[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
[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.
[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