Dr. Maria Reif


Foto von Maria Reif

Technische Universität München

Lehrstuhl für Theoretische Biophysik (T38) - Molekulardynamik (Prof. Zacharias)

Postadresse

Postal:
Ernst-Otto-Fischer-Straße 8
85748 Garching b. München

Research Interests

  • Free-energy calculation of (biomacro)molecular association: Methods and applications
  • Proline isomerization in proteins: Simulation methods and biological significance
  • Fluorophore-labelled proteins: Force-fields and protein-fluorophore interactions

Publications

Year

Authors, Title, Journal

2022

Reif, Maria M. and Zacharias, Martin
Improving the potential of mean force and nonequilibrium pulling simulations by simultaneous alchemical modifications.
J. Chem. Theory Comput., 2022, 18, pp. 3873, (doi:10.1021/acs.jctc.1c01194)

2022

Reif, Maria M. and Zacharias, Martin
Computational tools for accurate binding free-energy prediction.
In: Computational Methods for Estimating the Kinetic Parameters of Biological Systems, pp. 255; Methods Mol. Biol.; Vanhaelen, Quentin, Ed.; Springer Science + Business Media, NY, USA
(doi:10.1007/978-1-0716-1767-0)

2021

Christian Gebhardt, Martin Lehmann, Maria M. Reif, Martin Zacharias, Thorben Cordes
Molecular and spectroscopic characterization of green and red cyanine fluorophores from the Alexa Fluor and AF series
ChemPhysChem (2021), (doi: 10.1002/cphc.202000935)

2019

Reif, Maria M. and Fischer, Moritz and Fredriksson, Kai and Hagn, Franz and Zacharias, Martin
The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding
Journal of Molecular Biology, 431, pp. 223-243. (doi: 10.1016/j.jmb.2018.09.015)

2017

Reif, Maria M. and Kallies, Christopher and Knecht, Volker
Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study
Membranes, 2017, 7, pp. 5. Multidisciplinary Digital Publishing Institute (doi:10.3390/membranes7010005)

2017

Pechlaner, Maria and Reif, Maria M. and Oostenbrink, Chris
Reparametrisation of united-atom amine solvation in the GROMOS force field
Molecular Physics, 2017, 115, pp. 1144-1154. Taylor & Francis (doi:10.1080/00268976.2016.1255797)

2017

Margreitter, Christian and Reif, Maria M. and Oostenbrink, Chris
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field
Journal of computational chemistry, 2017, 38, pp. 714-720. Wiley Online Library (doi:10.1002/jcc.24733)

2016

Reif, Maria M. and Hünenberger, Philippe H.
Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited
The Journal of Physical Chemistry B, 2016, 120, pp. 8485-8517. ACS Publications (doi:10.1021/acs.jpcb.6b02156)

2016

Reif, Maria M. and Zacharias, Martin
Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules.
J Comput Chem, Jul, 2016, 37, pp. 1711-1724. (doi:10.1002/jcc.24390)

2015

Reif, Maria M. and Oostenbrink, Chris
Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization
Theor Chem Acc, Jan, 2015, 134. Springer Science + Business Media (doi:10.1007/s00214-014-1600-8)

2014

Reif, Maria M. and Oostenbrink, Chris
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies
Journal of Computational Chemistry, Oct, 2014, 35, pp. 2319-2332. Wiley-Blackwell (doi:10.1002/jcc.23756)

2014

Sündermann, Axel and Reif, Maria M. and Hofbauer, Stefan and Obinger, Christian and Oostenbrink, Chris
Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations
Biochemistry, July, 2014. (doi:10.1021/bi500467h)

2014

Reif, Maria M. and Oostenbrink, Chris
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.
J Comput Chem, Jan, 2014, 35, pp. 227-243. (doi:10.1002/jcc.23490)

2013

Reif, Maria M. and Winger, Moritz and Oostenbrink, Chris
Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins
Journal of Chemical Theory and Computation, Feb, 2013, 9, pp. 1247-1264. American Chemical Society (ACS) (doi:10.1021/ct300874c)

2012

Reif, Maria M. and Mach, Lukas and Oostenbrink, Chris
Molecular Insight into Propeptide-Protein Interactions in Cathepsins L and O
Biochemistry, Oct, 2012, 51, pp. 8636-8653. American Chemical Society (ACS) (doi:10.1021/bi300802a)

2012

Reif, Maria M. and Hünenberger, Philippe H. and Oostenbrink, Chris
New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
Journal of Chemical Theory and Computation, Oct, 2012, 8, pp. 3705-3723. American Chemical Society (ACS) (doi:10.1021/ct300156h)

2012

Dahlgren, Björn and Reif, Maria M. and Hünenberger, Philippe H. and Hansen, Niels
Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations
Journal of Chemical Theory and Computation, Oct, 2012, 8, pp. 3542-3564. American Chemical Society (ACS) (doi:10.1021/ct300260q)

2012

Gößler-Schöfberger, Ruth and Hesser, Günter and Reif, Maria M. and Friedmann, Jacqueline and Duscher, Bernadette and Toca-Herrera, Jose Luis and Oostenbrink, Chris and Jilek, Alexander
A stereochemical switch in the aDrs model system, a candidate for a functional amyloid
Archives of Biochemistry and Biophysics, Jun, 2012, 522, pp. 100-106. Elsevier BV (doi:10.1016/j.abb.2012.04.006)

2011

Reif, Maria M. and Hünenberger, Philippe H.
Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water
The Journal of Chemical Physics, 2011, 134, pp. 144104. AIP Publishing (doi:10.1063/1.3567022)

2011

Reif, Maria M. and Hünenberger, Philippe H.
Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions
The Journal of Chemical Physics, 2011, 134, pp. 144103. AIP Publishing (doi:10.1063/1.3567020)

2011

Hünenberger, P.H. and Reif, Maria M.
Single-ion solvation. Experimental and theoretical approaches to elusive thermodynamic quantities
Royal Society of Chemistry, (https://pubs.rsc.org/en/content/ebook/978-1-84755-187-0)

2009

Reif, Maria M. and Kräutler, Vincent and Kastenholz, Mika A. and Daura, Xavier and Hünenberger, Philippe H.
Molecular Dynamics Simulations of a Reversibly Folding beta-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
The Journal of Physical Chemistry B, Mar, 2009, 113, pp. 3112-3128. American Chemical Society (ACS) (doi:10.1021/jp807421a)

2006

Platts, James A. and Oldfield, Steven P. and Reif, Maria M. and Palmucci, Alessandra and Gabano, Elisabetta and Osella, Domenico
The RP-HPLC measurement and QSPR analysis of logPo/w values of several Pt(II) complexes
Journal of Inorganic Biochemistry, Jul, 2006, 100, pp. 1199-1207. Elsevier BV (doi:10.1016/j.jinorgbio.2006.01.035)

2005

Schnell, Christoph and Reif, Maria M. and Scharnagl, Christina and Friedrich, Josef
Local compressibilities in insulin as determined from pressure tuning hole burning experiments and MD simulations
Physical Chemistry Chemical Physics, 2005, 7, pp. 2217. Royal Society of Chemistry (RSC) (doi:10.1039/b502056p)

2005

Scharnagl, Christina and Reif, Maria M. and Friedrich, Josef
Stability of proteins: Temperature, pressure and the role of the solvent
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Jun, 2005, 1749, pp. 187-213. Elsevier BV (doi:10.1016/j.bbapap.2005.03.002)

2005

Scharnagl, Christina and Reif, Maria M. and Friedrich, Josef
Local Compressibilities of Proteins: Comparison of Optical Experiments and Simulations for Horse Heart Cytochrome-c
Biophysical Journal, Jul, 2005, 89, pp. 64-75. Elsevier BV (doi:10.1529/biophysj.104.057265)

2005

Milbradt, Alexander G. and Löweneck, Markus and Krupka, Simone S. and Reif, Maria M. and Sinner, Eva-Kathrin and Moroder, Luis and Renner, Christian
Photomodulation of conformational states. IV. Integrin-binding RGD-peptides with (4-aminomethyl)phenylazobenzoic acid as backbone constituent
Biopolymers, Apr, 2005, 77, pp. 304-313. Wiley-Blackwell (doi:10.1002/bip.20226)