PublicationsMark

Publications

Pre-2005 publications are available from the Groningen Biomolecular Sciences site

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In press

• Wassenaar, T., Daura, X., Padrós, E. and Mark, A. E. (2008)

Calcium binding to the Purple Membrane: A Molecular Dynamics study. PROTEINS (in press)

• Zhu, J., Fan, H., Xavier, P., Honig, B., Mark, A. E. (2008)

Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials PROTEINS (Accepted)

• Cemazar, M., Joshi, A., Daly, N., Mark, A. E. and Craik, D. (2008)

The Structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein. Structure (in press)

• Risselada, H.J., Mark, A.E. and Marrink, S.J. (2008)

The application of MFFA boundary potentials in MD simulations of lipid Vesicales. J. of Phys. Chem. B (in press)

2008

AM08.01 Wassenaar, T.A., Quax, W.J. and Mark, A.E. (2008)
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics study.
Proteins, Structure, Function, and Bioinformatics, 111, 6015-6025.
media:AM_08_01.pdf

AM08.02 Knecht, V., Risselada, H.J., Mark, A.E., and Marrink, S.J. (2008)
Electrophoretic mobility does not always reflect the charge on an oil droplet
Journal of Colloid and Interface Science, 318, 477-486.
media:AM_08_02.pdf

AM08.03 Mueller, D.S., Kampmann, T., Yennamalli, R., Young., P.R., Kobe B., Mark, A.E. (2008)
Histidine protonation and the activation of viral fusion proteins
Biochemical Society Transactions, 36, 43-45
media:AM_08_03.pdf

AM08.04 van Gunsteren. W.F., Dolenc, J., and Mark, A.E. (2008)
Molecular simulation as an aid to experimentalists
Current Opinion in Structural Biology, 18, 149-153
media:AM_08_04.pdf

2007

AM07.01 Periole, X. and Mark, A. E. (2007)
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
J. Chem. Phys. 126, 014903.
media:AM_07.01.pdf

AM07.02 Chipot, C., Mark, A.E., Pande, V.S. and Simonson, T. (2007)
Applications of Free Energy Calculations to Chemistry and Biology.
In: Free Energy Calculations Theory and Applications in Chemistry and Biology. (Chipot, C.; Pohorille, A. Eds.) Springer. pp. 463-492

AM07.03 Pineiro, A., Banquy, X., Perez-Casas, S., Tovar, E., Garcia, A., Villa, A., Amigo, A., Mark, A.E. and Costas, M. (2007)
On the Characterization of Host-Guest Complexes: Surface Tension, Calorimetry, and Molecular Dynamics of Cyclodextrins with a Non-ionic Surfactant.
J. Phys. Chem. B. 111, 4383-92.
media:AM_07_03.pdf

AM07.04 Leontiadou, H., Mark, A.E. and Marrink, S.J. (2007)
Ion transport across transmembrane pores.
Biophys. J. 92, 12, 4209-15.
media:AM_07_04.pdf

AM07.05 Villa, A., Fan, H., Wassenaar, T.A. and Mark, A. E. (2007)
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
J. Phys. Chem. B. 111, 6015-6025.
media:AM_07_05.pdf

AM07.06 Periole, X., Vendruscolo, M, and Mark, A. E. (2007)
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.
Proteins, Structure, Function, and Bioinformatics, 69, 536-550.
media:AM_07_06.pdf

2006

AM06.01 Wassenaar, T. A. and Mark, A. E. (2006)
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.
J. Comp. Chem. 27, 316-325.
media:AM_06_01.pdf

AM06.02 Villa, A., Mark, A. E., Saracino, G. A. A., Cosentino, U., Pitea, D., Moro, G. and Salmona, M. (2006)
Conformational polymorphism of the PrP106-126 peptide in different environments: A Molecular dynamics study.
J. Phys. Chem. B. 110, 1423-1428.
media:AM_06_02.pdf

AM06.03 Knecht, V., Mark, A. E. and Marrink, S. J. (2006)
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail.
J. Amer. Chem. Soc. 128, 2030-2034.
media:AM_06_03.pdf

AM06.04 Fan, H. and Mark A. E. (2006)
Mimicking the action of GroEL in molecular dynamics simulations: application to the refinement of protein structures.
Protein Sci. 15, 441-8.
media:AM_06_04.pdf

AM06.05 Fan, H., Wang, X. Q., Zhu, J., Robillard, G. T. and Mark, A. E. (2006)
Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface.
Protens-Structure and Bioinformatics, 64, 863-873.
media:AM_06_05.pdf

AM06.06 Leontiadou, H., Mark, A .E. and Marrink, S.J. (2006)
Antimicrobial peptides in action.
J. Am. Chem. Soc. 128, 12156-12161.
media:AM_06_06.pdf

AM06.07 Kampmann, T., Mueller, D. S., Mark, A. E., Young, P. R. and Kobe, B. (2006)
The role of histidine residues in low-pH-mediated viral membrane fusion.
Structure. 14, 1481-7.
media:AM_06_07.pdf

AM06.08 Siwko, M. E., Marrink, S. J., de Vries, A. H., Kozubek, A., Schoot Uiterkamp, A. J. and Mark A. E. (2006)
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study.
Biochim Biophys Acta. 1768, 198-206.
media:AM_06_08.pdf

2005

AM05.01 Donnini, S., Mark, A. E., Juffer, A. H. and Villa, A. (2005)
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
J. Comp. Chem. 26, 115-122.
media:AM_05_01.pdf

AM05.02 Kovalskyy, D., Dubyna, V., Kanibolotsky, D., Mark, A. E. and Kornelyuk, A. (2005)
A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ions in stabilizing the active site.
Proteins: Structure, Function, and Genetics. 58, 450-458.
media:AM_05_02.pdf

AM05.03 Soto, P., Cladera, J., Mark, A. E. and Daura, X. (2005)
Stability of SIV gp32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations.
Angew. Chem. Int. Ed. Engl. 17, 1089-1091.
media:AM_05_03.pdf

AM05.04 Knecht, V., Mueller, M., Bonn, M., Marrink, S. J. and Mark, A. E. (2005)
Simulation studies of pore and domain formation in a phospholipid monolayer.
J. Chem. Phys. 122, 024704 1-9.
media:AM_05_04.pdf

AM05.05 Pagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A. E., Berger, S. and Koksch, B. (2005)
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.
Org. Biomol. Chem. 3, 1189-1194.
media:AM_05_05.pdf

AM05.06 van den Bosch, M., Swart, M., Snijders, J. G., Berendsen, H.J.C., Mark, A. E., Oostenbrink, C., van Gunsteren, W. F. and Canters, G. W. (2005)
Calculation of the redox potential of the protein azurin and some mutants.
Chembiochem. 6, 738-746.
media:AM_05_06.pdf

AM05.07 de Vries, A. H., Yefimov, S., Mark, A. E. and Marrink, S. J. (2005)
Molecular structure of the lecithin ripple phase.
Proceedings of the National Academy of Sciences of the United States of America. 102, 5392-5396.
media:AM_05_07.pdf

AM05.08 Fan, H., Mark, A. E., Zhu, J. and Honig, B. (2005)
Comparative study of generalized Born models: Protein dynamics.
Proceedings of the National Academy of Sciences of the United States of America. 102, 19, 6760-6764.
media:AM_05_08.pdf

AM05.09 Marrink, S. J., Risselada, J. and Mark, A. E. (2005)
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
Chem. Phys. Lipids. 135, 223-244.
media:AM_05_09.pdf

AM05.10 van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C., (2005)
GROMACS: Fast, flexible, and free.
J. Comp. Chem. 26, 1701-1718.
media:AM_05_10.pdf

AM05.11 Pinero, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005)
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations.
Biophys. J. 89, 3701-3713 2005.
media:AM_05_11.pdf

2004

AM04.01 Fan, H. and Mark, A.E.
Refinement of homology-based protein structures by molecular dynamics simulation techniques
Protein Science 13 (2004) 211-220

AM04.02 Marrink, S.J., de Vries, A.H. and Mark, A.E.
Coarse Grained model for Semiquantitative Lipid Simulations
J. Phys. Chem. B 108 (2004) 750-760

AM04.03 de Vries, A.H., Mark, A.E. and Marrink, S.J
The Binary Mixing Behaviour of Phospholipids in a Bilayer: a Molecular Dynamics Study
J. Phys. Chem. B 108 (2004) 2454-2463

AM04.04 Fan, H. and Mark, A.E
Mimicking the action of folding chaperones in molecular dynamics study: Application to the refinement of Homology Based Protein Structures
Protein Science 13 (2004) 992-999

AM04.05 Leontiadou, H., Mark, A.E., and Marrink, S.J.
Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers
Biophys. J. 86 (2004) 2156-2164

AM04.06 Zangi, R. and Mark, A.E.
Electrofreezing of confined water
J. Chem. Phys. 120 (2004) 7123-7130

AM04.07 Vries, A.H., Mark, A.E. and Marrink, S.J.
Molecular dynamics simulation of spontaneous formation of a small DPPC vesicle in water in atomistic detail
J. Am. Chem. Sco. 126 (2004) 4488-4489

AM04.08 Groenhof, G., Bouxin-Cademartory, M., Hess, B., de Visser, S.P., Berendsen, H.J.C., Olivucci, M., Mark, A.E. and Robb, M.A.
Photoactivation of the Photoactive Yellow Protein: Why photo absorbtion triggers a trans-to-cis isomerization of the chromophore in the Protein
J. Am. Chem. Soc. 126 (2004) 4228-4233

AM04.09 Oostenbrink, C., Villa, A., Mark, A.E. and van Gusnteren, W.F.
A biomolecular force field based on the free enthalpy of hydration and solcation: the GROMOS force-field parameter sets 53A5 and 53A6
J. Comp. Chem. 25 (2004) 1656-1676

AM04.10 Marrink, S.J. and Mark, A.E.
Molecular view of hexagonal phase formation in phospholipid membranes
Biophys. J. 87 (2004) 3894-3900