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J. of Phys. Chem. B (in press)
J. of Phys. Chem. B (in press)


'''2008'''


* van Gunsteren. W.F., Dolenc, J., and Mark, A.E. (2008)
== '''2008''' ==
Molecular simulation as an aid to experimentalists
 
Current Opinion in Structural Biology, 18, 149-153
 
'''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.
 
'''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.


* Mueller, D.S., Kampmann, T., Yennamalli, R., Young., P.R., Kobe B., Mark, A.E. (2008)
'''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
Histidine protonation and the activation of viral fusion proteins
Biochemical Society Transactions, 36, 43-45
Biochemical Society Transactions, 36, 43-45


* Knecht, V., Risselada, H.J., Mark, A.E., and Marrink, S.J. (2008)
'''AM08.04''' van Gunsteren. W.F., Dolenc, J., and Mark, A.E. (2008)
Electrophoretic mobility does not always reflect the charge on an oil droplet
Molecular simulation as an aid to experimentalists
Journal of Colloid and Interface Science, 318, 477-486.
Current Opinion in Structural Biology, 18, 149-153


* 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.


'''2007'''
== '''2007''' ==


* 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.


* Villa, A., Fan, H., Wassenaar, T.A. and Mark, A. E. (2007)
'''AM07.01''' Periole, X. and Mark, A. E. (2007)
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the  force field?
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
J. Phys. Chem. B. 111, 6015-6025.
J. Chem. Phys. 126, 014903.


* Leontiadou, H., Mark, A.E. and Marrink, S.J. (2007)
'''AM07.02''' Chipot, C., Mark, A.E., Pande, V.S. and Simonson, T. (2007)  
Ion transport across transmembrane pores.
Applications of Free Energy Calculations to Chemistry and Biology.  
Biophys. J. 92, 12, 4209-15.
In: Free Energy Calculations Theory and Applications in Chemistry and Biology. (Chipot, C.; Pohorille, A. Eds.) Springer. pp. 463-492


* Pineiro, A., Banquy, X., Perez-Casas, S., Tovar, E., Garcia, A., Villa, A., Amigo, A., Mark,  A.E. and Costas, M. (2007)
'''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.
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.  
J. Phys. Chem. B. 111, 4383-92.  


* Chipot, C., Mark, A.E., Pande, V.S. and Simonson, T. (2007)  
'''AM07.04''' Leontiadou, H., Mark, A.E. and Marrink, S.J. (2007)
Applications of Free Energy Calculations to Chemistry and Biology.  
Ion transport across transmembrane pores.
In: Free Energy Calculations Theory and Applications in Chemistry and Biology. (Chipot, C.; Pohorille, A. Eds.) Springer. pp. 463-492
Biophys. J. 92, 12, 4209-15.  


* Periole, X. and Mark, A. E. (2007)
'''AM07.05''' Villa, A., Fan, H., Wassenaar, T.A. and Mark, A. E. (2007)
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the  force field?
J. Chem. Phys. 126, 014903.
J. Phys. Chem. B. 111, 6015-6025.


'''2006'''
'''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.


* Kampmann, T., Mueller, D. S., Mark, A. E., Young, P. R. and Kobe, B. (2006)
== '''2006''' ==
The role of histidine residues in low-pH-mediated viral membrane fusion.
Structure. 14, 1481-7.


* Siwko, M. E., Marrink, S. J., de Vries, A. H., Kozubek, A., Schoot Uiterkamp, A. J. and Mark A. E. (2006)
'''AM06.01''' Wassenaar, T. A. and Mark, A. E. (2006)
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study.
The effect of box shape on the dynamic properties of proteins simulated under periodic  boundary conditions.
Biochim Biophys Acta. 1768, 198-206.  
J. Comp. Chem. 27, 316-325.


* Leontiadou, H., Mark, A .E. and Marrink, S.J. (2006)
'''AM06.02''' Villa, A., Mark, A. E., Saracino, G. A. A., Cosentino, U., Pitea, D., Moro, G. and Salmona, M. (2006)
Antimicrobial peptides in action.
Conformational polymorphism of the PrP106-126 peptide in different environments: A          Molecular dynamics study.
J. Am. Chem. Soc.  128, 12156-12161.
J. Phys. Chem. B.  110, 1423-1428.


* Fan, H., Wang, X. Q., Zhu, J., Robillard, G. T. and Mark, A. E. (2006)
'''AM06.03''' Knecht, V., Mark, A. E. and Marrink, S. J. (2006)
Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface .
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail.
Protens-Structure and Bioinformatics, 64, 863-873.  
J. Amer. Chem. Soc.  128, 2030-2034.


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


* Knecht, V., Mark, A. E. and Marrink, S. J. (2006)
'''AM06.05''' Fan, H., Wang, X. Q., Zhu, J., Robillard, G. T. and Mark, A. E. (2006)
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail.
Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface .
J. Amer. Chem. Soc.  128, 2030-2034.
Protens-Structure and Bioinformatics, 64, 863-873.
 
'''AM06.06''' Leontiadou, H., Mark, A .E. and Marrink, S.J. (2006)
Antimicrobial peptides in action.
J. Am. Chem. Soc.  128, 12156-12161.


* Villa, A., Mark, A. E., Saracino, G. A. A., Cosentino, U., Pitea, D., Moro, G. and Salmona, M. (2006)
'''AM06.07''' Kampmann, T., Mueller, D. S., Mark, A. E., Young, P. R. and Kobe, B. (2006)
Conformational polymorphism of the PrP106-126 peptide in different environments: A          Molecular dynamics study.
The role of histidine residues in low-pH-mediated viral membrane fusion.
J. Phys. Chem. B. 110, 1423-1428.
Structure. 14, 1481-7.


* Wassenaar, T. A. and Mark, A. E. (2006)
'''AM06.08''' Siwko, M. E., Marrink, S. J., de Vries, A. H., Kozubek, A., Schoot Uiterkamp, A. J. and Mark A. E. (2006)
The effect of box shape on the dynamic properties of proteins simulated under periodic  boundary conditions.
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study.
J. Comp. Chem. 27, 316-325.
Biochim Biophys Acta. 1768, 198-206.  


'''2005'''
== '''2005''' ==


* Pinero, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005)
'''AM05.01''' Donnini, S., Mark, A. E., Juffer, A. H. and Villa, A. (2005)
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations.
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
Biophys. J.  89, 3701-3713 2005.
J. Comp. Chem.  26, 115-122.


* van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C.,  (2005)
'''AM05.02''' Kovalskyy, D., Dubyna, V., Kanibolotsky, D., Mark, A. E. and Kornelyuk, A. (2005)
GROMACS: Fast, flexible, and free.
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.
J. Comp. Chem.  26, 1701-1718.
Proteins: Structure, Function, and Genetics.  58, 450-458.


* Marrink, S. J., Risselada, J. and Mark, A. E. (2005)
'''AM05.03''' Soto, P., Cladera, J., Mark, A. E. and Daura, X. (2005)  
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
Stability of SIV gp32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations.
Chem. Phys. Lipids.  135, 223-244.
Angew. Chem. Int. Ed. Engl.  17, 1089-1091.


* Fan, H., Mark, A. E., Zhu, J. and Honig, B. (2005)
'''AM05.04''' Knecht, V., Mueller, M., Bonn, M., Marrink, S. J. and Mark, A. E. (2005)
Comparative study of generalized Born models: Protein dynamics.
Simulation studies of pore and domain formation in a phospholipid monolayer.
Proceedings of the National Academy of Sciences of the United States of America.  102, 19, 6760-6764.
J. Chem. Phys.  122, 024704 1-9.


* de Vries, A. H., Yefimov, S., Mark, A. E. and Marrink, S. J. (2005)
'''AM05.05''' Pagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A. E., Berger, S. and Koksch, B. (2005)
Molecular structure of the lecithin ripple phase.
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.
Proceedings of the National Academy of Sciences of the United States of America.  102, 5392-5396.
Org. Biomol. Chem.  3, 1189-1194.


* 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)
'''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.
Calculation of the redox potential of the protein azurin and some mutants.
Chembiochem.  6, 738-746.
Chembiochem.  6, 738-746.


* Pagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A. E., Berger, S. and Koksch, B. (2005)
'''AM05.07''' de Vries, A. H., Yefimov, S., Mark, A. E. and Marrink, S. J. (2005)
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.
Molecular structure of the lecithin ripple phase.
Org. Biomol. Chem.  3, 1189-1194.
Proceedings of the National Academy of Sciences of the United States of America.  102, 5392-5396.


* Knecht, V., Mueller, M., Bonn, M., Marrink, S. J. and Mark, A. E. (2005)
'''AM05.08''' Fan, H., Mark, A. E., Zhu, J. and Honig, B. (2005)
Simulation studies of pore and domain formation in a phospholipid monolayer.
Comparative study of generalized Born models: Protein dynamics.
J. Chem. Phys.  122, 024704 1-9.
Proceedings of the National Academy of Sciences of the United States of America.  102, 19, 6760-6764.


* Soto, P., Cladera, J., Mark, A. E. and Daura, X. (2005)  
'''AM05.09''' Marrink, S. J., Risselada, J. and Mark, A. E. (2005)
Stability of SIV gp32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations.
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
Angew. Chem. Int. Ed. Engl.  17, 1089-1091.
Chem. Phys. Lipids.  135, 223-244.


* Kovalskyy, D., Dubyna, V., Kanibolotsky, D., Mark, A. E. and Kornelyuk, A. (2005)
'''AM05.10''' van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C.,  (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.
GROMACS: Fast, flexible, and free.
Proteins: Structure, Function, and Genetics.  58, 450-458.
J. Comp. Chem.  26, 1701-1718.


* Donnini, S., Mark, A. E., Juffer, A. H. and Villa, A. (2005)
'''AM05.11''' Pinero, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005)
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations.
J. Comp. Chem.  26, 115-122.
Biophys. J.  89, 3701-3713 2005.

Revision as of 22:34, 21 July 2008

Publications

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

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.

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.

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

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


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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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