B3: Coarse-graining of solvent effects in force-probe molecular dynamics simulations

Force probe simulations using an adaptive resolution scheme
Marco Oestereich, J Gauss, Gregor Diezemann
Journal of Physics: Condensed Matter, (2021);
doi:10.1088/1361-648x/abed18

Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles
Ken Schäfer, Hima Bindu Kolli, Mikkel Killingmoe Christensen, Sigbjørn Løland Bore, Gregor Diezemann, Jürgen Gauss, Giuseppe Milano, Reidar Lund, Michele Cascella
Angewandte Chemie International Edition 59 (42), 18591-18598 (2020);
doi:10.1002/anie.202004522

↓ Show Abstract↑ Hide Abstract The shape and size of self-assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long-range interactions. Combin- ing small-angle X-ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabili- zation of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.

Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations
Ken Schäfer, Gregor Diezemann
Molecular Physics 118 (19-20), e1743886 (2020);
doi:10.1080/00268976.2020.1743886

↓ Show Abstract↑ Hide Abstract Single-molecule force spectroscopy and molecular simulations are well-established techniques to study the mechanical unfolding of supramolecular complexes in various fields of biomolecular physics. In the present study, we investigate the details of the force-dependent folding transition of a well-studied model system, a calix[4]arene catenane dimer, using atomistic force quench simu- lations. This protocol allows us to reach a range of much smaller forces than possible with the more common force ramp simulations where the force is changed with a constant velocity. We find that the folding pathway changes its character as a function of external force. For small forces (on the order of 50 pN), the folding transition occurs via the transition to a metastable intermediate structure in about 30% of the simulations. We characterise the structure of this intermediate and demonstrate its relevance by considering the averaged potential of mean force of the system as a function of a well-defined reaction coordinate. When the force increases, the importance of the intermediate diminishes and for high external forces (500 pN), our results can be interpreted in terms of a simple two-state model, that has also been used in earlier simulations on the same system.

Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
Stefan Jaschonek, Ken Schäfer, Gregor Diezemann
The Journal of Physical Chemistry B 123 (22), 4688-4694 (2019);
doi:10.1021/acs.jpcb.9b02676

Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations
Takashi Kato, Ken Schäfer, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 151 (4), 045102 (2019);
doi:10.1063/1.5111717

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment
Hima Bindu Kolli, Antonio de Nicola, Sigbjørn Løland Bore, Ken Schäfer, Gregor Diezemann, Jürgen Gauss, Toshihiro Kawakatsu, Zhong-Yuan Lu, You-Liang Zhu, Giuseppe Milano, Michele Cascella
Journal of Chemical Theory and Computation 14 (9), 4928-4937 (2018);
doi:10.1021/acs.jctc.8b00466

↓ Show Abstract↑ Hide Abstract We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycer- ol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolytes. According to the hybrid approach, the intramolecular interactions are treated by a standard molecular Hamiltonian, and the nonelectrostatic intermolec- ular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure, as recently proposed [Zhu et al. Phys. Chem. Chem. Phys. 2016, 18, 9799]. Our results show that, upon proper calibration of key parameters, electrostatic forces can be correctly reproduced. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. The inclusion of explicit electrostatics with good accuracy and low computational cost paves the way for a significant extension of the hybrid particle-field method to biological systems, where the polyelectrolyte component plays a fundamental role for both structural and dynamical molecular properties.

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Fabian Knoch, Ken Schäfer, Gregor Diezemann, Thomas Speck
The Journal of Chemical Physics 148 (4), 044109 (2018);
doi:10.1063/1.5010435

Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations
Lalita Uribe, Gregor Diezemann, Jürgen Gauss, Jens Preben Morth, Michele Cascella
Chemistry - A European Journal 24 (20), 5074-5077 (2018);
doi:10.1002/chem.201705159

Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers
Stefan Jaschonek, Michele Cascella, Jürgen Gauss, Gregor Diezemann, Giuseppe Milano
Biochemical and Biophysical Research Communications 498 (2), 327-333 (2018);
doi:10.1016/j.bbrc.2017.10.132

Force probe simulations using a hybrid scheme with virtual sites
Ken Schäfer, Marco Oestereich, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 147 (13), 134909 (2017);
doi:10.1063/1.4986194

Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
Stefan Jaschonek, Gregor Diezemann
The Journal of Chemical Physics 146 (12), 124901 (2017);
doi:10.1063/1.4978678

Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 120 (40), 10433-10441 (2016);
doi:10.1021/acs.jpcb.6b06784

Mechanical unfolding pathway of a model β-peptide foldamer
Lalita Uribe, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 142 (20), 204901 (2015);
doi:10.1063/1.4921371

Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 119 (26), 8313-8320 (2015);
doi:10.1021/acs.jpcb.5b04044