Critical Comparison of Biomembrane Force Fields: Protein–Lipid Interactions at the Membrane Interface

Angelica Sandoval-Perez; Kristyna Pluhackova; Rainer A. Böckmann

doi:10.1021/acs.jctc.7b00001

Critical Comparison of Biomembrane Force Fields: Protein–Lipid Interactions at the Membrane Interface

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.7b00001 ◽

2017 ◽

Vol 13 (5) ◽

pp. 2310-2321 ◽

Cited By ~ 28

Author(s):

Angelica Sandoval-Perez ◽

Kristyna Pluhackova ◽

Rainer A. Böckmann

Keyword(s):

Force Fields ◽

Membrane Interface ◽

Lipid Interactions ◽

Critical Comparison

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Vibrational Normal Modes of theD2h16 Phase of BaCeO3: a Critical Comparison of Force Fields

Journal of Raman Spectroscopy ◽

10.1002/(sici)1097-4555(199704)28:4<255::aid-jrs95>3.0.co;2-f ◽

1997 ◽

Vol 28 (4) ◽

pp. 255-276 ◽

Cited By ~ 24

Author(s):

F. Genet ◽

S. Loridant ◽

G. Lucazeau

Keyword(s):

Force Fields ◽

Normal Modes ◽

Critical Comparison

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Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane

The Journal of Physical Chemistry B ◽

10.1021/jp711492h ◽

2008 ◽

Vol 112 (32) ◽

pp. 9588-9602 ◽

Cited By ~ 88

Author(s):

Igor Vorobyov ◽

Libo Li ◽

Toby W. Allen

Keyword(s):

Force Fields ◽

Coarse Grained ◽

Side Chain ◽

Lipid Interactions ◽

Formidable Challenge

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A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

Physical Chemistry Chemical Physics ◽

10.1039/c7cp01532a ◽

2017 ◽

Vol 19 (21) ◽

pp. 13629-13639 ◽

Cited By ~ 12

Author(s):

Jie Hu ◽

Tao Chen ◽

Moye Wang ◽

Hue Sun Chan ◽

Zhuqing Zhang

Keyword(s):

Protein Folding ◽

Force Fields ◽

Coarse Grained ◽

Unfolded Proteins ◽

Critical Comparison ◽

Atomic Models ◽

Atomic Force

The predicted dimension of unfolded proteins is quite different using native-centric Gō-like models and transferrable (non-structure-based) models based on current atomic force fields.

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A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.6b01870 ◽

2016 ◽

Vol 120 (16) ◽

pp. 3888-3903 ◽

Cited By ~ 76

Author(s):

Kristyna Pluhackova ◽

Sonja A. Kirsch ◽

Jing Han ◽

Liping Sun ◽

Zhenyan Jiang ◽

...

Keyword(s):

Force Fields ◽

Critical Comparison ◽

Structure And Dynamics

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Use of the Magnetostatic Analogue In Electromagnetic Lens Engineering

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100068795 ◽

1970 ◽

Vol 28 ◽

pp. 360-361

Author(s):

John W. Coleman

Keyword(s):

Boundary Conditions ◽

High Performance ◽

Force Fields ◽

Optical Design ◽

Direct Conversion ◽

Design Engineering ◽

Design Data ◽

Scalar Potentials ◽

Geometric Elements ◽

At Will

In the design engineering of high performance electromagnetic lenses, the direct conversion of electron optical design data into drawings for reliable hardware is oftentimes difficult, especially in terms of how to mount parts to each other, how to tolerance dimensions, and how to specify finishes. An answer to this is in the use of magnetostatic analytics, corresponding to boundary conditions for the optical design. With such models, the magnetostatic force on a test pole along the axis may be examined, and in this way one may obtain priority listings for holding dimensions, relieving stresses, etc..The development of magnetostatic models most easily proceeds from the derivation of scalar potentials of separate geometric elements. These potentials can then be conbined at will because of the superposition characteristic of conservative force fields.

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Two-Dimensional Crystallization of Tetanus Toxin

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100119466 ◽

1985 ◽

Vol 43 ◽

pp. 528-529

Author(s):

Jeffry A. Reidler ◽

John P. Robinson

Keyword(s):

Electron Microscopy ◽

Tetanus Toxin ◽

Structural Information ◽

Three Dimensional ◽

Two Dimensional ◽

Membrane Interface ◽

3D Reconstructions ◽

Cellular Receptors ◽

Computer Reconstruction ◽

2D Crystals

We have prepared two-dimensional (2D) crystals of tetanus toxin using procedures developed by Uzgiris and Kornberg for the directed production of 2D crystals of monoclonal antibodies at an antigen-phospholipid monolayer interface. The tetanus toxin crystals were formed using a small mole fraction of the natural receptor, GT1, incorporated into phosphatidyl choline monolayers. The crystals formed at low concentration overnight. Two dimensional crystals of this type are particularly useful for structure determination using electron microscopy and computer image refinement. Three dimensional (3D) structural information can be derived from these crystals by computer reconstruction of photographs of toxin crystals taken at different tilt angles. Such 3D reconstructions may help elucidate the mechanism of entry of the enzymatic subunit of toxins into cells, particularly since these crystals form directly on a membrane interface at similar concentrations of ganglioside GT1 to the natural cellular receptors.

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