Molecular dynamics simulations of rubredoxin fromClostridium pasteurianum: Changes in structure and electrostatic potential duringredox reactions

AbstractDiffusion is the most fundamental mode of protein translocation within cells. Confined diffusion of proteins along the electrostatic potential constituted by the surface of microtubules, although modeled meticulously in molecular dynamics simulations, has not been experimentally observed in real-time. Here, we used interferometric scattering microscopy to directly visualize the movement of the microtubule-associated protein Ase1 along the microtubule surface at nanometer and microsecond resolution. We resolved millisecond confinements of Ase1 and fast leaps between these positions of dwelling preferentially occurring along the microtubule protofilaments, revealing Ase1’s mode of diffusive translocation along the microtubule’s periodic surface. The derived interaction potential closely matches the tubulin-dimer periodicity and the distribution of the electrostatic potential on the microtubule lattice. We anticipate that mapping the interaction landscapes for different proteins on microtubules, finding plausible energetic barriers of different positioning and heights, will provide valuable insights into regulating the dynamics of essential cytoskeletal processes, such as intracellular cargo trafficking, cell division, and morphogenesis, all of which rely on diffusive translocation of proteins along microtubules.

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Surface Electrostatic Potential and Water Orientation in the presence of Sodium Octanoate Dilute Monolayers Studied by Means of Molecular Dynamics Simulations

Langmuir ◽

10.1021/acs.langmuir.5b02904 ◽

2015 ◽

Vol 31 (40) ◽

pp. 10995-11004 ◽

Cited By ~ 9

Author(s):

Kalil Bernardino ◽

André F. de Moura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Potential ◽

Sodium Octanoate ◽

Dynamics Simulations ◽

Surface Electrostatic Potential

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Ibuprofen and sila-ibuprofen: polarization effects in the crystal and enzyme environments

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520621009379 ◽

2021 ◽

Vol 77 (6) ◽

Author(s):

Florian Kleemiss ◽

Pim Puylaert ◽

Daniel Duvinage ◽

Malte Fugel ◽

Kunihisa Sugimoto ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Potential ◽

Quantum Chemical ◽

Functional Group ◽

Water Soluble ◽

Biologically Active ◽

Polarization Effects ◽

Similarities And Differences ◽

Dynamics Simulations

Sila-ibuprofen is a new potential nonsteroidal anti-inflammatory drug which deviates from its parent ibuprofen in terms of the electrostatic potential around the carbon/silicon-switched C/Si—H group. Therefore, sila-ibuprofen is more water soluble and has a lower melting enthalpy. However, its binding and inhibition properties of cyclooxygenases appear to be very similar to regular ibuprofen. Therefore, in this study, intermolecular interactions and interaction densities of both ibuprofen and sila-ibuprofen in their biologically active forms, i.e. deprotonated and as the pure S-enantiomers are investigated. Quantum-crystallographically refined salts with argininium and 1-phenylethan-1-amoninium (PEA) counter-cations as crystalline models of the interactions with the guanidine functional group of arginine inside cyclooxygenases are presented. The similarities and differences between the polarization of ibuprofen and sila-ibuprofen in the crystal, enzyme, solvent and isolated environments are discussed based on quantum-chemical calculations. For the explicit crystal and enzyme environments, specifically, molecular dynamics simulations starting from the crystal models were combined with QM/MM calculations.

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