Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments

Zec, Nebojša; Mangiapia, Gaetano; Hendry, Alex C; Barker, Robert; Koutsioubas, Alexandros; Frielinghaus, Henrich; Campana, Mario; Roldan, Jose‐Luis Ortega; Büsch, Sebastian; Moulin, Jean‐François

doi:10.3390/membranes11070507

Cited by 6 publications

(5 citation statements)

References 85 publications

(113 reference statements)

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“…The above examples show that, despite of apparent intrinsic limitations [67], the combination of SAXS/SANS and MD has a great potential for a deeper understanding of solution structures and dynamics of protein complexes. It has to be added that solution structures obtained by PEPSI can be directly used as an input structure to derived force fields for MD simulations since it keeps the initial protein sequence.…”

Section: Combination With Molecular Dynamics Simulationsmentioning

confidence: 99%

Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods

Golub,

Pieper

2023

Molecules

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Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.

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Section: Combination With Molecular Dynamics Simulationsmentioning

confidence: 99%

Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods

Golub,

Pieper

2023

Molecules

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“…Although MD simulations have been successfully used to evaluate the nanoscopic (picoseconds and Ångstroms) structure and dynamics probed by scattering data [8,[20][21][22][23][24], the interaction potentials used by the simulations are generally optimized to reproduce macroscopic, thermodynamic properties and densities [12,13], sometimes with the aim of being able to cover a large portion of the phase diagram [13]. A model that is directly optimized to reproduce scattering experiments will likely yield a better description of the nanoscopic properties, albeit probably at the cost of generality.…”

Section: Introductionmentioning

confidence: 99%

Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments

et al. 2022

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The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.

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“…Such a conformation, including the various embedded proteins (receptors, ion channels, transporters, and other proteins), constitutes the so-called fluid-mosaic model [ 12 ]. Membrane fluidity represents one of the most critical membrane properties [ 9 ], and it is still the object of several studies [ 9 , 10 , 11 , 13 , 14 , 15 , 16 , 17 ]. Among numerous molecules relocating along the plasma membrane, we focus here on the motility of receptor proteins.…”

Section: Introductionmentioning

confidence: 99%

Modeling Receptor Motility along Advecting Lipid Membranes

et al. 2022

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This work aims to overview multiphysics mechanobiological computational models for receptor dynamics along advecting cell membranes. Continuum and statistical models of receptor motility are the two main modeling methodologies identified in reviewing the state of the art. Within the former modeling class, a further subdivision based on different biological purposes and processes of proteins’ motion is recognized; cell adhesion, cell contractility, endocytosis, and receptor relocations on advecting membranes are the most relevant biological processes identified in which receptor motility is pivotal. Numerical and/or experimental methods and approaches are highlighted in the exposure of the reviewed works provided by the literature, pertinent to the topic of the present manuscript. With a main focus on the continuum models of receptor motility, we discuss appropriate multiphyisics laws to model the mass flux of receptor proteins in the reproduction of receptor relocation and recruitment along cell membranes to describe receptor–ligand chemical interactions, and the cell’s structural response. The mass flux of receptor modeling is further supported by a discussion on the methodology utilized to evaluate the protein diffusion coefficient developed over the years.

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Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments

Cited by 6 publications

References 85 publications

Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods

Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods

Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments

Modeling Receptor Motility along Advecting Lipid Membranes

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