Microrheology analysis in molecular dynamics simulations: Finite box size correction

Ethier, Jeffrey G.; Nourian, Pouria; Islam, Rafikul; Khare, Rajesh; Schieber, Jay D.

doi:10.1122/8.0000158

Cited by 14 publications

(23 citation statements)

References 83 publications

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“…Following previous work on bead tracking simulations for polymeric systems 123 , we introduce a probe bead (with radius of 3, 4, and 5 σ ) within phase-separated condensates under bulk conditions (Fig. 1(e) Bottom panel).…”

Section: Resultsmentioning

confidence: 99%

“…Please note that despite self-interactions among probe beads are set to be purely repulsive, we only study this technique using a single probe bead (see the SM for further technical details). Following previous work on bead tracking simulations for polymeric systems 123 , we introduce a probe bead (with radius of 3, 4, and 5σ) within phase-separated condensates under bulk conditions (Fig. 1(e) Bottom panel).…”

Section: Bead Tracking (Bt) Methodsmentioning

confidence: 99%

“…Despite the fact that this technique has been experimentally applied to numerous soft matter and polymeric systems 119,120 (some of them including even chocolate 138 or mozzarella 139 ), its application to protein condensates has been much more limited 30,140 , mainly due to sample size requirements (bulk rheology measurements need, at least, volumes of the order of milliliters). In computer simulations, the OS technique has been mainly employed to characterise polymeric systems 117,123,[141][142][143] . In Fig.…”

Section: Oscillatory Shear (Os) Techniquementioning

confidence: 99%

“…In this work, we apply three different computational methods to evaluate the viscoelastic behaviour of biomolecular condensates formed by proteins and RNA. These methods are the integration of the shear stress relaxation modulus (SSRMI) 117,118 , the oscillatory shear (OS) technique 119,120 , and passive microrheology bead tracking (BT) 30,121–123 . Although these are well known in the field of polymer physics 117,124 , here we test them for the first time in the context of biomolecular condensates and progressive condensate maturation.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

Tejedor

Collepardo-Guevara

Ramı́rez

et al. 2022

Preprint

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Biomolecular condensates are important contributors to the internal organization of the cell material. While initially described as liquid-like droplets, the term biomolecular condensates is now used to describe a diversity of condensed phase assemblies with material properties extending from low to high viscous liquids, gels, and even glasses. Because the material properties of condensates are determined by the intrinsic behaviour of their molecules, characterising such properties is integral to rationalising the molecular mechanisms that dictate their functions and roles in health and disease. Here, we apply and compare three distinct computational methods to measure the viscoelasticity of biomolecular condensates in molecular simulations. These methods are the shear stress relaxation modulus integration (SSRMI), the oscillatory shear (OS) technique, and the bead tracking (BT) method. We find that, although all of these methods provide consistent results for the viscosity of the condensates, the SSRMI and OS techniques outperform the BT method in terms of computational efficiency and statistical uncertainty. We, thus, apply the SSRMI and OS techniques for a set of 12 different protein/RNA systems using a sequence-dependent high-resolution coarse-grained model. Our results reveal a strong correlation between condensate viscosity and density, as well as with protein/RNA length and the number of stickers vs. spacers in the amino-acid protein sequence. Moreover, we couple the SSRMI and the OS technique to nonequilibrium molecular dynamics simulations that mimic the progressive liquid-to-gel transition of protein condensates due to the accumulation of inter-protein β-sheets. We compare the behaviour of three different protein condensates -i.e., those formed by either hnRNPA1, FUS, or TDP-43 proteins- whose liquid-to-gel transitions are associated with the onset of amyotrophic lateral sclerosis and frontotemporal dementia. We find that both SSRMI and OS techniques successfully predict the transition from functional liquid-like behaviour to kinetically arrested states once the network of inter-protein β-sheets has percolated through the condensates. Overall, our work provides a comparison of different modelling rheological techniques to assess the viscosity of biomolecular condensates, a critical magnitude that provides information on the behaviour of biomolecules inside condensates.

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Section: Resultsmentioning

confidence: 99%

Section: Bead Tracking (Bt) Methodsmentioning

confidence: 99%

Section: Oscillatory Shear (Os) Techniquementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

Tejedor

Collepardo-Guevara

Ramı́rez

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Recently, Guo and coworkers theoretically and experimentally reported the adsorption and detection of melphalan anti-ovarian cancer drug by the B 12 N 12 and the doped XB 11 N 12 nanostructures by using B3LYP and B3PW91 functionals [26]. It was found that GeB 11 N 12 fullerene can be regarded as a suitable biosensor for detection of melphalan and as an acceptable drug delivery vehicle to decrease the metabolic activity of the OVCAR-3 cancer cells [107,108]. The high sensitivity of the electronic features of BN nanocages towards adsorption behaviour of various drugs such as amantadine [27], curcumin [28], exemestane [29], ifosfamide [30], hydroxyurea [31], sarin and chlorosarin [32], sulfasalazine [33], thiotepa [34], etc., makes them as potential drug carriers for such drug molecules.…”

Section: Introductionmentioning

confidence: 99%

Anti-inflammatory effect of functionalized sulfasalazine boron nitride nanocages on cardiovascular disease and breast cancer: An in-silico simulation

Hachem

Opulencia

Abdelbasset

et al. 2022

Journal of Molecular Liquids

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Implementation of probe rheology simulation technique in atomistically detailed molecular dynamics simulations

Nourian

Peters

2023

J Comput Chem

Self Cite

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The probe rheology simulation technique is a technique for measuring the viscosity of a fluid by measuring the motion of an inserted probe particle. This approach has the benefit of greater potential accuracy at a lower computational cost than other conventional simulation techniques used for the calculation of mechanical properties, such as the Green–Kubo approach and nonequilibrium molecular dynamics simulations, and the potential to allow for sampling local variations of properties. This approach is implemented and demonstrated for atomistically detailed models. The viscosity of four different simple Newtonian liquids is calculated from both the Brownian motion (passive mode) and the forced motion (active mode) of an embedded probe particle. The probe particle is loosely modeled as a nano‐sized diamond particle: a rough sphere cut out of an FCC lattice made of carbon atoms. The viscosities obtained from the motion of the probe particle are compared with those obtained from the periodic perturbation method, and good agreement between the two sets of values is observed once the probe‐fluid interaction strength (i.e., εitalicij in the pair‐wise Lennard–Jones interaction) is two times higher than their original values, and the artificial hydrodynamic interactions between the probe particle and its periodic images are accounted for. The success of the proposed model opens new opportunities for applying such a technique in the rheological characterization of local mechanical properties in atomistically detailed molecular dynamics simulations, which can be directly compared with or help guide experiments of similar nature.

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Microrheology analysis in molecular dynamics simulations: Finite box size correction

Cited by 14 publications

References 83 publications

Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

Anti-inflammatory effect of functionalized sulfasalazine boron nitride nanocages on cardiovascular disease and breast cancer: An in-silico simulation

Implementation of probe rheology simulation technique in atomistically detailed molecular dynamics simulations

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