Methods for characterizing the material properties of biomolecular condensates

Alshareedah, Ibraheem; Kaur, Taranpreet; Banerjee, Priya R.

doi:10.1016/bs.mie.2020.06.009

Cited by 53 publications

(56 citation statements)

References 59 publications

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“…1 B). For droplets displaying Newtonian fluid properties, this relaxation time is proportional to the ratio of the viscosity h over surface tension g (30) and can be written as…”

Section: Resultsmentioning

confidence: 99%

“…where l is the average diameter of the fusing droplets. Measurement of inverse capillary velocity (h/g) alone does not provide any direct information on the viscosity and/or surface tension of condensates, unless an independent assay is used to measure one of these quantities (30). To this end, we employed VPT microscopy, which enables the determination of the viscosity of the same condensates (31).…”

Section: Resultsmentioning

confidence: 99%

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Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates

Alshareedah

Thurston

Banerjee

2021

Biophysical Journal

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“…1 B). For droplets displaying Newtonian fluid properties, this relaxation time is proportional to the ratio of the viscosity h over surface tension g (30) and can be written as…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates

Alshareedah

Thurston

Banerjee

2021

Biophysical Journal

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“…Multivalent protein and nucleic acid molecules drive the formation of membraneless biomolecular condensates, which are implicated in a variety of cellular functions (Mitrea and Kriwacki, 2016). As micron-or sub-micron sized structures, condensates can function as viscous liquids, viscoelastic fluids, gels, liquid crystals, or solids (Alshareedah et al, 2021;Choi et al, 2020;Franzmann et al, 2018;Kaur et al, 2019;Kroschwald et al, 2018;Shen et al, 2020;Yu et al, 2021). Among the molecular drivers of phase separation are distinct types of intrinsically disordered proteins (IDPs) (Posey et al, 2018a) with the requisite sequence grammar (Greig et al, 2020;Kim et al, 2019;Martin et al, 2020;Martin and Mittag, 2018;Vernon et al, 2018;Wang et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Sequence grammar underlying unfolding and phase separation of globular proteins

Ruff

Choi

Cox

et al. 2021

Preprint

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SummaryProtein homeostasis involves regulation of the concentrations of unfolded states of globular proteins. Dysregulation can cause phase separation leading to protein-rich deposits. Here, we uncover the sequence-grammar that influences the triad of folding, binding, and phase equilibria of unfolded proteins in cells. We find that the interactions that drive deposit formation of ALS-associated superoxide dismutase 1 mutations are akin to those that drive phase separation and deposit formation in variants of a model protein, barnase. We examined a set of barnase variants to uncover the molecular interactions that drive phase separation of unfolded proteins and formation of unfolded protein deposits (UPODs). The formation of UPODs requires protein destabilization, to increase the concentration of unfolded states, and a requisite sequence grammar to enable cohesive interactions among unfolded proteins. We further find that molecular chaperones, Hsp40 and Hsp70, destabilize UPODs by binding preferentially to and processing unfolded proteins in the dilute phase.HighlightsUnfolded states of globular proteins undergo aggregation-mediated phase separation to form unfolded protein deposits (UPODs) in cells.The threshold concentration of unfolded proteins required to drive phase separation is governed by a combination of protein stability and the requisite grammar of cohesive motifs known as stickers that provide cohesive intermolecular interactions.The sequence grammar that contributes to phase separation of unfolded proteins shares features with those of proteins that drive the formation of functional biomolecular condensates.Molecular chaperones regulate the concentrations of free unfolded proteins in cells by binding preferentially to unfolded states in dilute phases thereby destabilizing UPOD formation mainly via binding-mediated polyphasic linkage.

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“…∑ l ≥ 2; l even C l θ 0 (l − 1)(l + 2) [14] The force exerted on either pole is F 0 = − p ex0 πR 2 1 − cos 2 θ 0 [15] This is obtained by integrating over each cap the axial component (i.e., along the pole-topole direction) of the force due to the external pressure. The net force in the lateral direction is zero due to axial symmetry.…”

Section: Theoretical Model I Model Under Static Forcesmentioning

confidence: 99%

“…Experimental measurements of material properties are crucial for deepening understanding of condensates. Both fluorescence microscopy 8,[11][12] and optical tweezers (OT) [13][14][15][16] have proven useful in dealing with the micron sizes of droplets. Analyzing the experimental data typically require a theoretical model for the statics or dynamics of the material states of condensates.…”

Section: Introductionmentioning

confidence: 99%

Determination of Condensate Material Properties from Droplet Deformation

Zhou

2020

J. Phys. Chem. B

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I derive theoretical results that relate the effective spring constant, χ, of protein droplets to their material properties. χ, defined as the ratio between a uniaxial applied force and the extent of the corresponding deformation, can be measured by optical tweezers. When the deformation is static, where the applied force is balanced by the interfacial tension of the droplet, the spring constant allows for the determination of the surface tension (γ). When a sinusoidal force is applied (at frequency ω), the dynamic spring constant χ(ω) is related to both γ and the complex shear modulus, G(ω) of the droplet. The results derived here enable accurate extraction of γ and G(ω) from χ(ω) data.

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Methods for characterizing the material properties of biomolecular condensates

Cited by 53 publications

References 59 publications

Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates

Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates

Sequence grammar underlying unfolding and phase separation of globular proteins

Determination of Condensate Material Properties from Droplet Deformation

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