Biomolecular Chemistry in Liquid Phase Separated Compartments

Nakashima, Karina K.; Vibhute, Mahesh A.; Spruijt, Evan

doi:10.3389/fmolb.2019.00021

Cited by 193 publications

(184 citation statements)

References 89 publications

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“…[21,52,53] Membrane-free droplets can hence be described as "open" reactors, capable of rapid molecular exchange with their environment without the need for active transport machineries (Figure 2A). [55] Low-molecular-weight solutes do not usually exhibit high levels of partitioning in neutral polymer ATPSs. [54] Althought he driving forces behind selectives olute partitioning remainp oorly understood, factors such as the charge, hydrophobicity,s ize or shape of biomolecular solutes, together with the chemical natureo ft he LLPS components,h ave been invoked to account for the solutes' uptake or exclusionb y aqueous droplets.…”

Section: Bridging the Gap With Living Cells:i Ntracellular Biomoleculmentioning

confidence: 99%

“…Experimental and theoretical studies in ATPSs showed only poor reactionr ate enhancement for a pair of enzymesi nvolved in ac oncertedc ascade reaction, due to the low degree of partitioning of enzymes in the droplets. [55,82] Elucidation and explanation of the connections between differential partitioning, upconcentration, crowding, chemical composition, protein conformation etc. [81] By compartmentalising dextranase in ac oacervate subcompartment within the dextran droplet, substrate inhibition was mitigated and dextranase-mediated interfacial dextran hydrolysis was restored.…”

Section: Bridging the Gap With Living Cells:i Ntracellular Biomoleculmentioning

confidence: 99%

“…At heoretical framework to account for selectivep artitioning, based on the standard free energy of the client solutes in the two phases, has recently been developed. [55] Low-molecular-weight solutes do not usually exhibit high levels of partitioning in neutral polymer ATPSs. [7] In contrast, complexc oacervate droplets have been found to sequester small solutes,i ncluding ions, [56] through complementary electrostatic interactions, together with hydrophobic effects associated with the lower dielectric constant of the droplets' interiors relative to the dilute phase.…”

Section: Biomolecular Partitioninga Nd Biochemical Reactions In Membrmentioning

confidence: 99%

“…Similar observations have also been reported in naturally occurring biomolecular condensates. [55,82] Elucidation and explanation of the connections between differential partitioning, upconcentration, crowding, chemical composition, protein conformation etc. and the structure,c onformational stabilitya nd activity of enzymes in membrane-free droplets is an area of increasing interest that should help in the designing of robust and versatile bioactive droplets capable of more advanced functions (e.g.,f eedback, control, logical operations etc.…”

Section: Biomolecular Partitioninga Nd Biochemical Reactions In Membrmentioning

confidence: 99%

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Dynamic Synthetic Cells Based on Liquid–Liquid Phase Separation

2019

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Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom‐up construction of cell‐like models capable of reproducing aspects of such dynamic organisation. Liquid–liquid phase‐separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher‐order structures and behaviour.

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Section: Bridging the Gap With Living Cells:i Ntracellular Biomoleculmentioning

confidence: 99%

Section: Bridging the Gap With Living Cells:i Ntracellular Biomoleculmentioning

confidence: 99%

Section: Biomolecular Partitioninga Nd Biochemical Reactions In Membrmentioning

confidence: 99%

Section: Biomolecular Partitioninga Nd Biochemical Reactions In Membrmentioning

confidence: 99%

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Dynamic Synthetic Cells Based on Liquid–Liquid Phase Separation

2019

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“…Several methodologies have been developed to sequester specific biochemical processes to defined locations and to emulate functions of natural cellular organelles (3). Examples include the use of coacervates (4)(5)(6), hydrogels (7)(8)(9), as well as protein (10,11) and polymer (12) assemblies to spatially organize biomolecules. In eukaryotic cells, compartmentalization is primarily achieved by lipid bilayer membranes that demarcate the boundary to the outside world and enclose classical organelles.…”

Section: Introductionmentioning

confidence: 99%

Lipid Sponge Droplets as Programmable Synthetic Organelles

Bhattacharya

Niederholtmeyer

Podolsky

et al. 2020

Preprint

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performed the biochemical, chemical, and imaging experiments. A.B., R.B., J.S., and S.K.S performed and analyzed the data for X-ray scattering experiments. A.B., H.N., and N.K.D wrote the manuscript. AbstractLiving cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and nonionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the co-localization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and selfassembling spatial organization with biochemical reaction systems. Significance statementOrganelles spatially and temporally orchestrate biochemical reactions in a cell to a degree of precision that is still unattainable in synthetic reaction systems. Additionally, organelles such as the endoplasmic reticulum (ER) contain highly interconnected and dense membrane networks that provide large reaction spaces for both transmembrane and soluble enzymes. We present lipid sponge droplets to emulate the functions of organelles such as the ER. We demonstrate that lipid sponge droplets can be programmed to internally concentrate specific proteins, host and accelerate biochemical transformations, and to rapidly and reversibly sequester and release proteins to control enzymatic reactions. The self-assembled and programmable nature of lipid sponge droplets will facilitate the integration of complex functions for bottom up synthetic biology.

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