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Article ; Online: Self-assembly coupled to liquid-liquid phase separation.

Hagan, Michael F / Mohajerani, Farzaneh

2023 Volume 19, Issue 5, Page(s) e1010652

Abstract: Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self- ... ...

Abstract	Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
MeSH term(s)	Protein Aggregates
Chemical Substances	Protein Aggregates
Language	English
Publishing date	2023-05-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010652
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Article ; Online: Optimization of non-equilibrium self-assembly protocols using Markov state models.

Trubiano, Anthony / Hagan, Michael F

The Journal of chemical physics

2022 Volume 157, Issue 24, Page(s) 244901

Abstract: The promise of self-assembly to enable the bottom-up formation of materials with prescribed architectures and functions has driven intensive efforts to uncover rational design principles for maximizing the yield of a target structure. Yet, despite many ... ...

Abstract	The promise of self-assembly to enable the bottom-up formation of materials with prescribed architectures and functions has driven intensive efforts to uncover rational design principles for maximizing the yield of a target structure. Yet, despite many successful examples of self-assembly, ensuring kinetic accessibility of the target structure remains an unsolved problem in many systems. In particular, long-lived kinetic traps can result in assembly times that vastly exceed experimentally accessible timescales. One proposed solution is to design non-equilibrium assembly protocols in which system parameters change over time to avoid such kinetic traps. Here, we develop a framework to combine Markov state model (MSM) analysis with optimal control theory to compute a time-dependent protocol that maximizes the yield of the target structure at a finite time. We present an adjoint-based gradient descent method that, in conjunction with MSMs for a system as a function of its control parameters, enables efficiently optimizing the assembly protocol. We also describe an interpolation approach to significantly reduce the number of simulations required to construct the MSMs. We demonstrate our approach with two examples; a simple semi-analytic model for the folding of a polymer of colloidal particles, and a more complex model for capsid assembly. Our results show that optimizing time-dependent protocols can achieve significant improvements in the yields of selected structures, including equilibrium free energy minima, long-lived metastable structures, and transient states.
MeSH term(s)	Capsid Proteins ; Capsid/chemistry ; Polymers/analysis
Chemical Substances	Capsid Proteins ; Polymers
Language	English
Publishing date	2022-12-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0130407
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Article: Equilibrium mechanisms of self-limiting assembly.

Hagan, Michael F / Grason, Gregory M

Reviews of modern physics

2021 Volume 93, Issue 2

Abstract: Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly ...

Abstract	Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of
Language	English
Publishing date	2021-06-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	209901-9
ISSN	0034-6861
ISSN	0034-6861
DOI	10.1103/revmodphys.93.025008
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Book ; Online: Optimization of Non-Equilibrium Self-Assembly Protocols Using Markov State Models

Trubiano, Anthony / Hagan, Michael F.

2022

Abstract: The promise of self-assembly to enable bottom-up formation of materials with prescribed architectures and functions has driven intensive efforts to uncover rational design principles for maximizing the yield of a target structure. Yet, despite many ... ...

Abstract	The promise of self-assembly to enable bottom-up formation of materials with prescribed architectures and functions has driven intensive efforts to uncover rational design principles for maximizing the yield of a target structure. Yet, despite many successful examples of self-assembly, ensuring kinetic accessibility of the target structure remains an unsolved problem in many systems. In particular, long-lived kinetic traps can result in assembly times that vastly exceed experimentally accessible timescales. One proposed solution is to design non-equilibrium assembly protocols in which system parameters change over time to avoid such kinetic traps. Here, we develop a framework to combine Markov state model (MSM) analysis with optimal control theory to compute a time-dependent protocol that maximizes the yield of the target structure at a finite-time. We present an adjoint-based gradient descent method that, in conjunction with MSMs for a system as a function of its control parameters, enables efficiently optimizing the assembly protocol. We also describe an interpolation approach to significantly reduce the number of simulations required to construct the MSMs. We demonstrate our approach on two examples; a simple semi-analytic model for the folding of a polymer of colloidal particles, and a more complex model for capsid assembly. Our results show that optimizing time-dependent protocols can achieve significant improvements in yields of selected structures, including equilibrium free energy minima, long-lived metastable structures, and transient states.
Keywords	Condensed Matter - Soft Condensed Matter ; Condensed Matter - Materials Science
Subject code	670
Publishing date	2022-10-11
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microcompartment assembly around multicomponent fluid cargoes.

Tsidilkovski, Lev / Mohajerani, Farzaneh / Hagan, Michael F

The Journal of chemical physics

2022 Volume 156, Issue 24, Page(s) 245104

Abstract: This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a ...

Abstract	This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein-shell protein and shell protein-cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid-liquid phase separation may play a role in the organization of the cellular cytoplasm.
MeSH term(s)	Bacteria/metabolism ; Bacterial Proteins/metabolism ; Kinetics ; Synthetic Biology ; Thermodynamics
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0089556
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Book ; Online: Design principles for transporting vesicles with enclosed active particles

Uplap, Sarvesh / Hagan, Michael F. / Baskaran, Aparna

2023

Abstract: We use coarse-grained molecular dynamics simulations to study the motility of a 2D vesicle containing self-propelled rods, as a function of the vesicle bending rigidity and the number density, length, and activity of the enclosed rods. Above a threshold ... ...

Abstract	We use coarse-grained molecular dynamics simulations to study the motility of a 2D vesicle containing self-propelled rods, as a function of the vesicle bending rigidity and the number density, length, and activity of the enclosed rods. Above a threshold value of the rod length, distinct dynamical regimes emerge, including a dramatic enhancement of vesicle motility characterized by a highly persistent random walk. These regimes are determined by clustering of the rods within the vesicle; the maximum motility state arises when there is one long-lived polar cluster. We develop a scaling theory that predicts the dynamical regimes as a function of control parameters, and shows that feedback between activity and passive membrane forces govern the rod organization. These findings yield design principles for building self-propelled superstructures using independent active agents under deformable confinement. Comment: 8 pages, 5 figures
Keywords	Condensed Matter - Soft Condensed Matter
Subject code	612
Publishing date	2023-03-28
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Polymorphic self-assembly of helical tubules is kinetically controlled.

Fang, Huang / Tyukodi, Botond / Rogers, W Benjamin / Hagan, Michael F

Soft matter

2022 Volume 18, Issue 35, Page(s) 6716–6728

Abstract: In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size ... ...

Abstract	In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size scale of the individual monomers. In many such cases, the finite dimension is selected by a preferred curvature of the monomers, which leads to self-closure of the assembly. In this article, we study an example class of self-closing assemblies: cylindrical tubules that assemble from triangular monomers. By combining kinetic Monte Carlo simulations, free energy calculations, and simple theoretical models, we show that a range of programmable size scales can be targeted by controlling the intricate balance between the preferred curvature of the monomers and their interaction strengths. However, their assembly is kinetically controlled-the tubule morphology is essentially fixed shortly after closure, resulting in a distribution of tubule widths that is significantly broader than the equilibrium distribution. We develop a simple kinetic model based on this observation and the underlying free-energy landscape of assembling tubules that quantitatively describes the distributions. Our results are consistent with recent experimental observations of tubule assembly from triangular DNA origami monomers. The modeling framework elucidates design principles for assembling self-limited structures from synthetic components, such as artificial microtubules that have a desired width and chirality.
MeSH term(s)	DNA/chemistry ; Kinetics ; Microtubules ; Models, Theoretical ; Monte Carlo Method
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-09-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d2sm00679k
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Article ; Online: From disks to channels: dynamics of active nematics confined to an annulus.

Joshi, Chaitanya / Zarei, Zahra / Norton, Michael M / Fraden, Seth / Baskaran, Aparna / Hagan, Michael F

Soft matter

2023 Volume 19, Issue 29, Page(s) 5630–5640

Abstract: Confinement can be used to systematically tame turbulent dynamics occurring in active fluids. Although periodic channels are the simplest geometries to study confinement numerically, the corresponding experimental realizations require closed racetracks. ... ...

Abstract	Confinement can be used to systematically tame turbulent dynamics occurring in active fluids. Although periodic channels are the simplest geometries to study confinement numerically, the corresponding experimental realizations require closed racetracks. Here, we computationally study 2D active nematics confined to such a geometry-an annulus. By systematically varying the annulus inner radius and channel width, we bridge the behaviors observed in the previously studied asymptotic limits of the annulus geometry: a disk and an infinite channel. We identify new steady-state behaviors, which reveal the influence of boundary curvature and its interplay with confinement. We also show that, below a threshold inner radius, the dynamics are insensitive to the presence of the inner hole. We explain this insensitivity through a simple scaling analysis. Our work sheds further light on design principles for using confinement to control the dynamics of active nematics.
Language	English
Publishing date	2023-07-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d3sm00477e
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Article ; Online: Engineering Metastability into a Virus-like Particle to Enable Triggered Dissociation.

Starr, Caleb A / Nair, Smita / Huang, Sheng-Yuan / Hagan, Michael F / Jacobson, Stephen C / Zlotnick, Adam

Journal of the American Chemical Society

2023 Volume 145, Issue 4, Page(s) 2322–2331

Abstract: For a virus-like particle (VLP) to serve as a delivery platform, the VLP must be able to release its cargo in response to a trigger. Here, we use a chemical biology approach to destabilize a self-assembling capsid for a subsequent triggered disassembly. ... ...

Abstract	For a virus-like particle (VLP) to serve as a delivery platform, the VLP must be able to release its cargo in response to a trigger. Here, we use a chemical biology approach to destabilize a self-assembling capsid for a subsequent triggered disassembly. We redesigned the dimeric hepatitis B virus (HBV) capsid protein (Cp) with two differentially addressable cysteines, C150 for reversibly crosslinking the capsid and C124 to react with a destabilizing moiety. The resulting construct, Cp150-V124C, assembles into icosahedral, 120-dimer VLPs that spontaneously crosslink via the C-terminal C150, leaving C124 buried at a dimer-dimer interface. The VLP is driven into a metastable state when C124 is reacted with the bulky fluorophore, maleimidyl BoDIPY-FL. The resulting VLP is stable until exposed to modest, physiologically relevant concentrations of reducing agent. We observe dissociation with FRET relaxation of polarization, size exclusion chromatography, and resistive-pulse sensing. Dissociation is slow, minutes to hours, with a characteristic lag phase. Mathematical modeling based on the presence of a nucleation step predicts disassembly dynamics that are consistent with experimental observations. VLPs transfected into hepatoma cells show similar dissociation behavior. These results suggest a generalizable strategy for designing a VLP that can release its contents in an environmentally responsive reaction.
MeSH term(s)	Capsid/chemistry ; Capsid Proteins/chemistry ; Hepatitis B virus/chemistry ; Cell Line ; Vaccines, Virus-Like Particle/analysis
Chemical Substances	Capsid Proteins ; Vaccines, Virus-Like Particle
Language	English
Publishing date	2023-01-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.2c10937
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Article ; Online: Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate).

Asor, Roi / Singaram, Surendra W / Levi-Kalisman, Yael / Hagan, Michael F / Raviv, Uri

The European physical journal. E, Soft matter

2023 Volume 46, Issue 11, Page(s) 107

Abstract: Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent, such as RNA, DNA, or a charged polymer. Electrostatic ... ...

Abstract	Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent, such as RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with a combinatorial number of intermediates. Hence, the mechanism of the reaction is poorly understood. In this paper, we combined solution small-angle X-ray scattering (SAXS), cryo-transmission electron microscopy (TEM), and computational modeling to determine the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by SAXS and cryo-TEM. To analyze the data, we performed Langevin dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures consistent with the experimental data. We found that close to physiological ionic strength, [Formula: see text] VLPs coexisted with VP1 pentamers. At lower or higher ionic strengths, incomplete particles coexisted with pentamers and [Formula: see text] particles. Including the simulated structures was essential to explain the SAXS data in a manner that is consistent with the cryo-TEM images.
MeSH term(s)	Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Capsid/chemistry ; Capsid/metabolism ; Styrene/analysis ; Styrene/metabolism ; Scattering, Small Angle ; X-Ray Diffraction ; Simian virus 40/chemistry ; Simian virus 40/genetics ; Simian virus 40/metabolism ; Virus Assembly
Chemical Substances	Capsid Proteins ; Styrene (44LJ2U959V)
Language	English
Publishing date	2023-11-02
Publishing country	France
Document type	Journal Article
ZDB-ID	2004003-9
ISSN	1292-895X ; 1292-8941
ISSN (online)	1292-895X
ISSN	1292-8941
DOI	10.1140/epje/s10189-023-00363-x
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