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Article ; Online: Polymer compaction and bridging-induced clustering of protein-inspired patchy particles.

Brackley, C A

Journal of physics. Condensed matter : an Institute of Physics journal

2020 Volume 32, Issue 31, Page(s) 314002

Abstract: ... simulations [Brackley et al 2013 Proc. Natl Acad. Sci. USA 110 E3605], where proteins modelled as spheres form ...

Abstract	There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro, and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo. In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the 'bridging-induced attraction'. The latter is a mechanism observed in previous simulations [Brackley et al 2013 Proc. Natl Acad. Sci. USA 110 E3605], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein-protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple 'patchy particles' interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.
Language	English
Publishing date	2020-03-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/1361-648X/ab7f6c
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Article ; Online: Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions.

Brackley, C A / Marenduzzo, D

Briefings in functional genomics

2020 Volume 19, Issue 2, Page(s) 111–118

Abstract: We review the mechanism and consequences of the 'bridging-induced attraction', a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer ...

Abstract	We review the mechanism and consequences of the 'bridging-induced attraction', a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. The clusters found in simulations also give rise to chromatin domains that conform well with the observation of A/B compartments in HiC experiments.
MeSH term(s)	Chromatin/chemistry ; Chromatin/metabolism ; Photobleaching ; Protein Processing, Post-Translational
Chemical Substances	Chromatin
Language	English
Publishing date	2020-01-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elz032
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Book ; Online: Polymer compaction and bridging-induced clustering of protein-inspired patchy particles

Brackley, C. A.

2019

Abstract: ... simulations [Brackley et al., Proc. Natl. Acad. Sci. USA 110 (2013)], where proteins modelled as spheres form ...

Abstract	There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro, and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo. In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the "bridging-induced attraction". The latter is a mechanism observed in previous simulations [Brackley et al., Proc. Natl. Acad. Sci. USA 110 (2013)], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein-protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple "patchy particles" interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.
Keywords	Condensed Matter - Soft Condensed Matter ; Quantitative Biology - Biomolecules
Subject code	612
Publishing date	2019-12-06
Publishing country	us
Document type	Book ; Online
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Article ; Online: Induction and maintenance of healing in erosive esophagitis in the United States.

Yadlapati, Rena / Hubscher, Elizabeth / Pelletier, Corey / Jacob, Rinu / Brackley, Allison / Shah, Shailja

Expert review of gastroenterology & hepatology

2022 Volume 16, Issue 10, Page(s) 967–980

Abstract: Introduction: Erosive esophagitis (EE) occurs when refluxate from the stomach causes T-lymphocyte infiltration of the esophageal mucosa, resulting in mucosal breaks. Currently, therapy with proton-pump inhibitors (PPIs) is the standard treatment for EE ... ...

Abstract	Introduction: Erosive esophagitis (EE) occurs when refluxate from the stomach causes T-lymphocyte infiltration of the esophageal mucosa, resulting in mucosal breaks. Currently, therapy with proton-pump inhibitors (PPIs) is the standard treatment for EE in the United States, but few comprehensive reviews exist on the efficacy of PPIs in US populations. Here, we present the most contemporary, thorough analysis of PPI efficacy rates, and identify and characterize patient subgroups at risk for poor healing outcomes. Areas covered: We searched the literature to identify studies reporting rates of endoscopic healing and maintained healing of EE with PPI therapies in the US and found a paucity of recent evidence and real-world evidence. Twenty-two studies from 2009 and earlier were included in the final dataset. Expert opinion: Rates of EE healing with PPIs were highest after 8 weeks of treatment, with over 80% of patients in most treatment arms demonstrating endoscopic healing, compared to lower efficacy (<80%) at 4 weeks. Rates of maintained healing with PPIs at 6 and 12 months were mostly lower than 80%, although the data were limited. Symptomatic patients and those with severe EE were less likely to achieve healing. Obese patients experienced similar healing rates as non-obese patients.
MeSH term(s)	Humans ; United States/epidemiology ; Esophagitis/diagnosis ; Esophagitis/drug therapy ; Esophagitis/complications ; Proton Pump Inhibitors/adverse effects ; Peptic Ulcer ; Upper Gastrointestinal Tract ; Barrett Esophagus/etiology
Chemical Substances	Proton Pump Inhibitors
Language	English
Publishing date	2022-10-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2481021-6
ISSN	1747-4132 ; 1747-4124
ISSN (online)	1747-4132
ISSN	1747-4124
DOI	10.1080/17474124.2022.2134115
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Article ; Online: Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces.

Brackley, C A / Lips, A / Morozov, A / Poon, W C K / Marenduzzo, D

Nature communications

2021 Volume 12, Issue 1, Page(s) 6812

Abstract: ... Thus, we predict that the electrostatic free energy of an RNA virus should increase by several thousands of k ...

Abstract	Understanding the interactions between viruses and surfaces or interfaces is important, as they provide the principles underpinning the cleaning and disinfection of contaminated surfaces. Yet, the physics of such interactions is currently poorly understood. For instance, there are longstanding experimental observations suggesting that the presence of air-water interfaces can generically inactivate and kill viruses, yet the mechanism underlying this phenomenon remains unknown. Here we use theory and simulations to show that electrostatics may provide one such mechanism, and that this is very general. Thus, we predict that the electrostatic free energy of an RNA virus should increase by several thousands of k
MeSH term(s)	Air ; Disinfection ; Hydrophobic and Hydrophilic Interactions ; RNA Viruses/chemistry ; Respiratory Aerosols and Droplets/chemistry ; Respiratory Aerosols and Droplets/virology ; Static Electricity ; Surface Properties ; Water
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2021-11-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-27052-7
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Article ; Online: Complex small-world regulatory networks emerge from the 3D organisation of the human genome.

Brackley, C A / Gilbert, N / Michieletto, D / Papantonis, A / Pereira, M C F / Cook, P R / Marenduzzo, D

Nature communications

2021 Volume 12, Issue 1, Page(s) 5756

Abstract: The discovery that overexpressing one or a few critical transcription factors can switch cell state suggests that gene regulatory networks are relatively simple. In contrast, genome-wide association studies (GWAS) point to complex phenotypes being ... ...

Abstract	The discovery that overexpressing one or a few critical transcription factors can switch cell state suggests that gene regulatory networks are relatively simple. In contrast, genome-wide association studies (GWAS) point to complex phenotypes being determined by hundreds of loci that rarely encode transcription factors and which individually have small effects. Here, we use computer simulations and a simple fitting-free polymer model of chromosomes to show that spatial correlations arising from 3D genome organisation naturally lead to stochastic and bursty transcription as well as complex small-world regulatory networks (where the transcriptional activity of each genomic region subtly affects almost all others). These effects require factors to be present at sub-saturating levels; increasing levels dramatically simplifies networks as more transcription units are pressed into use. Consequently, results from GWAS can be reconciled with those involving overexpression. We apply this pan-genomic model to predict patterns of transcriptional activity in whole human chromosomes, and, as an example, the effects of the deletion causing the diGeorge syndrome.
MeSH term(s)	Chromatin/chemistry ; Chromatin/metabolism ; Chromosomes, Human/chemistry ; Chromosomes, Human/metabolism ; Gene Regulatory Networks ; Genome, Human ; Genome-Wide Association Study ; Humans ; Models, Genetic ; Polymers/chemistry ; Polymers/metabolism ; Quantitative Trait Loci ; Transcription Factors/metabolism ; Transcription, Genetic
Chemical Substances	Chromatin ; Polymers ; Transcription Factors
Language	English
Publishing date	2021-10-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-25875-y
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Article ; Online: Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins.

Bonato, A / Brackley, C A / Johnson, J / Michieletto, D / Marenduzzo, D

Soft matter

2020 Volume 16, Issue 9, Page(s) 2406–2414

Abstract: We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to explain the ... ...

Abstract	We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to explain the extrusion of chromatin loops of hundreds of kilo-base-pairs (kbp), which may then be stabilised by interactions between cohesin and CTCF proteins. Here we show that the flexibility of the chromatin fibre strongly affects this dynamical process, and find that diffusive loop extrusion is more efficient on stiffer chromatin regions. We also show that the dynamics of loop formation are faster in confined and collapsed chromatin conformations but that this enhancement is counteracted by the increased crowding. We provide a simple theoretical argument explaining why stiffness and collapsed conformations favour diffusive extrusion. In light of the heterogeneous physical and conformational properties of eukaryotic chromatin, we suggest that our results are relevant to understand the looping and organisation of interphase chromosomes in vivo.
MeSH term(s)	Animals ; CCCTC-Binding Factor/chemistry ; CCCTC-Binding Factor/metabolism ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Chromatin/chemistry ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/chemistry ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosomes/chemistry ; Chromosomes/genetics ; Chromosomes/metabolism ; Diffusion ; Eukaryota/chemistry ; Eukaryota/genetics ; Eukaryota/metabolism ; Humans ; Models, Biological ; Cohesins
Chemical Substances	CCCTC-Binding Factor ; Cell Cycle Proteins ; Chromatin ; Chromosomal Proteins, Non-Histone
Language	English
Publishing date	2020-02-17
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/c9sm01875a
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Article ; Online: Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces

C. A. Brackley / A. Lips / A. Morozov / W. C. K. Poon / D. Marenduzzo

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 6

Abstract: We know that air-water interfaces can generically inactivate viruses, but the mechanisms behind this observation are unclear. Here the authors use simulations to uncover those mechanisms and find that the electrostatic repulsive free energy of an RNA ... ...

Abstract	We know that air-water interfaces can generically inactivate viruses, but the mechanisms behind this observation are unclear. Here the authors use simulations to uncover those mechanisms and find that the electrostatic repulsive free energy of an RNA virus increases by several thousands of kBT as it approaches an air-water interface, providing a mechanism for viral destabilization which may induce inactivation.
Keywords	Science ; Q
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Complex small-world regulatory networks emerge from the 3D organisation of the human genome

C. A. Brackley / N. Gilbert / D. Michieletto / A. Papantonis / M. C. F. Pereira / P. R. Cook / D. Marenduzzo

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 14

Abstract: Gene-regulatory networks are thought to be complex, and yet perturbation of just a few transcription factors (TFs) can have major consequences. Here the authors apply DNA polymer modelling and simulations to predict how 3D genome structure and TF-DNA ... ...

Abstract	Gene-regulatory networks are thought to be complex, and yet perturbation of just a few transcription factors (TFs) can have major consequences. Here the authors apply DNA polymer modelling and simulations to predict how 3D genome structure and TF-DNA interactions can give rise to transcriptional regulation operating over broad genomic regions, where small perturbations can have long-reaching effects.
Keywords	Science ; Q
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-equilibrium effects of molecular motors on polymers.

Foglino, M / Locatelli, E / Brackley, C A / Michieletto, D / Likos, C N / Marenduzzo, D

Soft matter

2019 Volume 15, Issue 29, Page(s) 5995–6005

Abstract: We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as ...

Abstract	We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as freely diffusing beads which, upon encountering the substrate, bind to it through a short-ranged attractive potential. When bound, motors and polymer beads experience an equal and opposite active force, directed tangential to the polymer; this leads to motion of the motors along the polymer contour. The inclusion of explicit motors differentiates our model from other recent active polymer models. We study, by means of Langevin dynamics simulations, the effect of the motor activity on both the conformational and dynamical properties of the substrate. We find that activity leads, in addition to the expected enhancement of polymer diffusion, to an effective reduction of its persistence length. We discover that this effective "softening" is a consequence of the emergence of double-folded branches, or hairpins, and that it can be tuned by changing the number of motors or the force they generate. Finally, we investigate the effect of the motors on the probability of knot formation. Counter-intuitively our simulations reveal that, even though at equilibrium a more flexible substrate would show an increased knotting probability, motor activity leads to a marked decrease in the occurrence of knotted conformations with respect to equilibrium.
Language	English
Publishing date	2019-07-11
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/c9sm00273a
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