Journal Club Group Meeting
Feb
25
1:00 PM13:00

Journal Club Group Meeting

Presenter: Rachel

Article: Supercharging enables organized assembly of synthetic biomolecules

Symmetrical protein oligomers are ubiquitous in biological systems and perform key structural and regulatory functions. However, there are few methods for constructing such oligomers. Here we have engineered completely synthetic, symmetrical oligomers by combining pairs of oppositely supercharged variants of a normally monomeric model protein through a strategy we term ‘supercharged protein assembly’ (SuPrA). We show that supercharged variants of green fluorescent protein can assemble into a variety of architectures including a well-defined symmetrical 16-mer structure that we solved using cryo-electron microscopy at 3.47 Å resolution. The 16-mer is composed of two stacked rings of octamers, in which the octamers contain supercharged proteins of alternating charges, and interactions within and between the rings are mediated by a variety of specific electrostatic contacts. The ready assembly of this structure suggests that combining oppositely supercharged pairs of protein variants may provide broad opportunities for generating novel architectures via otherwise unprogrammed interactions.

https://www.nature.com/articles/s41557-018-0196-3#Abs1

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Coffee & Coacervates
Feb
15
3:00 PM15:00

Coffee & Coacervates

This week will be discussing the theory and molecular driving forces for intracellular phase transitions. See you then!!

Link: https://deptaedit.princeton.edu/cbe/people/faculty/brangwynne/group/publications/Berry_RoPP_2018.pdf (Sections 1 and 2)

Abstract: Exciting recent developments suggest that phase transitions represent an important and ubiquitous mechanism underlying intracellular organization. We describe key experimental findings in this area of study, as well as the application of classical theoretical approaches for quantitatively understanding these data. We also discuss the way in which equilibrium thermodynamic driving forces may interface with the fundamentally out-of-equilibrium nature of living cells. In particular, time and/or space-dependent concentration profiles may modulate the phase behavior of biomolecules in living cells. We suggest future directions for both theoretical and experimental work that will shed light on the way in which biological activity modulates the assembly, properties, and function of viscoelastic states of living matter.

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Journal Club Group Meeting
Feb
4
1:00 PM13:00

Journal Club Group Meeting

Presenter: Vivian

Article: Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

https://www.cell.com/cell/pdf/S0092-8674(18)31456-9.pdf

Phase transitions involving biomolecular liquids are a fundamental mechanism underlying intracellular organization. In the cell nucleus, liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is implicated in assembly of the nucleolus, as well as transcriptional clusters, and other nuclear bodies. However, it remains unclear whether and how physical forces associated with nucleation, growth, and wetting of liquid condensates can directly restructure chromatin. Here, we use CasDrop, a novel CRISPR-Cas9-based optogenetic technology, to show that various IDPs phase separate into liquid condensates that mechanically exclude chromatin as they grow and preferentially form in low-density, largely euchromatic regions. A minimal physical model explains how this stiffness sensitivity arises from lower mechanical energy associated with deforming softer genomic regions. Targeted genomic loci can nonetheless be mechanically pulled together through surface tension-driven coalescence. Nuclear condensates may thus function as mechanoactive chromatin filters, physically pulling in targeted genomic loci while pushing out non-targeted regions of the neighboring genome.

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Coffee & Coacervates
Feb
1
3:30 PM15:30

Coffee & Coacervates

Come and join us for Coffee & Coacervates! This week we will be discussing a thermodynamic analysis of protein-polyelectrolyte interactions. This review discusses the mechanisms including theories and binding stages concerning the protein–polyelectrolyte (PE) interactions, as well as the applications for both complexation and coacervation states of protein–PE pairs.

https://www.mdpi.com/2073-4360/11/1/82

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Jan
28
1:00 PM13:00

Journal Club Group Meeting

Presenter: Nick

Article: Out-of-equilibrium microcompartments for the bottom-up integration of metabolic functions

Self-sustined metabolic pathways in microcompartments are the corner-stone for living systems. From a technological viewpoint, such pathways are a mandatory prerequisite for the reliable design of artificial cells functioning out-of-equilibrium. Here we develop a microfluidic platform for the miniaturization and analysis of metabolic pathways in man-made microcompartments formed of water-in-oil droplets. In a modular approach, we integrate in the microcompartments a nicotinamide adenine dinucleotide (NAD)-dependent enzymatic reaction and a NAD-regeneration module as a minimal metabolism. We show that the microcompartments sustain a metabolically active state until the substrate is fully consumed. Reversibly, the external addition of the substrate reboots the metabolic activity of the microcompartments back to an active state. We therefore control the metabolic state of thousands of independent monodisperse microcompartments, a step of relevance for the construction of large populations of metabolically active artificial cells.

https://www.nature.com/articles/s41467-018-04825-1

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Coffee & Coacervates: Complexation and coacervation of like-charged polyelectrolytes inspired by mussels
Jan
18
2:30 PM14:30

Coffee & Coacervates: Complexation and coacervation of like-charged polyelectrolytes inspired by mussels

Coffee & Coacervates is back for the semester! This week we will be discussing complexation and coacervation of two positively charged polyelectrolytes by overcoming longer-range electrostatic repulsion. This study was inspired by marine mussel adhesives, where complexation of the like-charged coacervate is most likely driven by strong cation–π interactions.

Where: Northwest Corner Building, 8th floor conference room

Paper link: https://www.pnas.org/content/113/7/E847.long

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AIChE Charged & Ion Containing Polymers / Polyelectrolytes and Polymer Electrolytes Sessions
Nov
1
8:00 AM08:00

AIChE Charged & Ion Containing Polymers / Polyelectrolytes and Polymer Electrolytes Sessions

  • David L. Lawrence Convention Center (map)
  • Google Calendar ICS

Join Vivek Sharma (@odeslab) and Allie (@obermeyergroup) for an exciting day of presentations on charged polymers.

The morning session (8-10:30 a.m. in Room 327) features an invited talk from Jian Qin and several presentations from faculty candidates.

The afternoon session (3-6 p.m. in Room 327) features presentations from lots of junior faculty in the field.

Allie will be presenting “Sequence and Structure Effects in the Complex Coacervation of Proteins with Polyions” at 5:00 p.m.

Vivek will present on “Extensional Relaxation Time, Pinch-Off Dynamics and Printability of Semi-Dilute Polyelectrolyte Solutions” at 4:00 p.m.

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Coffee & Coacervates
Sep
28
2:00 PM14:00

Coffee & Coacervates

Come for an informal discussion of relevant literature! This week we are going to discuss polyelectrolyte complexation, specifically the nature of the liquid-to-solid transitions.

Rheological characterization of liquid-to-solid transitions in bulk polyelectrolyte complexes

https://pubs.rsc.org/en/content/articlelanding/2017/sm/c7sm01285c#!divAbstract

Where: Northwest Corner Building, 8th floor conference room

If you are interested in attending and need building access, contact Nick Zervoudis

412-491-6785

nz2283@columbia.edu

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Journal Club Group Meeting
Sep
24
4:00 PM16:00

Journal Club Group Meeting

Presenters: Vivian and Nick

Articles: (1) From the Hammer lab: Controllable protein phase separation and modular recruitment to form responsive membraneless organelles Nature Commun. 2018, 9, 2985 and (2) From the Quin and Schmidt-Dannert labs: Self-Assembling Protein Scaffold System for Easy in Vitro Coimmobilization of Biocatalytic Cascade Enzymes ACS Catalysis, 2018, 8 5611

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Coffee & Coacervates
Sep
21
2:00 PM14:00

Coffee & Coacervates

Come for an informal discussion of relevant literature! This week we are going to attempt to discuss 2 shorter papers. The first is a short review on forming self-assembled block polymers in solution. The second discusses using complex coacervates as vehicles for drug delivery.

https://www.sciencedirect.com/science/article/pii/S1359029405000063

https://pubs.acs.org/doi/10.1021/mz500529v

Where: Northwest Corner Building, 8th floor conference room

If you are interested in attending and need building access, contact Nick Zervoudis

412-491-6785

nz2283@columbia.edu


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Journal Club Group Meeting
Sep
17
4:00 PM16:00

Journal Club Group Meeting

Presenters: Justin and Rachel

Articles: (1) From the Reineke and Lodge groups: Packaging pDNA by Polymeric ABC Micelles Simultaneously Achieves Colloidal Stability and Structural Control, JACS, 2018, 140, 11101. (2) From the Zhou and Guo groups: Thrombin-Responsive, Brain-Targeting Nanoparticles for Improved Stroke Therapy, ACS Nano, 2018, 12, 8723.

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Sep
14
1:00 PM13:00

Coffee & Coacervates

Come for an informal discussion of relevant literature! This week: a polymers paper on polyelectrolyte conformations and dilution regimes.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/polb.20853

Where: Northwest Corner Building, 8th floor conference room

If you are interested in attending and need building access, contact Nick Zervoudis

412-491-6785

nz2283@columbia.edu

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