Center for Catalysis in Biomimetic Confinement

Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.

Please see our new paper: Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment | The Journal of Physical Chemistry B pubs.acs.org/doi/10.1021/...

The CCBC makes Molecular Foundry News with: Harnessing Nature’s Nanofactories: Rapidly Assembling Bacterial Microcompartments

foundry.lbl.gov/2025/11/25/h...

POV: the PlateMaster watching me do its job 👀 #STEM #lab #lablife #pipet #research #science #sciencehumor #benchwork

Former Berkeley Lab Scientist John Clarke Wins 2025 Nobel Prize in Physics The Nobel Prize committee honored former Berkeley Lab scientist John Clarke for research in quantum tunneling in electric circuits.

🏅 Former Berkeley Lab senior scientist John Clarke has won the 2025 Nobel Prize in Physics. His research on quantum tunneling in electric circuits paved the way for today’s quantum computers and sensors. 🧠 This brings LBNL’s Nobel count to 17!

@nobelprize.bsky.social
@uofcalifornia.bsky.social

UC Berkeley’s Omar Yaghi shares 2025 Nobel Prize in Chemistry - Berkeley News Yaghi created a field called reticular chemistry, which involves stitching together molecular building blocks to form porous structures — metal-organic frameworks (MOFs) — with myriad applications.

🎉Congrats to @ucberkeleyofficial.bsky.social's Omar Yaghi, awarded the 2025 @nobelprize.bsky.social in Chemistry for pioneering reticular chemistry and creating metal–organic frameworks (MOFs). Yaghi led our @molecularfoundry.lbl.gov and is now an affiliate in the Lab’s Materials Sciences Division.

Happy Halloween from the CCBC!

Kyleigh gives talk at Molecular Foundry User Meeting #CCBC #Syntheticbiology #MolecularFoundry #LBL

Wilson or summer intern gives CCBC talk on AMF at LBL #CCBC #Syntheticbiology #LBL #AMF

Jay Keasling Named 2025 Department of Energy/National Academy of Inventors Innovator of the Year The honor is awarded each year to one person chosen from all employees of the Department of Energy, its 17 national laboratories, and other DOE sites, who has translated research into tangible impacts...

🎉 Congrats to Jay Keasling, DOE Office of Technology Commercialization and Academy of Inventors “Innovator of the Year!” Keasling, an authority on synthetic biology, @biosci.lbl.gov scientist and CEO of our Joint BioEnergy Institute, holds 75 patents and has founded or co-founded 12 startups. ⬇️

Tim gives talk at Molecular Foundry: "Polymorphism in bacterial microcompartment shell self-assembly"
#Molecularfoundry #LBL #CCBC

Scanning electron microscope image of copper nanostructures resembling clusters of tiny flowers. These intricate, petal-like formations are electrocatalysts used to reduce carbon dioxide into hydrocarbon fuels.

Close-up scanning electron microscope image of vertically aligned silicon nanowires, appearing as smooth, evenly spaced pillars. These nanowires facilitate oxidation reactions in an artificial photosynthesis system.

Our scientists and partners have created copper “nanoflowers” and silicon “nanowires” that work together to turn CO₂ + ☀️ into liquid fuels and other useful chemicals. newscenter.lbl.gov/2025/04/24/s...

📷: SEM images show flower-like copper electrocatalysts and wire-thin silicon pillars in action.

Scientists Develop Artificial Leaf That Uses Sunlight to Produce Valuable Chemicals Researchers built a device made of perovskite and copper that mimics a green leaf.

🌿 What if a leaf could do more than photosynthesize? This artificial leaf uses copper nanoflowers + perovskite crystals to turn CO₂ into C₂—used in plastics, jet fuel & more.

Built on 20+ yrs of collaboration science!
@molecularfoundry.lbl.gov @caltech.edu

🎉 Kudos to the researchers and operators of @als-lbnl.bsky.social's 9 structural biology beamlines on depositing 10k macromolecular structures solved by users in the @rcsbpdb.bsky.social to date! From fundamental insights 🧬 to drug discovery 💊 to de novo design 🧩, here’s to the next 10k! #BioMBIB

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'Enhanced Binding Site Identification in Protein–Ligand Complexes with a Combined Blind Docking and Dipolar Electron Paramagnetic Resonance Approach' from Journal of the American Chemical Society is currently free to read as an #ACSEditorsChoice.

📖 Read the article: buff.ly/oCcbM65

Promotional graphic with Energy & Fuels logo and text: "Special Issue: Celebrating Women in Energy Research"

In celebration of the contributions from Women researchers in the energy field, Energy & Fuels highlights a special issue featuring 32 female researchers worldwide, covering a wide range of energy research topics. #WomeninSTEM

Explore the collection: buff.ly/kdTsRdt

Hydrogen bonding helps explain why water behaves in the (sometimes strange) ways it does. But what exactly is hydrogen bonding and why does it happen? And how is this related to ice?

Watch the full video by our friends over at Reactions to learn more: buff.ly/rnKmO56

Job searching this wknd? We're #hiring a postdoctoral researcher in our #Emeryville-based Quantitative Modeling Group. Be part of an interdisciplinary team at the Joint BioEnergy Institute & Agile BioFoundry!

Learn more: go.lbl.gov/bioscijobs

#TeamBioSci @berkeleylab.lbl.gov #CareerOpportunities

Comparing the writing styles of highly and rarely cited papers in conservation biology For the everyday scientist, being published – and henceforth cited – is a major enterprise. An understanding of the components associated with highly-…

Really interesting analysis on how to make sure your papers are highly cited - www.sciencedirect.com/science/arti...

tl;dr: "include broad titles, use motivational language, use conceptual images, and included clear explanations of the broader context and relevance of their research"

CCBC's Michaela TerAvest gives talk: "Considering Bioenergetics in Engineering for Bioenergy" at ASBMB in Chicago! #asbmb25 #BMC #CCBC #bioenergy #SyntheticBiology #MSU

Why an overreliance on AI-driven modelling is bad for science Nature - Without clear protocols to catch errors, artificial intelligence’s growing role in science could do more harm than good.

Without clear protocols to catch errors, artificial intelligence’s growing role in science could do more harm than good

https://go.nature.com/42nGQt6

Where do proteins go in cells? Next-generation methods map the molecules’ hidden lives Nature - Spatial proteomics is helping biologists to uncover how cells work by mapping where proteins operate.

If you want to understand how cells function, you have to work out what proteins interact with — and where

https://go.nature.com/3RgNXOZ

Christin Monroe, an assistant professor of chemistry at Landmark College, (left) explains DNA base pairing to a student Rose Heathcliff (right) in her chemistry laboratory.

"Neurodivergent people problem-solve differently, which offers a valuable perspective in STEM."
—Christin Monroe, assistant professor of chemistry at @landmarkcollege.bsky.social
https://bit.ly/3GbymOa
#Neurodivergence #NeurodivergentInSTEM

A gorgeous cover on the latest issue of Biochemistry courtesy of MSU BMB's Michaela TerAvest and Michael Feig!

"Controlled Enzyme Cargo Loading in Engineered Bacterial Microcompartment Shells"

pubs.acs.org/doi/10.1021/...

New research; Kerfeld lab; "Interfacing bacterial microcompartment shell proteins with genetically encoded condensates"; Protein Science

New research from the Kerfeld lab published in Protein Science titled "Interfacing bacterial microcompartment shell proteins with genetically encoded condensates" buff.ly/3XlyoJl

Please See our latest cover in ACS Nano

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'Receptor-Mediated Transmembrane Activation of Protein Folding in Synthetic Cells' from Bioconjugate Chemistry is currently free to read as an #ACSEditorsChoice.

📖 Read the article: buff.ly/gu7Hw9D

Six roadblocks to net zero — and how to get around them Overcoming these obstacles in carbon markets can speed up decarbonization.

Overcoming these six obstacles in carbon markets can speed up decarbonization

https://go.nature.com/4c9ZfxY

A Community Resource for Secondary Metabolite Researchers - Biosciences Area The JGI's Secondary Metabolism Collaboratory (SMC) has launched as an interactive public database for the research community.

The @jgi.doe.gov recently launched the Secondary Metabolism Collaboratory (SMC) - an interactive public database with the largest repository of BGC sequence data

biosciences.lbl.gov/2025/03/03/a...

@berkeleylab.lbl.gov

📸 Join Nature’s photo competition for a chance to be featured in the magazine, win a print and online subscription to the journal, and take home £500

Submit your best #ScientistAtWork photo to photocompetition@nature.com. Entries close on Friday!

Communicating science for advocacy March 25, 2025 | 3 p.m. Eastern

Scientists – interested in ways to share your work to non-scientists and decision makers? Please join this webinar on Tues Mar 25 3PM ET from @asbmb.bsky.social, where I'll be joined by @amyjhawkins.bsky.social (U Utah) and Sean Gallagher (AAAS). Register at www.asbmb.org/meetings-eve...