Maddie Ceminsky
@mceminsky.bsky.social
PhD candidate in the Gunn lab at Cornell. Engineering carbon fixation. Biochemistry, structural biology. she/her
Reposted by Maddie Ceminsky
Pleased to see this collaboration with a great PhD student Pei Cing Ng, from Prof. Luning Liu's lab at Liverpool University published. Structure of the H. neapolitanus carbonic anhydrase and localisation in a mini-carboxysome: www.pnas.org/doi/epdf/10....
November 13, 2025 at 9:57 AM
Pleased to see this collaboration with a great PhD student Pei Cing Ng, from Prof. Luning Liu's lab at Liverpool University published. Structure of the H. neapolitanus carbonic anhydrase and localisation in a mini-carboxysome: www.pnas.org/doi/epdf/10....
Reposted by Maddie Ceminsky
Every day I understand the Butlerian Jihad more and more
November 10, 2025 at 4:26 PM
Every day I understand the Butlerian Jihad more and more
Reposted by Maddie Ceminsky
FLiP–MS uses a library of protein–protein interaction markers to understand protein complex dynamics go.nature.com/4dQabQw
rdcu.be/eJI3A
rdcu.be/eJI3A
Global profiling of protein complex dynamics with an experimental library of protein interaction markers - Nature Biotechnology
FLiP–MS uses a library of protein–protein interaction markers to understand protein complex dynamics.
go.nature.com
October 9, 2025 at 1:02 AM
FLiP–MS uses a library of protein–protein interaction markers to understand protein complex dynamics go.nature.com/4dQabQw
rdcu.be/eJI3A
rdcu.be/eJI3A
Reposted by Maddie Ceminsky
Reposted by Maddie Ceminsky
How does catalysis emerge from non-catalytic domains?
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
@claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity.
🔗 doi.org/10.1093/molbev/msaf215
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf215
#evobio #molbio
From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance
Abstract. How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were disco
doi.org
October 8, 2025 at 2:32 PM
How does catalysis emerge from non-catalytic domains?
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
This is super cool! I love the combination of computation and wet lab. The preference for slow codons in mitochondrial targeted proteins is thought provoking - presumably this could also be true of chloroplast targeted proteins
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
www.biorxiv.org
August 8, 2025 at 12:08 AM
This is super cool! I love the combination of computation and wet lab. The preference for slow codons in mitochondrial targeted proteins is thought provoking - presumably this could also be true of chloroplast targeted proteins
Reposted by Maddie Ceminsky
Awesome to see this epic piece of work, led by @cecclementi.bsky.social, finally appear in @natchem.nature.com.
The development of a general coarse-grained protein forcefield to describe folding, binding and conformation changes without solvent and all-atom, has been long anticipated!
The development of a general coarse-grained protein forcefield to describe folding, binding and conformation changes without solvent and all-atom, has been long anticipated!
Our development of machine-learned transferable coarse-grained models in now on Nat Chem! doi.org/10.1038/s415...
I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.
I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.
Navigating protein landscapes with a machine-learned transferable coarse-grained model - Nature Chemistry
The development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...
doi.org
July 18, 2025 at 11:25 AM
Awesome to see this epic piece of work, led by @cecclementi.bsky.social, finally appear in @natchem.nature.com.
The development of a general coarse-grained protein forcefield to describe folding, binding and conformation changes without solvent and all-atom, has been long anticipated!
The development of a general coarse-grained protein forcefield to describe folding, binding and conformation changes without solvent and all-atom, has been long anticipated!
Reposted by Maddie Ceminsky
New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models
How do related proteins with a common fold perform diverse biological functions? Although the average structure may be similar, structural excursions from this average may differ, giving rise to allos...
www.biorxiv.org
May 27, 2025 at 7:23 PM
New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
I can’t wait for a coot-free future
June 30, 2025 at 12:09 AM
I can’t wait for a coot-free future
Reposted by Maddie Ceminsky
Reposted by Maddie Ceminsky
A Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Advances in uncovering the mechanisms of macromolecular conformational entropy - Nature Chemical Biology
Protein conformational entropy plays a vital role in functions like binding and catalysis. This Perspective discusses three ways macromolecules use conformational entropy: prepaying entropic costs, re...
www.nature.com
April 25, 2025 at 3:35 PM
A Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Maddie Ceminsky
Outstanding work by @anyalb.bsky.social in my lab - she targeted enzymes to synthetic biomolecular condensates in plants and showed increases in metabolic pathway activity, likely due to protection of the introduced enzymes from proteolysis
#PlantScience
onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience
onlinelibrary.wiley.com/doi/10.1111/...
April 25, 2025 at 9:20 AM
Outstanding work by @anyalb.bsky.social in my lab - she targeted enzymes to synthetic biomolecular condensates in plants and showed increases in metabolic pathway activity, likely due to protection of the introduced enzymes from proteolysis
#PlantScience
onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Maddie Ceminsky
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
March 20, 2025 at 3:02 PM
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
Reposted by Maddie Ceminsky
You can download my protein structure-inspired artwork from pdb webpage:
pdb101.rcsb.org/sci-art/bezs...
@rcsbpdb.bsky.social
@pdbeurope.bsky.social
#sciart
pdb101.rcsb.org/sci-art/bezs...
@rcsbpdb.bsky.social
@pdbeurope.bsky.social
#sciart
PDB101: Irina Bezsonova Gallery
PDB-101: Training, Outreach, and Education portal of RCSB PDB
pdb101.rcsb.org
March 15, 2025 at 11:42 AM
You can download my protein structure-inspired artwork from pdb webpage:
pdb101.rcsb.org/sci-art/bezs...
@rcsbpdb.bsky.social
@pdbeurope.bsky.social
#sciart
pdb101.rcsb.org/sci-art/bezs...
@rcsbpdb.bsky.social
@pdbeurope.bsky.social
#sciart
Reposted by Maddie Ceminsky
Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.
#1 www.nature.com/articles/s41...
#1 www.nature.com/articles/s41...
March 3, 2024 at 8:37 AM
Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.
#1 www.nature.com/articles/s41...
#1 www.nature.com/articles/s41...
Reposted by Maddie Ceminsky
How Ironic that on the International Day of Women and Girls in Science, Woman's portraits have been taken down at NIH and Women is a forbidden word that if found in your NSF grant could get it revoked. #womeninstem
February 11, 2025 at 1:20 PM
How Ironic that on the International Day of Women and Girls in Science, Woman's portraits have been taken down at NIH and Women is a forbidden word that if found in your NSF grant could get it revoked. #womeninstem
Reposted by Maddie Ceminsky
Withdrawing US funding from the World Health Organization is a potential disaster for public health worldwide, due to the impact it will have on the important work the WHO does. Preventing the CDC from even *talking* with WHO personnel is a step much farther toward undermining global health & safety
CDC ordered to stop working with WHO immediately, upending expectations of an extended withdrawal
U.S. public health officials have been told to stop working with the World Health Organization, effective immediately. The surprise decision is focused on the U.S.
apnews.com
January 27, 2025 at 10:31 PM
Withdrawing US funding from the World Health Organization is a potential disaster for public health worldwide, due to the impact it will have on the important work the WHO does. Preventing the CDC from even *talking* with WHO personnel is a step much farther toward undermining global health & safety
Reposted by Maddie Ceminsky
Fun to see it out in print! I was really lucky to have an amazing team to work with on this. If this sort of work seems interesting to you or someone you know, please feel free to reach out (planning to staff a lab later this year).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A map of the rubisco biochemical landscape - Nature
A massively parallel assay developed to map the essential photosynthetic enzyme rubisco showed that non-trivial biochemical changes and improvements in CO2 affinity are possible, signposting further e...
www.nature.com
January 22, 2025 at 10:34 PM
Fun to see it out in print! I was really lucky to have an amazing team to work with on this. If this sort of work seems interesting to you or someone you know, please feel free to reach out (planning to staff a lab later this year).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Check out our hornwort Rubisco kinetics:
a) what catalytic tradeoff?
b) almost double the kcat by removing a chaperone
www.cell.com/molecular-pl...
Strong publication for Zhen Guo (Zen) Oh!
a) what catalytic tradeoff?
b) almost double the kcat by removing a chaperone
www.cell.com/molecular-pl...
Strong publication for Zhen Guo (Zen) Oh!
Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems
Hornworts are non-vascular land plants, which diverged from vascular plants approximately 500 million years ago, yet the CO2 fixing enzyme (Rubisco) in hornworts has received little prior attention. This study develops the synthetic biology system to heterologously express hornwort Rubiscos and demonstrates that hornwort Rubiscos have different biogenesis dependencies. Further analyses of the kinetics of hornwort Rubiscos show that Rubiscos are indeed phylogenetically constrained.
www.cell.com
December 15, 2024 at 4:33 AM