Molecular Ocean Lab

A review reporting on the discussions held at the recent @cecamevents.bsky.social workshop on enzymatic plastic degradation that we co-organized in Trieste is now available on #arxiv

Beyond the technical discussions, everyone appreciated the relaxed, collaborative atmosphere fostered by the small format and classroom setting. We hope this report inspires new initiatives and shared consortia toward open, bio-based plastic recycling.

Computations Meet Experiments to Advance the Enzymatic Depolymerization of Plastics One Atom at a Time Plastics are essential to modern life, yet poor disposal practices contribute to low recycling rates and environmental accumulation-biological degradation and by-product reuse offer a path to mitigate...

The paper highlighting key insights, future challenges, and research priorities identified during our recent CECAM workshop in Trieste is now available online. Take a look to see what’s coming next in the field of enzymatic plastic degradation:

arxiv.org/abs/2507.14413

Many thanks, everyone!

Chronic Lyme Disease Was Once Dismissed. More Doctors Are Coming Around. Newer trials are starting to track Lyme patients and investigate potential treatments

Thank you @briannaabbott.bsky.social for this wonderful piece, and highlighting what the MIT MAESTRO study means to our participants!
I love that my quote was about HOPE. I KNOW that this is a solvable problem. We need to work together to fix it!
www.wsj.com/health/chron...

Comparison of Molecular Recognition in Docking Versus Experimental CSD and PDB Data | Journal of Chemical Information and Modeling pubs.acs.org/doi/10.1021/...

Single-celled organisms set for greater role in gut health Long cast as villains, some protists, such as Blastocystis, are potentially beneficial to human health.

Protists!

www.nature.com/articles/d41...

Great news from the @crg.eu on @monicabettencourt.bsky.social appointment as the new director. This is excellent for the CRG and for catalan #science, for Monica is an excellent choice and a leader to a bright scientific future! #womeninscience

Cracking the code of Multiple Sclerosis with in silico medicine multiple sclerosis (ms) is often called the disease of a thousand faces. and for good reasons– no …

www.vph-institute.org/news/crackin...

After all, much of what we consider "ourselves" is microbial—the essential human microbiome. When infections occur they disrupt a complex ecological balance—altering the equilibrium that defines our natural state. We NEED healthy, robust, and interdisciplinary infectious disease research!

Infections cause everything Another reason why RFK Jrs. MAHA plan is misguided

Excellent piece by @julieparsonnet.bsky.social on infectious diseases as root causes of a number of chronic human diseases; pausing research on bacterial and viral infections will limit efforts to cure neurodegeneration, autoimmune, metabolic disease as well as cancer

substack.com/inbox/post/1...

🤯 Implications for OLE RNA as a natural integral membrane RNA from Ron Breaker's lab rnajournal.cshlp.org/content/earl...

Thanks for joining us Vicent! It was great to listen your fantastic talk!

Thanks to the organizers for the invitation: Francesco Colizzi (
@molecularocean.bsky.social ) Paula Blazquez-Sanchez and Giovanni Busi. It was fantastic!

Extensive compositionality in the vocal system of bonobos Compositionality, the capacity to combine meaningful elements into larger meaningful structures, is a hallmark of human language. Compositionality can be trivial (the combination’s meaning is the sum ...

Bonobos, our closest living relatives, exhibit communication that shares more structural similarities with human language than previously recognized.

www.science.org/doi/10.1126/...

Trois de nos plus grands scientifiques, Yasmine Belkaid (@pasteur.fr), Bana Jabri (@institutimagine.bsky.social) et Alain Puisieux (@institutcurie.bsky.social), prennent la parole pour appeler à des réponses courageuses des pouvoirs publics face aux attaques contre la recherche. ⬇️

This article does a great job describing the lives of young American scientists:

“You roll up your sleeves, try to make or discover something useful and then let the scientific community try to punch holes in your work to make sure that it’s sound”

This sound familiar: “However, it turns out that travel agencies charge far more than it would cost an academic to arrange their own travel and accommodation—sometimes staggeringly more”

Only a few days left to secure your spot at the most groundbreaking conference in the world! 😎 (Okay, maybe not 𝘵𝘩𝘢𝘵 much, but it’s going to be fun). Don’t miss out—register now before the deadline hits!

Outstanding list of speakers, and talks, and posters:
www.cecam.org/workshop-det...

It was great to contribute to the characterization of these new Cas9 molecular scissors from the deep ocean, alongside a dream team led by Silvia Acinas and Julian Ceron. @raticosdeciencia.bsky.social
www.icm.csic.es/en/news/gene...

Today I remembered my first QM parameterization of a small molecule failed miserably (turn volume ON for a full experience)

Very excited to share our review on "The Chemistry and Biology of the Tetrodotoxin Natural Product Family", where we discuss their potential for the development of analgesics, structure-activity relationships on NaV channels, biosynthetic hypotheses and chemical syntheses: tinyurl.com/ye6nwnwu.

We are finalizing the program of the @cecamevents.bsky.social RNA modelling across scales www.cecam.org/workshop-det... at SISSA, Trieste, Italy, May 19-22. Please note that we still have a few slots for in person attendance. We will accept applications for the next few weeks, until fully booked!

Still a few days remaining to apply for the RNA modelling across scales @cecamevents.bsky.social workshop at SISSA. Deadline March 23, hurry up!!

Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models.

Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp

a greeting card for eid-eh shoma mobarak wishing you a healthy and prosperous novruz ALT: a greeting card for eid-eh shoma mobarak wishing you a healthy and prosperous novruz

Norooz Mobarak! happy New Year!

Enzyme Enhancement Through Computational Stability Design Targeting NMR-Determined Catalytic Hotspots Enzymes are the quintessential green catalysts, but realizing their full potential for biotechnology typically requires improvement of their biomolecular properties. Catalysis enhancement, however, is often accompanied by impaired stability. Here, we show how the interplay between activity and stability in enzyme optimization can be efficiently addressed by coupling two recently proposed methodologies for guiding directed evolution. We first identify catalytic hotspots from chemical shift perturbations induced by transition-state-analogue binding and then use computational/phylogenetic design (FuncLib) to predict stabilizing combinations of mutations at sets of such hotspots. We test this approach on a previously designed de novo Kemp eliminase, which is already highly optimized in terms of both activity and stability. Most tested variants displayed substantially increased denaturation temperatures and purification yields. Notably, our most efficient engineered variant shows a ∼3-fold enhancement in activity (kcat ∼ 1700 s–1, kcat/KM ∼ 4.3 × 105 M–1 s–1) from an already heavily optimized starting variant, resulting in the most proficient proton-abstraction Kemp eliminase designed to date, with a catalytic efficiency on a par with naturally occurring enzymes. Molecular simulations pinpoint the origin of this catalytic enhancement as being due to the progressive elimination of a catalytically inefficient substrate conformation that is present in the original design. Remarkably, interaction network analysis identifies a significant fraction of catalytic hotspots, thus providing a computational tool which we show to be useful even for natural-enzyme engineering. Overall, our work showcases the power of dynamically guided enzyme engineering as a design principle for obtaining novel biocatalysts with tailored physicochemical properties, toward even anthropogenic reactions.

Our latest paper "Enzyme Enhancement Through Computational Stability Design Targeting NMR-Determined Catalytic Hotspots" now out in JACS @jacs.acspublications.org. Collaboration with Jose M. Sanchez-Ruiz in Granada, among others. pubs.acs.org/doi/full/10....

How to stop plastic pollution: three strategies that actually work Countries are meeting to agree the first ever global treaty on curbing plastic pollution. Research suggests where bans and incentives can make a difference.

www.nature.com/articles/d41...

Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and noncanonical base pairs that require protonation events to stabilize or perturb these interactions. Constant pH molecular dynamics (CpHMD) methods provide a reliable framework to explore the conformational and protonation spaces of dynamic structures and to perform robust calculations of pH-dependent properties, such as the pKa of titratable sites. Despite growing biological evidence concerning pH regulation of certain motifs and its role in biotechnological applications, pH-sensitive in silico methods have rarely been applied to nucleic acids. This work extends the stochastic titration CpHMD method to include RNA parameters from the standard χOL3 AMBER force field. We demonstrate its capability to capture titration events of nucleotides in single-stranded RNAs. We validate the method using trimers and pentamers with a single central titratable site while integrating a well-tempered metadynamics approach into the st-CpHMD methodology (CpH-MetaD) using PLUMED. This approach enhances the convergence of the conformational landscape and enables more efficient sampling of protonation-conformation coupling. Our pKa estimates are in agreement with experimental data, validating the method’s ability to reproduce electrostatic changes around a titratable nucleobase in single-stranded RNA. These findings provide molecular insight into intramolecular phenomena, such as nucleobase stacking and phosphate interactions, that dictate the experimentally observed pKa shifts between different strands. Overall, this work validates both the st-CpHMD method and the metadynamics integration as reliable tools for studying biologically relevant RNA systems.

Constant pH #metadynamics simulation of #RNA oligomers now published on @acs.org JCIM! Work done by @tf-silva.bsky.social with some help from @bussigio.bsky.social . doi.org/10.1021/acs.jcim.4c02185

Computations meet Experiments to Advance the Enzymatic Depolymerization of Plastics One Atom at a Time - SISSA, Trieste, CECAM Worskhop 6-8 May 2025

Interested in enzymatic plastic depolymerization? Join us at the @cecamevents.bsky.social meeting in Trieste, hosted at SISSA from May 6-8, 2025! Slots available for talks and posters—share your work with us! Co-organized with Paula Blazquez Sanchez and @bussigio.bsky.social
tinyurl.com/mrx8nucs

Water water water and RNA

www.nature.com/articles/s41...