Exciting news for our team at Texas A&M University! We are joining NATIVE-ID (Native-context Analysis and Therapeutic Intervention for Variant Ensembles in Intrinsically Disordered Proteins), an ARPA-H-funded initiative led by the UC Berkeley. @tamu.bsky.social

Innovative Genomics Institute@innovativegenomics.bsky.social · 3d ago

Most neurodegenerative diseases begin with misfolded proteins. A new project funded by the ARPA-H BIOGAMI program seeks to prevent neurodegenerative diseases by learning the language of disordered proteins in human cells at scale. Learn more: https://ow.ly/fLju50ZW7EC

(Part 1/2) Excited to share our recent work with Prof. Nicolas Fawzi’s group (nicolasluxfawzi.bsky.social), now out in Angewandte Chemie (onlinelibrary.wiley.com/doi/full/10....)! We show how RNA reshapes FUS condensate assembly and dynamics. Congrats to Tongyin, Kandarp, Samara, Qizan, Priyesh!

(Part 1/2) Excited to share our latest paper (doi.org/10.1063/5.03...), led by PhD student Shuo-Lin Weng and Dr. Shiv Rekhi! We introduce buffered Charge-Regulation Monte Carlo method to model dynamic charge regulation, buffer equilibria, and ion partitioning within condensates.

Excited to share our new preprint (www.biorxiv.org/content/10.6...). Using molecular dynamics simulations, we link reprogrammed protein interactions to condensate viscoelasticity and show that stiffer, gel-like condensates are preferentially packaged into neuronal exopher vesicles.

(Part 1/2) Excited to share our recent work with contributions from Dr. Busra Ozguney and Dr. Priyesh Mohanty, in collaboration with Prof. Nicolas Lux Fawzi’s group (@nicolasluxfawzi.bsky.social) at Brown University, now published in PNAS (doi.org/10.1073/pnas...)!

New from Fawzi + @mittalgrouptamu.bsky.social labs led by Busra Ozguney and Ryan Puterbaugh. Methionine oxidation in both helical conserved region and disordered regions of TDP-43 C-terminal domain decreases phase separation by perturbing different sets of contacts www.pnas.org/doi/10.1073/...

Methionine oxidation alters both helical assembly and disordered contacts in human TDP-43 C-terminal domain phase separation | PNAS

TAR DNA binding protein 43 (TDP-43), a key protein linked to ALS pathology, undergoes phase separation and forms functional assemblies via condensa...

pnas.org

Excited to share our recent preprint (biorxiv.org/content/10.6...), where we show that each of HP1α's binding partners (CAF-1, LBR, and Sgo1) tunes its phase separation differently, while electrostatic interactions ultimately dominate how phosphorylated HP1α forms condensates.

The role of electrostatic interactions in the phase separation of HP1α and its protein binding partners

Heterochromatin protein 1α (HP1α) is an intrinsic component of heterochromatin domains where it is involved in a diverse set of functions including heterochromatin spreading and organization, chromati...

biorxiv.org

We are hiring postdoctoral researchers. Please share!

Excited to share our latest preprint (doi.org/10.64898/202...) introducing buffered Charge-Regulation Monte Carlo (b-CR-MC), a rigorous, efficient framework showing how dynamic charge regulation drives protein condensates toward their isoelectric points!

Molecular Origins of pH Gradients in Charge-Regulated Biomolecular Condensates

Biomolecular condensates exhibit spontaneous electrochemical microenvironments characterized by asymmetric ion distributions and pH gradients that emerge from protein-sequence-dependent charge regulat...

doi.org

(Part 1/2) Excited to share our recent work led by Dr. Shiv Rekhi, now out in JACS (pubs.acs.org/doi/full/10....). We show that biomolecular condensates act as distinct solvation environments that reshape amino acid pKₐ values, favoring protonated states within the dense phase.

Excited to share our latest preprint (www.biorxiv.org/content/10.6...), which uses an interpretable graph neural network (GNN) to uncover the molecular features that govern the selective partitioning of small molecules into different biomolecular condensates.

(Part 1/2) Excited to share that a collaborative study led by the Prof. James Shorter Lab at UPenn on short RNA chaperones and TDP-43 aggregation is now published in Science (www.science.org/doi/full/10....).

The most recent volume of the Annual Review of Physical Chemistry is now online. The most read article so far is "Computational Modeling of Biomolecular Phase Separation: Current Progress and Open Challenges" by Rizuan et al. arevie.ws/4t44E0q @mittalgrouptamu.bsky.social

(Part 1/2) Excited to share our recent work led by PhD students Qizan Chen and Ryan Soucek, with Prof. Jeffrey D. Rimer (University of Houston), now out in JACS Au (pubs.acs.org/doi/full/10....). We show that molecular modifiers like riboflavin regulate ammonium urate crystallization.

Excited to share our latest preprint (www.biorxiv.org/content/10.6...) in collaboration with Prof. Marina Feric from Penn State University. In this work, we demonstrate how condensates assist in the assembly of the mitochondrial replication machinery.

(Part 1/2) Excited to share our recent work led by PhD students Azamat Rizuan and Shiv Rekhi, in collaboration with Prof. Joan-Emma Shea from UCSB, is now out in Annual Review of Physical Chemistry (www.annualreviews.org/content/jour...)

(Part 1/2) Excited to share our recent work done by Postdoc Dr. Anupam Mondal, in collaboration with Prof. Marcos M. Pires from the University of Virginia, is now out in Nature Communications (www.nature.com/articles/s41...).

(Part 1/2) Excited to share our recent work led by PhD student Beth Wei, in collaboration with Prof. Michael P. Howard from Auburn University, published in Molecular Systems Design & Engineering (pubs.rsc.org/en/content/a...).

(Part 1/2) Excited to share our work, led by PhD student Keerthivasan Muthukumar and postdoc Dr. Dinesh S. Devarajan, is now published in PNAS (www.pnas.org/doi/10.1073/...).

(Part 1/2) Excited to share new work by our PhD student Qizan Chen, in collaboration with Jeffery Rimer’s group, published in JPCC (pubs.acs.org/doi/full/10....). We study how subtle structural differences in uric acid tautomers affect ammonium urate crystals.

(Part 1/2) Excited to share our work (pubs.acs.org/doi/10.1021/...), led by PhD student Shuo-Lin Weng and postdoc Priyesh Mohanty. We used all-atom MD simulations to study the conformational dynamics and phase separation (PS) of full-length FUS protein.

(Part 1/2) Excited to share our recent work (pubs.acs.org/doi/full/10....) led by Ashish Shyam Tangade and Anupam Mondal. We developed a minimal coarse-grained model to simulate protein-DNA condensates.

Excited to share our recent work published in JACS Au (pubs.acs.org/doi/full/10....) led by PhD student Jiahui Wang! We reveal how small molecule cosolutes modulate the morphology of multicomponent condensates by tuning the relative interaction strengths between components.

Excited to share our recent work (www.sciencedirect.com/science/arti...) led by PhD student Busra Ozguney & postdoc Priyesh Mohanty! We reveal atomic-level insights into how GU-rich RNA binding modulates the conformational ensemble of TDP-43 RRMs, promoting function and preventing misfolding.

(1/2) We’re excited to share our recent work (elifesciences.org/reviewed-pre...) on HP1 phase separation, led by postdoc Tien Phan @tienphan.bsky.social ! We investigate LLPS differences among HP1 paralogs (HP1α, HP1β, HP1γ), key players in heterochromatin formation and gene regulation.

(1/2) We are excited to announce that our paper, led by PhD student Shiv Rekhi, has been published in PNAS: www.pnas.org/doi/10.1073/.... In this work we compute the transfer free energies of amino acid side chains from the dilute to the dense phase.