A New Model of PD-1 Inhibition: Unphosphorylated Tyrosines Block T-Cell Signaling Condensate Formation / Anti-PD-1, anti-PD-L1, biomolecular condensates,

Distinguishing near- versus off-critical phase behaviors of intrinsically disordered proteins, Mitra, Gaurav, Ghosh, Souradeep, Ruff, Kiersten M, Zhang, Ruoyao, Chauhan, Gaurav, Pappu, Rohit V

Pre-mRNA processing components in nuclear speckles encompass one or more folded RNA recognition motifs (RRMs) and disordered regions with specific seq…

Researchers at Washington University in St. Louis and St. Jude Children’s Research Hospital have found that biomolecular condensates play a role in suppressing the effects of ALS-causing mutations.

Washington University in St. Louis and Duke University researchers show how directed motions combined with protein interactions influence phase separation and the maintenance of biomolecular...

Experiments and computations show that the organization and dynamics of molecules within and at interfaces of biomolecular condensates are governed by differential interaction strengths leading to the...

Biomolecular condensates formed by intrinsically disordered protein condensates are known to be semidilute solutions, however, the molecular interactions in the dilute versus dense phases remain under...

Researchers at Washington University in St. Louis are discovering the electrochemical properties of biomolecular condensates which could help in development of cancer or ALS treatments.

Researchers at Washington University in St. Louis have developed a method to peer into biomolecular condensates, which could lead to a better understanding of condensate functions and their impairment...

Postdoctoral trainees share their experiences working in WashU’s Department of Biomedical Engineering

Intrinsically disordered regions (IDRs) of proteins are defined by functionally relevant molecular grammars. This refers to IDR-specific non-random amino acid compositions and non-random patterning of...

Nuclear speckles are enriched in serine / arginine rich splicing factors (SRSFs), such as SRSF1. Splicing factors and proteins such as TDP43 concentrate into distinct speckle territories to enable pre...

YouTube video by WebsEdge Science

We present the NetSci program–an open-source scientific software package designed for estimating mutual information (MI) between data sets using GPU acceleration and a k-nearest-neighbor algorithm. This approach significantly enhances calculation speed, achieving improvements of several orders of magnitude over traditional CPU-based methods, with data set size limits dictated only by available hardware. To validate NetSci, we accurately compute MI for an analytically verifiable two-dimensional Gaussian distribution and replicate the generalized correlation (GC) analysis previously conducted on the B1 domain of protein G. We also apply NetSci to molecular dynamics simulations of the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump, exploring the allosteric mechanisms and pathways influenced by ATP and 2′-deoxy-ATP (dATP) binding. Our analysis reveals distinct allosteric effects induced by ATP compared to dATP, with predicted information pathways from the bound nucleotide to the calcium-binding domain differing based on the nucleotide involved. NetSci proves to be a valuable tool for estimating MI and GC in various data sets and is particularly effective for analyzing intraprotein communication and information transfer.

It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facili...

The function of biomolecular systems, including biological macromolecules, often crucially depends on their dynamics. Nuclear Magnetic Resonance (NMR) is one of the most informative methods used to st...