Search bioRxiv⌕ Search

Biology subjects

Muthukumar, K.

Publications and source records attributed to Muthukumar, K..

2 recordsLinked to original sources

Sticky Interactions Govern Sequence-Dependent Dynamics in Biomolecular Condensates

Intrinsically disordered proteins (IDPs) play a central role in shaping the dynamics and material properties of biomolecular condensates. Understanding how sequence features determine these properties is critical for elucidating physiological function and guiding the rational design of synthetic condensates. Here, we use molecular dynamics simulations to investigate condensates formed by model IDPs with systematically varied chain length and charge patterning, two features characteristic of natural IDPs. Our results show that chain relaxation times, governed by sequence-dependent electrostatic interactions, quantitatively predict condensate viscosity and diffusivity. These condensates exhibit dynamics consistent with a crossover regime between Rouse and reptation behavior. While the Rouse model with idealized friction fails to capture sequence effects, the sticky Rouse model, which incorporates transient interchain contact lifetimes, accurately predicts chain reconfiguration times and, consequently, macroscopic material properties. This work establishes a predictive, sequence-resolved framework that links molecular interactions to condensate dynamics across length and time scales.

biophysics↗

SMuRF: Portable and accurate ensemble-based somatic variant calling

ABSTARCTO_ST_ABSSummaryC_ST_ABSSMuRF is an ensemble method for prediction of somatic point mutations (SNVs) and small insertions/deletions (indels) in cancer genomes. The method integrates predictions and auxiliary features from different somatic mutation callers using a Random Forest machine learning approach. SMuRF is trained on community-curated tumor whole genome sequencing data, is robust across cancer types, and achieves improved accuracy for both SNV and indel predictions of genome and exome-level data. The software is user-friendly and portable by design, operating as an add-on to the community-developed bcbio-nextgen somatic variant calling pipeline.\n\nContactskanderupamj@gis.a-star.edu.sg

bioinformatics↗