Y. C. Kim

Sequence-Dependent Conformational Transitions of Disordered Proteins During Condensation

This study investigates how sequence patterns in intrinsically disordered proteins affect their conformational transitions during condensation using a polyampholyte model.

How a disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization

The paper investigates how a disordered linker in the Polyhomeotic protein influences phase separation and oligomerization in Drosophila and human cells through in vitro reconstitution and molecular dynamics simulations.

Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization

This study investigates how charge distribution and DNA influence the phase separation and localization of HP1 paralogs using simulations.

A coarse-grained DNA model to study protein-DNA interactions and liquid-liquid phase separation

This paper introduces a coarse-grained DNA model compatible with existing protein models to study protein-DNA interactions and liquid-liquid phase separation.

Sequence-Dependent Material Properties of Biomolecular Condensates and their Relation to Dilute Phase Conformations

This study computationally examines how sequence composition of charged disordered proteins affects their condensate material properties and finds similar responses to charge segregation across different sequences.

Role of Strong Localized vs. Weak Distributed Interactions in Disordered Protein Phase Separation

This study compares phase separation in intrinsically disordered proteins using two models with different interaction strengths and distributions, finding that distributed interactions promote liquid-like condensates over a broader range of compositions.

Effect of Charge Distribution on the Dynamics of Polyampholytic Disordered Proteins

This study examines how charge distribution affects the dynamics of polyampholytic disordered proteins in dilute solutions, showing conformational and dynamic changes with increasing charge segregation.

A predictive coarse-grained model for position-specific effects of post-translational modifications on disordered protein phase separation

This paper develops a coarse-grained model to predict how position-specific post-translational modifications affect disordered protein phase separation.

Tandem-Cleavage Linkers Improve the In Vivo Stability and Tolerability of Antibody-Drug Conjugates

This paper develops tandem-cleavage linkers to improve ADC stability and tolerability, showing better hematopoietic safety in rat studies.

Molecular details of protein condensates probed by microsecond-long atomistic simulations

The paper uses all-atom simulations to study protein condensates, revealing structural and dynamic details of phase separation in two IDPs and showing agreement with experiments.

A novel HER2-targeted antibody-drug conjugate offers the possibility of clinical dosing at trastuzumab-equivalent exposure levels

This paper develops a novel HER2-targeted ADC, CAT-01-106, showing improved efficacy and tolerability compared to T-DM1 at equivalent payload dosing.

Hydropathy patterning complements charge patterning to describe conformational preferences of disordered proteins

The paper introduces a new order parameter, SHD, and combines it with charge patterning to predict the scaling behavior of intrinsically disordered proteins from their sequences.

Use of dual electron probes reveals role of ferritin in erythropoiesis

The paper uses dual electron probes to study ferritin distribution in human erythropoietic stem cells during differentiation, finding increased Fe3+ accumulation in lysosomal ferritin cores.

TDP-43 α-helical structure tunes liquid-liquid phase separation and function

This study shows that mutations in TDP-43's helical region modulate its phase separation and function, with implications for ALS and synthetic biology.

Computational modeling highlights disordered Formin Homology 1 domain’s role in profilin-actin transfer

The paper uses simulations to show FH1 domains facilitate profilin-actin transfer, with flexibility and proximity to FH2 affecting efficiency.

Sequence determinants of protein phase behavior from a coarse-grained model

This paper develops a coarse-grained computational model to simulate liquid-liquid phase separation of proteins, showing it can capture phase diagram changes due to mutations and domain presence.