A. Kang

Diffusing protein binders to intrinsically disordered proteins

The paper develops RFdiffusion to generate protein binders for IDPs/IDRs, achieving nanomolar affinity and functional applications in amylin and IL2RG.

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

This paper designs beta barrels and transmembrane nanopores using deep learning and parametric methods, achieving high success rates with experimental validation.

Design of intrinsically disordered region binding proteins

The paper designs proteins that bind intrinsically disordered regions with high affinity and specificity across diverse targets.

Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells

Structure-optimized CD27-based CAR-T cells targeting CD70 show >80-fold improved expansion in vivo and offer a potential therapy for high-risk multiple myeloma patients.

Brg1 regulates fibroblast-myofibroblast transition to promote renal fibrosis

This study shows Brg1 promotes fibroblast-myofibroblast transition in renal fibrosis and identifies Prune2 and PU.1 as downstream targets, with PFI-3 as a potential antifibrotic drug.

De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles

The paper designs nanomolar binders for diverse small molecules using a pseudocycle-based shape complementarity method, enabling direct conversion into sensing systems.

Small-molecule binding and sensing with a designed protein family

This paper designs a protein family that binds and senses small molecules using deep learning and physics-based methods, achieving nanomolar sensitivity for cortisol.

Improving protein expression, stability, and function with ProteinMPNN

This paper introduces ProteinMPNN, a deep learning model that improves protein expression, stability, and function by incorporating evolutionary and structural information.

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

This study benchmarks ProteinMPNN against Rosetta in designing two-component protein nanomaterials, showing comparable success with significantly reduced computation and no manual refinement.

Blueprinting expandable nanomaterials with standardized protein building blocks

This paper introduces standardized protein building blocks and geometric design principles to create expandable protein nanomaterials, validated through X-ray crystallography and electron microscopy.

Cyclic peptide structure prediction and design using AlphaFold

This paper modifies AlphaFold to predict and design cyclic peptides, achieving high accuracy in structure prediction and de novo design with experimental validation.

Design of stimulus-responsive two-state hinge proteins

This paper designs two-state hinge proteins that switch between structural states in response to ligands, demonstrating atomic-level accuracy and tunable kinetics and thermodynamics.

De novo designed ice-binding proteins from twist-constrained helices

This paper designs ice-binding proteins with controlled under-twisting of alpha-helices to enhance ice recrystallization inhibition.

Precisely patterned nanofibers made from extendable protein multiplexes

The paper designs extendable protein multiplexes with symmetric architectures to create precisely patterned nanofibers through controlled repeat propagation and hydrophilic patch placement.

Hallucinating protein assemblies

Deep network-based protein design generates symmetric homo-oligomers with high structural accuracy, demonstrating the potential for creating novel nanomachines and biomaterials.

Subcutaneous BCG vaccination protects against streptococcal pneumonia via regulating innate immune responses in the lung

This study shows subcutaneous BCG vaccination enhances innate protection against Streptococcus pneumoniae by accelerating neutrophilia in the lung, independent of monocyte training.

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

This study identifies cryptic transmembrane domains in designed protein nanoparticles that hinder secretion and introduces a computational tool, Degreaser, to remove them while maintaining stability, improving secretion efficiency.

Robust deep learning based protein sequence design using ProteinMPNN

A deep learning method for protein sequence design shows high performance in both simulations and experiments, applicable to various design challenges.

Engineered chimeras unveil swappable modular features of fatty acid and polyketide synthase acyl carrier proteins

This study designs chimeric acyl carrier proteins to swap modular features between different ACPs, enabling compatibility with specific enzymes for synthetic pathway engineering.

Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma

This study uses multi-omics approaches to identify regulators of CD38 surface expression in multiple myeloma and assess the impact of therapies on CD38 levels and signaling.

Single-dose respiratory mucosal delivery of next-generation viral-vectored COVID-19 vaccine provides robust protection against both ancestral and variant strains of SARS-CoV-2

This study evaluates a multivalent Ad-vectored vaccine delivered via respiratory mucosal route, showing robust protection against SARS-CoV-2 and variants in mice.

Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks

This paper describes a hierarchical method to design multi-scale symmetric protein complexes using repeat proteins and helical bundles, resulting in large symmetric assemblies like an icosahedral nanocage.

Modification of forests by people means only 40% of remaining forests have high ecosystem integrity

The paper quantifies global forest modification, finding 40.5% of remaining forests have high ecosystem integrity, mostly in specific regions, and highlights the need for policies to protect these areas.

Rapamycin rejuvenates oral health in aging mice

Short-term rapamycin treatment reverses periodontal bone loss, reduces inflammation, and shifts the oral microbiome to a more youthful state in aged mice.

The desmosomal cadherin Desmoglein-3 regulates YAP and phospho-YAP in keratinocyte responses to mechanical forces

This study shows that Dsg3 regulates YAP and phospho-YAP in keratinocyte mechanotransduction, affecting their response to mechanical forces and nuclear localization.

Spontaneous isomerization of long-lived proteins provides a molecular mechanism for the lysosomal failure observed in Alzheimer’s disease

This paper shows that isomerization of long-lived proteins in Alzheimer’s disease prevents lysosomal digestion, leading to lysosomal failure and linking AD to lysosomal storage disorders.

The Pemphigus Vulgaris antigen desmoglein-3 suppresses p53 function via the YAP-Hippo pathway

This study shows Dsg3 suppresses p53 function through the YAP-Hippo pathway, contributing to PV pathology by affecting skin homeostasis.