N. V. Dokholyan

Septins Enable T Cell Contact Guidance via Amoeboid-Mesenchymal Switch

This study shows that septins regulate T cell migration modes by switching between amoeboid and mesenchymal movement, with mesenchymal migration relying on microtubules and dynein motors.

Allosteric regulation of kinase activity in living cells

This paper discusses methods to map and regulate allosteric communications in proteins, particularly kinases, in live cells using engineered sensors for high spatiotemporal control.

Structural and Dynamic Insights Into α-Synuclein Dimer Conformations

The paper identifies a compact, stable dimeric conformation of α-synuclein that may promote dityrosine linkage and is implicated in Parkinson's disease.

Adaptation-proof SARS-CoV-2 vaccine design

This study designs SARS-CoV-2 vaccines targeting conserved spike protein regions to reduce mutation escape, using epitope grafting on diverse scaffolds and showing immune response and diagnostic utility.

Allosteric inactivation of an engineered optogenetic GTPase

This paper uses NMR spectroscopy to study how light-induced allosteric changes in the Cdc42Lov fusion protein inhibit GTPase signaling, revealing structural and dynamic mechanisms of optogenetic control.

Predicting 3D RNA structure from solely the nucleotide sequence using Euclidean distance neural networks

This paper introduces a neural network that predicts 3D RNA structure from sequence using Euclidean distance matrices, achieving high accuracy and speed.

Robust and Efficient Assessment of Potency (REAP): A Quantitative Tool for Dose-response Curve Estimation

The paper introduces a robust beta regression method for dose-response curve estimation and develops a web tool for its implementation.

AlphaFold Models Illuminate Half of Dark Human Proteins

The paper uses AlphaFold models to predict protein structures for understudied human proteins, finding that 95% of models with confidence scores above 80 are accurate at the fold level.

NeuralDock: Rapid and conformation-agnostic docking of small molecules

NeuralDock rapidly predicts protein-small molecule binding energy and affinity without prior ligand knowledge, validated against physical docking methods.

GM1 mediates the formation and maintenance of cytotoxic Aβ oligomers

This study shows GM1 promotes Aβ oligomer formation and maintains their stability on membranes, supporting the Aβ ion channel hypothesis and highlighting GM1 as a target for Alzheimer's disease research.

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

This study maps the conformational space of α-synuclein monomer using simulations and experimental validations, revealing stable conformations with slow interconversion times.

Various miRNAs are involved in efficient HCV replication

This study identifies miRNAs other than miR-122 that support HCV replication in non-hepatic cells by interacting with the viral 5UTR and stabilizing the IRES structure.

Prefusion spike protein stabilization through computational mutagenesis

The paper develops a pipeline to identify thermodynamically stabilizing mutations in the SARS-CoV-2 spike protein using bioinformatics, molecular dynamics, and a protein design tool.

Rational design and implementation of a chemically inducible hetero-trimerization system

This paper designs a chemically inducible trimerization system by splitting FRB and FKBP, enabling precise control of tri-organellar junctions and membrane lipid perturbations in live cells.

Mapping Co-regulation Pathways among Ligand Binding sites in RyR1

The paper maps co-regulation pathways among ligand binding sites in RyR1 using a graph-theoretical approach to understand how Ca2+, ATP, and caffeine synergistically regulate the channel.