Explanipedia

Constrained Evolutionary Funnels Shape Viral Immune Escape Open

Marian Huot, D. I. C. Wang, Eugene I. Shakhnovich, Rémi Monasson, Simona Cocco · 2025

Understanding how viral proteins adapt under immune pressure while preserving structural viability is crucial for anticipating the emergence of antibody-resistant variants. Here, we present a probabilistic framework that predicts the evolu…

Entropy-driven denaturation enables sustainable protein regeneration through rapid gel-solid transition Open

Yichong Wang, Junlang Liu, Michael M. Peters, Ryoma Ishii, D. I. C. Wang , et al. · 2025

Predicting high-fitness viral protein variants with Bayesian active learning and biophysics Open

Marian Huot, D. I. C. Wang, Jiacheng Liu, Eugene I. Shakhnovich · 2025

The early detection of high-fitness viral variants is critical for pandemic response, yet limited experimental resources at the onset of variant emergence hinder effective identification. To address this, we introduce an active learning fr…

Complete Enzyme Clustering Enhances Coenzyme Q Biosynthesis via Substrate Channeling Open

D. I. C. Wang, Andrea Gottinger, Jinki Jeong, Callum R. Nicoll, Junlang Liu , et al. · 2025

Metabolons - transient assemblies of sequential metabolic enzymes - facilitate the reactions of multi-step metabolic pathways, yet, how they mechanistically bolster metabolic flux remains unknown. Here, we investigate the molecular determi…

The R2R3 MYB GhMYB308 is a key regulator in lignin biosynthesis and modulates cotton plant architecture and fiber Open

Kundai Chelsea Nyamaharo, Yinshuai Huang, Qian Yang, Hongli Zheng, Nnaemeka Ekene Vitalis , et al. · 2025

Spatial Clustering of Interface Residues Enhances Few-Shot Prediction of Viral Protein Binding Open

Maxime Basse, D. I. C. Wang, Eugene I. Shakhnovich · 2025

A bstract Predicting protein binding affinities across large combinatorial mutation spaces remains a critical challenge in molecular biology, particularly for understanding viral evolution and antibody interactions. While combinatorial mut…

Few-Shot Viral Variant Detection via Bayesian Active Learning and Biophysics Open

Marian Huot, D. I. C. Wang, Jiacheng Liu, Eugene I. Shakhnovich · 2025

The early detection of high-fitness viral variants is critical for pandemic response, yet limited experimental resources at the onset of variant emergence hinder effective identification. To address this, we introduce an active learning fr…

More Structure, Less Accuracy: ESM3’s Binding Prediction Paradox Open

Thomas Loux, D. I. C. Wang, Eugene I. Shakhnovich · 2024

This paper investigates the impact of incorporating structural information into the protein-protein interaction predictions made by ESM3, a multimodal protein language model (pLM). We utilized various structural variants as inputs and comp…

Entropy Changes in Water Networks Promote Protein Denaturation Open

Yichong Wang, Junlang Liu, Michael M. Peters, Ryoma Ishii, D. I. C. Wang , et al. · 2024

For over a century, an explanation for how concentrated ions denature proteins has proven elusive. Here, we report a novel mechanism of protein denaturation driven by entropy changes in water networks. Experiments and simulations show that…

Biophysical principles predict fitness of SARS-CoV-2 variants Open

D. I. C. Wang, Marian Huot, Vaibhav Mohanty, Eugene I. Shakhnovich · 2024

SARS-CoV-2 employs its spike protein’s receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our …

Biophysical principles predict fitness of SARS-CoV-2 variants Open

D. I. C. Wang, Marian Huot, Vaibhav Mohanty, Eugene I. Shakhnovich · 2023

SARS-CoV-2 employs its spike protein’s receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our …

Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination Open

Mara Prentiss, D. I. C. Wang, Jonathan Fu, Chantal Prévost, Veronica Godoy‐Carter , et al. · 2023

In E . coli , double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting …

Effects of Vimentin Intermediate Filaments on the Structure and Dynamics of <i>In Vitro</i> Multicomponent Interpenetrating Cytoskeletal Networks Open

Yinan Shen, Huayin Wu, Peter J. Lu, D. I. C. Wang, Marjan Shayegan , et al. · 2021

We investigate the rheological properties of interpenetrating networks reconstituted from the main cytoskeletal components: filamentous actin, microtubules, and vimentin intermediate filaments. The elastic modulus is determined largely by …

Effect of Divalent Cations on the Structure and Mechanics of Vimentin Intermediate Filaments Open

Huayin Wu, Yinan Shen, D. I. C. Wang, Harald Herrmann, Robert D. Goldman , et al. · 2020

Effect of the divalent cations zinc and calcium on the structure and mechanics of reconstituted vimentin intermediate filaments Open

Huayin Wu, Yinan Shen, D. I. C. Wang, Harald Herrmann, Robert D. Goldman , et al. · 2019

Divalent cations in a concentration-dependent manner behave as effective crosslinkers of intermediate filaments (IFs) such as vimentin IF (VIF). These interactions have been mostly attributed to their multivalency. However, ion-protein int…

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