M. Scott Shell
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View article: Evolution of the Tri-PDZ Domain in PSD95 (DLG-4 Gene)
Evolution of the Tri-PDZ Domain in PSD95 (DLG-4 Gene) Open
Some genes encoding proteins within the co-evolved pre- and postsynaptic compartments are present in genomes long preceding the origination of the synapse within the animal kingdom. DLG4, gene encoding PSD-95, is one of the most abundant s…
View article: Fast phase prediction of charged polymer blends by white-box machine learning surrogates
Fast phase prediction of charged polymer blends by white-box machine learning surrogates Open
Compatibilized polymer blends are a complex, yet versatile and widespread category of material. When the components of a binary blend are immiscible, they are typically driven towards a macrophase-separated state, but with the introduction…
View article: Structure-specific Mini-Prion Model for Alzheimer’s Disease Tau Fibrils
Structure-specific Mini-Prion Model for Alzheimer’s Disease Tau Fibrils Open
A critical discovery of the past decade is that tau protein fibrils adopt disease-specific hallmark structures in each tauopathy. The faithful generation of synthetic fibrils adopting hallmark structures that can serve as targets for devel…
View article: Hydrophobicity in Intrinsically Disordered Protein Force Fields: Implications for Conformational Ensembles and Protein–Protein Interactions
Hydrophobicity in Intrinsically Disordered Protein Force Fields: Implications for Conformational Ensembles and Protein–Protein Interactions Open
Intrinsically disordered proteins (IDPs) lack a stable 3D structure under physiological conditions, making them challenging to study and simulate. In this study, we compare the hydrophobicity and water-protein interactions of amino acids i…
View article: Water-directed pinning is key to tau prion formation
Water-directed pinning is key to tau prion formation Open
Tau forms fibrillar aggregates that are pathological hallmarks of a family of neurodegenerative diseases known as tauopathies. The synthetic replication of disease-specific fibril structures is a critical gap for developing diagnostic and …
View article: Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale
Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale Open
The interaction between amino acids (AAs) and hydration water is fundamental to protein folding and protein-protein interactions. Here, we proposed a hydrophobicity scale for AAs based on their computed free energetic cost of dewetting. Th…
View article: A colloidal model for the equilibrium assembly and liquid-liquid phase separation of the reflectin A1 protein
A colloidal model for the equilibrium assembly and liquid-liquid phase separation of the reflectin A1 protein Open
Reflectin is an intrinsically disordered protein known for its ability to modulate the biophotonic camouflage of cephalopods based on its assembly-induced osmotic properties. Its reversible self-assembly into discrete, size-controlled clus…
View article: Inverse design of pore wall chemistry and topology through active learning of surface group interactions
Inverse design of pore wall chemistry and topology through active learning of surface group interactions Open
Design of next-generation membranes requires a nanoscopic understanding of the effect of biologically inspired heterogeneous surface chemistries and topologies (roughness) on local water and solute behavior. In particular, the rejection of…
View article: Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning
Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning Open
The ability to program chain conformation and structure through control over the monomer sequence of synthetic polymers has broad implications for next-generation material design. While related problems of protein-folding and de novo desig…
View article: Nanoscale water–polymer interactions tune macroscopic diffusivity of water in aqueous poly(ethylene oxide) solutions
Nanoscale water–polymer interactions tune macroscopic diffusivity of water in aqueous poly(ethylene oxide) solutions Open
PEO restructures water near the polymer, reducing free volume and slowing local water.
View article: Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy
Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy Open
Hydration water dynamics, structure, and thermodynamics are crucially important to understand and predict water-mediated properties at molecular interfaces.
View article: Molecularly informed field theory for estimating critical micelle concentrations of intrinsically disordered protein surfactants
Molecularly informed field theory for estimating critical micelle concentrations of intrinsically disordered protein surfactants Open
The critical micelle concentration (CMC) is a crucial parameter in understanding the self-assembly behavior of surfactants. In this study, we combine simulation and experiment to demonstrate the predictive capability of molecularly informe…
View article: Relationships between Water’s Structure and Solute Affinity at Polypeptoid Brush Surfaces
Relationships between Water’s Structure and Solute Affinity at Polypeptoid Brush Surfaces Open
Excellent antifouling surfaces are generally thought to create a tightly bound layer of water that resists solute adsorption, and highly hydrophilic surfaces such as those with zwitterionic functionalities are of significant current intere…
View article: Tau P301L mutation promotes core 4R tauopathy fibril fold through near-surface water structuring and conformational rearrangement
Tau P301L mutation promotes core 4R tauopathy fibril fold through near-surface water structuring and conformational rearrangement Open
Tau forms toxic fibrillar aggregates in a family of neurodegenerative diseases known as tauopathies. The faithful replication of tauopathy-specific fibril structures is a critical gap for developing diagnostic and therapeutic tools. This s…
View article: Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6
Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6 Open
The PHF6 (Val-Gln-Ile-Val-Tyr-Lys) motif, found in all isoforms of the microtubule-associated protein tau, forms an integral part of ordered cores of amyloid fibrils formed in tauopathies and is thought to play a fundamental role in tau ag…
View article: Local Water Structures Govern the Mixing Thermodynamics of Glycerol-Water Solutions
Local Water Structures Govern the Mixing Thermodynamics of Glycerol-Water Solutions Open
Glycerol is a major cryoprotective agent and is widely used to promote protein stabilization. Through a combined experimental and theoretical study, we show that global thermodynamic mixing properties of glycerol and water are dictated by …
View article: Local solvation structures govern the mixing thermodynamics of glycerol–water solutions
Local solvation structures govern the mixing thermodynamics of glycerol–water solutions Open
Based on THz-spectra we quantify hydrophilic solvation and correlate with mixing enthalpy.
View article: Phosphates form spectroscopically dark state assemblies in common aqueous solutions
Phosphates form spectroscopically dark state assemblies in common aqueous solutions Open
Phosphates and polyphosphates play ubiquitous roles in biology as integral structural components of cell membranes and bone, or as vehicles of energy storage via adenosine triphosphate and phosphocreatine. The solution phase space of phosp…
View article: Inverse Design of Pore Wall Chemistry To Control Solute Transport and Selectivity
Inverse Design of Pore Wall Chemistry To Control Solute Transport and Selectivity Open
Next-generation membranes for purification and reuse of highly contaminated water require materials with precisely tuned functionality to address key challenges, including the removal of small, charge-neutral solutes. Bioinspired multifunc…
View article: Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics
Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics Open
We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polym…