Biology subjects

Polizzi, N.

Publications and source records attributed to Polizzi, N..

6 recordsLinked to original sources

bioRxiv2026

De novo design of small-molecule-induced conformational change

Many biological proteins function by changing shape upon small-molecule binding. Here, we present a general strategy for designing de novo proteins that undergo small-molecule-induced conformational change. Our approach converts a preorganized small-molecule binding protein into a ligand-responsive shape-changer by adding a mobile lid domain that closes behind the ligand upon binding. Using this strategy, we converted an exatecan-binding protein into a drug-induced conformational switch. The lidded proteins showed considerably stronger binding affinity in the sub-nanomolar regime, 100-fold greater specificity to exatecan over a similar molecule, and ligand residence times up to several months, with tunable binding kinetics. We turned one design into a genetically encodable fluorescent biosensor of the drug, enabling potential clinical applications. Our results open the door to programming complex molecular function using vast chemical space.

bioengineering↗

bioRxiv2026

Molecular basis of mitochondrial leucine transport by human Sideroflexin 1

Leucine is a central nutrient signal and a ketogenic amino acid that fuels metabolism, yet how it is imported into mitochondria remains incompletely defined. Sideroflexins are conserved inner mitochondrial membrane proteins implicated in amino acid transport, but their mechanism and substrate specificity remain unclear. Using cryogenic electron microscopy, we determined the structure of SFXN1 in its matrix-open conformation. AlphaFold and Boltz co-folding of SFXN1 with a library of human metabolites identified leucine as a candidate substrate, findings supported by thermal stability measurements and mitochondrial transport assays. Comparison with a cytoplasmic-open-model reveals an alternating-access "toggle-switch" mechanism of transport. Together, these findings uncover the molecular basis of leucine transport by SFXN1 and provide a framework for understanding its role in metabolism and disease.

Molecular Biology↗

bioRxiv2026

De novo design of transmembrane accessory subunits for fold stabilization and expansion

Transmembrane (TM) proteins play essential roles in biology as transporters, ion channels, chaperones, enzymes, and mediators of signal transduction. However, membrane proteins often suffer from inefficient folding and intrinsic instability. Misfolding in cells can cause numerous loss-of-function pathologies. Likewise, denaturation upon purification in the laboratory is a critical barrier to structure determination and characterization of key biochemical mechanisms. Generalizable strategies to stabilize membrane proteins remain limited. Here, we developed an informatics-based de novo design strategy to create synthetic auxiliary subunits that interact with the TM helices of a model pentameric ion channel, thereby bolstering folding while maintaining channel function. Biochemical and structural characterization reveal the synthetic TM subunits can also be used to create larger multi-spanning designer proteins of custom topology. This proof-of-concept motivates the feasibility of computationally designed accessory TM helices as potential pharmacological chaperone "folding correctors" of membrane proteins in disease and as tools in structural biology.

biochemistry↗

bioRxiv2026

Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition

The ability to map protein identity, with resolution sufficient to infer interactions, would support analysis of how proteins work together, or malfunction, in biological processes and diseases. Although several emerging technologies aim towards single-molecule protein sequencing, they require proteins to be removed from the nanoscale spatial context of cells and tissues. Expansion microscopy (ExM) has facilitated a diversity of chemical analyses by isotropically separating molecules throughout a specimen after permeation via a charged hydrogel, followed by gel swelling. Here, we adapt key protein sequencing steps - Edman degradation and amino acid recognition - to the ExM gel context. Using testbed peptides in ExM gels, we show that N-terminal amino acids can be recognized over multiple cycles of in-gel Edman degradation. This principle-oriented study demonstrates sequencing chemistry on defined synthetic constructs, rather than endogenous proteins in biological samples. These results establish principles of in situ protein sequencing and provide a framework for future in situ protein sequencing developments, including the development of higher specificity and affinity amino acid binders.

biochemistry↗

bioRxiv2023

De novo design of drug-binding proteins with predictable binding energy and specificity

The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low M, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles. One Sentence SummaryWe use informatic sampling to design low nM drug-binding proteins, and physics-based calculations to accurately predict affinities.

biophysics↗

bioRxiv2023

De novo Design of Peptides that Bind Specific Conformers of α-Synuclein

Insoluble amyloids rich in cross-{beta} fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloid in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of -synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB database with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of -synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by -synuclein, tau, or A{beta}40. This designed peptide also markedly slowed the formation of -synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.

biophysics↗