Nanopore sequencing: flourishing in its teenage years

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Язык: Английский

---

De novo design of transmembrane fluorescence-activating proteins

Nature, Год журнала: 2025, Номер unknown

Опубликована: Фев. 19, 2025

Язык: Английский

---

Binding and sensing diverse small molecules using shape-complementary pseudocycles

Science, Год журнала: 2024, Номер 385(6706), С. 276 - 282

Опубликована: Июль 18, 2024

We describe an approach for designing high-affinity small molecule–binding proteins poised downstream sensing. use deep learning–generated pseudocycles with repeating structural units surrounding central binding pockets widely varying shapes that depend on the geometry and number of repeat units. dock molecules interest into most shape complementary these pseudocycles, design interaction surfaces high affinity, experimentally screen to identify designs highest affinity. obtain binders four diverse molecules, including polar flexible methotrexate thyroxine. Taking advantage modular structure pockets, we construct chemically induced dimerization systems low-noise nanopore sensors by splitting domains reassemble upon ligand addition.

Язык: Английский

---

Toward single-molecule protein sequencing using nanopores

Nature Biotechnology, Год журнала: 2025, Номер unknown

Опубликована: Март 17, 2025

Язык: Английский

---

Detection of protein oligomers with nanopores

Nature Reviews Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Март 5, 2025

Язык: Английский

---

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 23, 2024

Francis Crick's global parameterization of coiled coil geometry has been widely useful for guiding design new protein structures and functions. However, guided by similar beta barrel less successful, likely due to the deviations from ideal required maintain inter-strand hydrogen bonding without introducing backbone strain. Instead, barrels have designed using 2D structural blueprints; while this approach successfully generated fluorescent proteins, transmembrane nanopores, other structures, it requires expert knowledge provides only indirect control over shape. Here we show that simplicity shape structure provided parametric representations can be generalized beyond coils taking advantage rich sequence-structure relationships implicit in RoseTTAFold based methods. Starting parametrically backbones, both RFjoint inpainting RFdiffusion readily incorporate irregularities necessary proper folding with minimal deviation idealized geometries. We across a broad range sheet parameterizations, these methods achieve high silico experimental success rates, atomic accuracy confirmed an X-ray crystal novel topology, de novo 12, 14, 16 stranded nanopores conductances ranging 200 500 pS. By combining generation rates deep learning methods, our makes proteins where confers function, such as more precisely specifiable accessible.

Язык: Английский

---

Protein-induced membrane asymmetry modulates OMP folding kinetics and stability

Faraday Discussions, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Biological membranes are asymmetric structures, with asymmetry arising from differences in lipid identity each leaflet of the bilayer, as well non-uniform distribution lipids and small molecules membrane. Proteins can also induce modulate membrane based on their shape, sequence interactions lipids. How affects macromolecular behaviour is poorly understood because complexity natural systems, difficulties creating relevant bilayer systems vitro. Here, we present a method exploiting efficient, unidirectional folding transmembrane β-barrel outer protein, OmpA, to create proteoliposomes protein-induced dipoles known direction (arising variation engineered into OmpA loops). We then characterise kinetics stability different variants these proteoliposomes. find that both primary dipole which occurs play an important role for modulating rate folding. Critically, by complementarily matching charge protein it possible enhance folded OmpA. The results hint at how cells might exploit loop membrane-embedded proteins manipulate environments adaptation survival.

Язык: Английский

---

Enhanced Water Permeation in Positively Charged Water Channels: Insights into the Molecular Mechanism

Angewandte Chemie International Edition, Год журнала: 2025, Номер unknown

Опубликована: Март 7, 2025

The high selectivity and permeability of aquaporin proteins in water transport inspired the design artificial channels (AWCs). efficiency both AQPs AWCs is influenced by charged groups at pore entrance. Here, we explored mechanism charge effects pillar[5]arene using molecular dynamics (MD) simulations. simulations demonstrate that positively (Ch+) exhibit higher compared to negatively (Ch-). Ch+ stems from shorter hydrogen bond lifetimes between molecules entrance region. In line with this, rotational faster region Ch+. Further analyses revealed two factors contributing distinct Ch- channels: direct interactions NH3 +/COO- counter ions (Cl-/K+) around these groups. + exert less stable H-bond interaction than COO- group channels. K+ concentrated retard rotation more effectively Cl- These findings provide insights into principles high-performance level.

Язык: Английский

---

Enhanced Water Permeation in Positively Charged Water Channels: Insights into the Molecular Mechanism

Angewandte Chemie, Год журнала: 2025, Номер unknown

Опубликована: Март 7, 2025

Abstract The high selectivity and permeability of aquaporin proteins in water transport inspired the design artificial channels (AWCs). efficiency both AQPs AWCs is influenced by charged groups at pore entrance. Here, we explored mechanism charge effects pillar[5]arene using molecular dynamics (MD) simulations. simulations demonstrate that positively ( Ch + ) exhibit higher compared to negatively − ). stems from shorter hydrogen bond lifetimes between molecules entrance region. In line with this, rotational faster region . Further analyses revealed two factors contributing distinct channels: direct interactions NH 3 /COO counter ions (Cl /K around these groups. exert less stable H‐bond interaction than COO group channels. K concentrated retard rotation more effectively Cl These findings provide insights into principles high‐performance level.

Язык: Английский

---

Rational Design Principles for De Novo α-Helical Peptide Barrels with Dynamic Conductive Channels

Journal of the American Chemical Society, Год журнала: 2025, Номер unknown

Опубликована: Март 28, 2025

Despite advances in peptide and protein design, the rational design of membrane-spanning peptides that form conducting channels remains challenging due to our imperfect understanding sequence-to-structure relationships drive membrane insertion, assembly, conductance. Here, we describe computational experimental characterization a series coiled coil-based transmembrane α-helical barrels with conductive channels. Through combination obtain 5 7 helices, as characterized detergent micelles. In lipid bilayers, these assemblies exhibit two conductance states relative populations dependent on applied potential: (i) low-conductance correlate variations designed amino-acid sequences modeled coiled-coil barrel geometries, indicating stable barrels; (ii) high-conductance which single change size discrete steps. Notably, are similar for all contrast states. This indicates formation large, dynamic channels, observed natural barrel-stave These findings establish routes tune functional specific geometry.

Язык: Английский

---