Computational design of serine hydrolases

Science, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities RFdiffusion ensemble generation method for assessing site preorganization to starting from minimal descriptions. Experimental characterization revealed catalytic efficiencies ( k cat / K m ) up 2.2x10 5 M −1 s and crystal structures closely match models (Cα RMSDs < 1 Å). Selection structural compatibility across reaction coordinate enabled identification new catalysts in low-throughput screens five different folds distinct those natural hydrolases. Our de novo approach provides insight into geometric basis catalysis roadmap designing catalyze transformations.

Language: Английский

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Allostery

Quarterly Reviews of Biophysics, Journal Year: 2025, Volume and Issue: 58

Published: Jan. 1, 2025

Abstract Allostery describes the ability of biological macromolecules to transmit signals spatially through molecule from an allosteric site – a that is distinct orthosteric binding sites primary, endogenous ligands functional or active site. This review starts with historical overview and description classical example allostery hemoglobin other well-known examples (aspartate transcarbamoylase, Lac repressor, kinases, G-protein-coupled receptors, adenosine triphosphate synthase, chaperonin). We then discuss fringe allostery, including intrinsically disordered proteins inter-enzyme influence dynamics, entropy, conformational ensembles landscapes on mechanisms, capture essence field. Thereafter, we give over central methods for investigating molecular covering experimental techniques as well simulations artificial intelligence (AI)-based methods. conclude allostery-based drug discovery, its challenges opportunities: recent advent AI-based methods, compounds are set revolutionize discovery medical treatments.

Language: Английский

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Protein Design Accelerates the Development and Application of Optogenetic Tools

Computational and Structural Biotechnology Journal, Journal Year: 2025, Volume and Issue: 27, P. 717 - 732

Published: Jan. 1, 2025

Optogenetics has substantially enhanced our understanding of biological processes by enabling high-precision tracking and manipulation individual cells. It relies on photosensitive proteins to monitor control cellular activities, thereby paving the way for significant advancements in complex system research. Photosensitive play a vital role development optogenetics, facilitating establishment cutting-edge methods. Recent breakthroughs protein design have opened up opportunities develop protein-based tools that can precisely manipulate activities. These will significantly accelerate application optogenetic tools. This article emphasizes pivotal tools, offering insights into potential future directions. We begin providing an introduction historical fundamental principles followed exploration operational mechanisms key domains, which includes clarifying conformational changes they undergo response light, such as allosteric modulation dimerization processes. Building this foundation, we reveal enable creation even more sophisticated techniques.

Language: Английский

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Design of high-affinity binders to immune modulating receptors for cancer immunotherapy

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 26, 2025

Immune receptors have emerged as critical therapeutic targets for cancer immunotherapy. Designed protein binders can high affinity, modularity, and stability hence could be attractive components of therapeutics directed against these receptors, but traditional Rosetta based binder methods using small globular scaffolds difficulty achieving affinity on convex targets. Here we describe the development helical concave tailored to target sites typically involved in immune receptor interactions. We employed design proteins that bind TGFβRII, CTLA-4, PD-L1, low nanomolar picomolar affinities potent biological activity following experimental optimization. Co-crystal structures TGFβRII CTLA-4 complex with their respective closely match models. These designs should considerable utility downstream applications. regulate responses are key immunotherapy Here, authors designed creating high-affinity PD-L1. confirmed potential.

Language: Английский

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De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 21, 2023

Abstract A general method for designing proteins to bind and sense any small molecule of interest would be widely useful. Due the number atoms interact with, binding molecules with high affinity requires highly shape complementary pockets, transducing events into signals is challenging. Here we describe an integrated deep learning energy based approach complementarity binders that are poised downstream sensing applications. We employ generated psuedocycles repeating structural units surrounding central pockets; depending on geometry unit repeat number, these pockets span wide ranges sizes shapes. For a target interest, extensively sample pseudocycles generate large numbers customized potential ligand poses interacting interfaces then optimized binding. computationally design four diverse molecules, including first time polar flexible such as methotrexate thyroxine, which expressed at levels have nanomolar affinities straight out computer. Co-crystal structures nearly identical models. Taking advantage modular structure location constructed low noise nanopore sensors chemically induced dimerization systems by splitting domains assemble original pseudocycle pocket upon addition. One Sentence Summary use pseuodocycle-based optimizing ligands, can directly converted ligand-gated nanopores systems.

Language: Английский

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Identification and Understanding of Allostery Hotspots in Proteins: Integration of Deep Mutational Scanning and Multi-faceted Computational Analyses

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 168998 - 168998

Published: Feb. 1, 2025

Language: Английский

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Design of Multimodal Supramolecular Protein Assemblies via Enzyme–Substrate Interactions for Intracellular Antioxidant Regulation

Nano Letters, Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

Allosteric modulation of protein function, which involves effector binding triggering distant conformational changes, is crucial for cellular and metabolic control. However, achieving tunable control, structural diversity, precise intracellular regulation remains challenging. Here, we designed dynamic supramolecular assemblies driven by enzyme-substrate interactions antioxidant in cells. Using a glutathione S-transferase modified with cysteine mutation (GSTK77C), engineered an molecule (GMP4M) containing (GSH) moiety maleimide group linked PEG chain. This system forms hierarchical diverse morphologies, including nanowires, nanorings, nanobranches, nanotwists, switchable "ON/OFF" enzymatic activity modulated endogenous GSH. The maintain integrity under physiological conditions, show remarkable reversibility, outperform native GST stability environmental adaptability. approach provides versatile platform creating broad applications therapies biomedical interventions.

Language: Английский

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Bioengineering of long-chain polyunsaturated fatty acids in oilseed crops

Progress in Lipid Research, Journal Year: 2025, Volume and Issue: unknown, P. 101333 - 101333

Published: May 1, 2025

Language: Английский

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Synthetic Biology for Designing Allostery and its Potential Biomedical Applications

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 169225 - 169225

Published: May 1, 2025

Allosteric regulation of protein function, where a perturbation at one site induces conformational shift or alters dynamics distal functional site, plays key role in numerous biological processes. The ability to introduce allostery using synthetic biology principles holds significant potential both for biomedical and biotechnological applications, advancing our understanding natural allostery. By customizing target proteins sensing specific chemical physical signals, including ligand binding environmental cues, we aim allosterically modulate the function depending on selected triggers. This approach, unlike active-site targeting, offers greater specificity selectivity can couple diverse physiological Synthetic strategies have been developed recently designed allosteric regulation, design modulators such as domain insertion, generation de novo switches, application engineered mechanisms control cellular functions. We examine artificial intelligence (AI)-based generative other important milestones, challenges opportunities this field, highlighting how these approaches could be applied development new therapeutic strategies.

Language: Английский

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Programmable Split DNAzyme Modulators via Allosteric Cooperative Activation for mRNA Electrochemiluminescence Biosensing

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

DNAzymes, known for their programmability, stability, and cost-effectiveness, are powerful tools signal transduction in complex biological systems. However, application responding to target effectors is often hindered by limited catalytic efficiency susceptibility unintended activation. Here we propose an allosteric cooperative activation strategy program a split DNAzyme modulator (STATER) that enables sensitive accurate electrochemiluminescence (ECL) biosensing of interleukin-6 (IL-6) mRNA. Our design features STATER leverages DNA tetrahedron as central scaffold, equipped with two pairs T-shaped hairpin probes (TP) helper (HP). Specifically, the TP contains apurinic/apyrimidinic endonuclease 1 (APE1) recognition sites, IL-6 mRNA region, partzyme fragment, while HP corresponding paired fragment. Unlike conventional modulators rely on single effector activation, integrates mechanism, which ensures all preblocked components synergistically activated assembled within confined space, facilitating rapid specific reconstruction DNAzyme's active domain. Furthermore, upon APE1 mRNA, inactive partzymes undergo assembly via toehold exchange displacement reaction, switching cleavage reactivity STATER. This mechanism establishment threshold thereby minimizing nonspecific scenarios. studies demonstrate exhibits outstanding sensitivity selectivity detection using supramolecular gold nanoclusters network-based ECL platform. The biosensor provides linear span from × 10–13 10–7 M, limit low 3.26 10–14 highlighting STATER's potential detecting various analytes

Language: Английский

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