TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

Polarizable force fields advance our understanding of electrostatic interactions in molecular systems; however, their widespread application is limited by the complexity required modeling. We here present TinkerModeller (TKM), a versatile software package designed to streamline construction biological systems Tinker simulation software. The core functionality TKM lies its capacity generate input files for complex and facilitate conversion from classical polarizable fields. With user-friendly, standalone script, provides an intuitive interface that supports users modeling through postanalysis, creating comprehensive platform dynamics simulations within Tinker. Furthermore, includes electric field (EF) postanalysis module, introducing novel approach employs charge methods point approximations efficient internal EF estimation. This module offers computationally low-demand solution high-throughput Our work paves way broader, more accessible use introduces new method estimation, advancing explore effects materials science applications.

Language: Английский

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Intramolecular epistasis correlates with divergence of specificity in promiscuous and bifunctional NSAR/OSBS enzymes

Protein Science, Journal Year: 2025, Volume and Issue: 34(5)

Published: April 18, 2025

Understanding the functions and evolution of specificity-determining residues is essential for improving strategies to predict design enzyme functions. Whether function an amino acid residue retained during depends on intramolecular epistasis, which occurs when same contributes different phenotypes in genetic backgrounds. This study examines relationship between epistasis functional divergence by investigating a conserved specificity determinant five homologs from N-succinylamino racemase (NSAR)/o-succinylbenzoate synthase (OSBS) subfamily. NSAR activity originated as promiscuous (non-biological) ancestral OSBS. Some extant NSAR/OSBS subfamily enzymes still have OSBS biological activity, while some use both activities Others only but can catalyze reaction activity. Previously, we determined that R266 Amycolatopsis sp. T-1-60 enabling K263 act general acid/base catalyst. Here, show mutating decreased relative four enzymes, predicted. However, other exhibited related pleiotropy R266, including proton exchange rate catalytic lysines substrate, impact thermostability. The strength was associated with evolutionary enzymes. These results illustrate benefits comparing multiple understanding mechanisms specificity.

Language: Английский

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Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(24), P. 16670 - 16680

Published: June 7, 2024

To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory of protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field entire active site is tracked through dynamics, clustered using affinity propagation algorithm, subjected principal component analysis. This analysis reveals notable changes with DE, where distinct topologies influence transition state energetics mechanism. A chemically meaningful emerges takes lead facilitates crossing barrier transfer. Our findings underscore intrinsic dynamic's on enzyme function, ability switch mechanisms within same protein, crucial role design.

Language: Английский

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Local Electric Fields Drives the Proton-Coupled Electron Transfer within Cytochrome P450 Reductase

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(10), P. 7893 - 7900

Published: May 6, 2024

Cytochrome P450 enzymes play a pivotal role in biosynthetic and metabolic transformations. Especially, cytochrome reductase (CPR) acts as the key electron donor for oxygen activation by monoxygenases, but transfer mechanism within CPR is largely elusive. Here, extensive molecular dynamics (MD) quantum mechanics/molecular mechanics (QM/MM) calculations were performed to elucidate CPR's mechanism. We found that from FADH– FMN occurs through proton-coupled (PCET) Glu142 transfers proton via two-water-molecule chain, concurrent with FMN. The subsequent ET FADH• FMNH• involves an Asp675-mediated PCET process, where Ser457-assisted Asp675 coupled FMNH•. Notably, local electric field doubly protonated His180 significantly enhances reactions both kinetically thermodynamically. This study highlights vital of facilitating biological enzymatic reactions.

Language: Английский

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Design of a light and Ca ²⁺ switchable organic–peptide hybrid

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(5)

Published: Jan. 30, 2025

The design of organic–peptide hybrids has the potential to combine our vast knowledge protein with small molecule engineering create hybrid structures complex functions. Here, we describe computational a photoswitchable Ca 2+ -binding hybrid. designed molecule, designated switch (CaBS), combines an EF-hand motif from classical proteins such as calmodulin group that can be reversibly isomerized between spiropyran (SP) and merocyanine (MC) state in response different wavelengths light. MC/SP acts both photoswitch well optical sensor binding. Photoconversion SP corresponding MC unmasks acidic phenol, which CaBS uses integral part its site tertiary quaternary structure. By design, is monomeric, while -bound form obligate dimer, two sites formed at interface domain-swapped dimer. Thus, light were expected serve “AND gate” powers change backbone structure/dynamics, oligomerization state, fluorescence properties molecule. was using Rosetta molecular dynamics simulations, experimentally characterized by nuclear magnetic resonance, isothermal titration calorimetry, titrations. These data illustrate combining de novo develop sensors whose conformation, association respond multiple environmental cues.

Language: Английский

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Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

Computational enzyme design is a promising technique for producing novel enzymes industrial and clinical needs. A key challenge that this faces to consistently achieve the desired activity. Fundamental studies of natural revealed critical contributions from second-shell - even more distant residues their remarkable efficiency. In particular, such organize internal electrostatic field promote reaction. Engineering fields computationally proved be strategy, which, however, has some limitations. Charged necessarily form specific patterns local interactions may exploited structural integrity. As result, it impossible probe alone by substituting amino acids. We hypothesize an approach isolates influences residues' charges other could yield deeper insights. use molecular modeling with AI-enhanced QM/MM reaction sampling implement apply model serine protease subtilisin. find negative charge 8 Å away catalytic site crucial achieving enzyme's efficiency, contributing than 2 kcal/mol lowering barrier. contrast, positive second-closest charged residue opposes efficiency raising barrier 0.8 kcal/mol. This result invites discussion into role trade-offs might have taken place in evolution enzymes. Our transferable can help investigate preorganization believe study engineering direction advance both fundamental applied enzymology lead new powerful biocatalysts.

Language: Английский

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Electro-inductive Effects and Molecular Polarizability for Vibrational Probes on Electrode Surfaces

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(35), P. 9100 - 9104

Published: Aug. 28, 2024

A microscopic understanding of electric fields and molecular polarization at interfaces will aid in the design electrocatalytic systems. Herein, variants 4-mercaptobenzonitrile are designed to test different schemes for breaking continuous conjugation between a gold electrode surface nitrile group. Periodic density functional theory calculations predict applied potential dependencies CN vibrational frequencies similar those observed experimentally. The frequency response decreased more when was broken benzene ring group than ring, highlighting polarizability effects. systems with or dominated by electro-inductive effects through-space electrostatic effects, respectively. Analysis fractional charge transfer molecule as well occupancy antibonding orbital provides further insights. Balancing polarizability, electro-induction, electrostatics has broad implications electrocatalyst design.

Language: Английский

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Methods for Theoretical Treatment of Local Fields in Proteins and Enzymes

Chemical Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

Electric fields generated by protein scaffolds are crucial in enzymatic catalysis. This review surveys theoretical approaches for detecting, analyzing, and comparing electric fields, electrostatic potentials, their effects on the charge density within enzyme active sites. Pioneering methods like empirical valence bond approach rely evaluating ionic covalent resonance forms influenced field. Strategies employing polarizable force also facilitate field detection. The vibrational Stark effect connects computational simulations to experimental spectroscopy, enabling direct comparisons. We highlight how dynamics induce fluctuations local influencing activity. Recent techniques assess throughout site volume rather than only at specific bonds, machine learning helps relate these global reactivity. Quantum theory of atoms molecules captures entire electron landscape, providing a chemically intuitive perspective field-driven Overall, methodologies show protein-generated highly dynamic heterogeneous, understanding both aspects is critical elucidating mechanisms. holistic view empowers rational engineering tuning promising new avenues drug design, biocatalysis, industrial applications. Future directions include incorporating as explicit design targets enhance catalytic performance biochemical functionalities.

Language: Английский

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PyCPET─Computing Heterogeneous 3D Protein Electric Fields and Their Dynamics

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: April 8, 2025

Electrostatic preorganization is an exciting mode to understand the catalytic function of enzymes, yet limited tools exist computationally analyze it. In particular, no methods interpret geometry, dynamics, and fundamental components 3D electric fields, E⃗(r), in protein active sites. To address this, we present PyCPET (Python Computation Electric Field Topologies), a comprehensive, open-source toolbox E⃗(r) enzymes. We designed it around computational efficiency user friendliness with both CPU- GPU-accelerated codes. Our aim provide set functions for rich, descriptive analysis enzyme systems including benchmarking, distribution streamlines computation point principal component analysis, visualization. Finally, demonstrate its versatility by exploring nature electrostatic dynamics three cases: Cytochrome C, Co-substituted Liver Alcohol Dehydrogenase, HIV Protease. These test systems, along previous work, establish as essential toolkit in-depth visualization fields unlocking new avenues understanding contributions catalysis.

Language: Английский

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Machine-Learning Prediction of Protein Function from the Portrait of Its Intramolecular Electric Field

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 7, 2024

We introduce a machine learning framework designed to predict enzyme functionality directly from the heterogeneous electric fields inherent protein active sites. apply this method curated data set of heme-iron oxidoreductases, spanning three classes: monooxygenases, peroxidases, and catalases. Conventional analysis, focused on simplistic, point along Fe–O bond, is shown be inadequate for accurate activity prediction. Our model demonstrates that enzyme's 3-D field, alone, can accurately its function, without relying additional protein-specific information. Through feature selection, we uncover key field components not only validate previous studies but also underscore crucial role multiple beyond traditionally emphasized bond in heme enzymes. Furthermore, by integrating dynamics, principal component clustering, QM/MM calculations, reveal while dynamic complexities structures obscure predictions, still retains accuracy. This research significantly advances our understanding how scaffolds possess signature tailored their functions at site. Moreover, it presents novel electrostatics-based tool harness these predicting function.

Language: Английский

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