Molecular recognition between bacterial phosphorothioate DNA and sulfur-binding domain (SBD): competition between the water cage and chalcogen-hydrophobic packet

Li, Jiayi; Wan, Haibo; Zhang, Haoqing; Wang, Xiaolei; Liu, Guang; Wu, Geng; He, Xinyi; Deng, Zixin; Zhao, Yi‐Lei

doi:10.1039/d2cp00291d

Cited by 10 publications

(11 citation statements)

References 71 publications

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“…Low-energy conformers were optimized with the dispersion-included ωB97X-D functional in Gaussian 16 with the 6–31+G(d,p) basis set. , The prediction of reactive sites between the nucleophile and electrophile was studied by Hirshfeld charges, frontier molecular orbital (FMO) analysis, and Fukui functions (FFs). The details have been provided in previous works. − The isosurface maps were produced according to the outputs from Multiwfn calculations . We used the SMD solvation model to optimize the structure and calculate the frequency, obtaining the Gibbs free energy at 298 K via the GoodVibes program , Intrinsic reaction coordinate (IRC) calculations were conducted to determine the transition states.…”

Section: Methodsmentioning

confidence: 99%

High-Molecular-Weight and Light-Colored Disulfide-Bond-Embedded Polyesters: Accelerated Hydrolysis Triggered by Redox Responsiveness

Hu,

Luan,

et al. 2023

Biomacromolecules

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Disulfide bonds have attracted considerable attention due to their reduction responsiveness, but it is crucial and challenging to prepare disulfide-bond-based polyesters by melt polycondensation. Herein, the inherently poor thermal stability of the S–S bond in melting polycondensation was overcome. Moreover, poly(butylene succinate-co-dithiodipropionate) (PBSDi) with a light color and high molecular weights (Mn values up to 84.7 kg/mol) was obtained. These polyesters can be applied via melt processing with T d,5% > 318 °C. PBSDi10-PBSDi40 shows good crystallizability (crystallinity 56–38%) and compact lamellar thickness (2.9–3.2 nm). Compared with commercial poly(butylene adipate-co-terephthalate) (PBAT), the elevated mechanical and barrier performances of PBSDi make them better packaging materials. For the degradation behavior, the disulfide monomer obviously accelerates the enzyme degradation but has a weaker effect on hydrolysis. In 0.1 mol/L or higher concentrations of H2O2 solutions, the oxidation of disulfide bonds to sulfoxide and sulfone groups can be realized. This process results in a stronger nucleophilic attack, as confirmed by the Fukui function and DFT calculations. Additionally, the greater polarity and hydrophilicity of oxidation products, proved by noncovalent interaction analysis, accelerate the hydrolysis of polyesters. Moreover, glutathione-responsive breakage, from polymers to oligomers, is confirmed by an accelerated decline in molecular weight. Our research offers fresh perspectives on the effective synthesis of the disulfide polyester and lays a solid basis for the creation of high-performance biodegradable polyesters that degrade on demand.

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Section: Methodsmentioning

confidence: 99%

High-Molecular-Weight and Light-Colored Disulfide-Bond-Embedded Polyesters: Accelerated Hydrolysis Triggered by Redox Responsiveness

Hu,

Luan,

et al. 2023

Biomacromolecules

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“…Then, we built PBXI–CALB systems and carried out MD simulations to study the enzymatic degradation mechanisms. The prereaction state analysis , and noncovalent interaction (NCI) analysis , of PBXI–CALB were performed to reveal the origin of substrate preference (details of MD simulations and subsequent analyses are given in the Supporting Information). Isosurface maps were produced using the VMD 1.9.3 program and Multiwfn 3.7 software package …”

Section: Methodsmentioning

confidence: 99%

Efficient Synthesis of Itaconate Polyesters with Amine-Triggered Rapid Degradation and Outstanding Mechanical Properties: An Experimental and Theoretical Study on Degradation Mechanisms

Wang

et al. 2022

Macromolecules

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A range of degradable polyesters have been developed as sustainable alternatives for commercial plastics; however, limitations of composting facilities and uncontrolled degradation in the environment hindered their viability. In this study, biobased itaconic acid was selected as an active site to control the degradation of polyesters. A series of PBXI copolyesters with M w 's ranging from 4.86 to 8.31 × 10 4 g/mol and high intrinsic viscosities of more than 1.15 dL/g were successfully synthesized without any crosslinking by selecting appropriate reaction conditions, including condensation temperature and vacuum, effective inhibitor, and catalyst. The obtained copolyesters were semicrystalline, and their T m 's could be regulated from 42.5 to 179.5 °C. They exhibited outstanding elastic modulus (120−598 MPa) and tensile strength (17.9−51.4 MPa) among degradable polymers. Degradation experiments demonstrated that the incorporation of itaconate segments could facilitate both the hydrolysis and enzymatic degradation of polyesters. The state-of-the-art computation and analysis via molecular dynamics (MD) simulations of PBXI−CALB complexes elucidated the enzymatic degradation mechanism. Experimental results proved that, at room temperature, the degradation could be stimulated and regulated by amines without a catalyst and the M n 's of lactamization products rapidly decreased to less than 5000 g/mol within 24 h. Moreover, the copolymerized structure of copolyesters and solvent factors could influence the aza-Michael addition between amines and itaconate units. This work provides a strategy to synthesize biodegradable copolymers with the potential to undergo controlled and rapid in vivo degradation with outstanding mechanical properties.

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“…The prereaction state analysis and noncovalent interaction (NCI) analysis of PAATh-CALB were performed to reveal the origin of substrate preference. Details of MD simulations and NCI analyses are described in our previous work and provided in the Supporting Information. − Maps were produced using the VMD 1.9.3 program and Multiwfn 3.7 software package …”

Section: Experimental Sectionmentioning

confidence: 99%

Biobased Biodegradable Copolyesters from 2,5-Thiophenedicarboxylic Acid: Effect of Aliphatic Diols on Barrier Properties and Degradation

Wang,

Li,

Wang

et al. 2023

Biomacromolecules

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The demand for sustainable development has led to increasing attention in biobased polyesters due to their adjustable thermal and mechanical properties and biodegradability. In this study, we used a novel bioderived aromatic diacid, 2,5-thiophenedicarboxylic acid (TDCA) to synthesize a list of novel aromatic–aliphatic poly(alkylene adipate-co-thiophenedicarboxylate) (PAATh) copolyesters through a facile melt polycondensation method. PAAThs are random copolyesters with weight-average molecular weights of 58400 to 84200 g·mol–1 and intrinsic viscosities of 0.80 to 1.27 dL·g–1. All PAAThs exhibit sufficiently high thermal stability as well as the highest tensile strength of 6.2 MPa and the best gas barrier performances against CO2 and O2, 4.3- and 3.3-fold better than those of poly(butylene adipate-co-terephthalate) (PBAT). The biodegradability of PAAThs was fully evaluated through a degradation experiment and various experimental parameters, including residue weights, surface morphology, and molecular compositions. The state-of-the-art molecular dynamics (MD) simulations were applied to elucidate the different enzymatic degradation behaviors of PAAThs due to the effect of diols with different chain structures. The sterically hindered carbonyl carbon of the PHATh–enzyme complex was more susceptible to nucleophilic attack and exhibited a higher tendency to enter a prereaction state. This study has introduced a group of novel biobased copolyesters with their structure–property relationships investigated thoroughly, and the effect of diol components on the enzymatic degradation was revealed by computational analysis. These findings may lay the foundation for the development of promising substitutes for commercial biodegradable polyesters and shed light on their complicated degradation mechanisms.

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Molecular recognition between bacterial phosphorothioate DNA and sulfur-binding domain (SBD): competition between the water cage and chalcogen-hydrophobic packet

Abstract: Bacterial DNA phosphorothioation (PT) physiologically and stereo-specifically replaces a non-bridging oxygen in a phosphate link with a sulfur atom, which can be recognized by a highly conserved sulfur-binding domain (SBD)....

Cited by 10 publications

References 71 publications

High-Molecular-Weight and Light-Colored Disulfide-Bond-Embedded Polyesters: Accelerated Hydrolysis Triggered by Redox Responsiveness

High-Molecular-Weight and Light-Colored Disulfide-Bond-Embedded Polyesters: Accelerated Hydrolysis Triggered by Redox Responsiveness

Efficient Synthesis of Itaconate Polyesters with Amine-Triggered Rapid Degradation and Outstanding Mechanical Properties: An Experimental and Theoretical Study on Degradation Mechanisms

Biobased Biodegradable Copolyesters from 2,5-Thiophenedicarboxylic Acid: Effect of Aliphatic Diols on Barrier Properties and Degradation

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