Functional Studies on an Indel Loop between the Subtypes of <i>meso</i>-Diaminopimelate Dehydrogenase

Ma, Qinyuan; Wang, Xiaoxiao; Luan, Fang; Han, Ping; Zheng, Xue Bin; Yin, Yanmiao; Zhang, Xianghe; Zhang, Ya`ning; Gao, Xuemin

doi:10.1021/acscatal.2c01799

Cited by 11 publications

(15 citation statements)

References 33 publications

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“…Each paradigm has produced fundamental insights into how nature produces life and what goes wrong in disease, but each often overlooks mutations beyond simple missense substitutions. Recent work has underscored how essential other types of mutations are to evolutionary novelty and adaptation, as well as their utility for understanding diseases and protein engineering [1][2][3][4][5][6]. In addition to missense mutations, we must consider frameshifts, recombination, splice variations, and insertions and deletions to evaluate how mutations change proteins.…”

Section: Introductionmentioning

confidence: 99%

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

et al. 2023

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Insertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evolution. We develop a low cost and bias method, DIMPLE, for systematically generating deletions, insertions, and missense mutations in genes, which we test on a range of targets, including Kir2.1. We use DIMPLE to study how indels impact potassium channel structure, disease, and evolution. We find deletions are most disruptive overall, beta sheets are most sensitive to indels, and flexible loops are sensitive to deletions yet tolerate insertions.

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Section: Introductionmentioning

confidence: 99%

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

et al. 2023

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“…Each paradigm has produced fundamental insights into how nature produces life and what goes wrong in disease, but each often overlooks mutations beyond simple substitutions. Recent work has underscored how essential other types of mutations are to evolutionary novelty and adaptation, as well as their utility for understanding diseases and protein engineering (Seuma, Lehner, and Bolognesi 2022; Savino, Desmet, and Franceus 2022; Q. Ma et al 2022; Park and Hahn 2021; Z.…”

Section: Introductionmentioning

confidence: 99%

Deep Insertion, Deletion, and Missense Mutation Libraries for Exploring Protein Variation in Evolution, Disease, and Biology

Macdonald

Nedrud

Grimes

et al. 2022

Preprint

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Insertions and deletions (indels) are a major source of genetic variation in evolution and the cause of nearly 30 percent of Mendelian disease. Despite their importance, indels are left out of nearly every systematic mutational scan to date due to technical challenges associated with making indel-containing libraries, limiting our understanding of indels in disease, biology, and evolution. Here we present a library generation method, DIMPLE, that generates deletions, insertions, and missense at similar frequencies within any gene. To benchmark DIMPLE, we generated libraries within four genes (Kir2.1, VatD, TRPV1, and OPRM1) of varying length and evolutionary origin. DIMPLE produces libraries that are near complete, low cost, and low bias. We measured how missense mutations and indels of varying length impact the potassium channel Kir2.1 surface expression. Across all secondary structure, deletions are more disruptive than insertions, beta sheets are extremely sensitive to large deletions, and flexible loops allow insertions far more frequently than deletions. DIMPLE has low bias, ease of use, and low cost will enable high throughput probing of the importance of indels in disease and evolution.

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“…All bonds were constrained by the LINCS algorithm, and the total simulation time was 100 ns; conformations were saved every 10 ps. After the simulation was completed, the simulated trajectories were analyzed using VMD . The binding free energies were evaluated via the Molecular Mechanical Poisson–Boltzmann Surface Area (MM-PBSA) calculations …”

Section: Materials and Methodsmentioning

confidence: 99%

“…After the simulation was completed, the simulated trajectories were analyzed using VMD. 29 The binding free energies were evaluated via the Molecular Mechanical Poisson−Boltzmann Surface Area (MM-PBSA) calculations. 30 2.11.…”

Section: Structural Analysismentioning

confidence: 99%

Insights into the Unusual Activity of a Novel Homospermidine Synthase with a Promising Application to Produce Spermidine

Liu,

Hu,

Fang

et al. 2023

J. Agric. Food Chem.

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Spermidine is a naturally occurring polyamine with multiple biological activities and potential food and agricultural applications. However, sustainable and scalable spermidine production has not yet been attained. In this study, a homospermidine synthase (HSS) from Pseudomonas frederiksbergensis (PfHSS) capable of catalyzing the synthesis of spermidine from 1,3-diaminopropane and putrescine was identified based on multiple sequence alignment using Blastochloris viridis HSS (BvHSS) as a template. The optimal reaction pH and temperature for purified PfHSS were determined to be 8.5 and 45 °C, respectively, and K+ was able to promote the enzyme activity. Further analysis of the structural and functional relationships through molecular docking and molecular dynamics simulation indicates that glutamic acid at position 359 is the essential residue for the enzyme-catalyzed synthesis of spermidine. The whole-cell catalytic reaction yielded 1321.4 mg/L spermidine and 678.2 mg/L of homospermidine. This study presents a novel, promising, and sustainable biological method for producing spermidine.

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Functional Studies on an Indel Loop between the Subtypes of meso-Diaminopimelate Dehydrogenase

Cited by 11 publications

References 33 publications

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

Deep Insertion, Deletion, and Missense Mutation Libraries for Exploring Protein Variation in Evolution, Disease, and Biology

Insights into the Unusual Activity of a Novel Homospermidine Synthase with a Promising Application to Produce Spermidine

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