Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

Thompson, Michael C.; Barad, Benjamin A.; Wolff, Alexander M.; Cho, Hyun Sun; Schotte, Friedrich; Schwarz, Daniel M. C.; Anfinrud, Philip; Fraser, James S.

doi:10.1038/s41557-019-0329-3

Cited by 81 publications

(71 citation statements)

References 83 publications

(98 reference statements)

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“…Enzyme catalysis has been proven to be highly correlated with its conformation dynamics [51][52][53]. The salt-activated or -dependent properties of alginate lyase may be due to its salt-regulated conformational dynamics.…”

Section: Structural Insight Into the Salt-regulated Conformational Dymentioning

confidence: 99%

Characterization and Application of an Alginate Lyase, Aly1281 from Marine Bacterium Pseudoalteromonas carrageenovora ASY5

et al. 2020

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Alginate extracted from widely cultured brown seaweed can be hydrolyzed by alginate lyase to produce alginate oligosaccharides (AOS) with intriguing biological activities. Herein, a novel alginate lyase Aly1281 was cloned from marine bacterium Pseudoalteromonas carrageenovora ASY5 isolated from mangrove soil and found to belong to polysaccharide lyase family 7. Aly1281 exhibited maximum activity at pH 8.0 and 50 °C and have broad substrate specificity for polyguluronate and polymannuronate. Compared with other alginate lyases, Aly1281 exhibited high degradation specificity and mainly produced di-alginate oligosaccharides which displayed good antioxidant function to reduce ferric and scavenge radicals such as hydroxyl, ABTS+ and DPPH. Moreover, the catalytic activity and kinetic performance of Aly1281 were highly improved with the addition of salt, demonstrating a salt-activation property. A putative conformational structural feature of Aly1281 was found by MD simulation analysis for understanding the salt-activation effect.

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Section: Structural Insight Into the Salt-regulated Conformational Dymentioning

confidence: 99%

Characterization and Application of an Alginate Lyase, Aly1281 from Marine Bacterium Pseudoalteromonas carrageenovora ASY5

et al. 2020

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“…Additionally, a substantial effort has been made to expand time-resolved measurements to systems that do not have any photoactivity, making these experiments amenable to essentially any protein of interest. New perturbation methods that have been successfully utilized include temperature-jump 228 , rapid mixing 226 , 227 , ligand or substrate photocaging 229 , and rapid application of electric fields 230 . Finally, it is worth noting that the success of time-resolved crystallography has inspired the more recent development of time-resolved cryo-EM 231 .…”

Section: Developments In X-ray Crystallographymentioning

confidence: 99%

Advances in methods for atomic resolution macromolecular structure determination

2020

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Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.

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“…Recent detailed investigations of CypA dynamics have required both innovative biophysical techniques, and lengthy advanced sampling methodologies for simulations, and the use of polarizable force fields does not negate this necessity for adequate sampling. 74,[83][84][85] However, the accuracy of AMOEBA fields compared to DFT suggests that polarizable simulations provide a promising avenue to better explore the electrostatic contributions to mechanism across members of the cyclophilin family, in a computationally efficient way. AMOEBA showed significantly better agreement with DFT-calculated fields across the full range of systems, structures and field magnitudes tested, with non-overlapping 95 % confidence intervals in R 2 in the majority of cases, despite relatively small sample sizes.…”

Section: Implications For Cypa Mechanismmentioning

confidence: 99%

The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

Bradshaw

Dziedzic²,

Skylaris³

et al. 2020

Preprint

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<div><div><div><p>Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically-relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically-driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.</p></div></div></div>

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Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

Abstract: Figure S1. Typical X-ray energy spectrum of the pink beam (3% energy bandwidth) used for the reported SAXS/WAXS measurements.

Cited by 81 publications

References 83 publications

Characterization and Application of an Alginate Lyase, Aly1281 from Marine Bacterium Pseudoalteromonas carrageenovora ASY5

Characterization and Application of an Alginate Lyase, Aly1281 from Marine Bacterium Pseudoalteromonas carrageenovora ASY5

Advances in methods for atomic resolution macromolecular structure determination

The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

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