Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase

Jin, Hye Jin; Jang, Dogeun; Jeong, Jin Ho; Hong, Bok Sil; Yun, Yeoung‐Sang; Shin, Eun Ju; Choi, Kwan Yong

doi:10.1016/j.bbapap.2016.06.016

Cited by 4 publications

(2 citation statements)

References 42 publications

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“…However, enzyme activity is still a useful proxy to probe for accurate positioning when comparing aspartate to glutamate. Moreover, no known homologs of KSI contain a glutamate at the catalytic position (34). Thus, any designed solutions would be novel, and a fragment-based design protocol would not be able to rely on naturally occurring homologs that have already solved this particular problem.…”

Section: Resultsmentioning

confidence: 99%

Accurate positioning of functional residues with robotics-inspired computational protein design

Krivacic

Kundert

Pan

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Significance Computational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level geometries, which remains a major challenge. Here, we develop computational methods that design and predict local protein geometries with greater accuracy than existing methods. Then, as a proof of concept, we leverage these methods to design new protein conformations in the enzyme ketosteroid isomerase that change the protein’s preference for a key functional residue. Our computational methods are openly accessible and can be applied to the design of other intricate geometries customized for new user-defined protein functions.

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Section: Resultsmentioning

confidence: 99%

Accurate positioning of functional residues with robotics-inspired computational protein design

Krivacic

Kundert

Pan

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…3b). No known homologs of KSI contain a glutamate at the catalytic position 29 . Thus, any designed solutions would be novel and a fragment-based design protocol would not be able to rely on naturally occurring homologs that have already solved this particular problem.…”

Section: Application Of the Pip Protocolmentioning

confidence: 99%

Accurately positioning functional residues with robotics-inspired computational protein design

Krivacic

Kundert

Pan

et al. 2021

Preprint

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Accurate positioning of functional residues is critical for the design of new protein functions, but has remained difficult because of the prevalence of irregular local geometries in active sites. Here we introduce two computational methods that build local protein geometries from sequence with atomic accuracy: fragment kinematic closure (FKIC) and loophash kinematic closure (LHKIC). FKIC and LHKIC integrate two approaches: robotics-inspired kinematics of protein backbones and insertion of peptide fragments, and show up to 140-fold improvements in native-like predictions over either approach alone. We then integrate these methods into a new design protocol, pull-into-place (PIP), to position functionally important sidechains via design of new structured loop conformations. We validate PIP by remodeling a sizeable active site region in an enzyme and confirming the engineered new conformations of two designs with crystal structures. The described methods can be applied broadly to the design of many new protein geometries and functions.

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Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ5–3-ketosteroid isomerase

Peng

Cheng

Wang

et al. 2019

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase

Cited by 4 publications

References 42 publications

Accurate positioning of functional residues with robotics-inspired computational protein design

Accurate positioning of functional residues with robotics-inspired computational protein design

Accurately positioning functional residues with robotics-inspired computational protein design

Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ5–3-ketosteroid isomerase

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