PXD041767-2

PXD041767 is an original dataset announced via ProteomeXchange.

Title	Computational design of Matrix Metalloprotenaise-9 (MMP-9) resistant to auto-cleavage
Description	Matrix metalloproteinase-9 (MMP-9) is an endopeptidase that remodels the extracellular matrix and has been implicated as a major driver in cancer metastasis. Hence, there is a high demand for MMP-9 inhibitors for therapeutic purposes. For such drug design efforts, large amounts of MMP-9 are required. Yet, the catalytic domain of MMP-9 (MMP-9Cat) is an intrinsically unstable enzyme that tends to auto-cleave within minutes, making it difficult to use in drug design experiments and other biophysical studies. We set our goal to design MMP-9Catvariant that is active but stable to autocleavage. For this purpose, we first identified potential autocleavage sites on MMP-9Cat using mass spectroscopy and then eliminated the autocleavage site by predicting mutations that minimize autocleavage potential without reducing enzyme stability. Four computationally designed MMP-9Cat variants were experimentally constructed and evaluated for auto-cleavage and enzyme activity. Our best variant, Des2, with 2 mutations, was as active as the wild-type enzyme but did not exhibit auto-cleavage after seven days of incubation at 37°C. This MMP-9Cat variant, with an identical to MMP-9Cat WT active site, is an ideal candidate for drug design experiments targeting MMP-9 and enzyme crystallization experiments. The developed strategy for MMP-9Cat stabilization could be applied to redesign of other proteases to improve their stability for various biotechnological applications.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:09:33.963.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Solomon Oguche
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-24 03:57:34	ID requested
1	2023-10-24 12:33:44	announced
⏵ 2	2023-11-14 09:09:34	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:09:53	announced	2024-10-22: Updated project metadata.

Bonadio A, Oguche S, Lavy T, Kleifeld O, Shifman J, Computational design of matrix metalloprotenaise-9 (MMP-9) resistant to auto-cleavage. Biochem J, 480(14):1097-1107(2023) [pubmed]

submitter keyword: MMP-9, auto-cleavage,protein engineering, auto-degradation, enzyme engineering, matrix metalloproteases

Julia M shifman
contact affiliation	The Alexander Silberman Institute of Life Sciencs, the Hebrew University of Jerusalem Israel.
contact email	jshifman@mail.huji.ac.il
lab head
Solomon Oguche
contact affiliation	The Hebrew University of Jerusalem
contact email	solomon.oguche@mail.huji.ac.il
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD041767
     1. Label: PRIDE project
     2. Name: Computational design of Matrix Metalloprotenaise-9 (MMP-9) resistant to auto-cleavage