A caged substrate peptide for matrix metalloproteinases

Decaneto, Elena; Abbruzzetti, Stefania; Heise, Inge; Lubitz, Wolfgang; Viappiani, Cristiano; Knipp, Markus

doi:10.1039/c4pp00297k

Cited by 8 publications

(6 citation statements)

References 44 publications

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“…While this method avoids the need for genetic manipulation, it has been limited to in vitro and cell lysate applications thus far. Other applications of peptides containing light‐cleavable groups include optical control of cell signaling, protease activity, and cell motility . Simultaneous applications of two different caging groups (see Section 5.1) has enabled multiwavelength control of protein or peptide function…”

Section: Optical Control Of Proteins and Peptidesmentioning

confidence: 99%

Optochemical Control of Biological Processes in Cells and Animals

et al. 2018

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Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.

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Section: Optical Control Of Proteins and Peptidesmentioning

confidence: 99%

Optochemical Control of Biological Processes in Cells and Animals

et al. 2018

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“…The modified enzyme is fully active as demonstrated with a standard assay developed for MMPs based on a FRET mechanism. 24,25 In this assay, the consumption of a fluorogenic collagen-like peptide leads to an increase of fluorescence at 400 nm allowing the reaction kinetics to be monitored. Interestingly the cobalt enzyme has a lower substrate turnover frequency of approximately 20% and a 2 fold increase of the Michaelis Menten constant K M , (36 AE 15 vs. 85 AE 8 mM, Fig.…”

Section: Pccp Papermentioning

confidence: 99%

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

Decaneto

Vasilevskaya

Kutin

et al. 2017

Phys. Chem. Chem. Phys.

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Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.

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“…While this method avoids the need for genetic manipulation, it has been limited only to in vitro and cell lysate applications thus far. Other applications of peptides containing light-cleavable groups include the optical control of cell signaling, [87] protease activity, [88] and cell motility. [89] Simultaneous applications of two different caging groups (see section 5.1) has allowed for multi-wavelength control of protein or peptide function.…”

Section: Optical Activation Of Protein Functionmentioning

confidence: 99%

Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren

et al. 2018

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This article is protected by copyright. All rights reserved optochemical control of biology. In contrast to excellent previous reviews that focus on the chemistry of controlling biological function with light, [1] this review focuses on manipulation of cell and animal biology using photochemical approaches. Purely optogenetic approaches, not utilizing chemical operations, have been reviewed elsewhere. [2] 2. Optical control of small molecules Small molecule probes have been essential tools to perturb and control cellular processes, thereby providing an understanding of detailed biological function. Optical control of small molecule function provides an extra layer of precision to the molecular toolbox by enabling temporal and spatial control with high resolution, as discussed in the examples below. Small molecule protein dimerizers, inhibitors, metabolites, and metal ions have all been rendered lightresponsive through the chemical installation of caging groups and have been applied to the investigation of living systems. In contrast to photocaged nucleic acids, peptides, and proteins, small molecules have the added benefits of being synthetically more accessible and capable of being readily delivered into cells and animals. 2.1. Optical activation of rapamycin induced dimerization Chemical inducers of dimerization (CIDs) are prominent tools for chemical biologists to place biological processes under conditional control. [3] The most commonly utilized CID is rapamycin, which binds to FK506 binding protein (FKBP) and the FKBP-rapamycin binding domain of mTOR (FRB), forming a ternary complex. Due to the small size of FKBP and FRB, these domains have been fused to numerous proteins and subsequent heterodimerization was induced by rapamycin. Processes that have been placed under rapamycin control include Golgi/endoplasmic reticulum association to study mitosis, [4] phosphoinositide control of endocytic trafficking, [5] and inactivation of proteins by rerouting them to the mitochondria. [6] Caged rapamycin analogs allow for placement of these processes under optical control in order to enhance temporal and spatial resolution. The photocaged rapamycin analog 1 was generated through installation of a nitrobenzyl caging group at the C-40 position (Figure 1a). [7] When applied to cells, 1 still induced FKBP-FRB dimerization, indicating that the caging group alone wasn't sufficient to abrogate protein-small molecule interaction, which is consistent with previous modifications at C-40. [8] However, work by the Hahn lab had shown that a truncated FKBP, termed iFKBP, [9] exhibited increased flexibility in the loop that interacts with the C-40 position of rapamycin. This flexibility increased contacts for interaction with 1 and resulted in a distorted binding conformation that prevented formation of the ternary complex consisting of iFKBP, FRB, and 1. This system was then applied to the optical activation of FAK (focal adhesion kinase), using an engineered iFKBP-FAK fusion which rendered the kinase inactive until UV irradiation...

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A caged substrate peptide for matrix metalloproteinases

Cited by 8 publications

References 44 publications

Optochemical Control of Biological Processes in Cells and Animals

Optochemical Control of Biological Processes in Cells and Animals

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren

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