MechanoProDB: a web-based database for exploring the mechanical properties of proteins

Abstract

The mechanical stability of proteins is crucial for biological processes. To understand the mechanical functions of proteins, it is important to know the protein structure and mechanical properties. Protein mechanics is usually investigated through force spectroscopy experiments and simulations that probe the forces required to unfold the protein of interest. While there is a wealth of data in the literature on force spectroscopy experiments and steered molecular dynamics simulations of forced protein unfolding, this information is spread and difficult to access by non-experts. Here, we introduce MechanoProDB, a novel web-based database resource for collecting and mining data obtained from experimental and computational works. MechanoProDB provides a curated repository for a wide range of proteins, including muscle proteins, adhesion molecules and membrane proteins. The database incorporates relevant parameters that provide insights into the mechanical stability of proteins and their conformational stability such as the unfolding forces, energy landscape parameters and contour lengths of unfolding steps. Additionally, it provides intuitive annotations of the unfolding pathways of each protein, allowing users to explore the individual steps during mechanical unfolding. The user-friendly interface of MechanoProDB allows researchers to efficiently navigate, search and download data pertaining to specific protein folds or experimental conditions. Users can visualize protein structures using interactive tools integrated within the database, such as Mol*, and plot available data through integrated plotting tools. To ensure data quality and reliability, we have carefully manually verified and curated the data currently available on MechanoProDB. Furthermore, the database also features an interface that enables users to contribute new data and annotations, promoting community-driven comprehensiveness. The freely available MechanoProDB aims to streamline and accelerate research in the field of mechanobiology and biophysics by offering a unique platform for data sharing and analysis. MechanoProDB is freely available at https://mechanoprodb.ibdm.univ-amu.fr.

Figure 1.

Schematic representation of MechanoProDB. As a first step, data are extracted and annotated from literature sources. The structural and functional information is retrieved from the PDB using a Python script when the PDB accession code is available or introduced manually by the user.

Figure 2.

Screenshot of MechanoProDB’s main page. (a) Shows the ‘quick search’ button where an example of searching for proteins with single step unfolding and a contour length of 38 nm is shown. The unfolding pathway of interest here: is similar for three proteins and the available unfolding annotation of C2A is highlighted. The main table displays information including the PDB ID, unfolding forces, contour lengths, experimental conditions, domain amino acid coordinates and unfolding process annotations. (b) Shows the ‘cumulative search’ button where users can add more than one search criteria. (c) Shows the ‘column visibility’ button that enables users to show/hide the columns of interest. The ‘CSV’ and ‘Excel’ buttons allow users to download the data to their local machine in two different file formats.

Figure 3.

Screenshot showing a ‘cumulative search’ where three conditions are satisfied. The conditions are shown in the red box and their results are highlighted. The mechanical properties in addition to the unfolding annotation of the I27 module of titin are also displayed. The annotation has been obtained from the original references shown within the ‘pulling reference’ column. Links within these references redirect users to the available online version of the original manuscript.

Figure 4.

Two examples of the detail page that opens when clicking on the protein name. Displayed figures are extracted from the original reference for each protein. The dynamic force spectra are displayed, when available; otherwise, the force–extension plot is shown. For proteins with unfolding intermediates, the force–extension showing the forces and corresponding contour lengths is shown (A). For most of the proteins the DFS is displayed as shown in (B).

Figure 5.

Snapshot showing the sequence and structure for the first domain of synaptotagmin (C2A) using the Mol* plugin. This visualization enables users to examine sequence and three-dimensional structural conformation. In the example shown, Phenylalanine (F) is highlighted in both sequence and structure.

Figure 6.

Interactive plots in MechanoProDB. Illustration of the interactive plots within MechanoProDB: (A) Force versus velocity plot: each data point represents a protein entry, colored by functional classification. Double-clicking a functional class isolates it, while a single click hides it. (B) Pie chart displaying the percentage of protein fold categories according to SCOP classification. (C) Box plot depicting unfolding forces relative to protein fold, enabling cross-category comparisons. (D) Display of minimum and maximum forces categorized by functional class. Users can modify data representation by employing the pen tool, activated by hovering; see the red square on plot (A). (E) Box plot showing the distance to the transition state with respect to SCOP structural classification.