MPAD: Membrane Protein complex binding Affinity Database

FREQUENTLY ASKED QUESTIONS

  1. What is MPAD?
    2. MPAD is a searchable database of experimental binding affinity data for wild-type and mutant membrane protein-protein complexes compiled through extensive literature mining and intergration of data from previously published databases. MPAD integrates thermodynamic data to protein sequence and structural databases. We have also incorporated key membrane protein-specific features, experimental conditions, and literature information for each record.
  2. How does MPAD differ from other existing databases?
    3. Membrane proteins (MPs) are an essential class of proteins that play key role in cell signaling, molecular and ion transport across membranes, enzymatic activity, and several other functions. Most membrane proteins are thought to function in complexes. Mutations can alter the structure, function, and affinity of the protein-protein complexes, resulting in diseases. There are various databases developed specifically for membrane proteins in the literature, such as PDBTM, TOPDB, MpTherm, MutHTP, and others. However, no specific database exists on the binding affinity of membrane protein-protein complexes and their mutants, paving the way for the development of MPAD.
  3. What membrane protein-specific features are available in this database?
    4. The novelty of MPAD is that we have included numerous membrane protein-specific features such as topology (mutation site location), number of transmembrane segments in each protein, which were acquired from the PDBTM, TOPDB, HTP database and CCTOP server. The type of membrane protein, which is based on structural adaptation in the cell membrane obtained from UniProt and the literature. The functional classification (transporter, enzyme or receptor) for each protein is also provided.
  4. What are the units and notations used in MPAD for thermodynamic and kinetic parameters?
    5. Notation Parameter Related Formula Unit
    kon Association rate M -1 s-1
    koff Dissociation rate s-1
    KD Dissociation rate constant KD = koff/kon M
    ΔG Change in binding free energy ΔG = RTln(KD)
    where R = 0.0019 kcal/mol K     		kcal/mol
    ΔΔG Difference in binding free energy change between mutant and wild-type complex ΔΔG = ΔGmut - ΔGwt kcal/mol
    T Temperature K (Kelvin)
  5. How are mutations denoted in each entry?
    6. The mutations are specified using the format "chain id: wild-type residue - position - mutated residue". For example, a mutation on the 18th position in Chain B would be represented as "B:W18A", where Trp (W) is the wild-type residue in the 18th position, mutated to Ala (A). If the chain information is not available (in cases where the PDB ID is not available), then it is represented as "UniProt id: wild-type residue - position - mutated residue" (if the UniProt ID of the protein is available) else it is denoted by a * (e.g. *:W18A). Double and multiple mutants are denoted in the same with the separator in between (e.g. K168A, E174A). Deleted regions are mentioned by the region name or residues mentioned with position number (e.g. del (FGEST), del (E172)).
  6. Is it required to enter at least one keyword while searching the database?
    7. It is not necessary to enter any keyword. But, at least one of the search options under BUILD SEARCH QUERY menu must be selected. You can also specify which columns to display in the search results page. Some columns are selected by default. The number of results to be displayed per page can also be selected by user.
  7. I am unable to locate my complex of interest/ some entries lack kinetic data/ I would like to include my data in the database
    8. MPAD is under constant development. Despite our best efforts to ensure the accuracy and completeness, certain data may not be correct or complete. Please notify us if any of the data is wrong. If you have experimentally determined binding affinity data which is not available in our database, and wish to share the data with us, please contact us via our Upload Data form. We will verify the data and after confirmation from you, the data will be included in the database.
  8. How will I get the entire dataset of MPAD?
    9. Please contact us by filling the form in the Download Data page. You will receive a response shortly.