Database for Membrane Protein Thermodynamics for understanding folding and stability

Frequently Asked Questions

✪ What is MPTherm database?

MPTherm is a thermodynamic or stability database, which is specifically designed for membrane proteins and their mutants. It contains several thermodynamic parameters such as melting temperature, free energy change, change in enthalpy, midpoint, etc., and these data were collected from previously published research papers and ProTherm database. The current version contains more than 7000 data of both wild-type and mutation data in more than 320 membrane proteins. MPTherm links thermodynamic data to protein sequence and structural databases, and we have provided the topology information, type of the membrane protein structure, experimental conditions and literature information of each record. In addition, users can view the protein structure (if available) using the JSmol applet.

✪ Why do we need a specific database for membrane proteins?

The membrane proteins are existing in both hydrophilic and hydrophobic environment whereas, the globular proteins are hydrophilic. These proteins are having diverse functions such as cell signaling, transport the ions and molecules across the membrane and many others. In the literature, there are several databases such as PDBTM, TOPDB, MutHTP, etc. are developed for exclusively membrane proteins. However, there is no specific thermodynamic database for membrane proteins, which paves way to develop the MPTherm database. The database is used to understand the structural and functional mechanism and to design stable mutants of membrane proteins.

✪ How to identify the stabilizing and destabilizing mutations in MPTherm ?

To investigate the effect of mutation on protein stability, the thermodynamic parameters such as change in free energy (ΔΔG) or melting temperature (ΔTm) are computed. For example ΔΔG computed by the following equation.
ΔΔG= ΔGMutant - ΔGWild-type
If the ΔΔG value is negative (-) or positive (+) value, it represent that the mutant is considered as destabilizing or stabilizing mutation respectively.

✪ What are the units and notations used in MPTherm for thermodynamic parameters?

Notation Parameter Related Formula/ Explanation Unit
TmMelting temperature Midpoint temperature of the thermal unfolding for thermal denaturation methods℃
ΔTmChange in melting temperature due to mutation Tm Mutant - Tm Wild-type℃
ΔGChange in Free energy Free energy of unfolding at a certain concentration of a denaturantkcal/mol
ΔΔGDifference in free energy change between mutant and wild-type protein ΔGMutant - ΔGWild-typekcal/mol
ΔGH2OChange in Free energy Free energy of unfolding in the absence of a denaturantkcal/mol
ΔΔGH2ODifference in free energy change between mutant and wild-type protein ΔGH2O Mutant - ΔGH2O Wild-typekcal/mol
ΔHEnthalpy change of denaturation -kcal/mol
CmConcentration of denaturant at which 50% of the protein is unfolded -Molar (M)
ΔCpHeat capacity change of denaturation -kcal/mol
mSlope of dG on denaturant concentration -kcal/mol/M
TTemperature -℃


✪ What are the membrane protein-specific features available in this database?

We have included several membrane protein features such as topology (mutation site location) and number of transmembrane segments in the protein, which were retrieved from the PDBTM database, CCTOP ,TOPCONS and PRED-TMBB2 server. The type of membrane protein, which is based on structural adaptation in the cell membrane was collected from UniProt and literature.

✪ Which is browser compatibility of MPTherm ?

The database is implemented in HTML, PHP, MySQL, JavaScript and supports recent versions of major browsers such as IE10, Firefox, Chrome and Opera.

✪ Why am I not able to visualize the protein structure in the JSmol applet?

Please note that the Jsmol applet cannot provide a protein structure view if the PDB ID is not known. If you are aware of an experimentally-determined crystal structure for the complex, please write to us and we will assign the PDB structure to the entry(s).

✪ Why some of the data have incomplete experimental data information? Is there any option to include my data in the database?

MPTherm is under constant development. Despite our best efforts to ensure accuracy and completeness, certain data may be incomplete. If any data is incorrect, please let us know. Yes, if you have experimentally determined thermodynamic data for any membrane proteins and do not find your data in the database, please contact us by filling our Upload form. Thank you for your inputs.

✪ How will I get the entire dataset of MPTherm ?

Thank you for your interest in MPTherm database. Please contact us by filling the form in the Download page. You will receive a response shortly through the e-mail.