FREQUENTLY ASKED QUESTIONS
What is PROXiMATE?
PROXiMATE is a searchable database of thermodynamic and kinetic data (including binding affinity, association rate, dissociation rate, binding free energy change, change in enthalpy and entropy) for mutant protein-protein complexes. It contains experimental data from previously published databases and recent literature. The current version contains more than 6000 mutations in more than 160 heterodimer complexes. PROXiMATE links thermodynamic data to functional classification and can calculate DSSP secondary structure assignments and relative accessibility. It also connects to STRING to provide users with a view of the protein interaction network in the vicinity of the protein-protein complex. Users can view the complex structure using the JSmol applet.
What are protein-protein interactions?
Nearly every cellular process (cell signalling, cell-cell adhesion, transport, metabolism, ubiquitination etc.) involves protein-protein interactions, i.e. interactions between two or more protein molecules, usually mediated by various biophysical forces (such as electrostatics, Van der Waals forces, hydrogen bonds, hydrophobic interactions etc.). The interaction is characterized by the formation of a protein-protein complex. For detailed reviews of protein-protein interactions, see the following references.
- Jones,S. and Thornton,J.M. (1996) Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA., 93(1), 13-20.
- Stites,W.E. (1997) Protein-Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis. Chem. Rev., 97(5), 1233-1250.
- Ali,M.H. and Imperiali,B. (2005) Protein oligomerization: How and why. Bioorgan. Med. Chem., 13(17), 5013-5020.
- Keskin,O. et. al. (2008) Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact? Chem. Rev., 108(4), 1225-1244.
- Janin,J. (2009) Basic Principles of Protein-Protein Interaction. In R. Nussinov and G. Schreiber (Eds.), Computational Protein-Protein Interactions., 1-19, Boca Raton: CRC Press.
What are hot spots?
Hot spots are defined as residues in the protein-protein complex which cause a change in binding free energy of more than 1.5 kcal/mol when mutated to alanine. These residues are thought to be important for binding and are usually found at the core of the binding interface.
What are the units and notations used in PROXiMATE for thermodynamic and kinetic parameters?
| Notation | Parameter | Related Formula | Unit |
|---|---|---|---|
| kon | Association rate | 1/Ms | |
| koff | Dissociation rate | 1/s | |
| KD | Dissociation rate constant | KD = koff/kon | M |
| ΔG | Change in binding free energy | ΔG = R T ln(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 |
| ΔH | Change in enthalpy | kcal/mol | |
| ΔS | Change in entropy | cal/mol K | |
| T | Temperature | K (Kelvin) |
What are the functional classes of complexes present in PROXiMATE?
| Class | Description |
|---|---|
| Ag-Ab | Antigen-antibody complexes |
| EI | Enzyme-inhibitor complexes |
| GC | G-protein containing complexes |
| HR | Hormone receptor complexes |
| OE | Other enzyme-containing complexes (i.e. protein interacting with the enzyme is not a known inhibitor) |
| RC | Receptor-containing complexes (i.e. protein interacting with the receptor is not designated as a hormone) |
Complexes not assigned a specific class are considered to belong to a miscellaneous class.
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How are mutations denoted in each entry?
The mutations are specified using the format "chain: wild-type residue - position - mutated residue". For example, a mutation on the 15th position in Chain I would be represented as "I:W15A", where Trp (W) is the wild-type residue in the 15th position, mutated to Ala (A). If the chain information is not available (in cases where the PDB ID is not available), the chain is represented by a * (as in *:W15A, which means the mutation is in the 15th position in some chain for which a letter has not been assigned).
I am not able to see the complex structure in the JSmol applet.
Please note that the Jsmol applet cannot provide a complex 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).
I am not able to find my complex of interest/Certain entries do not have an experimental technique/Some entries do not have any energetic data associated with them/I would like to include my data in the database.
PROXiMATE is under constant development. Despite our best efforts to ensure accuracy and completeness, certain data may not be correct or complete. If any data is incorrect, please let us know. If you have experimentally determined thermodynamic data for any mutant protein-protein complexes and do not find your data in the database, please contact us by filling our Upload form. Thank you for your inputs.
How do you assign the secondary structure? How is the relative accessibility calculated?
We used Bio.PDB's DSSP module (from Biopython) to calculate relative accessibility and secondary structure assignments for the wild-type residue at the mutation position. Accessible Surface Area (ASA) is calculated from the default MAX_ACC values for each residue provided by the same module, taken from Sander and Rost, 1994 [Proteins, 20:216-226].
I can't find a link to Uniprot for antibodies.
Due to the large amount of variation possible in the protein sequences of antibody molecules, antibodies may not be associated with a particular Uniprot ID. Thus, the Uniprot link is not provided for these molecules.
I would like to access the entire dataset.
Thank you for your interest in PROXiMATE database. Please contact us by filling the form in the Download page. You will recieve a response shortly.