MENSAdb

MENSAdb provides comprehensive structural and physicochemical analyses of membrane protein homo- and heterodimers to elucidate principles of dimerization relevant to structural biology and drug discovery.

Key Features:

• Dataset Content: Contains structural data for 167 unique membrane proteins, comprising 63% homo-dimers and 37% hetero-dimers.
• Conservation of Residues: Quantifies residue conservation across membrane proteins to assess structural and functional importance.
• Accessible Solvent Area Descriptors: Computes accessible solvent area (ASA) descriptors to quantify residue and surface exposure.
• Average B-factors: Reports average B-factors to indicate local atomic mobility and structural flexibility.
• Intermolecular Contacts: Maps intermolecular contacts using 2.5 Å and 4.0 Å distance cut-offs to delineate dimer interfaces.
• Hydrophobic Contacts: Identifies non-polar interactions that stabilize membrane protein structures.
• Hydrogen Bonds: Detects hydrogen bonds at dimer interfaces.
• Salt Bridges: Detects salt bridge interactions at dimer interfaces.
• π-π and T-stacking: Identifies π-π stacking and T-stacking aromatic interactions at interfaces.
• Cation-π Interactions: Identifies cation-π interactions contributing to interface stability.
• Evolutionary and Physicochemical Profiling: Provides combined evolutionary conservation and physicochemical descriptors to characterize dimer formation principles.

Scientific Applications:

• Structural Biology: Characterizes dimer interfaces and residue-level determinants of membrane protein assembly.
• Drug Discovery: Defines interface features and interaction types that can inform targeting of membrane protein dimers.
• Biophysics: Enables analysis of intermolecular forces and dynamic properties underlying membrane protein stability.
• Predictive Modeling: Supplies feature sets (conservation, ASA, B-factors, contact types) for development of predictive models of dimerization.

Methodology:

Analyses include residue conservation, accessible solvent area descriptors, average B-factors, and identification/mapping of intermolecular contacts—hydrophobic contacts, hydrogen bonds, salt bridges, π-π stacking, T-stacking, and cation-π interactions—using 2.5 Å and 4.0 Å distance cut-offs.