EncoMPASS
Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry
The coordinates of membrane protein complexes are retrieved from the Orientations of Proteins in Membranes (OPM) database. The orientation of the structures in the membrane is either obtained from OPM or calculated independently using the PPM algorithm on the Protein Databank (PDB) entry. Each entry is then divided into single-chain structures, which are then grouped for comparison based on their major secondary structure composition (alpha or beta) and their estimated number of transmembrane domains.
All structures to be compared undergo pairwise sequence and structure alignments, using the programs MUSCLE and Fr-TM-Align, respectively. These analyses identify important structural and sequence relationships between known membrane protein structures, without relying on fold classification or clustering.
Three structural symmetry recognition programs, CE-Symm, SymD and QuatSymm are used with several sets of parameters to determine the symmetries and symmetric regions of both the entire complex and each chain therein. The data from these two programs are further processed in order to present a comprehensive and coherent overview of the structural symmetries that are likely to be important for membrane protein function. Finally, the results from this analysis are combined with the information obtained from the structural and sequence alignments to infer the symmetry-related regions in a given protein based on the symmetries discovered in related protein structures. The relationships detected during this procedure allow for transfer of known symmetries to structures in which the symmetry may be difficult to detect.
For more details see:
Aleksandrova, A. A., Sarti, E., & Forrest, L. R. (2024). EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry. Structure. doi: 10.1016/j.str.2024.01.011.
All structures to be compared undergo pairwise sequence and structure alignments, using the programs MUSCLE and Fr-TM-Align, respectively. These analyses identify important structural and sequence relationships between known membrane protein structures, without relying on fold classification or clustering.
Three structural symmetry recognition programs, CE-Symm, SymD and QuatSymm are used with several sets of parameters to determine the symmetries and symmetric regions of both the entire complex and each chain therein. The data from these two programs are further processed in order to present a comprehensive and coherent overview of the structural symmetries that are likely to be important for membrane protein function. Finally, the results from this analysis are combined with the information obtained from the structural and sequence alignments to infer the symmetry-related regions in a given protein based on the symmetries discovered in related protein structures. The relationships detected during this procedure allow for transfer of known symmetries to structures in which the symmetry may be difficult to detect.
For more details see:
Aleksandrova, A. A., Sarti, E., & Forrest, L. R. (2024). EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry. Structure. doi: 10.1016/j.str.2024.01.011.