TMalphaDB contains 430 structures of α-helix bundles. For a full list of proteins click
here.
To avoid redundancy, only one structure for each protein is selected according to resolution and resemblance to the native state. Each structure is characterized by the PDB identification code, protein name, Uniprot accession code, family name (according to OPM1) and organism.
Because the hydrophobic nature of the lipid bilayer conditions the structure and features of the membrane-embedded regions relative to the water-exposed ones2, the domain of the protein inserted in the lipid bilayer has been calculated using TMDET3. The relevance of TMalphaDB is its capability to search and analyze sequence motifs in these transmembrane (TM) segments of the protein. The search is performed using exclusively the single-letter amino acid code or/and in combination with
wildcard characters. Moreover, the search (advanced options) can be filtered by the proximity of the sequence motif to the beginning/end of the TM domain (as the structural parameters can be highly influenced by the loops) or the presence of certain amino acids within the sequence motif (as, for instance, Pro or/and Gly can distort the secondary structure conformation).
The output consists in a list of proteins, identified by PDB id and the sequence of the TM segment with the requested motif highlighted. The coordinates of the entire protein or/and the TM segments can be downloaded for each entry. Moreover, backbone φ and Ψ angles and side chain χ1 angle for the identified/selected TM segments can be downloaded. Bend and twist angles are two relevant parameters to measure distortions of TM helices, thus, these values are calculated for the identified/selected TM segments using HELANAL4. Finally, JSMol5 sessions containing the coordinates of the requested motif, and all residues and ligands in its environment can also be displayed.
TMbetaDB server is also available for beta-barrel TM proteins.
TMalphaDB is written by
Ivar Lugtenburg and Marc Perea. The project is leaded by
Mireia Olivella and currently maintained by
Eduardo Mayol
Download TMalphaDB
Interactions
Inter-residue interactions of this dataset have been analyzed in "Inter-residue interactions in alpha-helical transmembrane proteins" Mayol, E. et al (Bioinformatics 2018)
You can access the information from this link.
References
1Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625
2 Blondelle SE, Forood B, Houghten RA, Pérez-Payá. Secondary structure induction in aqueous vs membrane-like environments. Biopolymers, 1997. 42(4): 489-98.
3 Tusnády GE, Dosztányi Z, Simon I. TMDET: web server for detecting transmembrane regions of proteins by using 3D coordinates. Bioinformatics. 2005, 21(7):1276-7.
4 Bansal M, Kumar S, Velavan R (2000) HELANAL: a program to characterize helix geometry in proteins.J Biomol Struct Dyn. 2000 Apr;17(5):811-9.
5 Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T., & Sussman, J. L. (2013). JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry.
Last update: February 2017.
Last modified: October 2018.
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