PDB ID or protein name

1amt » Alamethicin

1amt » Alamethicin
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Topology in Secreted
Topologyout side
in side
1amt » Alamethicin
Hydrophobic Thickness or Depth 10.9 ± 2.9 Å
Tilt Angle 74 ± 13°
ΔGtransfer -17.1 kcal/mol
Links to 1amt PDB Sum, PDB, SCOP, MSD, OCA, MMDB
Topology subunit A (N-terminus out)
Resolution 1.5 Å
Other PDB entries representing this structure none
Number of subunits 1
Experimental Verification for 1amt » Alamethicin
This is the calculated membrane binding mode of monomeric alamethicin. At a higher concentration, the peptide forms oligomers that insert to the membrane in a different orientation, depending on the transmembrane potential (Barranger-Mathys and Cafiso 1996, Bechinger et al. 2001, Bak et al. 2001). Transfer energy of the peptide (~ -18.5 kcal/mol per monomer) is overestimated compared to the experimental value (~ -6 kcal/mol per monomer, Lewis and Cafiso 1999), because a significant part of the transfer energy must be spent to fold an alpha-helix from the coil that exists in aqueous solution, prior to insertion of the helix into the membrane.
4 references
Bak M, Bywater RP, Hohwy M, Thomsen JK, Adelhorst K, Jakobsen HJ, Sorensen OW, Nielsen NC. 2001. Conformation of alamethicin in oriented phospholipid bilayers determined by (15)N solid-state nuclear magnetic resonance. Biophys J. 81: 1684-1698. PubMed
Barranger-Mathys M and Cafiso DS. 1996. Membrane structure of voltage-gated channel forming peptides by site-directed spin-labeling. Biochemistry. 35: 498-505. PubMed
Bechinger B, Skladnev DA, Ogrel A, Li X, Rogozhkina EV, Ovchinnikova TV, ONeil JD, Raap J. 2001. 15N and 31P solid-state NMR investigations on the orientation of zervamicin II and alamethicin in phosphatidylcholine membranes. Biochemistry. 40:9428-37. PubMed
Lewis JR and Cafiso DS . 1999. Correlation between the free energy of a channel-forming voltage-gated peptide and the spontaneous curvature of bilayer lipids. Biochemistry 38: 5932-5938. PubMed
Comments on 1amt » Alamethicin
The peptide is inserted "monotopically" (it does not cross the bilayer). There are small energetic differences between the surface and transmembrane arrangements of the peptide, especially in the monomeric form. An H-bond between Gln residues in the dimer stabilizes the transmembrane orientation (the crystal structure is a trimer, but third molecule is shifted, which makes incorporation of the entire trimer in the membrane energetically less favorable).