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Computational studies of colicin insertion into membranes: the closed state.

ABSTRACT: Colicins are water-soluble toxins that, upon interaction with membranes, undergo a conformational change, insert, and form pores in them. Pore formation activity is localized in a bundle of 10 ?-helices named the pore-forming domain (PFD). There is evidence that colicins attach to the membrane via a hydrophobic hairpin embedded in the core of the PFD. Two main models have been suggested for the membrane-bound state: penknife and umbrella, differing in regard to the orientation of the hydrophobic hairpin with respect to the membrane. The arrangement of the amphipathic helices has been described as either a compact three-dimensional structure or a two-dimensional array of loosely interacting helices on the membrane surface. Using molecular dynamics simulations with an implicit membrane model, we studied the structure and stability of the conformations proposed earlier for four colicins. We find that colicins are initially driven towards the membrane by electrostatic interactions between basic residues and the negatively charged membrane surface. They do not have a unique binding orientation, but in the predominant orientations the central hydrophobic hairpin is parallel to the membrane. In the inserted state, the estimated free energy tends to be lower for the compact arrangements of the amphipathic helix, but the more expanded ones are in better agreement with experimental distance distributions. The difference in energy between penknife and umbrella conformations is small enough for equilibrium to exist between them. Elongation of the hydrophobic hairpin helices and membrane thinning were found unable to produce stabilization of the transmembrane configuration of the hydrophobic hairpin.

SUBMITTER: Prieto L

PROVIDER: S-EPMC2995820 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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Computational studies of colicin insertion into membranes: the closed state.

Prieto Lidia L Lazaridis Themis T

Proteins 20101012 1

Colicins are water-soluble toxins that, upon interaction with membranes, undergo a conformational change, insert, and form pores in them. Pore formation activity is localized in a bundle of 10 α-helices named the pore-forming domain (PFD). There is evidence that colicins attach to the membrane via a hydrophobic hairpin embedded in the core of the PFD. Two main models have been suggested for the membrane-bound state: penknife and umbrella, differing in regard to the orientation of the hydrophobic ...[more]

PMID: 20941706

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Project description:The benzoylcyanoxime, NC-C(=N-OH)-C(O)-C6H5 (later H(BCO)), represents a new ampolydentate ligand that received attention in the light of useful biological properties of its coordination compounds. Colorless H(BCO), upon deprotonation, gains color that depends on the counter-cation and the system in general. Five derivatives of H(BCO), with colorless organic and inorganic mono-cations - Cs, Tl, Ag, N(CH3)4 and As(C6H5)4 - were synthesized and characterized by the X-ray analysis, vibrational and electronic spectroscopy. Compounds exhibited unexpected and significant differences in color, both in solid state and in solutions, that were challenging to explain, thereby warranting detailed investigation including high-level DFT/TDFT computations. It was found that the BCO- anion demonstrates negative solvatochromic in polar protic ROH (R = H, CH3, C2H5, C3H7, C4H9) solvents, and appears yellow in color, as tetraalkylammonium or alkali metal salts. In polar aprotic solvents, such as CH3CN, DMF, and DMSO, solutions of the BCO- anion are red. The color originates from n→π* transition in the anion. Solid state structures evidenced a considerable dependence on planarity of the BCO- anion on its color, as well as on the character of bonding in the C-N-O fragment: yellow color is associated with an oxime (bond length C-N is shorter than N-O), while red color is due to the nitroso character (bond length C-N is longer than the N-O). An addition of ethanol to red solutions of the BCO-containing salts leads to the color change to yellow, which is the result of the formation of an H-bond between the C-N-O fragment of cyanoxime and the solvent, also leading to the flattening of the structure. An explanation for this new color-changing effect was offered, based on experimental evidence and TD/DFT calculations. Glossary: H(BCO) is 1-cyano-1-oximino-acetophenone, or benzoylcyanoxime; BCO- is anion of the benzoylcyanoxime; AsPh4 + is tetraphenylarsonium cation; MMe4 + is tetramethyammonium cation; ROH - alcohols; DMF - dimethylformamide; DMSO - dimethylsulfoxide; AN - acetonitrile; DFT -Density Functional Theory; TDDFT - Time-Dependent Density Functional Theory.

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Computational studies of colicin insertion into membranes: the closed state.

Publications

Computational studies of colicin insertion into membranes: the closed state.

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