Deprotonation Of Acid Residues Research Articles

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.

PH-dependent conformations of the amyloid beta(1-28) peptide fragment explored using molecular dynamics.

Molecular dynamics simulations were used to successfully reproduce the experimentally observed pH-dependent conformational behavior of a monomeric peptide in aqueous solution. Simulations were conducted at 298 K on a peptide corresponding to residues 1-28 of the amyloid beta-peptide [referred to as beta(1-28)], which is the primary component of the plaques associated with Alzheimer's disease. beta(1-28) was found to be entirely alpha-helical at low pH. Upon deprotonation of acidic residues at medium pH, helical structure was lost in the N-terminal region. At high pH, some secondary structure was recovered to yield two helices joined by a kink. These results are in good agreement with the NMR solution structure at low pH [Zagorski and Barrow (1992) Biochemistry 31, 5621-5631; Talafous et al. (1994) Biochemistry 33, 7788-7796] and CD and NMR evidence of an alpha-helix to beta-sheet transition at mid-range pH [Barrow et al. (1992) J. Mol. Biol. 225, 1075-1093]. Additional simulations were also able to regenerate folded species from partially unfolded conformers. A mechanism for the pH-dependent structural rearrangements is proposed that involves the creation of a hydrogen-bonded pair between Ser 8 and Glu 11. The evidence for the existence of a multiconformational equilibrium of folded and unfolded species of the peptide is discussed.

Dynamic properties of membrane proteins: reversible insertion into membrane vesicles of a colicin E1 channel-forming peptide.

The binding of colicin E1 and its COOH-terminal channel-forming peptides to artificial membrane vesicles has an optimum at acidic pH values. The Mr 18,000 thermolytic peptide inserted into membrane vesicles at pH 4.0 has a limited accessibility to exogenous protease. It is converted by trypsin cleavage after Lys-381 and Lys-382 to a lower Mr 14,000 peptide. However, when the pH of a vesicle suspension to which peptide has been bound at pH 4.0 is shifted to 6.0, the accessibility to protease increased greatly. This was shown (i) by the large decrease in the amount of Mr 14,000 or Mr 18,000 peptide after the pH 4----6 shift and treatment with trypsin or Pronase, consistent with (ii) a previously observed decrease in membrane-bound radiolabeled peptide after protease treatment. (iii) When a photoactivable nitrene-generating phospholipid probe was used to label the colicin peptide inserted into the bilayer, the extent of labeling decreased by a factor of 3 when the pH was shifted from 4.0 to 6.5. (iv) Colicin peptide added to vesicles at pH 4.0 can "hop" to other vesicles if the pH and ionic strength of donor vesicles are successively increased. It is proposed that deprotonation of acidic residues in contact with the hydrophobic bilayer or the membrane surface destabilizes the inserted channel and causes it to be extruded from the membrane. The pH-dependent extrusion of the inserted colicin channel provides an example of dynamic properties of an intrinsic membrane protein.