Closure to “
            <i>Pore Water Uptake by Agricultural Runoff</i>
            ” by A. D. Parr, C. Richardson, D. D. Lane, and D. Buchman (February 1987, Vol. 113, No. 1)

128

The peptide acetylYEAAAKEARAKEAAAKAamide exhibits the dichroic features characteristic of a monomeric helix/coil transition in aqueous solution. Nineteen variants of this peptide each containing a different residue at position 9 were prepared by solid-phase peptide synthesis and purified by reversed-phase chromatography. The thermal dependence of the far-ultraviolet dichroic spectrum of each of these peptides except that containing proline is characteristic for an alpha-helix/coil transition. The relative stability of the helical forms of these peptides does not correlate with the preference of the variable amino acid to occupy a middle position in a protein helix. It is likely that the specific interactions of the variable residue with its local environment obscure any inherent preference of the residue to reside in an alpha-helix.

Section: Resultsmentioning

confidence: 63%

Section: Resultsmentioning

confidence: 99%

Effect of central-residue replacements on the helical stability of a monomeric peptide

Merutka

Lipton²,

Shalongo³

et al. 1990

128

“…The scissors grip model (Vinson et al, 1989) postulates that the two basic regions of a bZip dimer form a-helices and track from the base of the leucine zipper in opposite directions along a DNA major groove. The model also postulates a sharp bend in the basic region helix at a conserved asparagine (e.g., N235 of GCN4) which serves in the model as an a-helical "N-cap" residue (Richardson & Richardson, 1988). This bend would allow more extensive contacts between the basic region and DNA.…”

Section: Resultsmentioning

confidence: 99%

Minimum length of a sequence-specific DNA binding peptide

Talanian¹,

McKnight²,

Rutkowski³

et al. 1992

NMR experiments show that a stable complex can be formed between a 14-base-pair oligonucleotide and a disulfide-bonded dimer of a peptide containing 27 residues of the basic region of the yeast transcriptional activator GCN4; the complex is in slow exchange on the NMR time scale. In contrast, a nonspecific complex is in fast exchange on the NMR time scale. DNase I footprinting experiments show that dimers of peptides containing as few as 20 residues of GCN4 bind DNA with sequence specificity similar to that of the intact protein. Circular dichroism experiments suggest that specific binding involves only 15 residues, corresponding to residues 231-245 of GCN4, in an alpha-helical conformation. These results limit substantially the region of GCN4 involved in sequence-specific DNA contacts and provide a uniquely simple model for studying protein-DNA interactions in detail.

“…We have no experimental evidence for differences in C-capping preferences, though statistical preferences in protein structures do show significant variation (Richardson & Richardson, 1988), but have included C-capping in the theory for completeness. We expect that variations in helix content due to C-capping will be observed in peptides in due course and that the theory described here will be appropriate for their analysis.…”

Section: Heteropolymersmentioning

confidence: 99%

Determination of Free Energies of N-Capping in .alpha.-Helixes by Modification of the Lifson-Roig Helix-Coil Theory To Include N- and C-Capping

Doig¹,

Chakrabartty²,

Klingler³

et al. 1994

179

258

We have previously shown that varying the N-terminal amino acid in alpha-helical peptides can cause large variations in helix content (Chakrabartty et al., 1993a). The Lifson-Roig theory for the helix-coil transition predicts, however, that substitutions at the N-terminus in an unacetylated peptide should have no effect on alpha-helix stability. We have therefore modified the theory to include these N-capping effects by assigning a statistical weight (the "n-value") to the amino acid immediately preceding a stretch of helical residues. The n-value measures the N-capping propensity of an amino acid, and like the helix propensity (w-value), it is independent of neighboring residues or positions in sequence. The new theory was used, with the experimental data for these substitutions, to calculate n-values and, hence, free energies for N-capping for the amino acids Gln, Ala, Val, Met, Pro, Ile, Leu, Thr, Gly, Ser, and Asn as well as for the acetyl group, which is commonly used to cap peptides. The free energies vary by approximately 1 kcal mol-1 from Gln (worst) to Asn (best), and the acetyl group is nearly as effective as Asn. N-Capping free energies were also found for Leu, Thr, Gly, Ser, and Asn when the N-terminus is charged at pH 5. The unfavorable effect of protonation of the N-terminus in an alpha-helix was found to be approximately 0.5 kcal mol-1. Our results agree well with a survey of N-capping preferences from protein crystal structures and are compared to results from site-directed mutagenesis of N-caps in proteins.