Modulation of the helical stability of a model peptide by ionic residues

Park, Soon Ho; Shalongo, William; Stellwagen, Earle

doi:10.1021/bi00210a044

Cited by 29 publications

(32 citation statements)

References 22 publications

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“…In the host peptide of Park et al (1993aPark et al ( , 1993b, helix fraying will tend to destabilize the A. Chakrabartty et ai. Table 2, s(AK), with those measured in (A) the multiple salt-bridge system of Gans et al (1991), s(E4K4), and (B) the triple salt-bridge system of Park et al (1993aPark et al ( , 1993b…”

Section: Comparison Of Results With Other Systemsmentioning

confidence: 99%

“…Therefore, neglect of ( i , i & 3) salt bridges and the helix-macrodipole interaction may have introduced a systematic error in the analysis that accounts for the 0.6-unit offset. Park et al (1993aPark et al ( , 1993b) measured helix propensities in a host peptide containing 3 possible Glu-Lys salt bridges (generic sequence: acetyl-YEAAAKEA?CAKEAAAK-amide, where X is a guest residue), using the standard Lifson-Roig theory. There is a moderate correlation between their and our results (Fig.…”

Section: Comparison Of Results With Other Systemsmentioning

confidence: 99%

“…( , 1993b, any side-chain interaction will be subsumed in the helix propensity measurement. Park et al (1993b) suggested that, by making linear extrapolations from measurements in high salt solutions, they removed all ionic effects. Scholtz et al .…”

Section: S(eak)mentioning

confidence: 99%

“…(1993) showed, however, that Glu--Lys+ salt-bridge interactions (i.e., H-bonded ion pairs) in helices are screened only partially by high salt. Because all the peptides examined by Park et al (1993aPark et al ( , 1993b contain salt bridges, it is likely that omission of salt-bridge interactions affected their measurements of helix propensities, the ionizing amino acids being affected the most.…”

Section: S(eak)mentioning

confidence: 99%

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Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions

1994

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Helix propensities of the amino acids have been measured in alanine-based peptides in the absence of helix-stabilizing side-chain interactions. Fifty-eight peptides have been studied. A modified form of the Lifson-Roig theory for the helix-coil transition, which includes helix capping (Doig AJ, Chakrabartty A, Klingler TM, Baldwin RL, 1994, Biochemistry 33:3396-3403), was used to analyze the results. Substitutions were made at various positions of homologous helical peptides. Helix-capping interactions were found to contribute to helix stability, even when the substitution site was not at the end of the peptide. Analysis of our data with the original Lifson-Roig theory, which neglects capping effects, does not produce as good a fit to the experimental data as does analysis with the modified Lifson-Roig theory. At 0 "C, Ala is a strong helix former, Leu and Arg are helix-indifferent, and all other amino acids are helix breakers of varying severity. Because Ala has a small side chain that cannot interact significantly with other side chains, helix formation by Ala is stabilized predominantly by the backbone ("peptide H-bonds"). The implication for protein folding is that formation of peptide H-bonds can largely offset the unfavorable entropy change caused by fixing the peptide backbone. The helix propensities of most amino acids oppose folding; consequently, the majority of isolated helices derived from proteins are unstable, unless specific side-chain interactions stabilize them.

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Section: Comparison Of Results With Other Systemsmentioning

confidence: 99%

Section: Comparison Of Results With Other Systemsmentioning

confidence: 99%

Section: S(eak)mentioning

confidence: 99%

Section: S(eak)mentioning

confidence: 99%

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Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions

1994

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“…The AEK peptide system [43,44] is an alaninebased peptide but it contains 3 pairs of Glu, Lys residues spaced i, i + 4, to make helix-stabilizing ion pair interactions. The s-values obtained with the AEK system include values for the ionizing amino acids, whereas the values obtained with the E,K, system do not.…”

Section: Helix Propensities Of the 20 Amino Acidsmentioning

confidence: 99%

α-Helix formation by peptides of defined sequence

Baldwin¹

1995

Biophysical Chemistry

109

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The factors controlling a-helix formation in water by peptides of defined sequence are beginning to be understood. The field is close to the point where the extent of helix formation can be predicted for peptides of any sequence. Our own approach to the problem, and the main results obtained by following this approach, are summarized below. The chief reason for studying a-helix formation by peptides is to understand precisely and in detail one part of the protein folding problem. Questions about peptide helix formation can be answered at a fundamental level, in terms of the physico-chemical mechanisms involved.

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The relative order of helical propensity of amino acids changes with solvent environment

Krittanai

Johnson

2000

Proteins

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A model peptide of sequence Ac-Y-VAXAK-VAXAK-VAXAK-NH(2), where X is substituted with one of nineteen amino acids (P excluded), was synthesized and titrated with methanol to study helical propensity as a function of solvent environment. The CD spectra of these peptides are largely random coil in 2 mM sodium phosphate buffer (pH 5.5) and show a conformational change to alpha-helix with increasing methanol content. Singular value decomposition was used to correct the CD spectra for the absorbing side chains of W, Y, F, C, and M, and this correction can be substantial. With correction both W and F become good helix formers. The free energy for helix propagation was calculated using the Lifson-Roig statistical model for each of the nineteen amino acids at each point in their titration. The results show that the rank order of helical propensity for the nineteen amino acids changes with solvent environment. This result will be particularly important if proteins undergo hydrophobic collapse before secondary structures are formed, because amino acids can then see different solvent environments as the secondary structures are formed. Related amino acids are found to have interesting correlations in the shape of their titration curves. This finding provides one explanation for the limiting 70% accuracy in predicting secondary structure from sequence, since the helical propensities used are calculated for an average solvent environment. Proteins 2000;39:132-141.

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Modulation of the helical stability of a model peptide by ionic residues

Cited by 29 publications

References 22 publications

Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions

Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions

α-Helix formation by peptides of defined sequence

The relative order of helical propensity of amino acids changes with solvent environment

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