The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain

Pauling, Linus; Corey, Robert B.; Branson, H. R.

doi:10.1073/pnas.37.4.205

Cited by 2,614 publications

(1,337 citation statements)

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“…By invoking the one-helical-sequence approximation, conformations that contain multiple helical segments are excluded from the partition function. In addition, the authors stated that "the minimum helical length is four residues in helical angles plus two caps" (Mufioz & Serrano, 1994), although three residues in helical angles (Pauling et al, 1951), plus two caps, are sufficient to form a single turn of helix. The effect of this assumption is to exclude all helices that contain a single hydrogen bond; only helices with two or more hydrogen bonds are allowed.…”

Section: A-helix: I R R~n S I +~L R U N S ~R M N S~+ 4 G U U C H E mentioning

confidence: 99%

Addition of side chain interactions to modified Lifson‐Roig helix‐coil theory: Application to energetics of Phenylalanine‐Methionine interactions

1995

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We introduce here i, i + 3 and i, i + 4 side chain interactions into the modified Lifson-Roig helix-coil theory of Doig et al. (1994, Biochemistry 33:3396-3403). The helixkoil equilibrium is a function of initiation, propagation, capping, and side chain interaction parameters. If each of these parameters is known, the helix content of any isolated peptide can be predicted. The model considers every possible conformation of a peptide, is not limited to peptides with only a single helical segment, and has physically meaningful parameters. We apply the theory to measure the i, i + 4 interaction energies between Phe and Met side chains. Peptides with these residues spaced i, i + 4 are significantly more helical than controls where they are spaced i, i + 5 . Application of the model yields A G for the Phe-Met orientation to be -0.75 kcal.mol", whereas that for the Met-Phe orientation is -0.54 kcal.mol-'. These orientational preferences can be explained, in part, by rotamer preferences for the interacting side chains. We place Phe-Met i , i + 4 at the N-terminus, the C-terminus, and in the center of the host peptide. The model quantitatively predicts the observed helix contents using a single parameter for the side chain-side chain interaction energy. This result indicates that the model works well even when the interaction is at different locations in the helix.

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Section: A-helix: I R R~n S I +~L R U N S ~R M N S~+ 4 G U U C H E mentioning

confidence: 99%

Addition of side chain interactions to modified Lifson‐Roig helix‐coil theory: Application to energetics of Phenylalanine‐Methionine interactions

1995

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“…11,12 This provides the basis of a universal mechanism for osmolyte-mediated protein stabilization by protecting osmolytes and destabilization by urea as the protein backbone is shared by all proteins, regardless of side chain sequence. [13][14][15] The evaluation of group transfer free energy values defined the now classic Tanford model for ureainduced protein denaturation. 16,17 In that model, the thermodynamic interaction of the side chains with the urea solution gave rise to the long held concept of favorable urea interaction with hydrophobic groups as a driving force in urea's denaturation effect.…”

Section: Introductionmentioning

confidence: 99%

Backbone additivity in the transfer model of protein solvation

et al. 2010

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The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (DG tr ) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and DG tr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of 254 cal/mol/M compares quite favorably with 243 cal/mol/M determined experimentally.

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“…Matched pairs of these keratins form heterodimers that constitute the basic building blocks of cytoskeletal intermediate filaments and epidermal derivatives of hair, nail and horn. Keratins have an important place in the history of the elucidation of protein structure as in 1951, Pauling et al suggested the first model for a-helix structure for wool a-keratins, in the absence of knowledge of the sequence of keratins [1]. The first sequence of a cytoskeletal keratin was determined in 1982 [2].…”

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confidence: 99%