Alpha-helix and mixed 3(10)/alpha-helix in cocrystallized conformers of Boc-Aib-Val-Aib-Aib-Val-Val-Val-Aib-Val-Aib-OMe.

Karle, Isabella L.; Flippen‐Anderson, Judith L.; Uma, K.; Balaram, Hemalatha; Balaram, Padmanabhan

doi:10.1073/pnas.86.3.765

Cited by 70 publications

(37 citation statements)

References 7 publications

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“…At the a/310 junction, however, bi- hydrogen bonds may not always form. This situation has been observed in at least one crystal structure (Karle et al, 1989) and is likely to depend on amino acid identity. The junction parameters must also include any energetic penalties resulting from bifurcating the hydrogen bonding pattern of the helix, or any geometric strain that is introduced.…”

Section: Meaning Of the Junction Parameters T And Tcmentioning

confidence: 97%

Models for the 3₁₀‐helix/coil, π‐helix/coil, and α‐helix/3₁₀‐helix/coil transitions in isolated peptides

Rohl

Doig

1996

Protein Science

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Models for the 310-helix/coil and a-helix/coil equilibria have been derived. The theory is based on classifying residues into helical or nonhelical (coil) conformations. Statistical weights are assigned to residues in a helical conformation with an associated helical hydrogen bond, a helical conformation with no hydrogen bond, an N-cap position, a C-cap position, or the reference coil conformation. The models for a-helix formation and 3,,-helix formation have also been combined to describe a three-state equilibrium in which a-helical, 3,,-helical, and coil conformations are populated. The results are compared with the modified Lifson-Roig theory for the a-helix/coil equilibrium. The comparison accounts for the experimental observations that 310-helices tend to be short and a-helices are not favored for any length. This work may provide a framework for quantitatively rationalizing experimental work on isolated 310-helices and mixed 310-/a-helices.Keywords: a-helix; helix-coil transition theory; N-cap; a-helix; 3,,-helix Polypeptide helices are stabilized by periodic hydrogen bonds between backbone CO and NH groups. They can be described by the number of residues per helical turn and the number of atoms contained in the ring made by each hydrogen bond (Bragg et al., 1950). The ideal a-helix has a periodicity of 3.6 residues per turn, encloses 13 atoms in a ring by formation of an i , i + 4 C=O.. .H-N hydrogen bond and is thus a 3.6,,-helix.The 3,,-helix is a more tightly wound helix, stabilized by i, i + 3 C=O. . .H-N hydrogen bonds, whereas the s-(4.4,,-)helix is wound less tightly with i, i + 5 C=O. . .H-N hydrogen bonds.The 3,,-helix was proposed and discussed (Huggins, 1943; Bragg et al., 1950;Donohue, 1953) earlier than the a-helix (Pauling et al., 1951). Although appreciably less common than a-helices, 3-4'70 of residues in crystal structures are in 3,,-helices (Barlow & Thornton, 1988; Karpen et al., 1992), making the 3,,-helix the fourth most common type of secondary structure in proteins after a-helices, @-sheets, and reverse turns. Most 3,,-helices are short, only three or four residues long, compared with a mean of ten residues in a-helices (Barlow & Thornton, 1988 Hubbard, 1984;Barlow & Thornton, 1988): 32% of helices in crystal structures were found to have a 3,,-type hydrogen bond at their N-termini and 34% at their C-termini (Baker & Hubbard, 1984). Strong amino acid preferences have been observed for different locations within a 3,,-helix in a recent survey of crystal structures (Karpen et al., 1992).3,,-Helices have also been studied in isolated peptides. It has been proposed that peptides made of the standard 20 L-amino acids can form 3,0-helices (Miick et al., 1992), or at least populate a significant amount of 3,,-helix at their N-and C-termini. The fraction of 3,,-helix present in a helical peptide is certainly strongly sequence dependent (Fiori et al., 1994;Zhou et al., 1994). 3,,-Helix formation can be induced by the introduction of a c,,,-disubstituted a-amino acid, of which a-ami...

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Section: Meaning Of the Junction Parameters T And Tcmentioning

confidence: 97%

Models for the 3₁₀‐helix/coil, π‐helix/coil, and α‐helix/3₁₀‐helix/coil transitions in isolated peptides

Rohl

Doig

1996

Protein Science

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“…. .OC hydrogen bonds can be formed between the head of one helix and the tail of another (Karle et al, 1989(Karle et al, , 1992a. In other crystals where succeeding peptides with 3,0-or a-helices are not in good register, only 1 intermolecular N H .…”

Section: Head-to-tail Hydrogen Bondingmentioning

confidence: 99%

Facile transition between 3₁₀‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)₂‐Phe‐Aib‐fragment

Karle¹,

Flippen‐Anderson²,

Gurunath³

et al. 1994

Protein Science

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A structural transition from a 3,0-helix to an a-helix has been characterized at high resolution for an octapeptide begins as a 3,,-helix and abruptly changes to an a-helix at carbonyl 0(3), which is the acceptor for both a 4 + 1 hydrogen bond with N(6)H and a 5 + 1 hydrogen with N(7)H, even though the last 8 residues have the same sequence in all 3 peptides. The average q5,$ angles in the decapeptide are -58", -28" for residues 1-3 and -63", -41 O for residues 4-10. The packing of helices in the crystals does not provide any obvious reason for the transition in helix type. Fourier transform infrared studies in the solid state also provide evidence for a 310-to a-helix transition with the amide I band appearing at 1,656-1,657 cm" in the 9-and 10-residue peptides, whereas in shorter sequences the band is observed at 1,667 cm-l.

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“…The α-dimethyl group is reminiscent of α-aminoisobutyric (Aib) residue – a known helix inducer. 13 We conjectured that the rigidification afforded by α-dimethyl substitution may also enhance helical stability in HBS peptides derived from carbonyl alkene isosteres. Overall, we evaluated five different constraints as part of these studies: E and Z carbonyl–alkene isosteres, with and without the dimethyl substitutions, and the dimethyl Z-alkene C–N isostere.…”

mentioning

confidence: 98%

An optimal hydrogen-bond surrogate for α-helices

Joy

Arora

2016

Chem. Commun.

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Alpha-helix and mixed 3(10)/alpha-helix in cocrystallized conformers of Boc-Aib-Val-Aib-Aib-Val-Val-Val-Aib-Val-Aib-OMe.

Cited by 70 publications

References 7 publications

Models for the 3₁₀‐helix/coil, π‐helix/coil, and α‐helix/3₁₀‐helix/coil transitions in isolated peptides

Models for the 3₁₀‐helix/coil, π‐helix/coil, and α‐helix/3₁₀‐helix/coil transitions in isolated peptides

Facile transition between 3₁₀‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)₂‐Phe‐Aib‐fragment

An optimal hydrogen-bond surrogate for α-helices

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Alpha-helix and mixed 3(10)/alpha-helix in cocrystallized conformers of Boc-Aib-Val-Aib-Aib-Val-Val-Val-Aib-Val-Aib-OMe.

Cited by 70 publications

References 7 publications

Models for the 310‐helix/coil, π‐helix/coil, and α‐helix/310‐helix/coil transitions in isolated peptides

Models for the 310‐helix/coil, π‐helix/coil, and α‐helix/310‐helix/coil transitions in isolated peptides

Facile transition between 310‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)2‐Phe‐Aib‐fragment

An optimal hydrogen-bond surrogate for α-helices

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Models for the 3₁₀‐helix/coil, π‐helix/coil, and α‐helix/3₁₀‐helix/coil transitions in isolated peptides

Models for the 3₁₀‐helix/coil, π‐helix/coil, and α‐helix/3₁₀‐helix/coil transitions in isolated peptides

Facile transition between 3₁₀‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)₂‐Phe‐Aib‐fragment