Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: Crystal structure of hepta‐ and octapeptides containing α‐aminoisobutyric acid

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

doi:10.1002/prot.340070107

Cited by 67 publications

(44 citation statements)

References 28 publications

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“…Although both peptides adopt helical structures, the Boc analogue adopts a 3 10 -helix with 4 3 1 hydrogen bonds, except for some unwinding at the C-terminus, while the Ac analogue forms a good ␣-helix. It is noteworthy that Aib-7A 18 is almost identical to Ac-Dpg-7, rather than to Dpg-7. A superposition of Aib-7A and Ac-Dpg-7, made with a least-squares fit of backbone atoms from N1 to C6a, shows an excellent fit between the two molecules from the N-terminus (despite having an Ac group in one and a Boc group in the other) to C6a (Figure 3), and despite the high R factor for Ac-Dpg-7.…”

Section: Crystal State Conformationsmentioning

confidence: 94%

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Comparison of helix-stabilizing effects of α,α-dialkyl glycines with linear and cycloalkyl side chains

et al. 2000

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Section: Crystal State Conformationsmentioning

confidence: 94%

“…18 The differences in the heptapeptide analogues are Ac/Boc and Dpg 4 /Aib 4 in Ac-Dpg-7 and Aib-7A, respectively.…”

Section: Figurementioning

confidence: 99%

Comparison of helix-stabilizing effects of α,α-dialkyl glycines with linear and cycloalkyl side chains

et al. 2000

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“…Briefly, they all form helices, predominantly a-helices, with occasional 3,o-helix segments that occur mostly at the N terminus. The specific location of the Aib residues in the sequence is not very important for helix formation; for example, in at least one case an exchange of Aib with Leu produces no conformational changes (Karle, Flippen-Anderson, Uma & Balaram, 1990b), the elimination of Aib from the middle of a 16-residue sequence does not disturb the helix (Karle, FlippenAnderson, Uma, Sukumar & Balaram, 1990) and the presence or absence of Aib at either end of the helix is immaterial (Karle, Flippen-Anderson, Uma & Balaram, 1990c). The number of Aib residues can be quite small.…”

Section: Helical Peptides Containing Aib Residuesmentioning

confidence: 99%

“…may be involved in ion channels formed by helices with predominantly apolar residues, or they may be involved in the helix-folding or unfolding processes. Observations of water insertions have also been made in the apolar structures of Boc-(Ala-Leu-Aib)2-OMe and Boc-Val-Ala-Leu-Aib-VaI-Ala-Leu-OMe (Karle, Flippen-Anderson, Uma & Balaram, 1989b, 1990c. In the latter structure, both the unhydrated and the hydrated backbones occur side by side in the same unit cell.…”

Section: Water Penetration Into Helix Backbonesmentioning

confidence: 99%

Folding, aggregation and molecular recognition in peptides

Karle¹

1992

Acta Crystallogr Sect B

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In past years, most of the X-ray structure determinations of oligopeptides were for cyclic peptides or for short linear peptides. Longer peptides usually presented many difficulties in obtaining suitable crystals since the molecules are intrinsically very flexible. More recently, it has been appreciated that the aminoisobutyric acid residue (Aib), which occurs naturally in many peptides of microbial origin, initiates helix folding. Several score of 7-to 15-residue linear peptides containing Aib have been synthesized, crystallized and had their structures determined to high resolution. Many of the peptide structures have been determined in more than one crystalline form. These peptide structures have yielded a plethora of information on types of helices, modes of hydration, water penetration into helical backbones, helices bent by Pro residues, parallel and antiparallel association of helices, effects of Leu residues on association of peptides, an example of a zipper assembly by side chains, and an example of a possible ion channel with a gating mechanism.

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“…Similarly, the tetrazole-based intramolecular photoclick chemistry was also applied to synthesize the side chain-crosslinked peptides [63]. Briefly, the tetrazole and acrylamide modified lysine or ornithine were incorporated into a model 3 10 -helical peptide [64,65]. After photoirradiation, the pyrazoline-cross-linked peptides were generated in high yields.…”

Section: Site-specific Labeling Of Proteins Via the Photoinduced Tetrmentioning

confidence: 99%

Photo-Triggered Click Chemistry for Biological Applications

Herner¹,

Qi²

2015

Cycloadditions in Bioorthogonal Chemistry

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In the last decade and a half, numerous bioorthogonal reactions have been developed with a goal to study biological processes in their native environment, i.e., in living cells and animals. Among them, the photo-triggered reactions offer several unique advantages including operational simplicity with the use of light rather than toxic metal catalysts and ligands, and exceptional spatiotemporal control through the application of an appropriate light source with pre-selected wavelength, light intensity and exposure time. While the photoinduced reactions have been studied extensively in materials research, e.g., on macromolecular surface, the adaptation of these reactions for chemical biology applications is still in its infancy. In this chapter, we review the recent efforts in the discovery and optimization the photo-triggered bioorthogonal reactions, with a focus on those that have shown broad utility in biological systems. We discuss in each cases the chemical and mechanistic background, the kinetics of the reactions and the biological applicability together with the limiting factors.

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Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: Crystal structure of hepta‐ and octapeptides containing α‐aminoisobutyric acid

Cited by 67 publications

References 28 publications

Comparison of helix-stabilizing effects of α,α-dialkyl glycines with linear and cycloalkyl side chains

Comparison of helix-stabilizing effects of α,α-dialkyl glycines with linear and cycloalkyl side chains

Folding, aggregation and molecular recognition in peptides

Photo-Triggered Click Chemistry for Biological Applications

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