2016
DOI: 10.1002/bip.22995
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Optimization of a β‐sheet‐cap for long loop closure

Abstract: Protein loops make up a large portion of the secondary structure in nature. But very little is known concerning loop closure dynamics and the effects of loop composition on fold stability. We have designed a small system with stable β-sheet structures, including features that allow us to probe these questions. Using paired Trp residues that form aromatic clusters on folding, we are able to stabilize two β-strands connected by varying loop lengths and composition (an example sequence: RWITVTI - loop - KKIRVWE).… Show more

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Cited by 12 publications
(13 citation statements)
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“…23 β-Hairpins displaying long loops (N ≥ 10-mer) are inherently challenging to prepare due to the large entropic penalty associated with their loop nucleation and folding. 53,54 For this reason, we recently developed several stabilizing -strap motifs specifically crafted for long loops to create amphipathic structures with hydrophobic residues such as W/W pairs on one face and ionic residues on the other.…”
Section: Chemical Synthesis Characterization and Biologicalmentioning
confidence: 99%
“…23 β-Hairpins displaying long loops (N ≥ 10-mer) are inherently challenging to prepare due to the large entropic penalty associated with their loop nucleation and folding. 53,54 For this reason, we recently developed several stabilizing -strap motifs specifically crafted for long loops to create amphipathic structures with hydrophobic residues such as W/W pairs on one face and ionic residues on the other.…”
Section: Chemical Synthesis Characterization and Biologicalmentioning
confidence: 99%
“…This motif decreases the fraying at the N-and C-end generally observed in β-hairpin peptides. More interestingly, it has been shown to stabilise βhairpins with quite long and flexible loops [253].…”
Section: Capping Motifsmentioning
confidence: 99%
“…Without the D‐Pro‐L‐Pro template to serve as the hairpin turn, we chose the Arg‐Arg residues in the middle of the sequence and replaced it with a D‐Arg‐L‐Arg sequence since a D‐amino acid followed by an L‐amino acid has been shown to promote the formation of a hairpin turn . These residues were chosen because they were present at the middle of the sequence and having a turn nucleating sequence in the middle of a loop has been shown to increase the hairpin fold stability of the adjacent residues . The initial variant, acyclin‐1, also had three variations within the strands at position 2 (V ➔ I), position 11 (L ➔ V), and position 13 (L ➔ Y).…”
Section: Resultsmentioning
confidence: 99%