title: 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). Using NMR and CD, both fold stability and folding dynamics can be investigated for these systems. With the 16 residue loop peptide (sequence: RWITVTI-(GGGGKK)2GGGG-KKIRVWE) remaining folded (ΔGU= 1.6 kJ/mol at 295K). To increase stability and extend the series to longer loops, we added an additional Trp/Trp pair in the loop flanking position. With this addition to the strands, the 16 residue loop (sequence: RWITVRIW-(GGGGKK)2GGGG-WKTIRVWE) supports a remarkably stable β-sheet (ΔGU= 6.3 kJ/mol at 295 K, Tm= ∼55°C). Given the abundance of loops in binding motifs and between secondary structures, these constructs can be powerful tools for peptide chemists to study loop effects; with the Trp/Trp pair providing spectroscopic probes for assessing both stability and dynamics by NMR.
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Jordan M
authors.initials: JM
authors.lastname: Anderson
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Shcherbakov
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Brandon L
authors.initials: BL
authors.lastname: Kier
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Jackson
authors.initials: J
authors.lastname: Kellock
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Irene
authors.initials: I
authors.lastname: Shu
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Aimee L
authors.initials: AL
authors.lastname: Byrne
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Eidenschink
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington.
authors.forename: Niels H
authors.initials: NH
authors.lastname: Andersen
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D010455:Peptides
keywords: Aryl Cluster; Trp/Trp; beta-Capping; beta-hairpin; long loops; peptide design