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Optimization of a β‐sheet‐cap for long loop closure
Author(s) -
Anderson Jordan M.,
Shcherbakov Alexander A.,
Kier Brandon L.,
Kellock Jackson,
Shu Irene,
Byrne Aimee L.,
Eidenschink Lisa A.,
Andersen Niels H.
Publication year - 2017
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22995
Subject(s) - chemistry , loop (graph theory) , folding (dsp implementation) , beta sheet , sequence (biology) , peptide , protein secondary structure , molecular dynamics , crystallography , residue (chemistry) , protein folding , stereochemistry , biophysics , computational chemistry , biochemistry , mathematics , combinatorics , electrical engineering , engineering , biology
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: R W ITVTI – loop – KKIRV W E). Using NMR and CD, both fold stability and folding dynamics can be investigated for these systems. With the 16 residue loop peptide (sequence: R W ITVTI‐(GGGGKK) 2 GGGG‐KKIRV W E) remaining folded (ΔG U = 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: R W ITVRI W ‐(GGGGKK) 2 GGGG‐ W KTIRV W E) supports a remarkably stable β‐sheet (Δ G U = 6.3 kJ/mol at 295 K, T m = ∼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.