Chemical Shifts Provide Fold Populations and Register of β Hairpins and β Sheets

Fesinmeyer, R. Matthew; Hudson, F. Michael; Olsen, Katherine A.; White, George C.; Euser, Anna G.; Andersen, Niels H.

doi:10.1007/s10858-005-3731-7

Cited by 58 publications

(97 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The locations examined are indicated by the distance between the Trp residues and the central turn residues (NG, HG, or pG in the examples that follow); non-H-bonded (NHB) locations are thus S AE even sites (see Fig. 3) (31). One attempt to place the W/W pair at a hydrogen-bonded (HB) site (S AE 5) is also recorded.…”

Section: Resultsmentioning

confidence: 99%

Stabilizing capping motif for β-hairpins and sheets

Kier

Shu²,

Eidenschink³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

158

View full text Add to dashboard Cite

Although much has been learned about the design of models of β-sheets during the last decade, modest fold stabilities in water and terminal fraying remain a feature of most β-hairpin peptides. In the case of hairpin capping, nature did not provide guidance for solving the problem. Some observations from prior turn capping designs, with further optimization, have provided a generally applicable, "unnatural" beta cap motif (alkanoyl-Trp at the N terminus and Trp-Thr-Gly at the C terminus) that provides a net contribution of 6 þ kJ∕mol to β-hairpin stability, surpassing all other interactions that stabilize β-hairpins including the covalent disulfide bond. The motif, made up entirely of natural residues, is specific to the termini of antiparallel β-strands and reduces fraying at the ends of hairpins and other β-sheet models. Utilizing this motif, 10-to 22-residue peptide scaffolds of defined stereochemistry that are greater than 98% folded in water have been prepared. The β-cap can also be used to staple together short antiparallel β-strands connected by a long flexible loop.beta sheets | capping stabilization | peptide hairpins | Trp/Trp interactions C apping motifs are well-known features of protein and peptide secondary structure; specifically, terminal alpha helix caps (especially N caps) are common both in proteins and designed peptides (1-4). The basis for helix capping is straightforward: countering the helix macrodipole and providing additional H-bonding interactions (1). Caps increase the fold population of isolated α-helical peptides and have been a boon to the design of α-helix models. β-Structures have capping requirements wholly different from those of helices; the ends of canonical β-sheets and hairpins do not have dipole moments or unsatisfied H bonds.The a priori design of model β-sheet systems (5), focused on hairpins, has lagged behind that of α-helix counterparts. The key discoveries that improved β-hairpin stabilities outside of protein contexts have been sequences with good turn propensities, for example D-Pro-Gly (pG) (6), heterochiral pP (7), and Aib-Gly (8) [or less favorably, Asn-Gly (NG) (5, 9)] and the incorporation of optimized cross-strand pairings [most notably Trp/Trp pairs flanking the turn (10-14)]. However, longer hairpin models are typically still frayed at the termini; to date, fully folded spectroscopic reference values have only been attained via cyclization (15-17). With the exception of cyclization, mutations at terminal sites have yielded only modest changes in hairpin stability; terminal coulombic effects (ΔΔG U ¼ 1.5-2.5 kJ∕mol) standing as the only generally observed capping effect (11,18,19). Pi-cation interactions have also been shown to provide significant hairpin stabilization (20), but instances in which the interaction appears near the ends of hairpins have provided only marginal stability increases (18,(21)(22)(23)). An unnatural π-cation interaction has also been shown to stabilize the turn in a tripeptide (24). There has been limited evidence for hairpin fold sta...

show abstract

Section: Resultsmentioning

confidence: 99%

Stabilizing capping motif for β-hairpins and sheets

Kier

Shu²,

Eidenschink³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

158

View full text Add to dashboard Cite

show abstract

“…Full 1 H spectral assignments were made by using a combination of 2D NOESY and TOCSY experiments. The resulting chemical shifts were converted to folding-associated shifts, given as chemical shift deviations (CSDs) from random coil norms, using the CSDb algorithm (32)(33)(34). The large diagnostic CSDs for cyclo-TC1 and its acyclic precursor (TC1) appear in Fig.…”

Section: Methodsmentioning

confidence: 99%

Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction

Scian

Lin

Trong

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data, including the structural basis for the increase in fold stability associated with motif cyclization and the manner in which a polar serine side chain is accommodated in the hydrophobic interior. A hexameric oligomer of the cyclic peptide is found in both crystal forms and indicates that under appropriate conditions, this minimized system may also serve as a model for protein-protein interactions.protein-protein interaction | folding simulation target | protein cyclization | peptide oligomerization | H-bonding motifs T rp-cage miniproteins (at 18-20 residue length) are among the smallest peptides to fold into a stable protein-like structure (1, 2); as a result, the Trp-cage fold has emerged as a protein folding paradigm (3, 4). Trp-cage species have been extensively studied experimentally (4-11) and computationally (12-19), but the conclusions regarding the folding process and results drawn from these studies are not in accord at the level that should be attainable for such a small system.The structural model used for testing computational folding methods has, in almost all cases, been that derived by NMR for the initially reported Trp-cage (TC5b), which displays a rather low fold stability, T m ¼ 43°C (1). Additional Trp-cage structures based on NMR measurements are now available (2,6,10,(20)(21)(22). All of these appear to possess a common fold topology that is supported by an extensive set of structuring-induced shifts (CSDs, chemical shift deviations from random coil norms) that are largely the result of ring current effects. The uniformity of these CSDs suggests a well-defined common structure. However, other spectroscopic measurements of Trp-cage molecules have been interpreted as being consistent with a folded structure undergoing a greater degree of dynamic fluctuation (7,8). In addition, "folded" structures from molecular dynamics simulations, with a few notable exceptions (18,19), fail to predict the ring current effects observed by NMR (2). The failure of numerous calculations to reproduce the NMR structures and contrary conclusions from other experimental methods is problematic and points to outstanding issues concerning the continuing* use of a Trp-cage as a benchmark for molecular dynamics folding simulations. Further structural studies of Trp-cage species are required to validate the target and to ascertain the key interatomic interactions leading to the folded state.Herein we report X-ray structure determinations for two crystal forms of a cyclized Trp-cage (23), cyclo-TC1 (-GDAYAQW-LADGGPSSGRPPPSG-). Raising additional questions about the oligomeric state of the molec...

show abstract

“…When tryptophan is in the C-terminal position next to alanine (16), the alanine -proton is shifted 0.10 ppm upfield. If instead tryptophan is in the N-terminal position next to alanine (15), then the alanine -proton is shifted even further upfield Alanine -Proton Random Coil Chemical Shifts 77 (0.15 ppm). Again, the upfield shifts are not additive when two tryptophan residues are incorporated.…”

Section: Neighboring Amino Acidsmentioning

confidence: 99%

“…[6][7][8] CSI is of particular importance for those designing peptides that form discrete and stable -hairpins, because with relatively straightforward 1D and 2D NMR studies, information about protein secondary structure can be quickly obtained. [9][10][11][12][13][14][15] While CSI also applies to amide proton (HN), - 13 C, carbonyl 13 C, and amide 15 NH chemical shifts, the current study focuses on -proton chemical shifts. 8,16,17 In CSI the -proton of a particular amino acid in the protein is referenced to the random coil value for that amino acid.…”

Section: Introductionmentioning

confidence: 99%

Effect of pH, urea, peptide length, and neighboring amino acids on alanine α‐proton random coil chemical shifts

et al. 2006

View full text Add to dashboard Cite

Accurate random coil α‐proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the α‐proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1–3. Changes in pH (2–6), urea (0–1M), and peptide length (n = 1–3) had no effect on Ala α‐proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 ± 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine α‐proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C‐terminal position (∼0.10 vs. 0.05 ppm N‐terminal), and the larger aromatic tryptophan caused greater effects in the N‐terminal position (0.15 ppm vs. 0.10 C‐terminal). Proline affected both significant upfield (0.06 ppm, N‐terminal) and downfield (0.25 ppm, C‐terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding. © 2006 Wiley Periodicals, Inc. Biopolymers 85: 72–80, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

show abstract

Chemical Shifts Provide Fold Populations and Register of β Hairpins and β Sheets

Cited by 58 publications

References 70 publications

Stabilizing capping motif for β-hairpins and sheets

Stabilizing capping motif for β-hairpins and sheets

Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction

Effect of pH, urea, peptide length, and neighboring amino acids on alanine α‐proton random coil chemical shifts

Contact Info

Product

Resources

About