Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

Duddy, William; Nissink, J. Willem M.; Allen, Frank H.; Milner‐White, E. James

doi:10.1110/ps.04920904

Cited by 67 publications

(93 citation statements)

References 31 publications

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“…The observed topology undeniably mimics a typicalturn and the Asx-turns structures. [45][46][47][48][49][50][51][52][53][54] Unexpectedly, the mimicked topology encompasses a 10-membered hydrogen-bonded ring, analogous to a typical -turn and the Asx-turns. Previously, we demonstrated the occurrence of a remarkably similar folded topology in Boc-Thr-Thr-OCH 3 and the main-chain torsion angles iþ1 $ À628, iþ1 $ 1378, iþ2 $ À1308, T $ 68, characterized the molecular conformation.…”

Section: 82mentioning

confidence: 99%

“…Of the four main-chain torsion angles ( iþ1 , iþ1 , iþ2 , iþ2 ) defining the mimicked 10-membered hydrogen-bonded motif, the three torsion angles ( iþ1 , iþ1 , iþ2 ) evidently correspond to the type II -turn or type II Asx-turn structures. 35 And according to MilnerWhite and coworkers, if there is mimicry, the torsion angles comprising the hydrogen-bonded ring motif should resemble the -turn structure. 35 …”

Section: Crystal Packingmentioning

confidence: 99%

“…35 And according to MilnerWhite and coworkers, if there is mimicry, the torsion angles comprising the hydrogen-bonded ring motif should resemble the -turn structure. 35 …”

Section: Crystal Packingmentioning

confidence: 99%

“…The involvement of O H functionality in diverse short-range hydrogen-bonding interactions i.e., either side-chain to main-chain or side-chain to side-chain, are shown to fabricate backbone secondary structural mimicry and novel structural motifs, in synthetic peptides and proteins. [29][30][31][32][33][34][35] Among the proteinogenic amino acids, Thr is the only amino acid that bears a C -branched amphiphilic stereogenic center (Thr vs. Ile or Val; depicted in Figure 1) and that is expected to impose stronger conformational constraints on the backbone conformations. An evaluation of modulation of intrinsic , propensities of various amino acids revealed that despite a high secondary structure propensity to form -sheet structures, the Thr residue showed a surprisingly low value for P , i.e., Thr exhibited a relatively low P value (57%) as compared to the C -branched Ile (77%) and Val (79%).…”

Section: Introductionmentioning

confidence: 99%

“…The analysis provides unambiguous experimental evidence favoring the existence of a novel structural motif that topologically mimics a typical -turn, i.e., stabilized by a main-chain to main-chain C i ¼ ¼O Á Á Á HÀ ÀN iþ3 interaction, 29,[45][46][47][48][49][50] and the Asx-turns, i.e., stabilized by a side-chain to main-chain C i þ 1 ¼ ¼O Á Á Á HÀ ÀN iþ3 interaction. 29,[51][52][53][54] An assessment of hydrogen-bond geometric parameters incline us to suggest that the perceived -turnlike topology is stabilized by an effective nonconventional CÀ ÀH Á Á Á O-type hydrogen bond, i.e., C i ¼ ¼O Á Á Á H-À ÀC iþ2 interaction. [55][56][57][58][59][60][61][62][63] As depicted in Figure 2, the mimicked topology also encompasses a noncovalent 10-membered ring.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of β‐turn and Asx‐turns mimicry in a model peptide: Stabilization via CH · · · O interaction

Thakur

Kishore

2006

Biopolymers

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The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins.

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Section: 82mentioning

confidence: 99%

Section: Crystal Packingmentioning

confidence: 99%

“…35 And according to MilnerWhite and coworkers, if there is mimicry, the torsion angles comprising the hydrogen-bonded ring motif should resemble the -turn structure. 35 …”

Section: Crystal Packingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Characterization of β‐turn and Asx‐turns mimicry in a model peptide: Stabilization via CH · · · O interaction

Thakur

Kishore

2006

Biopolymers

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Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Hagarman

Mathieu

Toal

et al. 2011

Chemistry A European J

160

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Local structure in unfolded proteins, especially turn segments, has been suggested to initiate the hierarchical protein-folding process. To determine the intrinsic propensity to form such turn structures, amide I' band profiles of the Raman, IR, and vibrational circular dichroism (VCD) spectra, and several structure-sensitive NMR J-coupling constants, have been measured for a series of GxG (x=D, N, T, C) peptides, in which the central x residues are abundant in various turn motifs in folded proteins. In addition, we revisited earlier measured GSG experimental data. To check whether this relatively high propensity for these residues to sample turns reflects an intrinsic propensity, the experimental data were analyzed in terms of conformational distributions that can be described as a superposition of two-dimensional Gaussian distributions associated with different so-called mesostates. The analysis reveals that the investigated residues sample dihedral angles similar to those found in the corner residues of various turns, namely, type I/I', II/II', and IV β-turns. Aspartic acid (D) was found to predominantly sample regions attributed to turns, including distributions at the upper border of the upper-right quadrant of the Ramachandran plot, which bear some resemblance to asx-turns observed in proteins. This conformation enables hydrogen bonding between the side-chain carboxylate and the C-terminal amide group. Altogether, the study shows that the high propensity for T, S, C, N, and D to be located in turn motifs reflects, to a substantial degree, an intrinsic property and supports the role of these residues as initiation sites for hierarchical folding processes that can lead to compact structures in the unfolded state of peptides and proteins.

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Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

Toal

Kubatova

Richter

et al. 2015

Chemistry A European J

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To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected "GxyG" host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest-neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above-the-average preference for turn-like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above-the-average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of (3) J(H(N) ,H(α) ) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII↔β equilibrium indicating a significant residue dependent temperature dependence of the peptides' conformational ensembles. These results suggest that nearest-neighbor interactions between unlike residues act as conformational randomizers close to the enthalpy-entropy compensation temperature, eliminating intrinsic biases in favor of largely balanced pPII/β dominated ensembles at physiological temperatures.

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Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

Cited by 67 publications

References 31 publications

Characterization of β‐turn and Asx‐turns mimicry in a model peptide: Stabilization via CH · · · O interaction

Characterization of β‐turn and Asx‐turns mimicry in a model peptide: Stabilization via CH · · · O interaction

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

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