Methods of peptide conformation studies.

Bierzyński, A

doi:10.18388/abp.2001_3870

Cited by 14 publications

(4 citation statements)

References 35 publications

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“…Conformational preferences of β‐turn containing structures can be studied in solid state by crystallography or in solution state by a variety of spectroscopic techniques such as NMR, IR, UV, or chiroptical spectroscopies . However, one needs to take into account an equilibrium between a folded turn structure and an open chain structure.…”

Section: Introductionmentioning

confidence: 99%

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

Berger

Mallick

et al. 2016

Biopolymers

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A set of cyclic tetrapeptides of the general form cyclo (Boc-Cys-Pro-X-Cys-OMe) with X being L-/D-Ala, L-/D-Val, and L-/D-Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs - namely a β-turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β-turn conformational preferences using NMR, VCD, and Raman spectroscopy. Our results provide evidence for a strong influence of a single stereocenter on the structures of the peptides whereas solvent polarity does not significantly affect them. Additionally, the solid state conformational preferences were studied by crystal structure analysis. Overall, a general trend for the conformational preferences of this set of peptides can be concluded from the results of the complementary investigations.

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Section: Introductionmentioning

confidence: 99%

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

Berger

Mallick

et al. 2016

Biopolymers

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“…CD spectroscopy was used to study the overall structural organization of hemoglobin (18)(19)(20). Although the CD signal could show an aggregation-and size-related scattering effect, light scattering allows more precise detection of protein particle size.…”

Section: Introductionmentioning

confidence: 99%

Body Temperature-Related Structural Transitions of Monotremal and Human Hemoglobin

Digel

Maggakis-Kelemen

Zerlin

et al. 2006

Biophysical Journal

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In this study, temperature-related structural changes were investigated in human, duck-billed platypus (Ornithorhynchus anatinus, body temperature T(b) = 31-33 degrees C), and echidna (Tachyglossus aculeatus, body temperature T(b) = 32-33 degrees C) hemoglobin using circular dichroism spectroscopy and dynamic light scattering. The average hydrodynamic radius (R(h)) and fractional (normalized) change in the ellipticity (F(obs)) at 222 +/- 2 nm of hemoglobin were measured. The temperature was varied stepwise from 25 degrees C to 45 degrees C. The existence of a structural transition of human hemoglobin at the critical temperature T(c) between 36-37 degrees C was previously shown by micropipette aspiration experiments, viscosimetry, and circular dichroism spectroscopy. Based on light-scattering measurements, this study proves the onset of molecular aggregation at T(c). In two different monotremal hemoglobins (echidna and platypus), the critical transition temperatures were found between 32-33 degrees C, which are close to the species' body temperature T(b). The data suggest that the correlation of the structural transition's critical temperature T(c) and the species' body temperature T(b) is not mere coincidence but, instead, is a more widespread structural phenomenon possibly including many other proteins.

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“…However, the CD measurement is only sensitive to the average properties of partial helical peptide and the optimal sensitivity is around 50% of the helix content . Contribution of very short helical segments to the CD spectra is small, which makes it difficult to detect short helical segments in solution using the traditional CD spectroscopy. Recently, a short helical segment consisting of four residues stabilized by a La 3+ ion has been studied by Baldwin and co-workers using CD measurements .…”

Section: Introductionmentioning

confidence: 99%

Solution Conformations of Wild-Type and Mutated Bak BH3 Peptides via Dynamical Conformational Sampling and Implication to Their Binding to Antiapoptotic Bcl-2 Proteins

et al. 2004

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The BH3 (Bcl-2 homology 3) domain of the Bcl-2 family of proteins plays a critical role in the regulation of programmed cell death, or apoptosis. A 16-residue peptide derived from the BH3 domain of the proapoptotic protein Bak potently binds to the antiapoptotic proteins Bcl-2 and Bcl-xL. While this Bak BH3 peptide adopts a well-defined helical conformation in the experimental NMR solution structure in complex with Bcl-xL, it does not adopt a stable helical conformation in water. Experimental structural determination of peptides without a stable and well-defined solution conformation remains a difficult task. In this paper, we investigated the solution conformations of this Bak BH3 peptide through extensive molecular dynamics (MD) simulations in water using a recently developed self-guided MD simulation (SGMD) method. Our simulations showed that the Bak peptide exhibits a partially formed helical structure with a fairly stable 6-residue helical segment at the N terminus and a less stable approximately 4-residue helical segment at the C terminus. Additionally, we also performed extensive SGMD simulations of two mutated Bak peptides, in which the arginine residue at position 5 is mutated to either an alanine or a glycine residue (R5A or R5G mutant) to investigate the influence of mutation on the solution conformations of the Bak peptide. We found that the R5G mutation greatly affects the solution conformations of the peptide, and the overall helix ratio decreases by a factor of 2 as compared to the wild-type Bak peptide. In contrast, the R5A mutation does not affect significantly the peptide solution conformations observed in the wild type. By use of a fluorescence-polarization-based binding assay, we quantitatively determined the binding affinities of these three Bak BH3 peptides to Bcl-xL protein. We found that the R5G and R5A mutants are 24 and 6 times less potent than the wild-type Bak peptide, respectively, suggesting that the helical ratio of the peptides is an important but not the only factor for their binding to Bcl-xL. Analysis of representative conformations of the R5A mutant suggested that the relatively stable helical segment close to the N terminus may greatly facilitate its binding to Bcl-xL.

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Methods of peptide conformation studies.

Cited by 14 publications

References 35 publications

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

Body Temperature-Related Structural Transitions of Monotremal and Human Hemoglobin

Solution Conformations of Wild-Type and Mutated Bak BH3 Peptides via Dynamical Conformational Sampling and Implication to Their Binding to Antiapoptotic Bcl-2 Proteins

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