Conformational Exchange on the Microsecond Time Scale in α-Helix and β-Hairpin Peptides Measured by13C NMR Transverse Relaxation†

Biochemistry ◽  
2001 ◽  
Vol 40 (9) ◽  
pp. 2844-2853 ◽  
Author(s):  
Irina Nesmelova ◽  
Alexei Krushelnitsky ◽  
Djaudat Idiyatullin ◽  
Francesco Blanco ◽  
Marina Ramirez-Alvarado ◽  
...  
Keyword(s):  
Time Scale ◽  
Conformational Exchange ◽  
Transverse Relaxation ◽  
Hairpin Peptides ◽  
Α Helix

Chiral "basket handle" binaphthyl porphyrins: synthesis, catalytic epoxidation and NMR conformational studies

2010 ◽  
Vol 14 (07) ◽  
pp. 646-659 ◽  
Author(s):  
Eric Rose ◽  
Emma Gallo ◽  
Nicolas Raoul ◽  
Léa Bouché ◽  
Ariane Pille ◽  
...  
Keyword(s):  
Time Scale ◽  
Room Temperature ◽  
Conformational Equilibrium ◽  
Variable Temperature ◽  
Conformational Exchange ◽  
Iron Catalysts ◽  
Nmr Studies ◽  
Conformational Studies ◽  
H Nmr ◽  
Catalytic Epoxidation

Three "basket handle" porphyrins have been prepared by condensation of tetrakis-(α,β,α,β-2-aminophenyl)porphyrin atropoisomer with 1,1′-binaphthyl, 2,2′-dimethoxy, -3,3′-dicarbonylchloride, -3,3′-diacetylchloride and -3,3′-dipropanoylchloride. The epoxidation of styrene with the three iron catalysts, obtained after metalation of the free porphyrins, occurs with good yields and moderate ee up to 54%. These porphyrins showed unexpected conformational differences, as revealed by NMR spectroscopy. In particular, variable temperature NMR studies showed that the methoxy group in one of them undergoes intermediate conformational exchange on the 1H NMR time scale at room temperature. Lowering the temperature to -50 °C revealed the presence of four states in slow exchange on the NMR time scale. These results evidence a dynamic conformational equilibrium of the binaphthyl handles that adopt different, asymmetric positions with respect to the porphyrin plane.

scholarly journals Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics

2019 ◽  
Vol 116 (12) ◽  
pp. 5356-5361 ◽  
Author(s):  
Maxim B. Prigozhin ◽  
Yi Zhang ◽  
Klaus Schulten ◽  
Martin Gruebele ◽  
Taras V. Pogorelov
Keyword(s):  
Pressure Drop ◽  
Time Scale ◽  
Tertiary Structure ◽  
Specific Protein ◽  
Pressure Jump ◽  
Characteristic Time Scale ◽  
Hydrophobic Core ◽  
Pressure Drops ◽  
Contact Formation ◽  
Α Helix

As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ6–85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α3D)], whose drying and core formation proceed in concert, λ6–85repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

scholarly journals NMR structure and dynamics of monomeric neutrophil-activating peptide 2

1999 ◽  
Vol 338 (3) ◽  
pp. 591-598 ◽  
Author(s):  
Helen YOUNG ◽  
Vikram ROONGTA ◽  
Thomas J. DALY ◽  
Kevin H. MAYO
Keyword(s):  
Solution Structure ◽  
Computational Modelling ◽  
Terminal Segment ◽  
Conformational Exchange ◽  
15N Nmr ◽  
Model Free ◽  
C Terminus ◽  
Internal Mobility ◽  
Α Helix ◽  
Β Sheet

Neutrophil-activating peptide 2 (NAP-2), which demonstrates a range of proinflammatory activities, is a 72-residue protein belonging to the α-chemokine family. Although NAP-2, like other α-chemokines, is known to self-associate into dimers and tetramers, it has been shown that the monomeric form is physiologically active. Here we investigate the solution structure of monomeric NAP-2 by multi-dimensional 1H-NMR and 15N-NMR spectroscopy and computational modelling. The NAP-2 monomer consists of an amphipathic, triple-stranded, anti-parallel β-sheet on which is folded a C-terminal α-helix and an aperiodic N-terminal segment. The backbone fold is essentially the same as that found in other α-chemokines. 15N T1, T2 and nuclear Overhauser effects (NOEs) have been measured for backbone NH groups and used in a model free approach to calculate order parameters and conformational exchange terms that map out motions of the backbone. N-terminal residues 1 to 17 and the C-terminus are relatively highly flexible, whereas the β-sheet domain forms the most motionally restricted part of the fold. Conformational exchange occurring on the millisecond time scale is noted at the top of the C-terminal helix and at proximal residues from β-strands 1 and 2 and the connecting loop. Dissociation to the monomeric state is apparently responsible for increased internal mobility in NAP-2 compared with dimeric and tetrameric states in other α-chemokines.

scholarly journals Broadband measurement of true transverse relaxation rates in systems with coupled protons: application to the study of conformational exchange

2021 ◽  
Author(s):  
Peter Kiraly ◽  
Guilherme Dal Poggetto ◽  
Laura Castañar ◽  
Mathias Nilsson ◽  
Andrea Deák ◽  
...  
Keyword(s):  
Spin Systems ◽  
Conformational Exchange ◽  
Relaxation Rates ◽  
Transverse Relaxation ◽  
Coupled Spin Systems

Existing methods for measuring transverse relaxation give incorrect results in coupled spin systems. Measuring true relaxation rates extends their utility.

What Is the Time Scale for α-Helix Nucleation?

2011 ◽  
Vol 133 (17) ◽  
pp. 6809-6816 ◽  
Author(s):  
David De Sancho ◽  
Robert B. Best
Keyword(s):  
Time Scale ◽  
Helix Nucleation ◽  
Α Helix

scholarly journals A new type of scorpion Na+-channel-toxin-like polypeptide active on K+ channels

2005 ◽  
Vol 388 (2) ◽  
pp. 455-464 ◽  
Author(s):  
Najet SRAIRI-ABID ◽  
Joseba Iñaki GUIJARRO ◽  
Rym BENKHALIFA ◽  
Massimo MANTEGAZZA ◽  
Amani CHEIKH ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Poor Quality ◽  
Conformational Exchange ◽  
Na Channel ◽  
K Channels ◽  
Voltage Gated ◽  
Ic50 Values ◽  
Kv1.3 Channels ◽  
Α Helix ◽  
Β Sheet

We have purified and characterized two peptides, named KAaH1 and KAaH2 (AaH polypeptides 1 and 2 active on K+ channels, where AaH stands for Androctonus australis Hector), from the venom of A. australis Hector scorpions. Their sequences contain 58 amino acids including six half-cysteines and differ only at positions 26 (Phe/Ser) and 29 (Lys/Gln). Although KAaH1 and KAaH2 show important sequence similarity with anti-mammal β toxins specific for voltage-gated Na+ channels, only weak β-like effects were observed when KAaH1 or KAaH2 (1 μM) were tested on brain Nav1.2 channels. In contrast, KAaH1 blocks Kv1.1 and Kv1.3 channels expressed in Xenopus oocytes with IC50 values of 5 and 50 nM respectively, whereas KAaH2 blocks only 20% of the current on Kv1.1 and is not active on Kv1.3 channels at a 100 nM concentration. KAaH1 is thus the first member of a new subfamily of long-chain toxins mainly active on voltage-gated K+ channels. NMR spectra of KAaH1 and KAaH2 show good dispersion of signals but broad lines and poor quality. Self-diffusion NMR experiments indicate that lines are broadened due to a conformational exchange on the millisecond time scale. NMR and CD indicate that both polypeptides adopt a similar fold with α-helical and β-sheet structures. Homology-based molecular models generated for KAaH1 and KAaH2 are in accordance with CD and NMR data. In the model of KAaH1, the functionally important residues Phe26 and Lys29 are close to each other and are located in the α-helix. These residues may constitute the so-called functional dyad observed for short α-KTx scorpion toxins in the β-sheet.

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