An introduction to one- and two-dimensional lineshape analysis of chemically exchanging systems

Waudby, Christopher A.; Alfonso, Ignacio

doi:10.1016/j.jmro.2023.100102

“…TGA runs displayed sudden weight loss at 300 °C, associated to the thermal degradation of BCP and azpy ligands, confirming the stability of the crystals up to those temperatures (Figure S6). Additionally, 13 C and 1 H MAS NMR spectra confirmed the purity of the samples and the absence of residual solvent molecules after activation (Figure S17 and S20a).…”

Section: Resultsmentioning

confidence: 65%

“…This diffuse density indicates a major disorder of the rotor, thus suggesting increased dynamics, instead of the commonly described hindering action of guest molecules. [11] High resolution 13 C MAS NMR is a method of choice to understand the environment explored by each carbon atom within the observation time-scale. Variable temperature experiments under magic angle spinning and cross polarization were performed on FTR-P2 and FTR-P2-I 2 from room temperature to 100 K at 13 C NMR frequencies of 75 MHz and 100 MHz (Figure 3 and Figures S29 and S31).…”

Section: Methodsmentioning

confidence: 99%

“…Contrarily, smaller CO 2 molecules sorbed by the MOF maintain the high symmetry structure and interact with BCP modulating their rotation speed, as observed by in situ synchrotron radiation PXRD of the CO 2 -loaded framework up to 10 bar. The dynamics of the molecular rotors, their trajectories and energy barriers were determined by a combined approach, which includes single crystal and synchrotron radiation powder X-ray diffraction, 13 C CP MAS down 100 K, 1 H T 1 relaxation times down to 4 K and DFT/MM modelling. Collectively, this work aimed to demonstrate how unconventional integration of rotors (mobile elements) and structural softness can govern a reversible stimulated switch of solid-state molecular motion at surprisingly low temperatures.…”

Section: Introductionmentioning

confidence: 99%

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Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Perego,

Daolio,

Bezuidenhout

et al. 2024

Angew Chem Int Ed

6

0

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Engineering coordinated rotational motion in porous architectures enables the fabrication of molecular machines in solids. A flexible two‐fold interpenetrated pillared Metal‐Organic Framework precisely organizes fast mobile elements such as bicyclopentane (BCP) (107Hz regime at 85 K), two distinct pyridyl rotors and E‐azo group involved in pedal‐like motion. Reciprocal sliding of the two sub‐networks, switched by chemical stimuli, modulated the sizes of the channels and finally the overall dynamical machinery. Actually, iodine‐vapor adsorption drives a dramatic structural rearrangement, displacing the two distinct subnets in a concerted piston‐like motion. Unconventionally, BCP mobility increases, exploring ultra‐fast dynamics (107 Hz) at temperatures as low as 44 K, while the pyridyl rotors diverge into a faster and slower dynamical regime by symmetry lowering. Indeed, one pillar ring gained greater rotary freedom as carried by the azo‐group in a crank‐like motion. A peculiar behavior was stimulated by pressurized CO2, which regulates BCP dynamics upon incremental site occupation. The rotary dynamics is intrinsically coupled to the framework flexibility as demonstrated by complementary experimental evidence (multinuclear solid‐state NMR down to very low temperatures, synchrotron radiation XRD, gas sorption) and computational modelling, which helps elucidate the highly sophisticated rotor‐structure interplay.

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“…For the spectra in the transition region (3.3–4.8 M urea concentration), peak integration was employed in Topspin to derive p F and p U from the area under the peaks. For the 19 F FL RfaH, the 19 F NMR spectra (Figure ) in the transition region were globally fit to the real part of the analytical solution of the Bloch-McConnell equation (for asymmetric two-site exchange) in the frequency domain ,− using an in-house Python script: Y false( ω false) = C 0 { k ex + p normalF [ R 2 U − i false( ω − ω normalU false) ] + p normalU [ R 2 F + i false( ω − ω normalF false) ] } / { k ex p F false[ R 2 normalF + i ( ω − ω F ) false] + k ex p U false[ R 2 normalU + i ( ω − ω U …”

Section: Methodsmentioning

confidence: 99%

“…For the spectra in the transition region (3.3–4.8 M urea concentration), peak integration was employed in Topspin to derive p F and p U from the area under the peaks. For the 19 F FL RfaH, the 19 F NMR spectra (Figure ) in the transition region were globally fit to the real part of the analytical solution of the Bloch-McConnell equation (for asymmetric two-site exchange) in the frequency domain ,− using an in-house Python script: …”

Section: Methodsmentioning

confidence: 99%

Line Shape Analysis of ¹⁹F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics

Bhuvaneshwari,

Shivamani,

Sengupta

2023

J. Phys. Chem. B

3

0

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The recent discovery of metamorphic proteins, which can switch between multiple conformations under native conditions, has challenged the well-established one sequence-one structure paradigm of protein folding. This is exemplified in the Cterminal domain of the multidomain transcription factor RfaH, which converts from an α-helical coiled-coil conformation in its autoinhibited state to a β-barrel conformation upon activation. Here, we use multisite line shape analysis of 19 F NMR-monitored equilibrium chemical denaturation measurements of two 19 Flabeled variants of full-length RfaH, to show that it folds/unfolds slowly on the NMR time scale, in an apparent all-or-none fashion at physiological pH and room temperature in the 3.3−4.8 M urea concentration range. The significant thermodynamic stability and slow unfolding rate (kinetic stability) are likely responsible for maintaining the closed autoinhibited state of RfaH, preventing spurious interactions with RNA polymerase (RNAP) when not functional. Our results provide a quantitative understanding of the folding-function relationship in the model fold-switching protein RfaH.

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Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Perego,

Daolio,

Bezuidenhout

et al. 2024

Angewandte Chemie

0

View full text Add to dashboard Cite

Engineering coordinated rotational motion in porous architectures enables the fabrication of molecular machines in solids. A flexible two‐fold interpenetrated pillared Metal‐Organic Framework precisely organizes fast mobile elements such as bicyclopentane (BCP) (107Hz regime at 85 K), two distinct pyridyl rotors and E‐azo group involved in pedal‐like motion. Reciprocal sliding of the two sub‐networks, switched by chemical stimuli, modulated the sizes of the channels and finally the overall dynamical machinery. Actually, iodine‐vapor adsorption drives a dramatic structural rearrangement, displacing the two distinct subnets in a concerted piston‐like motion. Unconventionally, BCP mobility increases, exploring ultra‐fast dynamics (107 Hz) at temperatures as low as 44 K, while the pyridyl rotors diverge into a faster and slower dynamical regime by symmetry lowering. Indeed, one pillar ring gained greater rotary freedom as carried by the azo‐group in a crank‐like motion. A peculiar behavior was stimulated by pressurized CO2, which regulates BCP dynamics upon incremental site occupation. The rotary dynamics is intrinsically coupled to the framework flexibility as demonstrated by complementary experimental evidence (multinuclear solid‐state NMR down to very low temperatures, synchrotron radiation XRD, gas sorption) and computational modelling, which helps elucidate the highly sophisticated rotor‐structure interplay.

show abstract

An introduction to one- and two-dimensional lineshape analysis of chemically exchanging systems

Cited by 11 publications

References 78 publications

Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Line Shape Analysis of ¹⁹F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics

Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

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An introduction to one- and two-dimensional lineshape analysis of chemically exchanging systems

Cited by 11 publications

References 78 publications

Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Line Shape Analysis of 19F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics

Solid State Machinery of Multiple Dynamic Elements in a Metal–Organic Framework

Contact Info

Product

Resources

About

Line Shape Analysis of ¹⁹F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics