Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Gauto, Diego F.; Lebedenko, Olga O.; Becker, Lea Marie; Ayala, Isabel; Lichtenecker, Roman; Skrynnikov, Nikolai R.; Schanda, Paul

doi:10.1016/j.yjsbx.2022.100079

Cited by 7 publications

(11 citation statements)

References 90 publications

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“…While the NMR data do not establish that the exchange is due to ring flips, MD simulations support the interpretation that F45 undergoes ring flips with a correlation time on the order of 1 μs, rather than nanoseconds. 24 The results on ubiquitin provide a nice example of very fast ring flips of aromatic side chains located close to the protein surface, showing that the barriers of rotation in these cases can approach that derived from the χ 2 dihedral angle potential function, but also be significantly higher.…”

Section: ■ Ring Flip Mechanismsmentioning

confidence: 88%

“…Solid-state NMR experiments offer complementary advantages to studying ring flips because dipolar couplings are averaged by molecular dynamics in such a way that the amplitude and anisotropy of the underlying motion can be determined. 23,24,39,46,47 Furthermore, molecular size is not a limiting factor in solid-state NMR, as long as the analysis is not hampered by spectral overlap due to the increased number of aromatic spins. Potential drawbacks in solid-state NMR include the effects of the dipolar and chemical shift anisotropy relaxation mechanisms, which become very efficient if ring flips occur in the microsecond regime, thereby rendering the signals unobservable.…”

Section: Investigations Of Ring Flipsmentioning

confidence: 99%

“…53,54 Nonaccelerated MD simulations allow for qualitative characterization of ring flips into fast (observed frequently in an MD trajectory) or slow (not or rarely observed) categories. 24,51 To date, MD simulations have not been able to reliably reproduce experimentally determined ring flip rate constants, 20,51 indicating that NMR data provide valuable benchmarks and further highlighting the need for continued, data-guided development of force fields. MD simulations can also be directly guided by NMR data, either through reweighting of conformational ensembles or introducing restraints.…”

Section: ■ Computational Studies To Augment and Interpret Nmr Datamentioning

confidence: 99%

“…The effect of crystal packing on ring flip dynamics in microcrystalline solid-state NMR samples is of potential concern. 24 The detailed intermolecular interactions of exposed aromatic rings can play significant roles in governing ring flip rate constants, 24,47,48 but it remains an open question to what extent crystal packing might influence the dynamics of buried rings; apparent discrepancies between solution-state and solidstate NMR data obtained for the small protein GB1 suggest that crystal packing might play a role also in this case. 46,49 Further comparative studies are needed in this area.…”

Section: Investigations Of Ring Flipsmentioning

confidence: 99%

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NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins

Akke

Weininger

2023

J. Phys. Chem. B

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Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180°rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wuẗhrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.

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Section: ■ Ring Flip Mechanismsmentioning

confidence: 88%

Section: Investigations Of Ring Flipsmentioning

confidence: 99%

Section: ■ Computational Studies To Augment and Interpret Nmr Datamentioning

confidence: 99%

Section: Investigations Of Ring Flipsmentioning

confidence: 99%

See 2 more Smart Citations

NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins

Akke

Weininger

2023

J. Phys. Chem. B

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“…For the small globular protein used as a case example in this proof of concept study, the protein dynamics are confirmed to be highly similar between solution and crystal. Conversely, for manifold future targets, including supramolecular assemblies, fibrils, and membrane proteins, whose plasticity is functionally modulated by the complexation/aggregation state, ssNMR-restrained ensemble MD simulations will be key to elucidating diverse biological questions, possibly also addressing the challenge of in silico reconstruction of the explicit crystal lattices. − …”

mentioning

confidence: 99%

Integrated Assessment of the Structure and Dynamics of Solid Proteins

Söldner

Grohe

Neidig

et al. 2023

J. Phys. Chem. Lett.

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Understanding macromolecular function, interactions, and stability hinges on detailed assessment of conformational ensembles. For solid proteins, accurate elucidation of the spatial aspects of dynamics at physiological temperatures is limited by the qualitative character or low abundance of solid-state nuclear magnetic resonance internuclear distance information. Here, we demonstrate access to abundant proton−proton internuclear distances for integrated structural biology and chemistry with unprecedented accuracy. Apart from highest-resolution single-state structures, the exact distances enable molecular dynamics (MD) ensemble simulations orchestrated by a dense network of experimental interproton distance boundaries gathered in the context of their physical lattices. This direct embedding of experimental ensemble distances into MD will provide access to representative, atomic-level spatial details of conformational dynamics in supramolecular assemblies, crystalline and lipidembedded proteins, and beyond.

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Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten

et al. 2023

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Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein-Protein-Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross-β Amyloidfibrillen HET-s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von "atmenden Bewegungen" auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR-Strukturensemble einer solchen Cross-β-Amyloidstruktur hervorgeht. EinleitungAromatische Seitenketten spielen eine wichtige Rolle für die Stabilität und Funktion von Proteinen: Sie befinden sich häufig in aktiven Zentren oder Eintrittsstellen von Enzymen oder Membrankanälen [1] und sind überrepräsentiert an Protein-Protein-Schnittstellen, [2] so dass aromatische Gruppen direkt an Bindungen oder enzymatischen Umsätzen beteiligt sind. Darüber hinaus stabilisieren sie Proteinstrukturen, indem sie π-π, [3,4] CH-π, [5,6] oder Kation-π [7] -Wechselwirkungen bilden und die Selbstorganisation von Amyloidprotei-nen fördern. [8] Durch die sperrige Natur von Phenylalaninen (Phe), Tyrosinen (Tyr) und Tryptophanen (Trp) hat ihre Dynamik einen interessanten Aspekt: Ringflips um 180°, die zur Umwandlung ununterscheidbarer Zustände (für Phe und Tyr) führen, sind mit erheblichen Energiebarrieren verbunden. Ringflips wurden bereits in den 1970er Jahren durch Kernspinresonanz (NMR; engl.: nuclear magnetic resonance) in Lösung beobachtet. [9][10][11] Man geht davon aus, dass sie "atmende Bewegungen" erfordern, d. h. vorübergehende konformationell angeregte Zustände des Proteins, die das Hohlvolumen zum Drehen des Ringes schaffen. Die

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Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Cited by 7 publications

References 90 publications

NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins

NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins

Integrated Assessment of the Structure and Dynamics of Solid Proteins

Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten

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