Characterization of low-lying excited states of proteins by high-pressure NMR

Williamson, Mike; Kitahara, Ryo

doi:10.1016/j.bbapap.2018.10.014

Cited by 32 publications

(37 citation statements)

References 114 publications

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“…In general, chemical shifts are sensitive parameters for monitoring the structural changes of proteins. Specifically, changes in the chemical shifts of amide 1 H and 15 N are correlated to changes in the strengths of hydrogen bonds as well as the backbone ϕ and ψ torsion angles, accompanied by mechanical compression and/or a transition into a different conformational state with a different compressibility. In order to observe these structural changes by changes in chemical shifts, the time scale of the structural changes should be much faster than the NMR chemical shift timescale (i.e., approximately in the millisecond range).…”

Section: Resultsmentioning

confidence: 99%

“…We have focused on the structural characterization of the high‐energy conformations of proteins using high‐pressure nuclear magnetic resonance (NMR) spectroscopy . Elevated pressure can shift a population of protein conformers from the basic folded conformer to a fully unfolded conformer because the former has a larger partial molar volume .…”

Section: Introductionmentioning

confidence: 99%

“…However, the structural details of the transient high‐energy conformations of ubiquitin, for example, folding‐intermediate and partially unfolded conformations, are severely limited because of their low population. They are nevertheless of considerable interest, because local minima in the energy landscape are usually functionally important . We previously reported that an alternatively folded conformation (N 2 ) accounted for ∼20% of the population of wild‐type ubiquitin at ambient pressure (298 K and pH 7.2), but ∼70% of the population of the ubiquitin Q41N variant (hereafter referred to as Q41N) at ambient pressure, and accounted for 97% of the population at 2500 bar (298 K and pH 7.2) .…”

Section: Introductionmentioning

confidence: 99%

“…4 We have focused on the structural characterization of the high-energy conformations of proteins using high-pressure nuclear magnetic resonance (NMR) spectroscopy. [6][7][8][9] Elevated pressure can shift a population of protein conformers from the basic folded conformer to a fully unfolded conformer because the former has a larger partial molar volume. 10 Although solution NMR, including high-pressure NMR, is a useful technique to elucidate the dynamic equilibrium of proteins, structural determination remains difficult since conformational heterogeneity and the microsecond-to-millisecond time scale motions of the polypeptide chain lead to peakbroadening and missing peaks in the NMR spectra.…”

Section: Introductionmentioning

confidence: 99%

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Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

et al. 2019

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Nuclear magnetic resonance (NMR) is a powerful tool to study three‐dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that ubiquitin has two folded conformations, N1 and N2 and plus another folded conformation, I, in which some amide group signals of residues 33–41 almost disappeared above 3 kbar at pH 4.5 and 273 K. Thus, well‐converged structural models could not be obtained for this region owing to the absence of distance restraints. Here, we reexamine the problem using the ubiquitin Q41N variant as a model for this locally disordered conformation, I. We demonstrate that the variant shows pressure‐induced loss of backbone amide group signals at residues 28, 33, 36, and 39–41 like the wild‐type, with a similar but smaller effect on CαH and CβH signals. In order to characterize this I structure, we measured paramagnetic relaxation enhancement (PRE) under high pressure to obtain distance restraints, and calculated the structure assisted by Bayesian inference. We conclude that the more disordered I conformation observed at pH 4.0, 278 K, and 2.5 kbar largely retained the N2 conformation, although the amide groups at residues 33–41 have more heterogeneous conformations and more contact with water, which differ from the N1 and N2 states. The PRE‐assisted strategy has the potential to improve structural characterization of proteins that lack NMR signals, especially for relatively more open and hydrated protein conformations.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

et al. 2019

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“…In NMR spectroscopy,h ighpressure NMR has been appliedt ob ias the energy landscape by disfavoring the ground state and favoring excited states to differentd egrees. [58,59] In so doing, it can alter the populations of different states, without adding much extra energyt ot he system,a nd thus make previously unobservable conformations observable, making it easier to characterize structureso fm inor (but functionally important) conformers.…”

Section: High-pressure Deer Confirms the Two Distinct Populations Of mentioning

confidence: 99%

Identifying Protein Conformational Dynamics Using Spin‐label ESR

Lai

Kuo

Chiang

2019

Chemistry An Asian Journal

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Spin‐label electron spin resonance (ESR) has emerged as a powerful tool to characterize protein dynamics. One recent advance is the development of ESR for resolving dynamical components that occur or coexist during a biological process. It has been applied to study the complex structural and dynamical aspects of membranes and proteins, such as conformational changes in protein during translocation from cytosol to membrane, conformational exchange between equilibria in response to protein‐protein and protein‐ligand interactions in either soluble or membrane environments, protein oligomerization, and temperature‐ or hydration‐dependent protein dynamics. As these topics are challenging but urgent for understanding the function of a protein on the molecular level, the newly developed ESR methods to capture individual dynamical components, even in low‐populated states, have become a great complement to other existing biophysical tools.

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Driving Protein Conformational Cycles in Physiology and Disease: “Frustrated” Amino Acid Interaction Networks Define Dynamic Energy Landscapes

2020

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A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or “conformational cycle,” required for function is proposed. It is suggested that the free‐energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free‐energy landscape. Some network connections are consistent in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states.

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Characterization of low-lying excited states of proteins by high-pressure NMR

Cited by 32 publications

References 114 publications

Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin

Identifying Protein Conformational Dynamics Using Spin‐label ESR

Driving Protein Conformational Cycles in Physiology and Disease: “Frustrated” Amino Acid Interaction Networks Define Dynamic Energy Landscapes

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