Fitting side-chain NMR relaxation data using molecular simulations

Kümmerer, Felix; Orioli, Simone; Harding-Larsen, David; Hoffmann, Falk; Gavrilov, Yulian; Teilum, Kaare; Lindorff‐Larsen, Kresten

doi:10.1101/2020.08.18.256024

Cited by 8 publications

(18 citation statements)

References 86 publications

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“…[54][55][56] We averaged the 240 original blocks of 10 ns into 10 blocks of 240 ns and performed a leave-N-out cross-validation with N=1…5 to evaluate the convergence of the side chain order parameters. 57 Specifically, for each N we split the 10 blocks in a reference set of 10-N and a test set of N blocks (the left-out blocks), averaged the S 2 axis,sim values within the two sets and computed the RMSD between the resulting average values of the order parameters. For the same N, this procedure was repeated for all the possible combinations of the left out blocks and the corresponding RMSDs are averaged to obtain <RMSD>.…”

Section: Methodsmentioning

confidence: 99%

“…The approach is similar to previously described methods for fitting ensembles using order parameters, 54,58 but using a reweighting approach similar to our recently described ABSURDer method. 57 The functional form for the target function that we here used is:…”

Section: Methodsmentioning

confidence: 99%

“…The parameter 𝜃 is used to set the balance between our trust in the prior and in the experimental data. See Kümmerer et al 57 and Orioli et al 59 for the further details.…”

Section: Simulationsmentioning

confidence: 99%

See 2 more Smart Citations

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

Gavrilov¹,

Kümmerer²,

Orioli³

et al. 2021

Preprint

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The conformational heterogeneity of a folded protein can affect both its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here we have examined whether changed native state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side-chains with molecular dynamics simulations to quantify the native state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: A reduction in conformational dynamics (and entropy) of the native state of L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native state entropy might be needed to improve the predictions of the effect of mutations on protein stability.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

Gavrilov¹,

Kümmerer²,

Orioli³

et al. 2021

Preprint

Self Cite

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“…Specifically, segmental tumbling of α-helical and extended chain conformations has been implied to lead to pronounced diffusion anisotropy effects for intraresidual and sequential 1 H− 1 H NOEs (Ying et al, 2014;Mantsyzov et al, 2014Mantsyzov et al, , 2015. At the same time, the 3D GAF model (Bremi and Brüschweiler, 1997;Lienin et al, 1998) has been invoked to further rationalize the presence of anisotropic dynamics on the local scale of the peptide plane. This model has recently been reframed by Salvi et al (2017) to analyze MD-simulated 15 N relaxation of a partially disordered protein.…”

Section: Introductionmentioning

confidence: 99%

Detecting anisotropic segmental dynamics in disordered proteins by cross-correlated spin relaxation

et al. 2021

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Abstract. Among the numerous contributions of Geoffrey Bodenhausen to NMR spectroscopy, his developments in the field of spin-relaxation methodology and theory will definitely have a long lasting impact. Starting with his seminal contributions to the excitation of multiple-quantum coherences, he and his group thoroughly investigated the intricate relaxation properties of these “forbidden fruits” and developed experimental techniques to reveal the relevance of previously largely ignored cross-correlated relaxation (CCR) effects, as “the essential is invisible to the eyes”. Here we consider CCR within the challenging context of intrinsically disordered proteins (IDPs) and emphasize its potential and relevance for the studies of structural dynamics of IDPs in the future years to come. Conventionally, dynamics of globularly folded proteins are modeled and understood as deviations from otherwise rigid structures tumbling in solution. However, with increasing protein flexibility, as observed for IDPs, this apparent dichotomy between structure and dynamics becomes blurred. Although complex dynamics and ensemble averaging might impair the extraction of mechanistic details even further, spin relaxation uniquely encodes a protein's structural memory. Due to significant methodological developments, such as high-dimensional non-uniform sampling techniques, spin relaxation in IDPs can now be monitored in unprecedented resolution. Not embedded within a rigid globular fold, conventional 15N spin probes might not suffice to capture the inherently local nature of IDP dynamics. To better describe and understand possible segmental motions of IDPs, we propose an experimental approach to detect the signature of anisotropic segmental dynamics by quantifying cross-correlated spin relaxation of individual 15N1HN and 13C′13Cα spin pairs. By adapting Geoffrey Bodenhausen's symmetrical reconversion principle to obtain zero frequency spectral density values, we can define and demonstrate more sensitive means to characterize anisotropic dynamics in IDPs.

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“…However, due to a general lack of analytical descriptions for IDP dynamics (Modig and Poulsen, 2008;Idiyatullin et al, 2001;Bussell and Eliezer, 2001;Kadeřávek et al, 2014;Khan et al, 2015), this notion has been of somewhat academic nature until the recent past. Continuous developments in molecular dynamics (MD) simulation protocols (Piana et al, 2015;Rauscher et al, 2015;Robustelli et al, 2018;Zerze et al, 2019;Piana et al, 2020;Gopal et al, 2021;Shea et al, 2021) demonstrate how this gap can finally be bridged, allowing us to validate, refine and/or analyze dynamic ensemble representations of proteins (Kämpf et al, 2018;Kümmerer et al, 2020;Salvi et al, 2016Salvi et al, , 2017. With the necessary timescales becoming increasingly accessible (Stone et al, 2007(Stone et al, , 2010Salomon-Ferrer et al, 2013;Eastman et al, 2017) and the spectral resolution provided by high-dimensional NUS experiments to overcome the problem of severe spectral overlap (Grudziąż et al, 2018), spin-relaxation in IDPs can be investigated in unprecedented fashion.…”

mentioning

confidence: 99%

Detecting segmental anisotropic diffusion in disordered proteins by cross-correlated spin-relaxation

Kauffmann¹,

Ceccolini²,

Kontaxis³

et al. 2021

Preprint

View full text Add to dashboard Cite

Abstract. Among the numerous contributions of Geoffrey Bodenhausen to NMR spectroscopy his developments in the field of spin-relaxation methodology and theory will definitely have a long lasting impact. Starting with his seminal contributions to the excitation of multiple-quantum coherences he and his group thoroughly investigated the intricate relaxation properties of these “forbidden fruits” and developed experimental techniques to reveal the relevance of previously largely ignored cross-correlated relaxation (CCR) effects, as “the essential is invisible to the eyes”. Here we want to discuss CCR within the challenging context of intrinsically disordered proteins (IDPs) and emphasize its potential and relevance for the studies of structural dynamics of IDPs in the future years to come. Conventionally, dynamics of globularly folded proteins are modeled and understood as deviations from otherwise rigid structures tumbling in solution. However, with increasing protein flexibility, as observed for IDPs, this apparent dichotomy between structure and dynamics becomes blurred. Although complex dynamics and ensemble averaging might impair the extraction of mechanistic details even further, spin-relaxation uniquely encodes a protein’s structural memory, i.e. the temporal persistence of concerted motions and structural arrangements. Due to significant methodological developments, such as high-dimensional non-uniform sampling techniques, spin-relaxation in IDPs can now be monitored in unprecedented resolution. Not embedded within a rigid globular fold, conventional 15N spin probes might not suffice to capture the inherently local nature of IDP dynamics. To better describe and understand possible segmental motions of IDPs, we propose an experimental approach to detect the signature of diffusion anisotropy by quantifying cross-correlated spin relaxation of individual 15N1HN and 13C'13Cα spin pairs. By adapting Geoffrey Bodenhausen’s symmetrical reconversion principle to obtain zero frequency spectral density values we can define and demonstrate more sensitive means to characterize segmental anisotropic diffusion in IDPs.

show abstract

Fitting side-chain NMR relaxation data using molecular simulations

Cited by 8 publications

References 86 publications

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

Detecting anisotropic segmental dynamics in disordered proteins by cross-correlated spin relaxation

Detecting segmental anisotropic diffusion in disordered proteins by cross-correlated spin-relaxation

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