Bayesian-Maximum-Entropy reweighting of IDP ensembles based on NMR chemical shifts

AbstractBayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.

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Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts

Entropy ◽

10.3390/e21090898 ◽

2019 ◽

Vol 21 (9) ◽

pp. 898 ◽

Cited By ~ 10

Author(s):

Ramon Crehuet ◽

Pedro J. Buigues ◽

Xavier Salvatella ◽

Kresten Lindorff-Larsen

Keyword(s):

Chemical Shift ◽

Maximum Entropy ◽

Chemical Shifts ◽

Intrinsically Disordered Protein ◽

Intrinsically Disordered ◽

Computational Data ◽

Chemical Shift Data ◽

Secondary Chemical Shifts ◽

Validation Set ◽

Secondary Chemical

Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.

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Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

Journal of Biomolecular NMR ◽

10.1007/s10858-019-00283-z ◽

2019 ◽

Vol 73 (12) ◽

pp. 713-725 ◽

Cited By ~ 4

Author(s):

Ruth Hendus-Altenburger ◽

Catarina B. Fernandes ◽

Katrine Bugge ◽

Micha B. A. Kunze ◽

Wouter Boomsma ◽

...

Keyword(s):

Chemical Shift ◽

Secondary Structure ◽

Intrinsically Disordered Proteins ◽

Chemical Shifts ◽

Random Coil ◽

Disordered Proteins ◽

Phosphoryl Group ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Secondary Chemical

Abstract Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.

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Empirical correlation between protein backbone 15N and 13C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

Journal of Biomolecular NMR ◽

10.1007/s10858-009-9324-0 ◽

2009 ◽

Vol 44 (2) ◽

pp. 95-99 ◽

Cited By ~ 20

Author(s):

Liya Wang ◽

John L. Markley

Keyword(s):

Chemical Shift ◽

Chemical Shifts ◽

Empirical Correlation ◽

Protein Backbone ◽

Secondary Chemical Shifts ◽

Secondary Chemical

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Backbone and nearly complete side-chain chemical shift assignments of the human death-associated protein 1 (DAP1)

Biomolecular NMR Assignments ◽

10.1007/s12104-020-09988-x ◽

2020 ◽

Author(s):

Christoph Wiedemann ◽

Johanna Voigt ◽

Jan Jirschitzka ◽

Sabine Häfner ◽

Oliver Ohlenschläger ◽

...

Keyword(s):

Chemical Shift ◽

Chemical Shifts ◽

Intrinsically Disordered Protein ◽

Potential Interaction ◽

Chemical Shift Assignments ◽

Cell Growth And Migration ◽

Structural Investigations ◽

Intrinsically Disordered ◽

Spectral Dispersion ◽

And Migration

AbstractDeath-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer. Here we describe the almost complete $${{^{1}}\text {H}}$$ 1 H , $${{^{13}}\text {C}}$$ 13 C , and $${{^{15}}\text {N}}$$ 15 N chemical shift assignments of the human DAP1. The limited spectral dispersion, mainly in the $${{^{1}}\text {H}{^{\text{N}}}}$$ 1 H N region, and the lack of defined secondary structure elements, predicted based on chemical shifts, identifies human DAP1 as an intrinsically disordered protein (IDP). This work lays the foundation for further structural investigations, dynamic studies, mapping of potential interaction partners or drug screening and development.

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Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered

Biomolecular NMR Assignments ◽

10.1007/s12104-021-10043-6 ◽

2021 ◽

Vol 15 (2) ◽

pp. 441-448

Author(s):

Christoph Wiedemann ◽

Kingsley Benjamin Obika ◽

Sandra Liebscher ◽

Jan Jirschitzka ◽

Oliver Ohlenschlãger ◽

...

Keyword(s):

Chemical Shift ◽

Intrinsically Disordered Protein ◽

Genome Project ◽

Side Chain ◽

Resonance Spectroscopy ◽

Chemical Shift Assignments ◽

Uncharacterized Protein ◽

Protein Coding ◽

Intrinsically Disordered ◽

Side Chain Chemical Shift

AbstractEven though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these “unknown” proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the $$^1$$ 1 H, $$^{13}$$ 13 C, $$^{15}$$ 15 N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.

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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1907251116 ◽

2019 ◽

Vol 116 (41) ◽

pp. 20446-20452 ◽

Cited By ~ 9

Author(s):

Utsab R. Shrestha ◽

Puneet Juneja ◽

Qiu Zhang ◽

Viswanathan Gurumoorthy ◽

Jose M. Borreguero ◽

...

Keyword(s):

Molecular Dynamics ◽

Intrinsically Disordered Proteins ◽

Chemical Shifts ◽

Intrinsically Disordered Protein ◽

Physical Models ◽

Dynamics Simulation ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Eukaryotic Proteomes ◽

Heterogeneous Ensemble

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

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