Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

Parra, R. Gonzalo; Schafer, Nicholas P.; Radusky, Leandro; Tsai, Ming-Yen; Guzovsky, A. Brenda; Wolynes, Peter G.; Ferreiro, Diego U.

doi:10.1093/nar/gkw304

Cited by 199 publications

(254 citation statements)

References 23 publications

(30 reference statements)

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“…21 The frustration can be readily quantified by computational tools such as the Frustratometer. 22 Residual frustration is not necessarily an accident of nature coming from some failure of evolutionary optimization but can signal an adaptation to facilitate ligand-induced functional allosteric changes of protein conformational states. 19 Because of the multibasin character of most functional proteins, the dynamics of native proteins is anisotropic.…”

Section: Introductionmentioning

confidence: 99%

Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors

et al. 2017

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Many eukaryotic transcription factors function after forming oligomers. The choice of protein partners is a nonrandom event that has distinct functional consequences for gene regulation. In the present work we examine three dimers of transcription factors in the NFκB family: p50p50, p50p65, and p65p65. The NFκB dimers bind to a myriad of genomic sites and switch the targeted genes on or off with precision. The p65p50 heterodimer of NFκB is the strongest DNA binder, and its unbinding is controlled kinetically by molecular stripping from the DNA induced by IκB. In contrast, the homodimeric forms of NFκB, p50p50 and p65p65, bind DNA with significantly less affinity, which places the DNA residence of the homodimers under thermodynamic rather than kinetic control. It seems paradoxical that the heterodimer should bind more strongly than either of the symmetric homodimers since DNA is a nearly symmetric target. Using a variety of energy landscape analysis tools, here we uncover the features in the molecular architecture of NFκB dimers that are responsible for these drastically different binding free energies. We show that frustration in the heterodimer interface gives the heterodimer greater conformational plasticity, allowing the heterodimer to better accommodate the DNA. We also show how the elastic energy and mechanical strain in NFκB dimers can be found by extracting the principal components of the fluctuations in Cartesian coordinates as well as fluctuations in the space of physical contacts, which are sampled via simulations with a predictive energy landscape Hamiltonian. These energetic contributions determine the specific detailed mechanisms of binding and stripping for both homo- and heterodimers.

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Section: Introductionmentioning

confidence: 99%

Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors

et al. 2017

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“…We computed 'local energetic frustration' in the RAS proteins for each variant using the Ferreiro-Wolynes algorithm [18,58,59], which estimates how favorable a specific contact (or an aminoacid residue) is relative to the set of all possible contacts (or an amino-acid residue) in that location and compares it to the energies of a set of 'decoy' states. All 20 amino acids are considered at each site in RAS for the calculation of frustration.…”

Section: Structure-based Scoresmentioning

confidence: 99%

Integration of Multi-level Molecular Scoring for the Interpretation of RAS-Family Genetic Variation

Tripathi

Dsouza

Urrutia

et al. 2019

Preprint

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Protein-coding genetic variants are the first considered in most studies and Precision Medicine workflows, but their interpretation is primarily driven by DNA sequence-based analytical tools and annotations. Thus, more specific and mechanistic interpretations should be attainable by integrating DNA-based scores with scores from the protein 3D structure. However, reliable and reproducible standardization of methods that use 3D structure for genomic variation is still lacking. Further, we believe that the current paradigm of aiming to directly predict the pathogenicity of variants skips the critical step of inferring, with precision, molecular mechanisms of dysfunction. Thus, we report herein the development and evaluation of single and composite 3D structurebased scores and their integration with protein and DNA sequence-based scores to better understand not only if a genomic variant alters a protein, but how. We believe this is a critical step for understanding mechanistic changes due to genomic variants, designing functional validation tests, and for improving disease classifications. We applied this approach to the RAS gene family encoding seven distinct proteins and their 935 unique missense variants present somatically in cancer, in rare diseases (termed RASopathies), and in the currently healthy adult population. This knowledge shows that protein structure-based scores are distinct from information available from genomic annotation, that they are useful for interpreting genomic variants, and they should be taken into consideration in future guidelines for genomic data interpretation. Significance StatementGenetic information from patients is a powerful data type for understanding individual differences in disease risk and treatment, but most of the genetic variation we observe has no mechanistic interpretation. This lack of interpretation limits the use of genomics data in clinical care. Standard methods for genomics data interpretation take advantage of annotations available for the human reference genome, but they do not consider the 3D protein molecule. We believe that changes to the 3D molecule must be considered, to augment current practice and lead to more precise interpretation. In this work, we present our initial process for systematic multi-level molecular scores, including 3D, to interrogate 935 RAS-family variants that are relevant in both cancer and rare diseases. \body

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“…Local frustration analysis of the modelled serpin: protease complexes was conducted with the Frustratometer2 web server 91 . Essentially, the energetic frustration is obtained by the comparison of the native state interactions to a set of generated "decoy" states where the identities of each residue are mutated.…”

Section: Frustration Calculationmentioning

confidence: 99%

Reactive Centre Loop Dynamics and Serpin Specificity

Marijanovic

Fodor

Riley

et al. 2018

Preprint

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Serine proteinase inhibitors (serpins), typically fold to a metastable native state and undergo a major conformational change in order to inhibit target proteases. However, conformational labiality of the native serpin fold renders them susceptible to misfolding and aggregation, and underlies misfolding diseases such as α1-antitrypsin deficiency. Serpin specificity towards its protease target is dictated by its flexible and solvent exposed reactive centre loop (RCL), which forms the initial interaction with the target protease during inhibition. Previous studies have attempted to alter the specificity by mutating the RCL to that of a target serpin, but the rules governing specificity are not understood well enough yet to enable specificity to be engineered at will. In this paper, we use conserpin, a synthetic, thermostable serpin, as a model protein with which to investigate the determinants of serpin specificity by engineering its RCL.Replacing the RCL sequence with that from α1-antitrypsin fails to restore specificity against trypsin or human neutrophil elastase. Structural determination of the RCL-engineered conserpin and molecular dynamics simulations indicate that, although the RCL sequence may partially dictate specificity, local electrostatics and RCL dynamics may dictate the rate of insertion during protease inhibition, and thus whether it behaves as an inhibitor or a substrate.Engineering serpin specificity is therefore substantially more complex than solely manipulating the RCL sequence, and will require a more thorough understanding of how conformational dynamics achieves the delicate balance between stability, folding and function required by the exquisite serpin mechanism of action.

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Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

Cited by 199 publications

References 23 publications

Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors

Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors

Integration of Multi-level Molecular Scoring for the Interpretation of RAS-Family Genetic Variation

Reactive Centre Loop Dynamics and Serpin Specificity

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