Protein frustratometer: a tool to localize energetic frustration in protein molecules

Jenik, Michael; Parra, R. Gonzalo; Radusky, Leandro; Turjanski, Adrián; Wolynes, Peter G.; Ferreiro, Diego U.

doi:10.1093/nar/gks447

Cited by 142 publications

(171 citation statements)

References 17 publications

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“…An algorithm to do this is implemented in the frustratometer (32), which estimates the energetic contribution of contacts to the stability of the native state and compares these energies in the native structure to the distribution of energies that would be obtained by performing residue substitutions in the local environment. Native contacts whose energies are sufficiently deep in the energetically stabilizing part of the distribution are called minimally frustrated and are drawn as green lines on the structure, whereas the native contacts that are found sufficiently far in the energetically destabilizing region are called frustrated and are drawn as red lines.…”

Section: Structures Dynamics and Thermodynamicsmentioning

confidence: 99%

“…Native contacts whose energies are sufficiently deep in the energetically stabilizing part of the distribution are called minimally frustrated and are drawn as green lines on the structure, whereas the native contacts that are found sufficiently far in the energetically destabilizing region are called frustrated and are drawn as red lines. The quantitative details of this algorithm including electrostatic effects have been discussed in previous papers (30,32,33). The frustration patterns of the NF-κB were analyzed in the structure of free NF-κB, NF-κB bound with the DNA, and NF-κB bound with IκB.…”

Section: Structures Dynamics and Thermodynamicsmentioning

confidence: 99%

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Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network

Potoyan

Zheng

Komives

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

119

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Genetic switches based on the NF-κB/ IκB/ DNA system are master regulators of an array of cellular responses. Recent kinetic experiments have shown that IκB can actively remove NF-κB bound to its genetic sites via a process called "molecular stripping." This allows the NF-κB/ IκB/ DNA switch to function under kinetic control rather than the thermodynamic control contemplated in the traditional models of gene switches. Using molecular dynamics simulations of coarse-grained predictive energy landscape models for the constituent proteins by themselves and interacting with the DNA we explore the functional motions of the transcription factor NF-κB and its various binary and ternary complexes with DNA and the inhibitor IκB. These studies show that the function of the NF-κB/ IκB/ DNA genetic switch is realized via an allosteric mechanism. Molecular stripping occurs through the activation of a domain twist mode by the binding of IκB that occurs through conformational selection. Free energy calculations for DNA binding show that the binding of IκB not only results in a significant decrease of the affinity of the transcription factor for the DNA but also kinetically speeds DNA release. Projections of the free energy onto various reaction coordinates reveal the structural details of the stripping pathways. T he binding and release of protein transcription factors from DNA are fundamental molecular processes by which genes are regulated in the cell. The pioneering studies of Jacob, Monod, Ptashne, and Gilbert explained how these two processes, seeming inverses of each other, while being maintained in local chemical equilibrium, could still lead to robust genetic switches by coupling to protein synthesis and degradation, which are kinetically controlled far from equilibrium processes (1-4). This classic picture, with the law of mass action at its core (5, 6), suggests that understanding the molecular mechanism of the binding and release of transcription factors is of secondary interest compared with understanding the thermodynamics of protein-DNA recognition. The recent discovery of proteininduced release of a DNA-bound transcription factor in the NF-κB=IκB=DNA genetic switch changes this picture (7). The induced process, called "molecular stripping," opens up the possibility of molecular kinetic control of binding and release, thus overturning the classic paradigm based only on thermodynamic control. In this paper, we use molecular dynamics simulations of coarse-grained but predictive energy landscape models of the proteins along with their interacting DNA to explore first how the NF-κB transcription factor binds individually both to DNA and to its inhibitor IκB and then to study how an approaching IκB can strip the NF-κB from a DNA molecule to which it has already been bound, by forming an intermediate ternary complex. These simulations show that each of the binary binding events involves conformational selection of different NF-κB global conformations. Molecular stripping then occurs that is induced by forming the ternar...

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Section: Structures Dynamics and Thermodynamicsmentioning

confidence: 99%

Section: Structures Dynamics and Thermodynamicsmentioning

confidence: 99%

Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network

Potoyan

Zheng

Komives

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

119

View full text Add to dashboard Cite

show abstract

“…It is now textbook knowledge (Williamson, 2012) that proteins are dynamic and that structural states should be treated as ensembles that fluctuate around energy minima. This behavior is described by the energy landscape theory (Frauenfelder et al 1991), which can be applied to protein dynamics using the principle of minimal frustration (Ferreiro et al 2007(Ferreiro et al , 2014Jenik et al 2012). NMR spectroscopy has developed in parallel with the energy landscape theory, and the two research fields are now converging to provide an unprecedented understanding of protein function.…”

Section: Introductionmentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

143

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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“…S7. Misfolding: To identify on the structure the regions that are mainly involved in the transient misfolding, we highlighted in green the residues with more than 50% nonnative interactions in the early transition state of β T = 0.45; frustration was calculated from the web server www.frustratometer.tk (22) and residues forming highly frustrated interactions are reported in green (see also Fig. S1).…”

Section: Methodsmentioning

confidence: 99%

“…This result was achieved by characterizing the structures of both the early and late events of folding using Φ-value analysis (20) and restrained molecular dynamics simulations (21). By analyzing the structures of the different states along the folding process we found an unexpected number of nonnative interactions that slow down folding and superpose with the highly frustrated regions, as detected by the frustratometer server (22). The nonnative regions, which display peculiar Φ values, either negative or greater than unity, were predicted on the basis of the transition state structures determined from the Φ values, and subsequently confirmed by a second round of amino acid…”

mentioning

confidence: 99%

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

Gianni

Camilloni

Giri

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Folding and function may impose different requirements on the amino acid sequences of proteins, thus potentially giving rise to conflict. Such a conflict, or frustration, can result in the formation of partially misfolded intermediates that can compromise folding and promote aggregation. We investigate this phenomenon by studying frataxin, a protein whose normal function is to facilitate the formation of iron-sulfur clusters but whose mutations are associated with Friedreich's ataxia. To characterize the folding pathway of this protein we carry out a Φ-value analysis and use the resulting structural information to determine the structure of the folding transition state, which we then validate by a second round of rationally designed mutagenesis. The analysis of the transition-state structure reveals that the regions involved in the folding process are highly aggregation-prone. By contrast, the regions that are functionally important are partially misfolded in the transition state but highly resistant to aggregation. Taken together, these results indicate that in frataxin the competition between folding and function creates the possibility of misfolding, and that to prevent aggregation the amino acid sequence of this protein is optimized to be highly resistant to aggregation in the regions involved in misfolding.

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Protein frustratometer: a tool to localize energetic frustration in protein molecules

Cited by 142 publications

References 17 publications

Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network

Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network

Protein dynamics and function from solution state NMR spectroscopy

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

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