Distinguishing induced fit from conformational selection

Gianni, Stefano; Dogan, Jakob; Jemth, Per

doi:10.1016/j.bpc.2014.03.003

Cited by 146 publications

(169 citation statements)

References 40 publications

(63 reference statements)

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“…The catalytically active state of adenylate kinase (AdK), the enzyme in focus here, is a closed conformation, for which the structure (with bound ligand) has been determined by X-ray crystallography (13). Sampling of a closed conformation in a ligand-free "apo enzyme" is one of the prerequisites for the conformational selection model (14), in which functionally active states are populated in the absence of substrate. In this model, substrate binding redistributes the statistical weights in a manner that favors active conformations.…”

mentioning

confidence: 99%

Structural basis for ligand binding to an enzyme by a conformational selection pathway

Kovermann

Grundström

Sauer‐Eriksson

et al. 2017

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

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Proteins can bind target molecules through either induced fit or conformational selection pathways. In the conformational selection model, a protein samples a scarcely populated high-energy state that resembles a target-bound conformation. In enzymatic catalysis, such high-energy states have been identified as crucial entities for activity and the dynamic interconversion between ground states and high-energy states can constitute the ratelimiting step for catalytic turnover. The transient nature of these states has precluded direct observation of their properties. Here, we present a molecular description of a high-energy enzyme state in a conformational selection pathway by an experimental strategy centered on NMR spectroscopy, protein engineering, and X-ray crystallography. Through the introduction of a disulfide bond, we succeeded in arresting the enzyme adenylate kinase in a closed high-energy conformation that is on-pathway for catalysis. A 1.9-Å X-ray structure of the arrested enzyme in complex with a transition state analog shows that catalytic sidechains are properly aligned for catalysis. We discovered that the structural sampling of the substrate free enzyme corresponds to the complete amplitude that is associated with formation of the closed and catalytically active state. In addition, we found that the trapped high-energy state displayed improved ligand binding affinity, compared with the wild-type enzyme, demonstrating that substrate binding to the high-energy state is not occluded by steric hindrance. Finally, we show that quenching of fast time scale motions observed upon ligand binding to adenylate kinase is dominated by enzyme-substrate interactions and not by intramolecular interactions resulting from the conformational change.enzymatic catalysis | ligand binding | structural biology | adenylate kinase S ubstantial proportions of cellular processes depend on chemical reactions that in aqueous solution often are several orders of magnitude too slow to support biological life (1). This difference between "chemical" and "biological" time scales is bridged by acceleration of the rates of chemical reactions by enzymes (2). The catalytic power of an enzyme depends on a significant reduction of the free energy barrier for the chemical reaction (2). Several factors collectively contribute to an enzyme's efficiency as catalysts, including balanced substrate-binding affinity to ensure selectivity but at the same time avoid kinetic traps, optimal alignment of substrates, activation of a substrate's functional groups, and dehydration of active sites. All of these factors to some degree depend on conformational dynamics of the enzyme (3), where dynamics is defined as the time-dependent displacement of atomic coordinates. Structural excursions from enzymatic ground states to high-energy states have been observed with NMR spectroscopy, and in a few cases, were shown to be rate limiting for catalytic turnover (3-7). Furthermore, it has been proposed that the conformational dynamics required for substrate bindin...

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confidence: 99%

Structural basis for ligand binding to an enzyme by a conformational selection pathway

Kovermann

Grundström

Sauer‐Eriksson

et al. 2017

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

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“…In striking contrast to the temperature-dependent unfolding of the free domain, CD and 1 H NMR studies indicated that the native-like structure was largely intact in the specific DNA complex. Such structure was either regained on specific DNA binding (induced fit) or captured by the specific DNA site to predominate in the equilibrium complex (conformational selection) (71). These biophysical mechanisms are of evolutionary interest as the near-native functional properties of unstable or unfolded polypeptides may rationalize how the exquisite structural organization of modern proteins emerged through stepwise stabilization of nascent partial folds (72).…”

Section: Discussionmentioning

confidence: 99%

Human Sex Determination at the Edge of Ambiguity

Racca¹,

Chen²,

Yang

et al. 2016

Journal of Biological Chemistry

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A general problem is posed by analysis of transcriptional thresholds governing cell fate decisions in metazoan development. A model is provided by testis determination in therian mammals. Its key step, Sertoli cell differentiation in the embryonic gonadal ridge, is initiated by SRY, a Y-encoded architectural transcription factor. Mutations in human SRY cause gonadal dysgenesis leading to XY female development (Swyer syndrome). Here, we have characterized an inherited mutation compatible with either male or female somatic phenotypes as observed in an XY father and XY daughter, respectively. The mutation (a crevice-forming substitution at a conserved back surface of the SRY high mobility group box) markedly destabilizes the domain but preserves specific DNA affinity and induced DNA bend angle. On transient transfection of diverse human and rodent cell lines, the variant SRY exhibited accelerated proteasomal degradation (relative to wild type) associated with increased ubiquitination; in vitro susceptibility to ubiquitin-independent ("default") cleavage by the 20S core proteasome was unchanged. The variant's gene regulatory activity (as assessed in a cellular model of the rat embryonic XY gonadal ridge) was reduced by 2-fold relative to wild-type SRY at similar levels of mRNA expression. Chemical proteasome inhibition restored native-like SRY expression and transcriptional activity in association with restored occupancy of a sex-specific enhancer element in principal downstream gene Sox9, demonstrating that the variant SRY exhibits essentially native activity on a per molecule basis. Our findings define a novel mechanism of impaired organogenesis, accelerated ubiquitindirected proteasomal degradation of a master transcription factor leading to a developmental decision poised at the edge of ambiguity.

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“…101 The coupled folding and binding of IDRs can be described by 2 mechanisms: induced fit and conformational selection. [102][103][104][105] In addition to mediating promiscuous interactions, IDRs can confer high-specificity, low-affinity, rapid reversibility, and multi-valency to protein-protein interactions. [106][107][108] Thus the presence of IDRs in FOXO3a greatly enhances its capability of binding to other proteins, and several FOXO3a-mediated interactions are discussed below.…”

Section: Protein-protein Interactionsmentioning

confidence: 99%