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Induced-fit Model01:13

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Natural selection influences the frequencies of particular alleles and phenotypes within populations in several different ways. Primarily, natural selection can be directional, stabilizing, or disruptive. Directional selection favors one extreme trait and shifts the population towards that phenotype while selecting against individuals displaying alternate traits. Stabilizing selection favors an intermediate trait with a narrow range of variation. Deviation from the optimal phenotype towards an...
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When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Distinguishing induced fit from conformational selection.

Stefano Gianni1, Jakob Dogan2, Per Jemth3

  • 1Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

Biophysical Chemistry
|April 22, 2014
PubMed
Summary

This study introduces a kinetic method to differentiate protein conformational selection from induced fit mechanisms. The approach analyzes binding rate constants under varying protein and ligand concentrations to distinguish these common protein-ligand interaction models.

Keywords:
Conformational selectionInduced fitKineticsProtein–protein interactions

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Area of Science:

  • Biochemistry
  • Biophysics
  • Structural Biology

Background:

  • Protein-ligand interactions frequently involve protein conformational changes.
  • Distinguishing between conformational selection and induced fit mechanisms is challenging, especially with hyperbolic binding kinetics.
  • Recent interest in protein domain conformational sampling and intrinsically disordered proteins highlights the need for clarity on binding mechanisms.

Purpose of the Study:

  • To present a novel kinetic method for unequivocally distinguishing induced fit from conformational selection.
  • To provide a tool for analyzing protein-ligand binding mechanisms based on observed conformational changes.

Main Methods:

  • Measuring the observed rate constant (λ) for protein-ligand binding.
  • Systematically varying protein and ligand concentrations in separate experimental setups.
  • Analyzing the dependence of λ on varying concentrations to identify distinct kinetic signatures.

Main Results:

  • Induced fit mechanisms consistently show a hyperbolic dependence of λ as concentrations increase.
  • Conformational selection mechanisms exhibit distinct kinetic behaviors when protein or ligand concentrations are independently varied.
  • The method offers a way to differentiate these mechanisms, supported by literature examples.

Conclusions:

  • The described kinetic method can unequivocally distinguish induced fit from conformational selection in specific cases.
  • This approach aids in understanding the nuances of protein-ligand binding and conformational dynamics.
  • Further application and discussion of limitations are necessary for broader use.