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配体诱导的蛋白质过渡态稳定将结合途径从构象选择切换到诱导契合。

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit.

机构信息

Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.

出版信息

Proc Natl Acad Sci U S A. 2024 Apr 2;121(14):e2317747121. doi: 10.1073/pnas.2317747121. Epub 2024 Mar 25.


DOI:10.1073/pnas.2317747121
PMID:38527204
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10998626/
Abstract

Protein-ligand complex formation is fundamental to biological function. A central question is whether proteins spontaneously adopt binding-competent conformations to which ligands bind conformational selection (CS) or whether ligands induce the binding-competent conformation induced fit (IF). Here, we resolve the CS and IF binding pathways by characterizing protein conformational dynamics over a wide range of ligand concentrations using NMR relaxation dispersion. We determined the relative flux through the two pathways using a four-state binding model that includes both CS and IF. Experiments conducted without ligand show that galectin-3 exchanges between the ground-state conformation and a high-energy conformation similar to the ligand-bound conformation, demonstrating that CS is a plausible pathway. Near-identical crystal structures of the apo and ligand-bound states suggest that the high-energy conformation in solution corresponds to the apo crystal structure. Stepwise additions of the ligand lactose induce progressive changes in the relaxation dispersions that we fit collectively to the four-state model, yielding all microscopic rate constants and binding affinities. The ligand affinity is higher for the bound-like conformation than for the ground state, as expected for CS. Nonetheless, the IF pathway contributes greater than 70% of the total flux even at low ligand concentrations. The higher flux through the IF pathway is explained by considerably higher rates of exchange between the two protein conformations in the ligand-associated state. Thus, the ligand acts to decrease the activation barrier between protein conformations in a manner reciprocal to enzymatic transition-state stabilization of reactions involving ligand transformation.

摘要

蛋白质-配体复合物的形成是生物功能的基础。一个核心问题是,蛋白质是否会自发地采用结合能力构象,使配体结合(构象选择,CS),或者配体是否诱导结合能力构象(诱导契合,IF)。在这里,我们通过使用 NMR 弛豫分散来表征在广泛的配体浓度范围内蛋白质构象动力学,解决了 CS 和 IF 结合途径的问题。我们使用包括 CS 和 IF 的四态结合模型来确定两条途径的相对通量。没有配体的实验表明,半乳凝素-3在基态构象和类似于配体结合构象的高能构象之间交换,这表明 CS 是一种可行的途径。无配体时的近相同的apo 和配体结合状态的晶体结构表明,溶液中的高能构象对应于 apo 晶体结构。逐步加入配体乳糖会引起弛豫分散的逐渐变化,我们将其集体拟合到四态模型中,得到所有微观速率常数和结合亲和力。配体亲和力对于结合样构象高于基态,这与 CS 预期的一致。尽管如此,即使在低配体浓度下,IF 途径的通量也超过 70%。IF 途径的通量较高是由于在配体结合状态下两种蛋白质构象之间的交换速率大大提高。因此,配体以与涉及配体转化的酶促过渡态稳定化相反的方式,降低蛋白质构象之间的活化势垒。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/eb5aa80817fb/pnas.2317747121fig05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/2f257541cf03/pnas.2317747121fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/36fbd4e4f578/pnas.2317747121fig02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/6027da13cc03/pnas.2317747121fig03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/233da853c733/pnas.2317747121fig04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/eb5aa80817fb/pnas.2317747121fig05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/2f257541cf03/pnas.2317747121fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/36fbd4e4f578/pnas.2317747121fig02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/6027da13cc03/pnas.2317747121fig03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/233da853c733/pnas.2317747121fig04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/196c/10998626/eb5aa80817fb/pnas.2317747121fig05.jpg

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Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit.

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[3]
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[4]
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本文引用的文献

[1]
Cosolvent Dimethyl Sulfoxide Influences Protein-Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein-Ligand Encounter.

Biochemistry. 2023-1-3

[2]
Biological Magnetic Resonance Data Bank.

Nucleic Acids Res. 2023-1-6

[3]
A litmus test for classifying recognition mechanisms of transiently binding proteins.

Nat Commun. 2022-7-1

[4]
Mapping the energy landscape of protein-ligand binding linear free energy relationships determined by protein NMR relaxation dispersion.

RSC Chem Biol. 2020-12-23

[5]
Algebraic expressions for Carr-Purcell-Meiboom-Gill relaxation dispersion for N-site chemical exchange.

J Magn Reson. 2020-12

[6]
Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding.

J Am Chem Soc. 2019-1-23

[7]
General Expressions for Carr-Purcell-Meiboom-Gill Relaxation Dispersion for N-Site Chemical Exchange.

Biochemistry. 2018-8-7

[8]
Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions.

Elife. 2018-2-20

[9]
Comprehensive analysis of NMR data using advanced line shape fitting.

J Biomol NMR. 2017-10

[10]
Kinetic Insights into the Binding between the nSH3 Domain of CrkII and Proline-Rich Motifs in cAbl.

Biophys J. 2016-11-1

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