Literature DB >> 25573261

Global ITC fitting methods in studies of protein allostery.

Lee Freiburger1, Karine Auclair2, Anthony Mittermaier2.   

Abstract

Allostery is a nearly ubiquitous feature of biological systems in which ligand binding or covalent modification at one site alters the activities of distant sites in a macromolecule or macromolecular complex. The molecular mechanisms underlying this phenomenon have been studied for decades. Nevertheless there are many aspects that remain poorly understood. ITC yields detailed information on the thermodynamics of biomacromolecular interactions and their coupling to additional equilibria, therefore in principle it is a powerful tool for better understanding how allostery is achieved. A particularly powerful approach involves simultaneously fitting multiple ITC data sets together with those of complementary techniques, especially nuclear magnetic resonance and circular dichroism spectroscopies. In this review, we describe several group-fitting methods for discriminating between different binding models and for improving the accuracy of thermodynamic parameters extracted from variable-temperature ITC data. The techniques were applied to the antibiotic resistance-causing enzyme aminoglycoside-6'-acetyltransferase Ii, uncovering the existence of competition between opposing mechanisms and ligand-dependent switching of the underlying mechanism. These novel observations underline the potential of combining ITC and spectroscopic techniques to study allostery.
Copyright © 2014 Elsevier Inc. All rights reserved.

Keywords:  Aminoglycoside acetyltransferase; CD; Cooperativity; ITC; NMR

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Year:  2015        PMID: 25573261      PMCID: PMC5182068          DOI: 10.1016/j.ymeth.2014.12.018

Source DB:  PubMed          Journal:  Methods        ISSN: 1046-2023            Impact factor:   3.608


  57 in total

1.  Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble.

Authors:  H Pan; J C Lee; V J Hilser
Journal:  Proc Natl Acad Sci U S A       Date:  2000-10-24       Impact factor: 11.205

Review 2.  Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010.

Authors:  Rajesh Ghai; Robert J Falconer; Brett M Collins
Journal:  J Mol Recognit       Date:  2012-01       Impact factor: 2.137

Review 3.  Heat capacity in proteins.

Authors:  Ninad V Prabhu; Kim A Sharp
Journal:  Annu Rev Phys Chem       Date:  2005       Impact factor: 12.703

Review 4.  Applications of isothermal titration calorimetry in protein science.

Authors:  Yi Liang
Journal:  Acta Biochim Biophys Sin (Shanghai)       Date:  2008-07       Impact factor: 3.848

5.  Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.

Authors:  J H Ha; R S Spolar; M T Record
Journal:  J Mol Biol       Date:  1989-10-20       Impact factor: 5.469

Review 6.  Mechanisms of cooperativity and allosteric regulation in proteins.

Authors:  M F Perutz
Journal:  Q Rev Biophys       Date:  1989-05       Impact factor: 5.318

7.  Rapid measurement of binding constants and heats of binding using a new titration calorimeter.

Authors:  T Wiseman; S Williston; J F Brandts; L N Lin
Journal:  Anal Biochem       Date:  1989-05-15       Impact factor: 3.365

8.  Overexpression and characterization of the chromosomal aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium.

Authors:  G D Wright; P Ladak
Journal:  Antimicrob Agents Chemother       Date:  1997-05       Impact factor: 5.191

Review 9.  Structural and energetic basis of allostery.

Authors:  Vincent J Hilser; James O Wrabl; Hesam N Motlagh
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

10.  Molecular recognition via coupled folding and binding in a TPR domain.

Authors:  Matthew J Cliff; Mark A Williams; John Brooke-Smith; David Barford; John E Ladbury
Journal:  J Mol Biol       Date:  2005-01-18       Impact factor: 5.469

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  13 in total

1.  Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

Authors:  Chad A Brautigam; Huaying Zhao; Carolyn Vargas; Sandro Keller; Peter Schuck
Journal:  Nat Protoc       Date:  2016-04-07       Impact factor: 13.491

2.  Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity.

Authors:  Elihu C Ihms; Ian R Kleckner; Paul Gollnick; Mark P Foster
Journal:  Biophys J       Date:  2017-04-11       Impact factor: 4.033

Review 3.  Applications of NMR and computational methodologies to study protein dynamics.

Authors:  Chitra Narayanan; Khushboo Bafna; Louise D Roux; Pratul K Agarwal; Nicolas Doucet
Journal:  Arch Biochem Biophys       Date:  2017-05-05       Impact factor: 4.013

Review 4.  In Vitro Analytical Approaches to Study Plant Ligand-Receptor Interactions.

Authors:  Pedro Jimenez Sandoval; Julia Santiago
Journal:  Plant Physiol       Date:  2020-02-07       Impact factor: 8.340

5.  Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.

Authors:  Levani Zandarashvili; Dan Nguyen; Kurtis M Anderson; Mark A White; David G Gorenstein; Junji Iwahara
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

6.  CALX-CBD1 Ca2+-Binding Cooperativity Studied by NMR Spectroscopy and ITC with Bayesian Statistics.

Authors:  Marcus V C Cardoso; Jose D Rivera; Phelipe A M Vitale; Maximilia F S Degenhardt; Layara A Abiko; Cristiano L P Oliveira; Roberto K Salinas
Journal:  Biophys J       Date:  2020-06-10       Impact factor: 4.033

7.  Isothermal Titration Calorimetry.

Authors:  Christopher M Johnson
Journal:  Methods Mol Biol       Date:  2021

8.  Multi-site binding of epigallocatechin gallate to human serum albumin measured by NMR and isothermal titration calorimetry.

Authors:  Joshua D Eaton; Mike P Williamson
Journal:  Biosci Rep       Date:  2017-05-11       Impact factor: 3.840

9.  Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism.

Authors:  Carlos A H Fernandes; Wallance M Pazin; Thiago R Dreyer; Renata N Bicev; Walter L G Cavalcante; Consuelo L Fortes-Dias; Amando S Ito; Cristiano L P Oliveira; Roberto Morato Fernandez; Marcos R M Fontes
Journal:  Sci Rep       Date:  2017-03-03       Impact factor: 4.379

10.  Positive Cooperativity in Substrate Binding by Human Thymidylate Synthase.

Authors:  Jeffrey P Bonin; Paul J Sapienza; Emily Wilkerson; Dennis Goldfarb; Li Wang; Laura Herring; Xian Chen; Michael B Major; Andrew L Lee
Journal:  Biophys J       Date:  2019-08-22       Impact factor: 3.699

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