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Title: Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics

Abstract

The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The “tip of the whip” that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the binding of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. Furthermore NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.

Authors:
 [1];  [2];  [2];  [3];  [3]; ORCiD logo [3]; ORCiD logo [1]
  1. City College of New York, CUNY, New York, NY (United States)
  2. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1349622
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 429; Journal Issue: 7; Journal ID: ISSN 0022-2836
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; nanoscale protein motion; disordered protein; protein binding kinetics; neutron spin echo spectroscopy; protein dynamics

Citation Formats

Callaway, David J. E., Matsui, Tsutomu, Weiss, Thomas, Stingaciu, Laura R., Stanley, Christopher B., Heller, William T., and Bu, Zimei. Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics. United States: N. p., 2017. Web. https://doi.org/10.1016/j.jmb.2017.03.003.
Callaway, David J. E., Matsui, Tsutomu, Weiss, Thomas, Stingaciu, Laura R., Stanley, Christopher B., Heller, William T., & Bu, Zimei. Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics. United States. https://doi.org/10.1016/j.jmb.2017.03.003
Callaway, David J. E., Matsui, Tsutomu, Weiss, Thomas, Stingaciu, Laura R., Stanley, Christopher B., Heller, William T., and Bu, Zimei. Wed . "Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics". United States. https://doi.org/10.1016/j.jmb.2017.03.003. https://www.osti.gov/servlets/purl/1349622.
@article{osti_1349622,
title = {Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics},
author = {Callaway, David J. E. and Matsui, Tsutomu and Weiss, Thomas and Stingaciu, Laura R. and Stanley, Christopher B. and Heller, William T. and Bu, Zimei},
abstractNote = {The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The “tip of the whip” that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the binding of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. Furthermore NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.},
doi = {10.1016/j.jmb.2017.03.003},
journal = {Journal of Molecular Biology},
number = 7,
volume = 429,
place = {United States},
year = {2017},
month = {3}
}

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Works referenced in this record:

Classification of Intrinsically Disordered Regions and Proteins
journal, December 2013

  • van der Lee, Robin; Buljan, Marija; Lang, Benjamin
  • Chemical Reviews, Vol. 114, Issue 13
  • DOI: 10.1021/cr400525m

Intrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept
journal, June 2008


Mechanism of coupled folding and binding of an intrinsically disordered protein
journal, May 2007

  • Sugase, Kenji; Dyson, H. Jane; Wright, Peter E.
  • Nature, Vol. 447, Issue 7147
  • DOI: 10.1038/nature05858

Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity
journal, May 2007

  • Borg, M.; Mittag, T.; Pawson, T.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 23
  • DOI: 10.1073/pnas.0702580104

Regulation of protein–protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes
journal, January 2013

  • Nishi, Hafumi; Fong, Jessica H.; Chang, Christiana
  • Molecular BioSystems, Vol. 9, Issue 7
  • DOI: 10.1039/c3mb25514j

The importance of intrinsic disorder for protein phosphorylation
journal, February 2004


Allosteric post-translational modification codes
journal, October 2012


The regulation of protein phosphorylation
journal, July 2009

  • Johnson, Louise N.
  • Biochemical Society Transactions, Vol. 37, Issue 4
  • DOI: 10.1042/BST0370627

Organizing the cell cortex: the role of ERM proteins
journal, April 2010

  • Fehon, Richard G.; McClatchey, Andrea I.; Bretscher, Anthony
  • Nature Reviews Molecular Cell Biology, Vol. 11, Issue 4
  • DOI: 10.1038/nrm2866

Regulation of G Protein-Coupled Receptor Function by Na + /H + Exchange Regulatory Factors
journal, August 2011

  • Ardura, Juan A.; Friedman, Peter A.
  • Pharmacological Reviews, Vol. 63, Issue 4
  • DOI: 10.1124/pr.110.004176

A molecular switch in the scaffold NHERF1 enables misfolded CFTR to evade the peripheral quality control checkpoint
journal, May 2015

  • Loureiro, Cláudia A.; Matos, Ana Margarida; Dias-Alves, Ângela
  • Science Signaling, Vol. 8, Issue 377
  • DOI: 10.1126/scisignal.aaa1580

The Role of the NHERF Family of PDZ Scaffolding Proteins in the Regulation of Salt and Water Transport: Lessons Learned from Knockout Mice
journal, May 2009


β-Oestradiol rescues ΔF508CFTR functional expression in human cystic fibrosis airway CFBE41o− cells through the up-regulation of NHERF1
journal, July 2008

  • Fanelli, Teresa; Cardone, Rosa Angela; Favia, Maria
  • Biology of the Cell, Vol. 100, Issue 7
  • DOI: 10.1042/BC20070095

PDZ interactions regulate rapid turnover of the scaffolding protein EBP50 in microvilli
journal, July 2012

  • Garbett, Damien; Bretscher, Anthony
  • The Journal of Cell Biology, Vol. 198, Issue 2
  • DOI: 10.1083/jcb.201204008

The tails of apical scaffolding proteins EBP50 and E3KARP regulate their localization and dynamics
journal, November 2013

  • Garbett, Damien; Sauvanet, Cécile; Viswanatha, Raghuvir
  • Molecular Biology of the Cell, Vol. 24, Issue 21
  • DOI: 10.1091/mbc.e13-06-0330

Dynamics of ezrin and EBP50 in regulating microvilli on the apical aspect of epithelial cells
journal, January 2014

  • Viswanatha, Raghuvir; Bretscher, Anthony; Garbett, Damien
  • Biochemical Society Transactions, Vol. 42, Issue 1
  • DOI: 10.1042/BST20130263

An unusually powerful mode of low-frequency sound interference due to defective hair bundles of the auditory outer hair cells
journal, June 2014

  • Kamiya, K.; Michel, V.; Giraudet, F.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 25
  • DOI: 10.1073/pnas.1405322111

A Conformational Switch in the Scaffolding Protein NHERF1 Controls Autoinhibition and Complex Formation
journal, December 2009

  • Bhattacharya, Shibani; Dai, Zhongping; Li, Jianquan
  • Journal of Biological Chemistry, Vol. 285, Issue 13
  • DOI: 10.1074/jbc.M109.074005

Identification of EBP50: A PDZ-containing Phosphoprotein that Associates with Members of the Ezrin-Radixin-Moesin Family
journal, October 1997

  • Reczek, David; Berryman, Mark; Bretscher, Anthony
  • Journal of Cell Biology, Vol. 139, Issue 1
  • DOI: 10.1083/jcb.139.1.169

The EBP50-moesin interaction involves a binding site regulated by direct masking on the FERM domain
journal, March 2004


Structural Basis for NHERF Recognition by ERM Proteins
journal, April 2006


Phosphoinositide binding and phosphorylation act sequentially in the activation mechanism of ezrin
journal, March 2004

  • Fievet, Bruno T.; Gautreau, Alexis; Roy, Christian
  • The Journal of Cell Biology, Vol. 164, Issue 5
  • DOI: 10.1083/jcb.200307032

Open Conformation of Ezrin Bound to Phosphatidylinositol 4,5-Bisphosphate and to F-actin Revealed by Neutron Scattering
journal, August 2012

  • Jayasundar, Jayant James; Ju, Jeong Ho; He, Lilin
  • Journal of Biological Chemistry, Vol. 287, Issue 44
  • DOI: 10.1074/jbc.M112.380972

Ezrin Induces Long-Range Interdomain Allostery in the Scaffolding Protein NHERF1
journal, September 2009

  • Li, Jianquan; Callaway, David J. E.; Bu, Zimei
  • Journal of Molecular Biology, Vol. 392, Issue 1
  • DOI: 10.1016/j.jmb.2009.07.005

Activation of Nanoscale Allosteric Protein Domain Motion Revealed by Neutron Spin Echo Spectroscopy
journal, November 2010


The scaffolding protein EBP50 regulates microvillar assembly in a phosphorylation-dependent manner
journal, October 2010

  • Garbett, Damien; LaLonde, David P.; Bretscher, Anthony
  • The Journal of Cell Biology, Vol. 191, Issue 2
  • DOI: 10.1083/jcb.201004115

Dynamic Na+-H+ Exchanger Regulatory Factor-1 Association and Dissociation Regulate Parathyroid Hormone Receptor Trafficking at Membrane Microdomains
journal, October 2011

  • Ardura, Juan A.; Wang, Bin; Watkins, Simon C.
  • Journal of Biological Chemistry, Vol. 286, Issue 40
  • DOI: 10.1074/jbc.M111.264978

Activation-independent Parathyroid Hormone Receptor Internalization Is Regulated by NHERF1 (EBP50)
journal, October 2003

  • Sneddon, W. Bruce; Syme, Colin A.; Bisello, Alessandro
  • Journal of Biological Chemistry, Vol. 278, Issue 44
  • DOI: 10.1074/jbc.M306019200

G Protein-coupled Receptor Kinase 6A Phosphorylates the Na + /H + Exchanger Regulatory Factor via a PDZ Domain-mediated Interaction
journal, August 1999

  • Hall, Randy A.; Spurney, Robert F.; Premont, Richard T.
  • Journal of Biological Chemistry, Vol. 274, Issue 34
  • DOI: 10.1074/jbc.274.34.24328

Phosphorylation and Cell Cycle-dependent Regulation of Na+/H+ Exchanger Regulatory Factor-1 by Cdc2 Kinase
journal, November 2001

  • He, Junqi; Lau, Anthony G.; Yaffe, Michael B.
  • Journal of Biological Chemistry, Vol. 276, Issue 45
  • DOI: 10.1074/jbc.M106859200

Protein kinase C regulates the phosphorylation and oligomerization of ERM binding phosphoprotein 50
journal, May 2005

  • Fouassier, Laura; Nichols, Matthew T.; Gidey, Elizabeth
  • Experimental Cell Research, Vol. 306, Issue 1
  • DOI: 10.1016/j.yexcr.2005.02.011

Phosphorylation of EBP50 negatively regulates β-PIX-dependent Rac1 activity in anoikis
journal, February 2012

  • Chen, J-Y; Lin, Y-Y; Jou, T-S
  • Cell Death & Differentiation, Vol. 19, Issue 6
  • DOI: 10.1038/cdd.2012.4

Visualizing the nanoscale: protein internal dynamics and neutron spin echo spectroscopy
journal, February 2017


Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy
journal, November 2005

  • Bu, Z.; Biehl, R.; Monkenbusch, M.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 49
  • DOI: 10.1073/pnas.0503388102

Ligand-Induced Dynamic Changes in Extended PDZ Domains from NHERF1
journal, July 2013

  • Bhattacharya, Shibani; Ju, Jeong Ho; Orlova, Natalia
  • Journal of Molecular Biology, Vol. 425, Issue 14
  • DOI: 10.1016/j.jmb.2013.04.001

Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering
journal, May 2007

  • Bernadó, Pau; Mylonas, Efstratios; Petoukhov, Maxim V.
  • Journal of the American Chemical Society, Vol. 129, Issue 17
  • DOI: 10.1021/ja069124n

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace
journal, July 2006

  • Maupetit, J.; Gautier, R.; Tuffery, P.
  • Nucleic Acids Research, Vol. 34, Issue Web Server
  • DOI: 10.1093/nar/gkl289

Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition
journal, October 2001


Reliable determination of binding affinity and kinetics using surface plasmon resonance biosensors
journal, August 1997


Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors
journal, February 1997


The binding mechanisms of intrinsically disordered proteins
journal, January 2014

  • Dogan, Jakob; Gianni, Stefano; Jemth, Per
  • Phys. Chem. Chem. Phys., Vol. 16, Issue 14
  • DOI: 10.1039/C3CP54226B

Folding and Binding of an Intrinsically Disordered Protein: Fast, but Not ‘Diffusion-Limited’
journal, January 2013

  • Rogers, Joseph M.; Steward, Annette; Clarke, Jane
  • Journal of the American Chemical Society, Vol. 135, Issue 4
  • DOI: 10.1021/ja309527h

Rapid, electrostatically assisted association of proteins
journal, May 1996

  • Schreiber, Gideon; Fersht, Alan R.
  • Nature Structural Biology, Vol. 3, Issue 5
  • DOI: 10.1038/nsb0596-427

Fundamental Aspects of Protein−Protein Association Kinetics
journal, March 2009

  • Schreiber, G.; Haran, G.; Zhou, H. -X.
  • Chemical Reviews, Vol. 109, Issue 3
  • DOI: 10.1021/cr800373w

Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions
journal, January 2008


Physicochemical mechanisms of protein regulation by phosphorylation
journal, August 2014


An Entropic Mechanism to Generate Highly Cooperative and Specific Binding from Protein Phosphorylations
journal, November 2006


Post-translational modifications induce significant yet not extreme changes to protein structure
journal, September 2012


Structural Basis of the pH-Dependent Assembly of a Botulinum Neurotoxin Complex
journal, November 2014


Architectures of Whole-Module and Bimodular Proteins from the 6-Deoxyerythronolide B Synthase
journal, May 2014

  • Edwards, Andrea L.; Matsui, Tsutomu; Weiss, Thomas M.
  • Journal of Molecular Biology, Vol. 426, Issue 11
  • DOI: 10.1016/j.jmb.2014.03.015

An integrated high-throughput data acquisition system for biological solution X-ray scattering studies
journal, March 2012

  • Martel, Anne; Liu, Ping; Weiss, Thomas M.
  • Journal of Synchrotron Radiation, Vol. 19, Issue 3
  • DOI: 10.1107/S0909049512008072

ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis
journal, April 2007

  • Petoukhov, Maxim V.; Konarev, Peter V.; Kikhney, Alexey G.
  • Journal of Applied Crystallography, Vol. 40, Issue s1
  • DOI: 10.1107/S0021889807002853

GNOM – a program package for small-angle scattering data processing
journal, October 1991


The extended Q -range small-angle neutron scattering diffractometer at the SNS
journal, July 2010


Mantid—Data analysis and visualization package for neutron scattering and μ SR experiments
journal, November 2014

  • Arnold, O.; Bilheux, J. C.; Borreguero, J. M.
  • Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 764
  • DOI: 10.1016/j.nima.2014.07.029

Molecular Conformation of the Full-Length Tumor Suppressor NF2/Merlin—A Small-Angle Neutron Scattering Study
journal, July 2014

  • Ali Khajeh, Jahan; Ju, Jeong Ho; Atchiba, Moussoubaou
  • Journal of Molecular Biology, Vol. 426, Issue 15
  • DOI: 10.1016/j.jmb.2014.05.011

Structure-specific DNA-induced Conformational Changes in Taq Polymerase Revealed by Small Angle Neutron Scattering
journal, July 2004

  • Ho, Derek L.; Byrnes, W. Malcolm; Ma, Wu-po
  • Journal of Biological Chemistry, Vol. 279, Issue 37
  • DOI: 10.1074/jbc.M404565200

The spin-echo spectrometer at the Spallation Neutron Source (SNS)
journal, December 2012

  • Ohl, M.; Monkenbusch, M.; Arend, N.
  • Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 696
  • DOI: 10.1016/j.nima.2012.08.059

Nanoscale protein domain motion and long-range allostery in signaling proteins—a view from neutron spin echo spectroscopy
journal, January 2015


Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin 1 1Edited by M. F. Moody
journal, September 2001

  • Bu, Zimei; Cook, Jeremy; Callaway, David J. E.
  • Journal of Molecular Biology, Vol. 312, Issue 4
  • DOI: 10.1006/jmbi.2001.5006

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

    Works referencing / citing this record:

    Dynamics of proteins in solution
    journal, January 2019


    Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly
    journal, June 2019

    • Bhattacharya, Shibani; Stanley, Christopher B.; Heller, William T.
    • Journal of Biological Chemistry, Vol. 294, Issue 29
    • DOI: 10.1074/jbc.ra119.008218