1
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Toyama Y, Rangadurai AK, Kay LE. Measurement of 1H α transverse relaxation rates in proteins: application to solvent PREs. JOURNAL OF BIOMOLECULAR NMR 2022; 76:137-152. [PMID: 36018482 DOI: 10.1007/s10858-022-00401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
It has recently been demonstrated that accurate near surface electrostatic potentials can be calculated for proteins from solvent paramagnetic relaxation enhancements (PREs) of amide protons measured using spin labels of similar structures but different charges (Yu et al. in Proc Natl Acad Sci 118(25):e2104020118, 2021). Here we develop methodology for extending such measurements to intrinsically disordered proteins at neutral pH where amide spectra are of very poor quality. Under these conditions it is shown that accurate PRE values can be measured using the haCONHA experiment that has been modified for recording 1Hα transverse relaxation rates. The optimal pulse scheme includes a spin-lock relaxation element for suppression of homonuclear scalar coupled evolution for all 1Hα protons, except those derived from Ser and Thr residues, and minimizes the radiation damping field from water magnetization that would otherwise increase measured relaxation rates. The robustness of the experiment is verified by developing a second approach using a band selective adiabatic decoupling scheme for suppression of scalar coupling modulations during 1Hα relaxation and showing that the measured PRE values from the two methods are in excellent agreement. The near surface electrostatic potential of a 103-residue construct comprising the C-terminal intrinsically disordered region of the RNA-binding protein CAPRIN1 is obtained at pH 5.5 using both 1HN and 1Hα-based relaxation rates, and at pH 7.4 where only 1Hα rates can be quantified, with very good agreement between potentials obtained under all experimental conditions.
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Affiliation(s)
- Yuki Toyama
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Atul Kaushik Rangadurai
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.
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2
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Bobone S, Pannone L, Biondi B, Solman M, Flex E, Canale VC, Calligari P, De Faveri C, Gandini T, Quercioli A, Torini G, Venditti M, Lauri A, Fasano G, Hoeksma J, Santucci V, Cattani G, Bocedi A, Carpentieri G, Tirelli V, Sanchez M, Peggion C, Formaggio F, den Hertog J, Martinelli S, Bocchinfuso G, Tartaglia M, Stella L. Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein-Protein Interactions. J Med Chem 2021; 64:15973-15990. [PMID: 34714648 PMCID: PMC8591604 DOI: 10.1021/acs.jmedchem.1c01371] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective for disease-associated SHP2 mutants. Considering that pathogenic lesions cause signaling hyperactivation due to increased levels of SHP2 association with cognate proteins, we developed peptide-based molecules with nanomolar affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation, and an affinity for pathogenic variants of SHP2 that is 2-20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool for investigating the role of protein-protein interactions in the function of SHP2.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
| | - Maja Solman
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Elisabetta Flex
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Viviana Claudia Canale
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Chiara De Faveri
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Tommaso Gandini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Andrea Quercioli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giuseppe Torini
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Jelmer Hoeksma
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Valerio Santucci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giada Cattani
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alessio Bocedi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Giovanna Carpentieri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy.,Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Valentina Tirelli
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Massimo Sanchez
- Centre of Core Facilities, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Jeroen den Hertog
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy.,Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Simone Martinelli
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome 00133, Italy
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3
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T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. J Phys Chem B 2021; 125:9641-9651. [PMID: 34423989 DOI: 10.1021/acs.jpcb.1c01227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (Oaxis2) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. Here, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM-peptide complexes. Oaxis2 of CaM in the ligand-free (Oaxis,U2) and ligand-bound (Oaxis,B2) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. ΔOaxis2 = Oaxis,B2 - Oaxis,U2 follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced Oaxis,U2 → Oaxis,B2 transition decreases with increasing magnitude of ΔOaxis2, indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between ΔOaxis2 and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein-ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein-ligand binding.
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Affiliation(s)
- Rajitha Rajeshwar T
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
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4
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Sakhrani VV, Hilario E, Caulkins BG, Hatcher-Skeers ME, Fan L, Dunn MF, Mueller LJ. Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:341-354. [PMID: 32415580 PMCID: PMC7451264 DOI: 10.1007/s10858-020-00320-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly 2H,13C,15N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S2) are predicted. Titration with the 3-indole-D-glycerol 3'-phosphate analog, N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), leads to chemical shift perturbations indicative of conformational changes from which an estimate of the dissociation constant is obtained. Comparisons of the backbone chemical-shifts, RCI-S2 values, and site-specific relaxation times with and without F9 reveal allosteric changes including modulation in secondary structures and loop rigidity induced upon ligand binding. A comparison is made to the X-ray crystal structure of the α-subunit in the full TS αββα bi-enzyme complex and to two new X-ray crystal structures of the isolated TS α-subunit reported in this work.
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Affiliation(s)
- Varun V Sakhrani
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Eduardo Hilario
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Bethany G Caulkins
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Mary E Hatcher-Skeers
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Li Fan
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Michael F Dunn
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Leonard J Mueller
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA.
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5
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Marasco M, Carlomagno T. Specificity and regulation of phosphotyrosine signaling through SH2 domains. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100026. [PMID: 32647828 PMCID: PMC7337045 DOI: 10.1016/j.yjsbx.2020.100026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 10/26/2022]
Abstract
Phosphotyrosine (pY) signaling is instrumental to numerous cellular processes. pY recognition occurs through specialized protein modules, among which the Src-homology 2 (SH2) domain is the most common. SH2 domains are small protein modules with an invariant fold, and are present in more than a hundred proteins with different function. Here we ask the question of how such a structurally conserved, small protein domain can recognize distinct phosphopeptides with the breath of binding affinity, specificity and kinetic parameters necessary for proper control of pY-dependent signaling and rapid cellular response. We review the current knowledge on structure, thermodynamics and kinetics of SH2-phosphopeptide complexes and conclude that selective phosphopeptide recognition is governed by both structure and dynamics of the SH2 domain, as well as by the kinetics of the binding events. Further studies on the thermodynamic and kinetic properties of SH2-phosphopeptide complexes, beyond their structure, are required to understand signaling regulation.
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Affiliation(s)
- Michelangelo Marasco
- Leibniz University Hannover, Institute of Organic Chemistry and Centre for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Institute of Organic Chemistry and Centre for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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6
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Tchaicheeyan O, Meirovitch E. An SRLS Study of 2H Methyl-Moiety Relaxation and Related Conformational Entropy in Free and Peptide-Bound PLCγ1C SH2. J Phys Chem B 2016; 120:10695-10705. [DOI: 10.1021/acs.jpcb.6b08264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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7
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Huculeci R, Cilia E, Lyczek A, Buts L, Houben K, Seeliger MA, van Nuland N, Lenaerts T. Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity. Structure 2016; 24:1947-1959. [PMID: 27692963 DOI: 10.1016/j.str.2016.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 07/13/2016] [Accepted: 08/10/2016] [Indexed: 12/30/2022]
Abstract
Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information. We reveal that binding the phosphorylated tail of Fyn perturbs a residue cluster near the linker connecting the SH2 and SH3 domains of Fyn, which is known to be relevant in the regulation of the activity of Fyn. Biochemical perturbation experiments validate that those residues are essential for inhibition of Fyn, leading to a gain of function upon mutation. These findings reveal how side-chain dynamics may facilitate the allosteric regulation of the different members of the Src kinase family.
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Affiliation(s)
- Radu Huculeci
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium
| | - Elisa Cilia
- MLG, Départment d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe CP212, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics Brussels (IB(2)), ULB-VUB, La Plaine Campus, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
| | - Agatha Lyczek
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, BST 8-140, Stony Brook, NY 11794-8651, USA
| | - Lieven Buts
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium
| | - Klaartje Houben
- NMR spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, BST 8-140, Stony Brook, NY 11794-8651, USA
| | - Nico van Nuland
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium.
| | - Tom Lenaerts
- MLG, Départment d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe CP212, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics Brussels (IB(2)), ULB-VUB, La Plaine Campus, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium; AI-lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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8
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Abstract
Proteins with a modular architecture of multiple domains connected by linkers often exhibit diversity in the relative positions of domains, while the domain tertiary structure remains unchanged. The biological function of these modular proteins, or the regulation of their activity, depends on the variation in domain orientation and separation. Accordingly, careful characterization of interdomain motion and correlated fluctuations of multidomain systems is relevant for understanding the functional behavior of modular proteins. Molecular dynamics (MD) simulations provides a powerful approach to study these motions in atomic detail. Nevertheless, the common procedure for analyzing fluctuations from MD simulations after rigid-body alignment fails for multidomain proteins; it greatly overestimates correlated positional fluctuations in the presence of relative domain motion. We show here that expressing the atomic motions of a multidomain protein as a combination of displacement within the domain reference frame and motion of the relative domains correctly separates the internal motions to allow a useful description of correlated fluctuations. We illustrate the methodology of separating the domain fluctuations and local fluctuations by application to the tandem SH2 domains of human Syk protein kinase and by characterizing an effect of phosphorylation on the dynamics. Correlated motions are assessed from a distance covariance rather than the more common vector-coordinate covariance. The approach makes it possible to calculate the proper correlations in fluctuations internal to a domain as well as between domains.
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Affiliation(s)
- Amitava Roy
- Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, NIAID, National Institutes of Health , Hamilton, Montana 59840, United States
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9
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Varma S, Botlani M, Leighty RE. Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning. Proteins 2014; 82:3241-54. [DOI: 10.1002/prot.24541] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/10/2014] [Accepted: 02/14/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sameer Varma
- Department of Cell Biology; Microbiology and Molecular Biology, University of South Florida; Tampa Florida 33620
| | - Mohsen Botlani
- Department of Cell Biology; Microbiology and Molecular Biology, University of South Florida; Tampa Florida 33620
| | - Ralph E. Leighty
- Department of Cell Biology; Microbiology and Molecular Biology, University of South Florida; Tampa Florida 33620
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10
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T. RR, Smith JC, Krishnan M. Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins. J Am Chem Soc 2014; 136:8590-605. [DOI: 10.1021/ja5024783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rajitha Rajeshwar T.
- Center
for Computational Natural Sciences and Bioinformatics, International
Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Marimuthu Krishnan
- Center
for Computational Natural Sciences and Bioinformatics, International
Institute of Information Technology, Gachibowli, Hyderabad 500 032, India
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11
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Weininger U, Blissing AT, Hennig J, Ahlner A, Liu Z, Vogel HJ, Akke M, Lundström P. Protein conformational exchange measured by 1H R1ρ relaxation dispersion of methyl groups. JOURNAL OF BIOMOLECULAR NMR 2013; 57:47-55. [PMID: 23904100 DOI: 10.1007/s10858-013-9764-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/17/2013] [Indexed: 06/02/2023]
Abstract
Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations by NMR relaxation dispersion experiments. Processes at the faster end of this range are more challenging to study, because higher RF field strengths are required to achieve refocusing of the exchanging magnetization. Here we describe a rotating-frame relaxation dispersion experiment for (1)H spins in methyl (13)CHD2 groups, which improves the characterization of fast exchange processes. The influence of (1)H-(1)H rotating-frame nuclear Overhauser effects (ROE) is shown to be negligible, based on a comparison of R 1ρ relaxation data acquired with tilt angles of 90° and 35°, in which the ROE is maximal and minimal, respectively, and on samples containing different (1)H densities surrounding the monitored methyl groups. The method was applied to ubiquitin and the apo form of calmodulin. We find that ubiquitin does not exhibit any (1)H relaxation dispersion of its methyl groups at 10 or 25 °C. By contrast, calmodulin shows significant conformational exchange of the methionine methyl groups in its C-terminal domain, as previously demonstrated by (1)H and (13)C CPMG experiments. The present R 1ρ experiment extends the relaxation dispersion profile towards higher refocusing frequencies, which improves the definition of the exchange correlation time, compared to previous results.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 22100, Lund, Sweden
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12
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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13
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Stauch B, Orts J, Carlomagno T. The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method. JOURNAL OF BIOMOLECULAR NMR 2012; 54:245-256. [PMID: 23001323 PMCID: PMC3483107 DOI: 10.1007/s10858-012-9662-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/13/2012] [Indexed: 05/31/2023]
Abstract
Protein internal motions influence observables of NMR experiments. The effect of internal motions occurring at the sub-nanosecond timescale can be described by NMR order parameters. Here, we report that the use of order parameters derived from Molecular Dynamics (MD) simulations of two holo-structures of Protein Kinase A increase the discrimination power of INPHARMA, an NMR based methodology that selects docked ligand orientations by maximizing the correlation of back-calculated to experimental data. By including internal motion in the back-calculation of the INPHARMA transfer, we obtain a more realistic description of the system, which better represents the experimental data. Furthermore, we propose a set of generic order parameters, derived from MD simulations of globular proteins, which can be used in the back-calculation of INPHARMA NOEs for any protein-ligand complex, thus by-passing the need of obtaining system-specific order parameters for new protein-ligand complexes.
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Affiliation(s)
- Benjamin Stauch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Present Address: European Bioinformatics Institute (EBI), Hinxton, UK
| | - Julien Orts
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Present Address: Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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14
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Liao X, Long D, Li DW, Brüschweiler R, Tugarinov V. Probing side-chain dynamics in proteins by the measurement of nine deuterium relaxation rates per methyl group. J Phys Chem B 2011; 116:606-20. [PMID: 22098066 DOI: 10.1021/jp209304c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate the feasibility of the measurement of up to nine deuterium spin relaxation rates in 13CHD2 and 13CH2D methyl isotopomers of small proteins. In addition to five measurable 2H relaxation rates in a 13CH2D methyl group (Millet, O.; Muhandiram, D. R.; Skrynnikov, N. R.; Kay, L. E. J. Am. Chem. Soc. 2002, 124, 6439-48), the measurement of additional four rates of (nearly) single-exponentially decaying magnetization terms in methyl groups of the 13CHD2 variety is reported. Consistency relationships between 2H spin relaxation rates measured in the two different types of methyl groups are derived and verified experimentally for a subset of methyl-containing side chains in the protein ubiquitin. A detailed comparison of methyl-bearing side-chain dynamics parameters obtained from relaxation measurements in 13CH2D and 13CHD2 methyls of ubiquitin at 10, 27, and 40 °C reveals that transverse 2H relaxation rates in 13CHD2 groups are reliable and accurate reporters of the amplitudes of methyl 3-fold axis motions (S(axis)2) for protein molecules with global molecular tumbling times τ(C) >~9 ns. For smaller molecules, simple correction of transverse 2H relaxation rates in 13CHD2 groups is sufficient for the derivation of robust measures of order. Residue-specific distributions of S(axis)2 are consistent with atomic-detail molecular dynamics (MD) results. Both 13CHD2- and 13CH2D-derived S(axis)2 values are in good overall agreement with those obtained from 1 μs MD simulations at all the three temperatures, although some differences in the site-specific temperature dependence between MD- and 2H-relaxation-derived S(axis)2 values are observed.
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Affiliation(s)
- Xinli Liao
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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15
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Long D, Li DW, Walter KFA, Griesinger C, Brüschweiler R. Toward a predictive understanding of slow methyl group dynamics in proteins. Biophys J 2011; 101:910-5. [PMID: 21843482 DOI: 10.1016/j.bpj.2011.06.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/27/2011] [Accepted: 06/29/2011] [Indexed: 11/28/2022] Open
Abstract
The development of the most recent generation of molecular mechanics force fields promises an increasingly predictive understanding of the protein dynamics-function relationship. Based on extensive validation against various types of experimental data, the AMBER force field ff99SB was benchmarked in recent years as a favorable force field for protein simulations. Recent improvements of the side chain and backbone potentials, made by different groups, led to the ff99SB-ILDN and ff99SBnmr1 force fields, respectively. The combination of these potentials into a unified force field, termed ff99SBnmr1-ILDN, was used in this study to perform a microsecond time scale molecular dynamics simulation of free ubiquitin in explicit solvent for validation against an extensive set of experimental NMR methyl group residual dipolar couplings. Our results show a high level of consistency between the experimental data and the values predicted from the molecular dynamics trajectory reflecting a systematically improved performance of ff99SBnmr1-ILDN over the original ff99SB force field. Moreover, the unconstrained ff99SBnmr1-ILDN MD ensemble achieves a similar level of agreement as the recently introduced EROS ensemble, which was constructed based on a large body of NMR data as constraints, including the methyl residual dipolar couplings. This suggests that ff99SBnmr1-ILDN provides a high-quality representation of the motions of methyl-bearing protein side chains, which are sensitive probes of protein-protein and protein-ligand interactions.
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Affiliation(s)
- Dong Long
- Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
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16
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Myslinski JM, DeLorbe JE, Clements JH, Martin SF. Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area. J Am Chem Soc 2011; 133:18518-21. [PMID: 22007755 DOI: 10.1021/ja2068752] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Thermodynamic parameters were determined for complex formation between the Grb2 SH2 domain and Ac-pTyr-Xaa-Asn derived tripeptides in which the Xaa residue is an α,α-cycloaliphatic amino acid that varies in ring size from three- to seven-membered. Although the six- and seven-membered ring analogs are approximately equipotent, binding affinities of those having three- to six-membered rings increase incrementally with ring size because increasingly more favorable binding enthalpies dominate increasingly less favorable binding entropies, a finding consistent with an enthalpy-driven hydrophobic effect. Crystallographic analysis reveals that the only significant differences in structures of the complexes are in the number of van der Waals contacts between the domain and the methylene groups in the Xaa residues. There is a positive correlation between buried nonpolar surface area and binding free energy and enthalpy, but not with ΔC(p). Displacing a water molecule from a protein-ligand interface is not necessarily reflected in a favorable change in binding entropy. These findings highlight some of the fallibilities associated with commonly held views of relationships of structure and energetics in protein-ligand interactions and have significant implications for ligand design.
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Affiliation(s)
- James M Myslinski
- Chemistry and Biochemistry Department, Institute of Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
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17
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Auer R, Tollinger M, Kuprov I, Konrat R, Kloiber K. Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange. JOURNAL OF BIOMOLECULAR NMR 2011; 51:35-47. [PMID: 21947913 PMCID: PMC3180638 DOI: 10.1007/s10858-011-9539-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 07/13/2011] [Indexed: 05/24/2023]
Abstract
Although originally designed for broadband inversion and decoupling in NMR spectroscopy, recent methodological developments have introduced adiabatic fast passage (AFP) pulses into the field of protein dynamics. AFP pulses employ a frequency sweep, and have not only superior inversion properties with respect to offset effects, but they are also easily implemented into a pulse sequence. As magnetization is dragged from the +z to the -z direction, Larmor precession is impeded since magnetization becomes spin-locked, which is a potentially useful feature for the investigation of microsecond to millisecond dynamics. A major drawback of these pulses as theoretical prediction is concerned, however, results from their time-dependent offset: simulations of spin density matrices under the influence of a time-dependent Hamiltonian with non-commuting elements are costly in terms of computational time, rendering data analysis impracticable. In this paper we suggest several ways to reduce the computational time without compromising accuracy with respect to effects such as cross-correlated relaxation and modulation of the chemical shift.
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Affiliation(s)
- Renate Auer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Martin Tollinger
- Department of Organic Chemistry, Leopold Franzens Universitaet Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
| | - Ilya Kuprov
- Oxford e-Research Centre, University of Oxford, 7 Keble Road, Oxford, OX1 3QG UK
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
| | - Karin Kloiber
- Department of Organic Chemistry, Leopold Franzens Universitaet Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
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18
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Tzeng SR, Kalodimos CG. Protein dynamics and allostery: an NMR view. Curr Opin Struct Biol 2010; 21:62-7. [PMID: 21109422 DOI: 10.1016/j.sbi.2010.10.007] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/24/2010] [Indexed: 11/19/2022]
Abstract
Allostery, the process by which distant sites within a protein system are energetically coupled, is an efficient and ubiquitous mechanism for activity regulation. A purely mechanical view of allostery invoking only structural changes has developed over the decades as the classical view of the phenomenon. However, a fast growing list of examples illustrate the intimate link between internal motions over a wide range of time scales and function in protein-ligand interactions. Proteins respond to perturbations by redistributing their motions and they use fluctuating conformational states for binding and conformational entropy as a carrier of allosteric energy to modulate association with ligands. In several cases allosteric interactions proceed with minimal or no structural changes. We discuss emerging paradigms for the central role of protein dynamics in allostery.
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Affiliation(s)
- Shiou-Ru Tzeng
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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19
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Wen Y, Li J, Xiong M, Peng Y, Yao W, Hong J, Lin D. Solution structure and dynamics of the I214V mutant of the rabbit prion protein. PLoS One 2010; 5:e13273. [PMID: 20949107 PMCID: PMC2951349 DOI: 10.1371/journal.pone.0013273] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 09/12/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The conformational conversion of the host-derived cellular prion protein (PrP(C)) into the disease-associated scrapie isoform (PrP(Sc)) is responsible for the pathogenesis of transmissible spongiform encephalopathies (TSEs). Various single-point mutations in PrP(C)s could cause structural changes and thereby distinctly influence the conformational conversion. Elucidation of the differences between the wild-type rabbit PrP(C) (RaPrP(C)) and various mutants would be of great help to understand the ability of RaPrP(C) to be resistant to TSE agents. METHODOLOGY/PRINCIPAL FINDINGS We determined the solution structure of the I214V mutant of RaPrP(C)(91-228) and detected the backbone dynamics of its structured C-terminal domain (121-228). The I214V mutant displays a visible shift of surface charge distribution that may have a potential effect on the binding specificity and affinity with other chaperones. The number of hydrogen bonds declines dramatically. Urea-induced transition experiments reveal an obvious decrease in the conformational stability. Furthermore, the NMR dynamics analysis discloses a significant increase in the backbone flexibility on the pico- to nanosecond time scale, indicative of lower energy barrier for structural rearrangement. CONCLUSIONS/SIGNIFICANCE Our results suggest that both the surface charge distribution and the intrinsic backbone flexibility greatly contribute to species barriers for the transmission of TSEs, and thereby provide valuable hints for understanding the inability of the conformational conversion for RaPrP(C).
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Affiliation(s)
- Yi Wen
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jun Li
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Minqian Xiong
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yu Peng
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wenming Yao
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jing Hong
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Donghai Lin
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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20
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Wang M, Prorok M, Castellino FJ. NMR backbone dynamics of VEK-30 bound to the human plasminogen kringle 2 domain. Biophys J 2010; 99:302-12. [PMID: 20655859 PMCID: PMC2895381 DOI: 10.1016/j.bpj.2010.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 03/12/2010] [Accepted: 04/08/2010] [Indexed: 10/19/2022] Open
Abstract
To gain insights into the mechanisms for the tight and highly specific interaction of the kringle 2 domain of human plasminogen (K2(Pg)) with a 30-residue internal peptide (VEK-30) from a group A streptococcal M-like protein, the dynamic properties of free and bound K2(Pg) and VEK-30 were investigated using backbone amide (15)N-NMR relaxation measurements. Dynamic parameters, namely the generalized order parameter, S(2), the local correlation time, tau(e), and the conformational exchange contribution, R(ex), were obtained for this complex by Lipari-Szabo model-free analysis. The results show that VEK-30 displays distinctly different dynamic behavior as a consequence of binding to K2(Pg), manifest by decreased backbone flexibility, particularly at the binding region of the peptide. In contrast, the backbone dynamics parameters of K2(Pg) displayed similar patterns in the free and bound forms, but, nonetheless, showed interesting differences. Based on our previous structure-function studies of this interaction, we also made comparisons of the VEK-30/K2(Pg) dynamics results from different kringle modules complexed with small lysine analogs. The differences in dynamics observed for kringles with different ligands provide what we believe to be new insights into the interactions responsible for protein-ligand recognition and a better understanding of the differences in binding affinity and binding specificity of kringle domains with various ligands.
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Affiliation(s)
| | | | - Francis J. Castellino
- W. M. Keck Center for Transgene and the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
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21
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Kaneko T, Huang H, Zhao B, Li L, Liu H, Voss CK, Wu C, Schiller MR, Li SSC. Loops govern SH2 domain specificity by controlling access to binding pockets. Sci Signal 2010; 3:ra34. [PMID: 20442417 DOI: 10.1126/scisignal.2000796] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cellular functions require specific protein-protein interactions that are often mediated by modular domains that use binding pockets to engage particular sequence motifs in their partners. Yet, how different members of a domain family select for distinct sequence motifs is not fully understood. The human genome encodes 120 Src homology 2 (SH2) domains (in 110 proteins), which mediate protein-protein interactions by binding to proteins with diverse phosphotyrosine (pTyr)-containing sequences. The structure of the SH2 domain of BRDG1 bound to a peptide revealed a binding pocket that was blocked by a loop residue in most other SH2 domains. Analysis of 63 SH2 domain structures suggested that the SH2 domains contain three binding pockets, which exhibit selectivity for the three positions after the pTyr in a peptide, and that SH2 domain loops defined the accessibility and shape of these pockets. Despite sequence variability in the loops, we identified conserved structural features in the loops of SH2 domains responsible for controlling access to these surface pockets. We engineered new loops in an SH2 domain that altered specificity as predicted. Thus, selective blockage of binding subsites or pockets by surface loops provides a molecular basis by which the diverse modes of ligand recognition by the SH2 domain may have evolved and provides a framework for engineering SH2 domains and designing SH2-specific inhibitors.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
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22
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Auer R, Hansen DF, Neudecker P, Korzhnev DM, Muhandiram DR, Konrat R, Kay LE. Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R1rho methods. JOURNAL OF BIOMOLECULAR NMR 2010; 46:205-216. [PMID: 20033258 DOI: 10.1007/s10858-009-9394-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/01/2009] [Indexed: 05/28/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond exchange processes between a major, populated ground state and one or more minor, low populated and often invisible 'excited' conformers. Analysis of CPMG data-sets also provides the magnitudes of the chemical shift difference(s) between exchanging states (|Deltavarpi|), that inform on the structural properties of the excited state(s). The sign of Deltavarpi is, however, not available from CPMG data. Here we present one-dimensional NMR experiments for measuring the signs of (1)H(N) and (13)C(alpha) Deltavarpi values using weak off-resonance R (1rho ) relaxation measurements, extending the spin-lock approach beyond previous applications focusing on the signs of (15)N and (1)H(alpha) shift differences. The accuracy of the method is established by using an exchanging system where the invisible, excited state can be converted to the visible, ground state by altering conditions so that the signs of Deltavarpi values obtained from the spin-lock approach can be validated with those measured directly. Further, the spin-lock experiments are compared with the established H(S/M)QC approach for measuring the signs of chemical shift differences. For the Abp1p and Fyn SH3 domains considered here it is found that while H(S/M)QC measurements provide signs for more residues than the spin-lock data, the two different methodologies are complementary, so that combining both approaches frequently produces signs for more residues than when the H(S/M)QC method is used alone.
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Affiliation(s)
- Renate Auer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, 1030, Vienna, Austria
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23
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Sheppard D, Sprangers R, Tugarinov V. Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:1-45. [PMID: 20633347 DOI: 10.1016/j.pnmrs.2009.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 07/29/2009] [Indexed: 05/29/2023]
Affiliation(s)
- Devon Sheppard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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24
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Tzeng SR, Kalodimos CG. Dynamic activation of an allosteric regulatory protein. Nature 2009; 462:368-72. [PMID: 19924217 DOI: 10.1038/nature08560] [Citation(s) in RCA: 305] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/07/2009] [Indexed: 11/09/2022]
Abstract
Allosteric regulation is used as a very efficient mechanism to control protein activity in most biological processes, including signal transduction, metabolism, catalysis and gene regulation. Allosteric proteins can exist in several conformational states with distinct binding or enzymatic activity. Effectors are considered to function in a purely structural manner by selectively stabilizing a specific conformational state, thereby regulating protein activity. Here we show that allosteric proteins can be regulated predominantly by changes in their structural dynamics. We have used NMR spectroscopy and isothermal titration calorimetry to characterize cyclic AMP (cAMP) binding to the catabolite activator protein (CAP), a transcriptional activator that has been a prototype for understanding effector-mediated allosteric control of protein activity. cAMP switches CAP from the 'off' state (inactive), which binds DNA weakly and non-specifically, to the 'on' state (active), which binds DNA strongly and specifically. In contrast, cAMP binding to a single CAP mutant, CAP-S62F, fails to elicit the active conformation; yet, cAMP binding to CAP-S62F strongly activates the protein for DNA binding. NMR and thermodynamic analyses show that despite the fact that CAP-S62F-cAMP(2) adopts the inactive conformation, its strong binding to DNA is driven by a large conformational entropy originating in enhanced protein motions induced by DNA binding. The results provide strong evidence that changes in protein motions may activate allosteric proteins that are otherwise structurally inactive.
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Affiliation(s)
- Shiou-Ru Tzeng
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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25
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DeLorbe JE, Clements JH, Teresk MG, Benfield AP, Plake HR, Millspaugh LE, Martin SF. Thermodynamic and Structural Effects of Conformational Constraints in Protein−Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. J Am Chem Soc 2009; 131:16758-70. [DOI: 10.1021/ja904698q] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John E. DeLorbe
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - John H. Clements
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Martin G. Teresk
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Aaron P. Benfield
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Hilary R. Plake
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Laura E. Millspaugh
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Stephen F. Martin
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
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26
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Amero CD, Byerly DW, McElroy CA, Simmons A, Foster MP. Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase. Biochemistry 2009; 48:7595-607. [PMID: 19627112 DOI: 10.1021/bi900600b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide deformylase (PDF) is an enzyme that is responsible for removing the formyl group from nascently synthesized polypeptides in bacteria, attracting much attention as a potential target for novel antibacterial agents. Efforts to develop potent inhibitors of the enzyme have progressed on the basis of classical medicinal chemistry, combinatorial chemistry, and structural approaches, yet the validity of PDF as an antibacterial target hangs, in part, on the ability of inhibitors to selectively target this enzyme in favor of structurally related metallohydrolases. We have used (15)N NMR spectroscopy and isothermal titration calorimetry to investigate the high-affinity interaction of EcPDF with actinonin, a naturally occurring potent EcPDF inhibitor. Backbone amide chemical shifts, residual dipolar couplings, hydrogen-deuterium exchange, and (15)N relaxation reveal structural and dynamic effects of ligand binding in the immediate vicinity of the ligand-binding site as well as at remote sites. A comparison of the crystal structures of free and actinonin-bound EcPDF with the solution data suggests that most of the consequences of the ligand binding to the protein are lost or obscured during crystallization. The results of these studies improve our understanding of the thermodynamic global minimum and have important implications for structure-based drug design.
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Affiliation(s)
- Carlos D Amero
- Biophysics Program, The Ohio StateUniversity, Columbus, Ohio 43210, USA
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27
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Gunning PT, Glenn MP, Siddiquee KAZ, Katt WP, Masson E, Sebti SM, Turkson J, Hamilton AD. Targeting protein-protein interactions: suppression of Stat3 dimerization with rationally designed small-molecule, nonpeptidic SH2 domain binders. Chembiochem 2009; 9:2800-3. [PMID: 19006150 DOI: 10.1002/cbic.200800291] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Patrick T Gunning
- Department of Chemistry, Yale University, P. O. Box 208017, New Haven, CT 06520-8107, USA
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28
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Taylor JD, Ababou A, Fawaz RR, Hobbs CJ, Williams MA, Ladbury JE. Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: implications for drug design. Proteins 2008; 73:929-40. [PMID: 18536014 DOI: 10.1002/prot.22119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SH2 domains provide fundamental recognition sites in tyrosine kinase-mediated signaling pathways which, when aberrant, give rise to disease states such as cancer, diabetes, and immune deficiency. Designing specific inhibitors that target the SH2 domain-binding site, however, have presented a major challenge. Despite well over a decade of intensive research, clinically useful SH2 domain inhibitors have yet to become available. A better understanding of the structural, dynamic, and thermodynamic contributions to ligand binding of individual SH2 domains will provide some insight as to whether inhibitor development is possible. We report the first high resolution solution structure of the apo-v-Src SH2 domain. This is accompanied by the analysis of backbone dynamics and pK(a) values within the apo- and peptide-bound states. Our results indicate that the phosphotyrosine (pY) pocket is tightly structured and hence not adaptable to exogenous ligands. On the other hand, the pocket which accommodates residues proximal and C-terminal of the pY (pY + 3) or so-called specificity determining region, is a large dynamic-binding surface. This appears to allow a high level of promiscuity in binding. Binding of a series of synthetic, phosphotyrosyl, peptidomimetic compounds designed to explore interactions in the pY + 3 pocket further demonstrates the ability of the SH2 domain to accommodate diverse ligands. The thermodynamic parameters of these interactions show dramatic enthalpy/entropy compensation. These data suggest that the v-Src SH2 domain does not have a highly specific secondary-binding site, which clearly presents a major hurdle to design selective inhibitors.
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Affiliation(s)
- Jonathan D Taylor
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
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29
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Echodu D, Goobes G, Shajani Z, Pederson K, Meints G, Varani G, Drobny G. Furanose dynamics in the HhaI methyltransferase target DNA studied by solution and solid-state NMR relaxation. J Phys Chem B 2008; 112:13934-44. [PMID: 18844399 PMCID: PMC2735271 DOI: 10.1021/jp801723x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Both solid-state and solution NMR relaxation measurements are routinely used to quantify the internal dynamics of biomolecules, but in very few cases have these two techniques been applied to the same system, and even fewer attempts have been made so far to describe the results obtained through these two methods through a common theoretical framework. We have previously collected both solution 13C and solid-state 2H relaxation measurements for multiple nuclei within the furanose rings of several nucleotides of the DNA sequence recognized by HhaI methyltransferase. The data demonstrated that the furanose rings within the GCGC recognition sequence are very flexible, with the furanose rings of the cytidine, which is the methylation target, experiencing the most extensive motions. To interpret these experimental results quantitatively, we have developed a dynamic model of furanose rings based on the analysis of solid-state 2H line shapes. The motions are modeled by treating bond reorientations as Brownian excursions within a restoring potential. By applying this model, we are able to reproduce the rates of 2H spin-lattice relaxation in the solid and 13C spin-lattice relaxation in solution using comparable restoring force constants and internal diffusion coefficients. As expected, the 13C relaxation rates in solution are less sensitive to motions that are slower than overall molecular tumbling than to the details of global molecular reorientation, but are somewhat more sensitive to motions in the immediate region of the Larmor frequency. Thus, we conclude that the local internal motions of this DNA oligomer in solution and in the hydrated solid state are virtually the same, and we validate an approach to the conjoint analysis of solution and solid-state NMR relaxation and line shapes data, with wide applicability to many biophysical problems.
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Affiliation(s)
- Dorothy Echodu
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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30
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Liang X, Van Doren SR. Mechanistic insights into phosphoprotein-binding FHA domains. Acc Chem Res 2008; 41:991-9. [PMID: 18656966 DOI: 10.1021/ar700148u] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[Structure: see text]. FHA domains are protein modules that switch signals in diverse biological pathways by monitoring the phosphorylation of threonine residues of target proteins. As part of the effort to gain insight into cellular avoidance of cancer, FHA domains involved in the cellular response to DNA damage have been especially well-characterized. The complete protein where the FHA domain resides and the interaction partners determine the nature of the signaling. Thus, a key biochemical question is how do FHA domains pick out their partners from among thousands of alternatives in the cell? This Account discusses the structure, affinity, and specificity of FHA domains and the formation of their functional structure. Although FHA domains share sequence identity at only five loop residues, they all fold into a beta-sandwich of two beta-sheets. The conserved arginine and serine of the recognition loops recognize the phosphorylation of the threonine targeted. Side chains emanating from loops that join beta-strand 4 with 5, 6 with 7, or 10 with 11 make specific contacts with amino acids of the ligand that tailor sequence preferences. Many FHA domains choose a partner in extended conformation, somewhat according to the residue three after the phosphothreonine in sequence (pT + 3 position). One group of FHA domains chooses a short carboxylate-containing side chain at pT + 3. Another group chooses a long, branched aliphatic side chain. A third group prefers other hydrophobic or uncharged polar side chains at pT + 3. However, another FHA domain instead chooses on the basis of pT - 2, pT - 3, and pT + 1 positions. An FHA domain from a marker of human cancer instead chooses a much longer protein fragment that adds a beta-strand to its beta-sheet and that presents hydrophobic residues from a novel helix to the usual recognition surface. This novel recognition site and more remote sites for the binding of other types of protein partners were predicted for the entire family of FHA domains by a bioinformatics approach. The phosphopeptide-dependent dynamics of an FHA domain, SH2 domain, and PTB domain suggest a common theme: rigid, preformed binding surfaces support van der Waals contacts that provide favorable binding enthalpy. Despite the lack of pronounced conformational changes in FHA domains linked to binding events, more subtle adjustments may be possible. In the one FHA domain tested, phosphothreonine peptide binding is accompanied by increased flexibility just outside the binding site and increased rigidity across the beta-sandwich. The folding of the same FHA domain progresses through near-native intermediates that stabilize the recognition loops in the center of the phosphoprotein-binding surface; this may promote rigidity in the interface and affinity for targets phosphorylated on threonine.
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Affiliation(s)
- Xiangyang Liang
- Department of Biochemistry, 105 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211
| | - Steven R. Van Doren
- Department of Biochemistry, 105 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211
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31
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Friedland GD, Linares AJ, Smith CA, Kortemme T. A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol 2008; 380:757-74. [PMID: 18547586 DOI: 10.1016/j.jmb.2008.05.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 04/08/2008] [Accepted: 05/07/2008] [Indexed: 10/22/2022]
Abstract
The considerable flexibility of side-chains in folded proteins is important for protein stability and function, and may have a role in mediating allosteric interactions. While sampling side-chain degrees of freedom has been an integral part of several successful computational protein design methods, the predictions of these approaches have not been directly compared to experimental measurements of side-chain motional amplitudes. In addition, protein design methods frequently keep the backbone fixed, an approximation that may substantially limit the ability to accurately model side-chain flexibility. Here, we describe a Monte Carlo approach to modeling side-chain conformational variability and validate our method against a large dataset of methyl relaxation order parameters derived from nuclear magnetic resonance (NMR) experiments (17 proteins and a total of 530 data points). We also evaluate a model of backbone flexibility based on Backrub motions, a type of conformational change frequently observed in ultra-high-resolution X-ray structures that accounts for correlated side-chain backbone movements. The fixed-backbone model performs reasonably well with an overall rmsd between computed and predicted side-chain order parameters of 0.26. Notably, including backbone flexibility leads to significant improvements in modeling side-chain order parameters for ten of the 17 proteins in the set. Greater accuracy of the flexible backbone model results from both increases and decreases in side-chain flexibility relative to the fixed-backbone model. This simple flexible-backbone model should be useful for a variety of protein design applications, including improved modeling of protein-protein interactions, design of proteins with desired flexibility or rigidity, and prediction of correlated motions within proteins.
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Affiliation(s)
- Gregory D Friedland
- Graduate Group in Biophysics, University of California at San Francisco, 1700 4th St, UCSF MC 2540, San Francisco, CA 94158-2330, USA
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32
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Wang T, Weaver DS, Cai S, Zuiderweg ERP. Quantifying Lipari-Szabo modelfree parameters from 13CO NMR relaxation experiments. JOURNAL OF BIOMOLECULAR NMR 2006; 36:79-102. [PMID: 17013680 DOI: 10.1007/s10858-006-9047-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 06/09/2006] [Indexed: 05/12/2023]
Abstract
It is proposed to obtain effective Lipari-Szabo order parameters and local correlation times for relaxation vectors of protein (13)CO nuclei by carrying out a (13)CO-R(1) auto relaxation experiment, a transverse (13)CO CSA/13CO-13Calpha CSA/dipolar cross correlation and a transverse (13)CO CSA/(13)CO-(15)N CSA/dipolar cross correlation experiment. Given the global rotational correlation time from (15)N relaxation experiments, a new program COMFORD (CO-Modelfree Fitting Of Relaxation Data) is presented to fit the (13)CO data to an effective order parameter S2CO, an effective local correlation time and the orientation of the CSA tensor with respect to the molecular frame. It is shown that the effective S2CO is least sensitive to rotational fluctuations about an imaginary Calpha-Calpha axis and most sensitive to rotational fluctuations about an imaginary axis parallel to the NH bond direction. As such, the Calpha-Calpha information is fully complementary to the (15)N relaxation order parameter, which is least sensitive to fluctuations about the NH axis and most sensitive to fluctuations about the Calpha-Calpha axis. The new paradigm is applied on data of Ca(2+) saturated Calmodulin, and on available literature data for Ubiquitin. Our data indicate that the S2CO order parameters rapport on slower, and sometimes different, motions than the (15)N relaxation order parameters. The CO local correlation times correlate well with the calmodulin's secondary structure.
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Affiliation(s)
- Tianzhi Wang
- Biophysics Research Division, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109-1055, USA
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33
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Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL. Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. J Mol Biol 2006; 364:337-51. [PMID: 17011581 DOI: 10.1016/j.jmb.2006.08.076] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/17/2006] [Accepted: 08/26/2006] [Indexed: 11/21/2022]
Abstract
A number of computational and experimental studies have identified intramolecular communication "pathways" or "networks" important for transmitting allostery. Here, we have used mutagenesis and NMR relaxation methods to investigate the scope and nature of the communication networks found in the second post-synaptic density-95/discs large/zonula occludens-1 (PDZ) domain of the human protein tyrosine phosphatase 1E protein (hPTP1E) (PDZ2). It was found that most mutations do not have a significant energetic contribution to peptide ligand binding. Three mutants that showed significant changes in binding also displayed context-dependent dynamic effects. Both a mutation at a partially exposed site (H71Y) and a buried core position (I35V) had a limited response in side-chain (2)H-based dynamics when compared to wild-type PDZ2. In contrast, a change at a second core position (I20F) that had previously been shown to be part of an energetic and dynamic network, resulted in extensive changes in side-chain dynamics. This response is reminiscent to that seen previously upon peptide ligand binding. These results shed light on the nature of the PDZ2 dynamic network and suggest that position 20 in PDZ2 acts as a "hub" that is energetically and dynamically critical for transmitting changes in dynamics throughout the PDZ domain.
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Affiliation(s)
- Ernesto J Fuentes
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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34
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Ahmed A, Gohlke H. Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins 2006; 63:1038-51. [PMID: 16493629 DOI: 10.1002/prot.20907] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of a two-step approach for multiscale modeling of macromolecular conformational changes is based on recent developments in rigidity and elastic network theory. In the first step, static properties of the macromolecule are determined by decomposing the molecule into rigid clusters by using the graph-theoretical approach FIRST and an all-atom representation of the protein. In this way, rigid clusters are not limited to consist of residues adjacent in sequence or secondary structure elements as in previous studies. Furthermore, flexible links between rigid clusters are identified and can be modeled as such subsequently. In the second step, dynamical properties of the molecule are revealed by the rotations-translations of blocks approach (RTB) using an elastic network model representation of the coarse-grained protein. In this step, only rigid body motions are allowed for rigid clusters, whereas links between them are treated as fully flexible. The approach was tested on a data set of 10 proteins that showed conformational changes on ligand binding. For efficiency, coarse-graining the protein results in a remarkable reduction of memory requirements and computational times by factors of 9 and 27 on average and up to 25 and 125, respectively. For accuracy, directions and magnitudes of motions predicted by our approach agree well with experimentally determined ones, despite embracing in extreme cases >50% of the protein into one rigid cluster. In fact, the results of our method are in general comparable with when no or a uniform coarse-graining is applied; and the results are superior if the movement is dominated by loop or fragment motions. This finding indicates that explicitly distinguishing between flexible and rigid regions is advantageous when using a simplified protein representation in the second step. Finally, motions of atoms in rigid clusters are also well predicted by our approach, which points to the need to consider mobile protein regions in addition to flexible ones when modeling correlated motions.
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Affiliation(s)
- Aqeel Ahmed
- Department of Biology and Computer Science, J. W. Goethe-University, Frankfurt, Germany
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35
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Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M. Relation between native ensembles and experimental structures of proteins. Proc Natl Acad Sci U S A 2006; 103:10901-6. [PMID: 16829580 PMCID: PMC1544146 DOI: 10.1073/pnas.0511156103] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Indexed: 11/18/2022] Open
Abstract
Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of "high-sequence similarity Protein Data Bank" (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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36
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Igumenova TI, Frederick KK, Wand AJ. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 2006; 106:1672-99. [PMID: 16683749 PMCID: PMC2547146 DOI: 10.1021/cr040422h] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tatyana I Igumenova
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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37
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Kim Y, Kovrigin EL, Eletr Z. NMR studies of Escherichia coli acyl carrier protein: dynamic and structural differences of the apo- and holo-forms. Biochem Biophys Res Commun 2006; 341:776-83. [PMID: 16455053 DOI: 10.1016/j.bbrc.2006.01.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Accepted: 01/03/2006] [Indexed: 11/29/2022]
Abstract
Two indicators of conformational variability of Escherichia coli acyl carrier protein (ACP) have been investigated, namely backbone dynamics and chemical shift variations of ACP. Hydrophobic interactions between the 4'-PP prosthetic group and the hydrophobic pocket enclosed by the amphipathic helices resulted in chemical shift perturbations in the residues near the prosthetic group binding sites and contact sites in the hydrophobic pockets upon conversion from apo- to holo-forms. At pH 7.9, destabilization of ACP due to negative charge repulsions and the deprotonated state of His 75 resulted in observed chemical shift changes in the C-terminal region. Model-free analysis showed that the alpha(1)alpha(2) loop region near the prosthetic group binding site in ACP shows the greatest flexibility (lowest S(2) values) and this result may suggest these flexibilities are required for structural rearrangements when the acyl chain binds to the prosthetic group of ACP. Flexibility of ACP shown in this study is essential for its ability to interact with functionally different enzyme partners specifically and weakly in the rapid delivery of acyl chain from one partner to another.
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Affiliation(s)
- Yangmee Kim
- Department of Chemistry and Bio/Molecular Informatics Center, Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, Republic of Korea.
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38
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Groesch TD, Zhou F, Mattila S, Geahlen RL, Post CB. Structural basis for the requirement of two phosphotyrosine residues in signaling mediated by Syk tyrosine kinase. J Mol Biol 2005; 356:1222-36. [PMID: 16410013 DOI: 10.1016/j.jmb.2005.11.095] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 11/30/2005] [Accepted: 11/30/2005] [Indexed: 11/30/2022]
Abstract
The protein-tyrosine kinase Syk couples immune recognition receptors to multiple signal transduction pathways, including the mobilization of calcium and the activation of NFAT. The ability of Syk to regulate signaling is influenced by its phosphorylation on tyrosine residues within the linker B region. The phosphorylation of both Y342 and Y346 is necessary for optimal signaling from the B cell receptor for antigen. The SH2 domains of multiple signaling proteins share the ability to bind this doubly phosphorylated site. The NMR structure of the C-terminal SH2 domain of PLCgamma (PLCC) bound to a doubly phosphorylated Syk peptide reveals a novel mode of phosphotyrosine recognition. PLCC undergoes extensive conformational changes upon binding to form a second phosphotyrosine-binding pocket in which pY346 is largely desolvated and stabilized through electrostatic interactions. The formation of the second binding pocket is distinct from other modes of phosphotyrosine recognition in SH2-protein association. The dependence of signaling on simultaneous phosphorylation of these two tyrosine residues offers a new mechanism to fine-tune the cellular response to external stimulation.
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Affiliation(s)
- Teresa D Groesch
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Cancer Center and Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
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39
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Perazzolo C, Wist J, Loth K, Poggi L, Homans S, Bodenhausen G. Effects of protein-pheromone complexation on correlated chemical shift modulations. JOURNAL OF BIOMOLECULAR NMR 2005; 33:233-42. [PMID: 16341752 DOI: 10.1007/s10858-005-3355-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 09/12/2005] [Indexed: 05/05/2023]
Abstract
Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{C'N} and DQC{C'N}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand).
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Affiliation(s)
- Chiara Perazzolo
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, BCH, 1015, Lausanne, Switzerland
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40
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Ding Z, Lee GI, Liang X, Gallazzi F, Arunima A, Van Doren SR. PhosphoThr peptide binding globally rigidifies much of the FHA domain from Arabidopsis receptor kinase-associated protein phosphatase. Biochemistry 2005; 44:10119-34. [PMID: 16042389 PMCID: PMC2813517 DOI: 10.1021/bi050414a] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A net increase in the backbone rigidity of the kinase-interacting FHA domain (KI-FHA) from the Arabidopsis receptor kinase-associated protein phosphatase (KAPP) accompanies the binding of a phosphoThr peptide from its CLV1 receptor-like kinase partner, according to (15)N NMR relaxation at 11.7 and 14.1 T. All of the loops of free KI-FHA display evidence of nanosecond-scale motions. Many of these same residues have residual dipolar couplings that deviate from structural predictions. Binding of the CLV1 pT868 peptide seems to reduce nanosecond-scale fluctuations of all loops, including half of the residues of recognition loops. Residues important for affinity are found to be rigid, i.e., conserved residues and residues of the subsite for the key pT+3 peptide position. This behavior parallels SH2 and PTB domain recognition of pTyr peptides. PhosphoThr peptide binding increases KI-FHA backbone rigidity (S(2)) of three recognition loops, a loop nearby, seven strands from the beta-sandwich, and a distal loop. Compensating the trend of increased rigidity, binding enhances fast mobility at a few sites in four loops on the periphery of the recognition surface and in two loops on the far side of the beta-sandwich. Line broadening evidence of microsecond- to millisecond-scale fluctuations occurs across the six-stranded beta-sheet and nearby edges of the beta-sandwich; this forms a network connected by packing of interior side chains and H-bonding. A patch of the slowly fluctuating residues coincides with the site of segment-swapped dimerization in crystals of the FHA domain of human Chfr. Phosphopeptide binding introduces microsecond- to millisecond-scale fluctuations to more residues of the long 8/9 recognition loop of KI-FHA. The rigidity of this FHA domain appears to couple as a whole to pThr peptide binding.
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Affiliation(s)
| | | | - Xiangyang Liang
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Fabio Gallazzi
- Molecular Biology Program, 125 Chemistry, 601 S. College Ave., University of Missouri, Columbia, Missouri, 65211 USA
| | - A. Arunima
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Steven R. Van Doren
- To whom correspondence should be addressed, E-mail: , Phone: 1 (573) 882-5113, FAX: 1 (573) 884-4812
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41
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Best RB, Clarke J, Karplus M. What Contributions to Protein Side-chain Dynamics are Probed by NMR Experiments? A Molecular Dynamics Simulation Analysis. J Mol Biol 2005; 349:185-203. [PMID: 15876377 DOI: 10.1016/j.jmb.2005.03.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 02/28/2005] [Accepted: 03/01/2005] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The results reproduce the variation in core side-chain dynamics observed by NMR and highlight the relevance of anharmonic motion and transitions between local minima for explaining NMR side-chain order parameters. A method is described for calculating converged order parameters by use of replica exchange molecular dynamics in conjunction with an implicit solvent model. These simulations allow the influence of various factors, such as the flexibility of side-chains and their free volume, on the mobility to be tested by perturbing the system. Deletion mutations are found to have the largest effect on the more densely packed FNfn10. Some counterintuitive effects are seen, such as an increase in order parameters close to deletion mutation sites, but these can be rationalized in terms of direct interactions with the modified side-chains. A statistical analysis of published order parameters supports the conclusions drawn from the simulations.
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Affiliation(s)
- Robert B Best
- MRC Centre for Protein Engineering, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
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42
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Kay LE. NMR studies of protein structure and dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 173:193-207. [PMID: 15780912 DOI: 10.1016/j.jmr.2004.11.021] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Indexed: 05/24/2023]
Abstract
Recent advances in solution NMR spectroscopy have significantly extended the spectrum of problems that can now be addressed with this technology. In particular, studies of proteins with molecular weights on the order of 100 kDa are now possible at a level of detail that was previously reserved for much smaller systems. An example of the sort of information that is now accessible is provided in a study of malate synthase G, a 723 residue enzyme that has been a focal point of research efforts in my laboratory. Details of the labeling schemes that have been employed and optimal experiments for extraction of structural and dynamics information on this protein are described. NMR studies of protein dynamics, in principle, give insight into the relation between motion and function. A description of deuterium-based spin relaxation methods for the investigation of side chain dynamics is provided. Examples where millisecond (ms) time scale dynamics play an important role and where relaxation dispersion NMR spectroscopy has been particularly informative, including applications involving the membrane enzyme PagP and mutants of the Fyn SH3 domain that fold on a ms time scale, are presented.
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Affiliation(s)
- Lewis E Kay
- Contribution from the Protein Engineering Network Centers of Excellence and the Department of Medical Genetics, The University of Toronto, Toronto, Ont., Canada M5S 1A8.
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43
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Ran X, Song J. Structural insight into the binding diversity between the Tyr-phosphorylated human ephrinBs and Nck2 SH2 domain. J Biol Chem 2005; 280:19205-12. [PMID: 15764601 DOI: 10.1074/jbc.m500330200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The binding interaction between the Nck2 SH2 domain and the phosphorylated ephrinB initiates a critical pathway for the reverse signaling network mediated by Eph receptor-ephrinB. Previously, the NMR structure and Tyr phosphorylations of the human ephrinB cytoplasmic domain have been studied. To obtain a complete story, it would be of significant interest to determine the structure of the Nck2 SH2 domain that shows a low sequence identity to other SH2 domains with known structures. Here, we report the determination of the solution structure of the human Nck2 SH2 domain and investigate its interactions with three phosphorylated ephrinB fragments by NMR spectroscopy. The results indicate that: 1) although the human Nck2 SH2 domain adopts a core tertiary fold common to all SH2 domains, it owns some unique properties such as a shorter C-terminal helix and unusual electrostatic potential surface. However, the most striking finding is that the C-terminal tail of the human Nck2 SH2 domain adopts a short antiparallel beta-sheet that, to the best of our knowledge, has never been identified in other SH2 domains. The truncation study suggests that one function of the C-terminal tail is to control the folding/solubility of the SH2 domain. 2) In addition to [Tyr(P)304]ephrinB2(301-322) and [Tyr(P)316]ephrinB2(301-322), here we identified [Tyr(P)330]ephrinB2(324-333) also capable of binding to the SH2 domain. The detailed NMR study indicated that the binding mechanisms for the three ephrinB fragments might be different. The binding with [Tyr(P)304]-ephrinB2(301-322) and [Tyr(P)316]ephrinB2(301-322) might be mostly involved in the residues over the N-half of the SH2 domain and provoked a significant increase in the backbone and side chain dynamics of the SH2 domain on the microsecond-millisecond time scale. In contrast, binding with [Tyr(P)330]ephrinB2(324-333) might have most residues over both halves engaged but induced less profound conformational dynamics on the mus-ms time scale.
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Affiliation(s)
- Xiaoyuan Ran
- Department of Biochemistry, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
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44
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Mittermaier A, Kay LE. The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase. Protein Sci 2004; 13:1088-99. [PMID: 15044737 PMCID: PMC2280047 DOI: 10.1110/ps.03502504] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have used (15)N- and (2)H-NMR spin relaxation experiments to study the response of backbone and side-chain dynamics when a leucine or valine is substituted for a completely buried phenylalanine residue in the SH3 domain from the Fyn tyrosine kinase. Several residues show differences in the time scales and temperature dependences of internal motions when data for the three proteins are compared. Changes were also observed in the magnitude of dynamics, with the valine, and to a lesser extent leucine mutant, showing enhanced flexibility compared to the wild-type (WT) protein. The motions of many of the same amide and methyl groups are affected by both mutations, identifying a set of loci where dynamics are sensitive to interactions involving the targeted side chain. These results show that contacts within the hydrophobic core affect many aspects of internal mobility throughout the Fyn SH3 domain.
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Affiliation(s)
- Anthony Mittermaier
- Departments of Biochemistry, Chemistry and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
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45
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
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46
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Gohlke H, Kuhn LA, Case DA. Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 2004; 56:322-37. [PMID: 15211515 DOI: 10.1002/prot.20116] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Changes in flexibility upon protein-protein complex formation of H-Ras and the Ras-binding domain of C-Raf1 have been investigated using the molecular framework approach FIRST (Floppy Inclusion and Rigid Substructure Topology) and molecular dynamics simulations (MD) of in total approximately 35 ns length. In a computational time of about one second, FIRST identifies flexible and rigid regions in a single, static three-dimensional molecular framework, whose vertices represent protein atoms and whose edges represent covalent and non-covalent (hydrogen bond and hydrophobic) constraints and fixed bond angles within the protein. The two methods show a very good agreement with respect to the identification of changes in flexibility in both binding partners on a local scale. This implies that flexibility can be successfully predicted by identifying which bonds limit motion within a molecule and how they are coupled. In particular, as identified by MD, the beta-sheet in Raf shows considerably more pronounced orientational correlations in the bound state compared to the unbound state. Similarly, FIRST assigns the beta-sheet to the largest rigid cluster of the complex. Interestingly, FIRST allows us to identify that interactions across the interface (but not conformational changes upon complex formation) result in the observed rigidification. Since regions of the beta-sheet of Raf that do not interact directly with Ras become rigidified, this also demonstrates the long-range aspect to rigidity percolation. Possible implications of the change of flexibility of the Ras-binding domain of Raf on the activation of Raf upon complex formation are discussed. Finally, the sensitivity of FIRST results with respect to the representation of non-covalent interactions used as constraints is probed.
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Affiliation(s)
- Holger Gohlke
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Fuentes EJ, Der CJ, Lee AL. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J Mol Biol 2004; 335:1105-15. [PMID: 14698303 DOI: 10.1016/j.jmb.2003.11.010] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric communication is a fundamental process that proteins use to propagate signals from one site to functionally important distal sites. Although allostery is usually associated with multimeric proteins and enzymes, "long-range" communication may be a fundamental property of proteins. In some cases, communication occurs with minimal structural change. PDZ (post-synaptic density-95/discs large/zonula occludens-1) domains are small, protein-protein binding modules that can use multiple surfaces for docking diverse molecules. Furthermore, these domains have long-range energetic couplings that link the ligand-binding site to distal regions of the structure. Here, we show that allosteric behavior in a representative member of the PDZ domain family may be directly detected using side-chain methyl dynamics measurements. The changes in side-chain dynamics parameters in the second PDZ domain from the human tyrosine phosphatase 1E (hPTP1E) were determined upon binding a peptide target. Long-range dynamic effects were detected that correspond to previously observed pair-wise energetic couplings. These results provide one of the first experimental examples for the potential role of ps-ns timescale dynamics in propagating long-range signals within a protein, and reinforce the idea that dynamic fluctuations in proteins contribute to allosteric signal transduction.
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Affiliation(s)
- Ernesto J Fuentes
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Sheinerman FB, Al-Lazikani B, Honig B. Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains. J Mol Biol 2004; 334:823-41. [PMID: 14636606 DOI: 10.1016/j.jmb.2003.09.075] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Here, we present an approach for the prediction of binding preferences of members of a large protein family for which structural information for a number of family members bound to a substrate is available. The approach involves a number of steps. First, an accurate multiple alignment of sequences of all members of a protein family is constructed on the basis of a multiple structural superposition of family members with known structure. Second, the methods of continuum electrostatics are used to characterize the energetic contribution of each residue in a protein to the binding of its substrate. Residues that make a significant contribution are mapped onto the protein sequence and are used to define a "binding site signature" for the complex being considered. Third, sequences whose structures have not been determined are checked to see if they have binding-site signatures similar to one of the known complexes. Predictions of binding affinity to a given substrate are based on similarities in binding-site signature. An important component of the approach is the introduction of a context-specific substitution matrix suitable for comparison of binding-site residues. The methods are applied to the prediction of phosphopeptide selectivity of SH2 domains. To this end, the energetic roles of all protein residues in 17 different complexes of SH2 domains with their cognate targets are analyzed. The total number of residues that make significant contributions to binding is found to vary from nine to 19 in different complexes. These energetically important residues are found to contribute to binding through a variety of mechanisms, involving both electrostatic and hydrophobic interactions. Binding-site signatures are found to involve residues in different positions in SH2 sequences, some of them as far as 9A away from a bound peptide. Surprisingly, similarities in the signatures of different domains do not correlate with whole-domain sequence identities unless the latter is greater than 50%. An extensive comparison with the optimal binding motifs determined by peptide library experiments, as well as other experimental data indicate that the similarity in binding preferences of different SH2 domains can be deduced on the basis of their binding-site signatures. The analysis provides a rationale for the empirically derived classification of SH2 domains described by Songyang & Cantley, in that proteins in the same group are found to have similar residues at positions important for binding. Confident predictions of binding preference can be made for about 85% of SH2 domain sequences found in SWISSPROT. The approach described in this work is quite general and can, in principle, be used to analyze binding preferences of members of large protein families for which structural information for a number of family members is available. It also offers a strategy for predicting cross-reactivity of compounds designed to bind to a particular target, for example in structure-based drug design.
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Affiliation(s)
- Felix B Sheinerman
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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Abstract
Over the last two decades, a new and unifying concept of cellular organization has emerged in which modular protein-protein interactions provide an underlying framework through which signaling pathways are assembled and controlled. In this scheme, posttranslational modifications such as phosphorylation commonly exert their biological effects by regulating molecular interactions, exemplified by the ability of phosphotyrosine sites to bind selectively to SH2 domains. Although these interactions are rather simple in isolation, they can nonetheless be exploited to generate complex cellular systems. Here, I discuss experiments that have led to this view of dynamic cellular behavior and identify some current and future areas of interest in cell signaling.
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Affiliation(s)
- Tony Pawson
- Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada.
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Thuduppathy GR, Hill RB. Applications of NMR spin relaxation methods for measuring biological motions. Methods Enzymol 2004; 384:243-64. [PMID: 15081691 PMCID: PMC3061832 DOI: 10.1016/s0076-6879(04)84015-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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