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Gautier C, Gianni S. A short structural extension dictates the early stages of folding of a PDZ domain. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140852. [PMID: 36055518 DOI: 10.1016/j.bbapap.2022.140852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
PDZ domains are highly abundant protein-protein interaction modules in human. One of the most extensively characterized PDZ domain, the third PDZ domain from PSD-95 (PDZ3), contains an α-helical C-terminal extension that has a key role in the function of the domain. Here we compared the folding of PDZ3 with a truncated variant (PDZ3Δα3), lacking the additional helix, by means of the so-called Φ-value analysis, an experimental technique that allows inferring the structure of folding transition states. Experiments reveal subtle but detectable differences in the folding of PDZ3Δα3 versus PDZ3, as probed by structural characterization of the folding transition states. These differences appear more remarkable in the early stages of folding, with a detectable shift of the folding nucleus. The presented results allow demonstrating that the native state exerts a weak bias at the early stages of folding, which appear to be characterized by alternative pathways.
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Affiliation(s)
- Candice Gautier
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
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2
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Raj N, Click TH, Yang H, Chu JW. Structure-mechanics statistical learning uncovers mechanical relay in proteins. Chem Sci 2022; 13:3688-3696. [PMID: 35432911 PMCID: PMC8966636 DOI: 10.1039/d1sc06184d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/10/2022] [Indexed: 12/31/2022] Open
Abstract
A protein's adaptive response to its substrates is one of the key questions driving molecular physics and physical chemistry. This work employs the recently developed structure-mechanics statistical learning method to establish a mechanical perspective. Specifically, by mapping all-atom molecular dynamics simulations onto the spring parameters of a backbone-side-chain elastic network model, the chemical moiety specific force constants (or mechanical rigidity) are used to assemble the rigidity graph, which is the matrix of inter-residue coupling strength. Using the S1A protease and the PDZ3 signaling domain as examples, chains of spatially contiguous residues are found to exhibit prominent changes in their mechanical rigidity upon substrate binding or dissociation. Such a mechanical-relay picture thus provides a mechanistic underpinning for conformational changes, long-range communication, and inter-domain allostery in both proteins, where the responsive mechanical hotspots are mostly residues having important biological functions or significant mutation sensitivity. Protein residues exhibit specific routes of mechanical relay as the adaptive responses to substrate binding or dissociation. On such physically contiguous connections, residues experience prominent changes in their coupling strengths.![]()
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Affiliation(s)
- Nixon Raj
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Timothy H Click
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
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3
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Kumawat A, Chakrabarty S. Protonation-Induced Dynamic Allostery in PDZ Domain: Evidence of Perturbation-Independent Universal Response Network. J Phys Chem Lett 2020; 11:9026-9031. [PMID: 33043672 DOI: 10.1021/acs.jpclett.0c02885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dynamic allostery is a relatively new paradigm where certain external perturbations may lead to modulation of conformational dynamics at a distant part of a protein without significant changes in the overall structure. While most well-characterized examples of dynamic allostery involve binding with other entities like small molecules, peptides, or nucleic acids, in this work we demonstrate that chemical modifications like protonation may lead to significant dynamical allosteric response in a PDZ domain protein. Tuning the protonation states of two histidine residues (H317 and H372), we identify the allosteric pathways responsible for the dynamic response. Interestingly, the same set of residues that constitute the allosteric response network upon ligand binding seem to be responsible for protonation-induced dynamic allostery. Thus, we propose the existence of an inherent universal response network in signaling proteins, where the same set of residues can respond to varying types of external perturbations in terms of rearrangement of hydrogen-bonded network and redistribution of electrostatic interaction energies.
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Affiliation(s)
- Amit Kumawat
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
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4
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Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate. Proc Natl Acad Sci U S A 2020; 117:19963-19969. [PMID: 32747559 PMCID: PMC7443948 DOI: 10.1073/pnas.2004138117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Much of our current knowledge on protein folding is based on work focused on isolated domains. In this study, using a combination of NMR and kinetic experiments, we depict the folding pathway of a multidomain construct comprising two PDZ domains in tandem, belonging to the protein Whirlin. We demonstrate the presence of a misfolded intermediate that competes with productive folding. Interestingly, we show that, unexpectedly, this misfolded state retains the native-like functional ability to bind its physiological ligand, representing a clear example of a functionally competent misfolded state. On the basis of these results and a comparative analysis of the amino acidic sequences of Whirlin from different species, we propose a possible physiological role of the misfolded intermediate. Although more than 75% of the proteome is composed of multidomain proteins, current knowledge of protein folding is based primarily on studies of isolated domains. In this work, we describe the folding mechanism of a multidomain tandem construct comprising two distinct covalently bound PDZ domains belonging to a protein called Whirlin, a scaffolding protein of the hearing apparatus. In particular, via a synergy between NMR and kinetic experiments, we demonstrate the presence of a misfolded intermediate that competes with productive folding. In agreement with the view that tandem domain swapping is a potential source of transient misfolding, we demonstrate that such a kinetic trap retains native-like functional activity, as shown by the preserved ability to bind its physiological ligand. Thus, despite the general knowledge that protein misfolding is intimately associated with dysfunction and diseases, we provide a direct example of a functionally competent misfolded state. Remarkably, a bioinformatics analysis of the amino acidic sequence of Whirlin from different species suggests that the tendency to perform tandem domain swapping between PDZ1 and PDZ2 is highly conserved, as demonstrated by their unexpectedly high sequence identity. On the basis of these observations, we discuss on a possible physiological role of such misfolded intermediate.
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5
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Li T, Li R, Zhu T, Cui X, Li C, Cui Y, Wu B. Improving the System Performance of the Asymmetric Biosynthesis of d-Pantoic Acid by Using Artificially Self-Assembled Enzymes in Escherichia coli. ACS Biomater Sci Eng 2019; 6:219-224. [DOI: 10.1021/acsbiomaterials.9b01754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Tong Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xuexian Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chuijian Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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6
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Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. J Biosci 2017. [DOI: 10.1007/s12038-017-9727-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Addressing the role of the α-helical extension in the folding of the third PDZ domain from PSD-95. Sci Rep 2017; 7:12593. [PMID: 28974728 PMCID: PMC5626748 DOI: 10.1038/s41598-017-12827-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/14/2017] [Indexed: 01/22/2023] Open
Abstract
PDZ domains are one of the most important protein-protein interaction domains in human. While presenting a conserved three dimensional structure, a substantial number of PDZ domains display structural extensions suggested to be involved in their folding and binding mechanisms. The C-terminal α-helix extension (α3) of the third PDZ domain from PSD-95 (PDZ3) has been reported to have a role in function of the domain as well as in the stabilization of the native fold. Here we report an evaluation of the effect of the truncation of this additional helix on the folding and unfolding kinetics of PDZ3. Fluorescent variants of full length and truncated PDZ3 were produced and stopped-flow fluorescence measurements were made under different experimental conditions (pH, ionic strength and temperature) to investigate the folding kinetics of the respective variant. The results show that folding of PDZ3 is robust and that the mechanism is only marginally affected by the truncation, which contributes to a destabilization of the native state, but otherwise do not change the overall observed kinetics. Furthermore, the increase in the unfolding rate constants, but not the folding rate constant upon deletion of α3 suggests that the α-helical extension is largely unstructured in the folding transition state.
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8
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Toto A, Mattei A, Jemth P, Gianni S. Understanding the role of phosphorylation in the binding mechanism of a PDZ domain. Protein Eng Des Sel 2016; 30:1-5. [PMID: 27760803 DOI: 10.1093/protein/gzw055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/14/2022] Open
Abstract
The PDZ domain is one of the most common protein-protein interaction domains in mammalian species. While several studies have demonstrated the importance of phosphorylation in interactions involving PDZ domains, there is a paucity of detailed mechanistic data addressing how the PDZ interaction is affected by phosphorylation. Here, we address this question by equilibrium and kinetic binding experiments using PDZ2 from protein tyrosine phosphatase L1 and its interaction with a peptide from the natural ligand RIL. The results show that phosphorylation of a serine residue in the RIL peptide has dual and opposing effects: it increases both the association and dissociation rate constants, which leads to an overall weakening of binding. Furthermore, we performed binding experiments with a RIL peptide in which the serine was replaced by a glutamate, a commonly used method to mimic phosphorylation in proteins. Strikingly, both the affinity and the ionic strength dependence of the affinity differed markedly for the phosphoserine and glutamate peptides. These results show that, in this particular case, glutamate is a poor mimic of serine phosphorylation.
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Affiliation(s)
- Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Fondazione Cenci Bolognetti, Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy
| | - Annalisa Mattei
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Fondazione Cenci Bolognetti, Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Fondazione Cenci Bolognetti, Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome, Italy
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9
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Pedersen SW, Moran GE, Sereikaitė V, Haugaard-Kedström LM, Strømgaard K. Importance of a Conserved Lys/Arg Residue for Ligand/PDZ Domain Interactions as Examined by Protein Semisynthesis. Chembiochem 2016; 17:1936-1944. [DOI: 10.1002/cbic.201600322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Søren W. Pedersen
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Griffin E. Moran
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Vita Sereikaitė
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Linda M. Haugaard-Kedström
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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10
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Toto A, Pedersen SW, Karlsson OA, Moran GE, Andersson E, Chi CN, Strømgaard K, Gianni S, Jemth P. Ligand binding to the PDZ domains of postsynaptic density protein 95. Protein Eng Des Sel 2016; 29:169-75. [PMID: 26941280 DOI: 10.1093/protein/gzw004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 01/22/2016] [Indexed: 11/13/2022] Open
Abstract
Cellular scaffolding and signalling is generally governed by multidomain proteins, where each domain has a particular function. Postsynaptic density protein 95 (PSD-95) is involved in synapse formation and is a typical example of such a multidomain protein. Protein-protein interactions of PSD-95 are well studied and include the following three protein ligands: (i)N-methyl-d-aspartate-type ionotropic glutamate receptor subunit GluN2B, (ii) neuronal nitric oxide synthase and (iii) cysteine-rich protein (CRIPT), all of which bind to one or more of the three PDZ domains in PSD-95. While interactions for individual PDZ domains of PSD-95 have been well studied, less is known about the influence of neighbouring domains on the function of the respective individual domain. We therefore performed a systematic study on the ligand-binding kinetics of PSD-95 using constructs of different size for PSD-95 and its ligands. Regarding the canonical peptide-binding pocket and relatively short peptides (up to 15-mer), the PDZ domains in PSD-95 by and large work as individual binding modules. However, in agreement with previous studies, residues outside of the canonical binding pocket modulate the affinity of the ligands. In particular, the dissociation of the 101 amino acid CRIPT from PSD-95 is slowed down at least 10-fold for full-length PSD-95 when compared with the individual PDZ3 domain.
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Affiliation(s)
- Angelo Toto
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Uppsala SE-75123, Sweden Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Sapienza, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, University of Rome, Rome 00185, Italy
| | - Søren W Pedersen
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - O Andreas Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Uppsala SE-75123, Sweden
| | - Griffin E Moran
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Uppsala SE-75123, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Uppsala SE-75123, Sweden
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Sapienza, Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, University of Rome, Rome 00185, Italy Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Uppsala SE-75123, Sweden
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11
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Pedersen SW, Pedersen SB, Anker L, Hultqvist G, Kristensen AS, Jemth P, Strømgaard K. Probing backbone hydrogen bonding in PDZ/ligand interactions by protein amide-to-ester mutations. Nat Commun 2015; 5:3215. [PMID: 24477114 DOI: 10.1038/ncomms4215] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/07/2014] [Indexed: 01/30/2023] Open
Abstract
PDZ domains are scaffolding modules in protein-protein interactions that mediate numerous physiological functions by interacting canonically with the C-terminus or non-canonically with an internal motif of protein ligands. A conserved carboxylate-binding site in the PDZ domain facilitates binding via backbone hydrogen bonds; however, little is known about the role of these hydrogen bonds due to experimental challenges with backbone mutations. Here we address this interaction by generating semisynthetic PDZ domains containing backbone amide-to-ester mutations and evaluating the importance of individual hydrogen bonds for ligand binding. We observe substantial and differential effects upon amide-to-ester mutation in PDZ2 of postsynaptic density protein 95 and other PDZ domains, suggesting that hydrogen bonding at the carboxylate-binding site contributes to both affinity and selectivity. In particular, the hydrogen-bonding pattern is surprisingly different between the non-canonical and canonical interaction. Our data provide a detailed understanding of the role of hydrogen bonds in protein-protein interactions.
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Affiliation(s)
- Søren W Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Stine B Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Louise Anker
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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12
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Chi CN, Vögeli B, Bibow S, Strotz D, Orts J, Güntert P, Riek R. A Structural Ensemble for the Enzyme Cyclophilin Reveals an Orchestrated Mode of Action at Atomic Resolution. Angew Chem Int Ed Engl 2015; 54:11657-61. [DOI: 10.1002/anie.201503698] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/05/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Celestine N. Chi
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
| | - Beat Vögeli
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
| | - Stefan Bibow
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
| | - Julien Orts
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max‐von‐Laue‐Strasse 9, 60438 Frankfurt am Main (Germany)
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, ETH‐Hönggerberg, 8093 Zürich (Switzerland)
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13
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Chi CN, Vögeli B, Bibow S, Strotz D, Orts J, Güntert P, Riek R. A Structural Ensemble for the Enzyme Cyclophilin Reveals an Orchestrated Mode of Action at Atomic Resolution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Blöchliger N, Xu M, Caflisch A. Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophys J 2015; 108:2362-70. [PMID: 25954893 PMCID: PMC4423040 DOI: 10.1016/j.bpj.2015.03.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 12/15/2022] Open
Abstract
We have captured the binding of a peptide to a PDZ domain by unbiased molecular dynamics simulations. Analysis of the trajectories reveals on-pathway encounter complex formation, which is driven by electrostatic interactions between negatively charged carboxylate groups in the peptide and positively charged side chains surrounding the binding site. In contrast, the final stereospecific complex, which matches the crystal structure, features completely different interactions, namely the burial of the hydrophobic side chain of the peptide C-terminal residue and backbone hydrogen bonds. The simulations show that nonnative salt bridges stabilize kinetically the encounter complex during binding. Unbinding follows the inverse sequence of events with the same nonnative salt bridges in the encounter complex. Thus, in contrast to protein folding, which is driven by native interactions, the binding of charged peptides can be steered by nonnative interactions, which might be a general mechanism, e.g., in the recognition of histone tails by bromodomains.
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Affiliation(s)
| | - Min Xu
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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15
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Di Silvio E, Toto A, Bonetti D, Morrone A, Gianni S. Understanding the effect of alternative splicing in the folding and function of the second PDZ from protein tyrosine phosphatase-BL. Sci Rep 2015; 5:9299. [PMID: 25788329 PMCID: PMC4365404 DOI: 10.1038/srep09299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
PDZ domains are the most prominent biological structural domains involved in protein-protein interactions in the human cell. The second PDZ domain of the protein tyrosine phosphatase BL (PDZ2) interacts and binds the C-termini of the tumour suppressor protein APC and of the LIM domain-containing protein RIL. One isoform of PDZ2 (PDZ2as) involves an alternative spliced form that exhibits an insertion of 5 residues in a loop. PDZ2as abrogates binding to its partners, even if the insertion is directly located in its binding pocket. Here, we investigate the folding and function of PDZ2as, in comparison to the previously characterized PDZ2 domain. Data reveal that, whilst the thermodynamic stability of PDZ2as appears as nearly identical to that of PDZ2, the insertion of 5 amino acids induces formation of some weak transient non-native interactions in the folding transition state, as mirrored by a concomitant increase of both the folding and unfolding rate constants. From a functional perspective, we show that the decrease in affinity is caused by a pronounced decrease of the association rate constants (by nearly ten fold), with no effect on the microscopic dissociation rate constants. The results are briefly discussed in the context of previous work on PDZ domains.
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Affiliation(s)
- Eva Di Silvio
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Angelo Toto
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Angela Morrone
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Stefano Gianni
- 1] Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy [2] Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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16
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Di Silvio E, Bonetti D, Toto A, Morrone A, Gianni S. The mechanism of binding of the second PDZ domain from the Protein Tyrosine Phosphatase-BL to the Adenomatous Polyposis Coli tumor suppressor. Protein Eng Des Sel 2014; 27:249-53. [DOI: 10.1093/protein/gzu022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Pedersen SW, Hultqvist G, Strømgaard K, Jemth P. The role of backbone hydrogen bonds in the transition state for protein folding of a PDZ domain. PLoS One 2014; 9:e95619. [PMID: 24748272 PMCID: PMC3991670 DOI: 10.1371/journal.pone.0095619] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/27/2014] [Indexed: 12/24/2022] Open
Abstract
Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.
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Affiliation(s)
- Søren W. Pedersen
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (KS); (PJ)
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
- * E-mail: (KS); (PJ)
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18
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Hultqvist G, Haq SR, Punekar AS, Chi CN, Engström Å, Bach A, Strømgaard K, Selmer M, Gianni S, Jemth P. Energetic pathway sampling in a protein interaction domain. Structure 2014; 21:1193-1202. [PMID: 23810696 DOI: 10.1016/j.str.2013.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/24/2013] [Accepted: 05/29/2013] [Indexed: 01/10/2023]
Abstract
The affinity and specificity of protein-ligand interactions are influenced by energetic crosstalk within the protein domain. However, the molecular details of such intradomain allostery are still unclear. Here, we have experimentally detected and computationally predicted interaction pathways in the postsynaptic density 95/discs large/zonula occludens 1 (PDZ)-peptide ligand model system using wild-type and circularly permuted PDZ proteins. The circular permutant introduced small perturbations in the tertiary structure and a concomitant rewiring of allosteric pathways, allowing us to describe how subtle changes may reshape energetic signaling. The results were analyzed in the context of other members of the PDZ family, which were found to contain distinct interaction pathways for different peptide ligands. The data reveal a fascinating scenario whereby several energetic pathways are sampled within one single domain and distinct pathways are activated by specific protein ligands.
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Affiliation(s)
- Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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19
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Eildal JNN, Hultqvist G, Balle T, Stuhr-Hansen N, Padrah S, Gianni S, Strømgaard K, Jemth P. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations. J Am Chem Soc 2013; 135:12998-3007. [PMID: 23705582 DOI: 10.1021/ja402875h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions.
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Affiliation(s)
- Jonas N N Eildal
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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20
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Møller TC, Wirth VF, Roberts NI, Bender J, Bach A, Jacky BPS, Strømgaard K, Deussing JM, Schwartz TW, Martinez KL. PDZ domain-mediated interactions of G protein-coupled receptors with postsynaptic density protein 95: quantitative characterization of interactions. PLoS One 2013; 8:e63352. [PMID: 23691031 PMCID: PMC3653948 DOI: 10.1371/journal.pone.0063352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/02/2013] [Indexed: 11/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome. Their signaling is regulated by scaffold proteins containing PDZ domains, but although these interactions are important for GPCR function, they are still poorly understood. We here present a quantitative characterization of the kinetics and affinity of interactions between GPCRs and one of the best characterized PDZ scaffold proteins, postsynaptic density protein 95 (PSD-95), using fluorescence polarization (FP) and surface plasmon resonance (SPR). By comparing these in vitro findings with colocalization of the full-length proteins in cells and with previous studies, we suggest that the range of relevant interactions might extend to interactions with K i = 450 µM in the in vitro assays. Within this range, we identify novel PSD-95 interactions with the chemokine receptor CXCR2, the neuropeptide Y receptor Y2, and four of the somatostatin receptors (SSTRs). The interaction with SSTR1 was further investigated in mouse hippocampal neurons, where we found a clear colocalization between the endogenously expressed proteins, indicating a potential for further investigation of the role of this interaction. The approach can easily be transferred to other receptors and scaffold proteins and this could help accelerate the discovery and quantitative characterization of GPCR-PDZ interactions.
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Affiliation(s)
- Thor C. Møller
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Volker F. Wirth
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Nina I. Roberts
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Julia Bender
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Anders Bach
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte P. S. Jacky
- Department of Neuroscience and Pharmacology & Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jan M. Deussing
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- Clinical Cooperation Group Molecular Neurogenetics, Institute of Developmental Genetics, Helmholtz Center Munich, Munich, Germany
| | - Thue W. Schwartz
- Department of Neuroscience and Pharmacology & Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Karen L. Martinez
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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21
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Ivarsson Y, Wawrzyniak AM, Kashyap R, Polanowska J, Betzi S, Lembo F, Vermeiren E, Chiheb D, Lenfant N, Morelli X, Borg JP, Reboul J, Zimmermann P. Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments. PLoS One 2013; 8:e54581. [PMID: 23390500 PMCID: PMC3563628 DOI: 10.1371/journal.pone.0054581] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND PDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the prevalence, specificity, affinity, and molecular determinants of PDZ-PtdInsPs interactions and on their impact on PDZ-protein interactions is very limited. METHODOLOGY/PRINCIPAL FINDINGS We screened the human proteome for PtdInsPs interacting PDZ domains by a combination of in vivo cell-localization studies and in vitro dot blot and Surface Plasmon Resonance (SPR) experiments using synthetic lipids and recombinant proteins. We found that PtdInsPs interactions contribute to the cellular distribution of some PDZ domains, intriguingly also in nuclear organelles, and that a significant subgroup of PDZ domains interacts with PtdInsPs with affinities in the low-to-mid micromolar range. In vitro specificity for the head group is low, but with a trend of higher affinities for more phosphorylated PtdInsPs species. Other membrane lipids can assist PtdInsPs-interactions. PtdInsPs-interacting PDZ domains have generally high pI values and contain characteristic clusters of basic residues, hallmarks that may be used to predict additional PtdInsPs interacting PDZ domains. In tripartite binding experiments we established that peptide binding can either compete or cooperate with PtdInsPs binding depending on the combination of ligands. CONCLUSIONS/SIGNIFICANCE Our screen substantially expands the set of PtdInsPs interacting PDZ domains, and shows that a full understanding of the biology of PDZ proteins will require a comprehensive insight into the intricate relationships between PDZ domains and their peptide and lipid ligands.
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Affiliation(s)
- Ylva Ivarsson
- Department of Human Genetics, K. U. Leuven, Leuven, Belgium
| | | | - Rudra Kashyap
- Department of Human Genetics, K. U. Leuven, Leuven, Belgium
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Jolanta Polanowska
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Stéphane Betzi
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Frédérique Lembo
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Elke Vermeiren
- Department of Human Genetics, K. U. Leuven, Leuven, Belgium
| | - Driss Chiheb
- Department of Human Genetics, K. U. Leuven, Leuven, Belgium
| | - Nicolas Lenfant
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Xavier Morelli
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Jean-Paul Borg
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Jérôme Reboul
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
| | - Pascale Zimmermann
- Department of Human Genetics, K. U. Leuven, Leuven, Belgium
- Inserm, U1068, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, CRCM, Marseille, France
- * E-mail:
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22
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Lloret N, Frederiksen RS, Møller TC, Rieben NI, Upadhyay S, De Vico L, Jensen JH, Nygård J, Martinez KL. Effects of buffer composition and dilution on nanowire field-effect biosensors. NANOTECHNOLOGY 2013; 24:035501. [PMID: 23263553 DOI: 10.1088/0957-4484/24/3/035501] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nanowire-based field-effect transistors (FETs) can be used as ultra-sensitive and label-free biosensors for detecting protein-protein interactions. A way to increase the performance of such sensors is to dilute the sensing buffer drastically. However, we show here that this can have an important effect on the function of the proteins. Moreover, it is demonstrated that this dilution significantly affects the pH stability of the sensing buffer, which consequently impacts the charge of the protein and thus the response and signal-to-noise ratio in the sensing experiments. Three model systems are investigated experimentally to illustrate the impact on ligand-protein and protein-protein interactions. Simulations are performed to illustrate the effect on the performance of the sensors. Combining various parameters, the current study provides a means for evaluating and selecting the most appropriate buffer composition for bioFET measurements.
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Affiliation(s)
- Noémie Lloret
- Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
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23
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Wawrzyniak AM, Kashyap R, Zimmermann P. Phosphoinositides and PDZ domain scaffolds. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 991:41-57. [PMID: 23775690 DOI: 10.1007/978-94-007-6331-9_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery that PSD-95/Discs large/ZO-1 (PDZ) domains can function as lipid-binding modules, in particular interacting with phosphoinositides (PIs), was made more than 10 years ago (Mol Cell 9(6): 1215-1225, 2002). Confirmatory studies and a series of functional follow-ups established PDZ domains as dual specificity modules displaying both peptide and lipid binding, and prompted a rethinking of the mode of action of PDZ domains in the control of cell signaling. In this chapter, after introducing PDZ domains, PIs and methods for studying protein-lipid interactions, we focus on (i) the prevalence and the specificity of PDZ-PIs interactions, (ii) the molecular determinants of PDZ-PIs interactions, (iii) the integration of lipid and peptide binding by PDZ domains, (iv) the common features of PIs interacting PDZ domains and (v) the regulation and functional significance of PDZ-PIs interactions.
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24
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Shammas S, Rogers J, Hill S, Clarke J. Slow, reversible, coupled folding and binding of the spectrin tetramerization domain. Biophys J 2012; 103:2203-14. [PMID: 23200054 PMCID: PMC3512043 DOI: 10.1016/j.bpj.2012.10.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/02/2012] [Accepted: 10/10/2012] [Indexed: 11/16/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) are significantly unstructured under physiological conditions. A number of these IDPs have been shown to undergo coupled folding and binding reactions whereby they can gain structure upon association with an appropriate partner protein. In general, these systems display weaker binding affinities than do systems with association between completely structured domains, with micromolar K(d) values appearing typical. One such system is the association between α- and β-spectrin, where two partially structured, incomplete domains associate to form a fully structured, three-helix bundle, the spectrin tetramerization domain. Here, we use this model system to demonstrate a method for fitting association and dissociation kinetic traces where, using typical biophysical concentrations, the association reactions are expected to be highly reversible. We elucidate the unusually slow, two-state kinetics of spectrin assembly in solution. The advantages of studying kinetics in this regime include the potential for gaining equilibrium constants as well as rate constants, and for performing experiments with low protein concentrations. We suggest that this approach would be particularly appropriate for high-throughput mutational analysis of two-state reversible binding processes.
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Affiliation(s)
| | | | | | - J. Clarke
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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25
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Chi CN, Haq SR, Rinaldo S, Dogan J, Cutruzzolà F, Engström Å, Gianni S, Lundström P, Jemth P. Interactions outside the boundaries of the canonical binding groove of a PDZ domain influence ligand binding. Biochemistry 2012; 51:8971-9. [PMID: 23046383 DOI: 10.1021/bi300792h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ) domain is a protein-protein interaction module with a shallow binding groove where protein ligands bind. However, interactions that are not part of this canonical binding groove are likely to modulate peptide binding. We have investigated such interactions beyond the binding groove for PDZ3 from PSD-95 and a peptide derived from the C-terminus of the natural ligand CRIPT. We found via nuclear magnetic resonance experiments that up to eight residues of the peptide ligand interact with the PDZ domain, showing that the interaction surface extends far outside of the binding groove as defined by the crystal structure. PDZ3 contains an extra structural element, a C-terminal helix (α3), which is known to affect affinity. Deletion of this helix resulted in the loss of several intermolecular nuclear Overhauser enhancements from peptide residues outside of the binding pocket, suggesting that α3 forms part of the extra binding surface in wild-type PDZ3. Site-directed mutagenesis, isothermal titration calorimetry, and fluorescence intensity experiments confirmed the importance of both α3 and the N-terminal part of the peptide for the affinity. Our data suggest a general mechanism in which different binding surfaces outside of the PDZ binding groove could provide sites for specific interactions.
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Affiliation(s)
- Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
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26
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Ivarsson Y. Plasticity of PDZ domains in ligand recognition and signaling. FEBS Lett 2012; 586:2638-47. [PMID: 22576124 PMCID: PMC7094393 DOI: 10.1016/j.febslet.2012.04.015] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 11/19/2022]
Abstract
The PDZ domain is a protein-protein interacting module that plays an important role in the organization of signaling complexes. The recognition of short intrinsically disordered C-terminal peptide motifs is the archetypical PDZ function, but the functional repertoire of this versatile module also includes recognition of internal peptide sequences, dimerization and phospholipid binding. The PDZ function can be tuned by various means such as allosteric effects, changes of physiological buffer conditions and phosphorylation of PDZ domains and/or ligands, which poses PDZ domains as dynamic regulators of cell signaling. This review is focused on the plasticity of the PDZ interactions.
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Affiliation(s)
- Ylva Ivarsson
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
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27
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Beauchamp DL, Khajehpour M. The effect of lithium ions on the hydrophobic effect: does lithium affect hydrophobicity differently than other ions? Biophys Chem 2012; 163-164:35-43. [DOI: 10.1016/j.bpc.2012.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 02/06/2012] [Accepted: 02/06/2012] [Indexed: 10/14/2022]
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28
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Mostarda S, Gfeller D, Rao F. Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains. PLoS Comput Biol 2012; 8:e1002429. [PMID: 22412368 PMCID: PMC3297566 DOI: 10.1371/journal.pcbi.1002429] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/30/2012] [Indexed: 12/17/2022] Open
Abstract
A general paradigm to understand protein function is to look at properties of isolated well conserved domains, such as SH3 or PDZ domains. While common features of domain families are well understood, the role of subtle differences among members of these families is less clear. Here, molecular dynamics simulations indicate that the binding mechanism in PSD95-PDZ3 is critically regulated via interactions outside the canonical binding site, involving both the poorly conserved β₂-β₃ loop and an extra-domain helix. Using the CRIPT peptide as a prototypical ligand, our simulations suggest that a network of salt-bridges between the ligand and this loop is necessary for binding. These contacts interconvert between each other on a time scale of a few tens of nanoseconds, making them elusive to X-ray crystallography. The loop is stabilized by an extra-domain helix. The latter influences the global dynamics of the domain, considerably increasing binding affinity. We found that two key contacts between the helix and the domain, one involving the β₂-β₃ loop, provide an atomistic interpretation of the increased affinity. Our analysis indicates that both extra-domain segments and loosely conserved regions play critical roles in PDZ binding affinity and specificity.
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Affiliation(s)
- Stefano Mostarda
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
| | - David Gfeller
- Molecular Modeling, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Rao
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
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29
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Chi CN, Bach A, Engström Å, Strømgaard K, Lundström P, Ferguson N, Jemth P. Biophysical characterization of the complex between human papillomavirus E6 protein and synapse-associated protein 97. J Biol Chem 2010; 286:3597-606. [PMID: 21113079 DOI: 10.1074/jbc.m110.190264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The E6 protein of human papillomavirus (HPV) exhibits complex interaction patterns with several host proteins, and their roles in HPV-mediated oncogenesis have proved challenging to study. Here we use several biophysical techniques to explore the binding of E6 to the three PDZ domains of the tumor suppressor protein synapse-associated protein 97 (SAP97). All of the potential binding sites in SAP97 bind E6 with micromolar affinity. The dissociation rate constants govern the different affinities of HPV16 and HPV18 E6 for SAP97. Unexpectedly, binding is not mutually exclusive, and all three PDZ domains can simultaneously bind E6. Intriguingly, this quaternary complex has the same apparent hydrodynamic volume as the unliganded PDZ region, suggesting that a conformational change occurs in the PDZ region upon binding, a conclusion supported by kinetic experiments. Using NMR, we discovered a new mode of interaction between E6 and PDZ: a subset of residues distal to the canonical binding pocket in the PDZ(2) domain exhibited noncanonical interactions with the E6 protein. This is consistent with a larger proportion of the protein surface defining binding specificity, as compared with that reported previously.
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Affiliation(s)
- Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
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30
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Extensions of PDZ domains as important structural and functional elements. Protein Cell 2010; 1:737-51. [PMID: 21203915 DOI: 10.1007/s13238-010-0099-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Accepted: 07/21/2010] [Indexed: 12/21/2022] Open
Abstract
'Divide and conquer' has been the guiding strategy for the study of protein structure and function. Proteins are divided into domains with each domain having a canonical structural definition depending on its type. In this review, we push forward with the interesting observation that many domains have regions outside of their canonical definition that affect their structure and function; we call these regions 'extensions'. We focus on the highly abundant PDZ (PSD-95, DLG1 and ZO-1) domain. Using bioinformatics, we find that many PDZ domains have potential extensions and we developed an openly-accessible website to display our results ( http://bcz102.ust.hk/pdzex/ ). We propose, using well-studied PDZ domains as illustrative examples, that the roles of PDZ extensions can be classified into at least four categories: 1) protein dynamics-based modulation of target binding affinity, 2) provision of binding sites for macro-molecular assembly, 3) structural integration of multi-domain modules, and 4) expansion of the target ligand-binding pocket. Our review highlights the potential structural and functional importance of domain extensions, highlighting the significance of looking beyond the canonical boundaries of protein domains in general.
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31
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Bach A, Stuhr-Hansen N, Thorsen TS, Bork N, Moreira IS, Frydenvang K, Padrah S, Christensen SB, Madsen KL, Weinstein H, Gether U, Strømgaard K. Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1. Org Biomol Chem 2010; 8:4281-8. [PMID: 20668766 DOI: 10.1039/c0ob00025f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, we described the first small-molecule inhibitor, (E)-ethyl 2-cyano-3-(3,4-dichlorophenyl)acryloylcarbamate (1), of the PDZ domain of protein interacting with Calpha-kinase 1 (PICK1), a potential drug target against brain ischemia, pain and cocaine addiction. Herein, we explore structure-activity relationships of 1 by introducing subtle modifications of the acryloylcarbamate scaffold and variations of the substituents on this scaffold. The configuration around the double bond of 1 and analogues was settled by a combination of X-ray crystallography, NMR and density functional theory calculations. Thereby, docking studies were used to correlate biological affinities with structural considerations for ligand-protein interactions. The most potent analogue obtained in this study showed an improvement in affinity compared to 1 and is currently a lead in further studies of PICK1 inhibition.
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Affiliation(s)
- Anders Bach
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
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Chi CN, Bach A, Gottschalk M, Kristensen AS, Strømgaard K, Jemth P. Deciphering the kinetic binding mechanism of dimeric ligands using a potent plasma-stable dimeric inhibitor of postsynaptic density protein-95 as an example. J Biol Chem 2010; 285:28252-60. [PMID: 20576616 DOI: 10.1074/jbc.m110.124040] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dimeric ligands can be potent inhibitors of protein-protein or enzyme-substrate interactions. They have increased affinity and specificity toward their targets due to their ability to bind two binding sites simultaneously and are therefore attractive in drug design. However, few studies have addressed the kinetic mechanism of interaction of such bivalent ligands. We have investigated the binding interaction of a recently identified potent plasma-stable dimeric pentapeptide and PDZ1-2 of postsynaptic density protein-95 (PSD-95) using protein engineering in combination with fluorescence polarization, isothermal titration calorimetry, and stopped-flow fluorimetry. We demonstrate that binding occurs via a two-step process, where an initial binding to either one of the two PDZ domains is followed by an intramolecular step, which produces the bidentate complex. We have determined all rate constants involved in the binding reaction and found evidence for a conformational transition of the complex. Our data demonstrate the importance of a slow dissociation for a successful dimeric ligand but also highlight the possibility of optimizing the intramolecular association rate. The results may therefore aid the design of dimeric inhibitors in general.
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Affiliation(s)
- Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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Sterling HJ, Batchelor JD, Wemmer DE, Williams ER. Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1045-9. [PMID: 20226685 PMCID: PMC2893594 DOI: 10.1016/j.jasms.2010.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 01/29/2010] [Accepted: 02/04/2010] [Indexed: 05/25/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a powerful method for analyzing the active forms of macromolecular complexes of biomolecules. However, these solutions often contain high concentrations of salts and/or detergents that adversely effect ESI performance by making ion formation less reproducible, causing severe adduction or ion suppression. Many methods for separating complexes from nonvolatile additives are routinely used with ESI-MS, but these methods may not be appropriate for complexes that require such stabilizers for activity. Here, the effects of buffer loading using concentrations of ammonium acetate ranging from 0.22 to 1.41 M on the ESI mass spectra of a solution containing a domain truncation mutant of a sigma(54) activator from Aquifex aeolicus were studied. This 44.9 kDa protein requires the presence of millimolar concentrations of Mg(2+), BeF(3)(-), and ADP, (at approximately 60 degrees C) to assemble into an active homo-hexamer. Addition of ammonium acetate can improve signal stability and reproducibility, and can significantly lower adduction and background signals. However, at higher concentrations, the relative ion abundance of the hexamer is diminished, while that of the constituent monomer is enhanced. These results are consistent with loss of enzymatic activity as measured by ATP hydrolysis and indicate that the high concentration of ammonium acetate interferes with assembly of the hexamer. This shows that buffer loading with ammonium acetate is effective for obtaining ESI signal for complexes that require high concentrations of essential salts, but can interfere with formation of, and/or destabilize complexes by disrupting crucial electrostatic interactions at high concentration.
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Affiliation(s)
- Harry J Sterling
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720, USA
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Gallardo R, Ivarsson Y, Schymkowitz J, Rousseau F, Zimmermann P. Structural Diversity of PDZ-Lipid Interactions. Chembiochem 2010; 11:456-67. [DOI: 10.1002/cbic.200900616] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Babai N, Kanevsky N, Dascal N, Rozanski GJ, Singh DP, Fatma N, Thoreson WB. Anion-sensitive regions of L-type CaV1.2 calcium channels expressed in HEK293 cells. PLoS One 2010; 5:e8602. [PMID: 20066046 PMCID: PMC2798859 DOI: 10.1371/journal.pone.0008602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/09/2009] [Indexed: 11/21/2022] Open
Abstract
L-type calcium currents (ICa) are influenced by changes in extracellular chloride, but sites of anion effects have not been identified. Our experiments showed that CaV1.2 currents expressed in HEK293 cells are strongly inhibited by replacing extracellular chloride with gluconate or perchlorate. Variance-mean analysis of ICa and cell-attached patch single channel recordings indicate that gluconate-induced inhibition is due to intracellular anion effects on Ca2+ channel open probability, not conductance. Inhibition of CaV1.2 currents produced by replacing chloride with gluconate was reduced from ∼75%–80% to ∼50% by omitting β subunits but unaffected by omitting α2δ subunits. Similarly, gluconate inhibition was reduced to ∼50% by deleting an α1 subunit N-terminal region of 15 residues critical for β subunit interactions regulating open probability. Omitting β subunits with this mutant α1 subunit did not further diminish inhibition. Gluconate inhibition was unchanged with expression of different β subunits. Truncating the C terminus at AA1665 reduced gluconate inhibition from ∼75%–80% to ∼50% whereas truncating it at AA1700 had no effect. Neutralizing arginines at AA1696 and 1697 by replacement with glutamines reduced gluconate inhibition to ∼60% indicating these residues are particularly important for anion effects. Expressing CaV1.2 channels that lacked both N and C termini reduced gluconate inhibition to ∼25% consistent with additive interactions between the two tail regions. Our results suggest that modest changes in intracellular anion concentration can produce significant effects on CaV1.2 currents mediated by changes in channel open probability involving β subunit interactions with the N terminus and a short C terminal region.
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Affiliation(s)
- Norbert Babai
- Department of Ophthalmology & Visual Science, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Nataly Kanevsky
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Nathan Dascal
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - George J. Rozanski
- Department of Cellular & Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Dhirendra P. Singh
- Department of Ophthalmology & Visual Science, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Nigar Fatma
- Department of Ophthalmology & Visual Science, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Wallace B. Thoreson
- Department of Ophthalmology & Visual Science, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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Eo HS, Kim S, Koo H, Kim W. A machine learning based method for the prediction of G protein-coupled receptor-binding PDZ domain proteins. Mol Cells 2009; 27:629-34. [PMID: 19533032 DOI: 10.1007/s10059-009-0091-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 05/01/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are part of multi-protein networks called 'receptosomes'. These GPCR interacting proteins (GIPs) in the receptosomes control the targeting, trafficking and signaling of GPCRs. PDZ domain proteins constitute the largest protein family among the GIPs, and the predominant function of the PDZ domain proteins is to assemble signaling pathway components into close proximity by recognition of the last four C-terminal amino acids of GPCRs. We present here a machine learning based approach for the identification of GPCR-binding PDZ domain proteins. In order to characterize the network of interactions between amino acid residues that contribute to the stability of the PDZ domain-ligand complex and to encode the complex into a feature vector, amino acid contact matrices and physicochemical distance matrix were constructed and adopted. This novel machine learning based method displayed high performance for the identification of PDZ domain-ligand interactions and allowed the identification of novel GPCR-PDZ domain protein interactions.
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Affiliation(s)
- Hae-Seok Eo
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
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Travaglini-Allocatelli C, Ivarsson Y, Jemth P, Gianni S. Folding and stability of globular proteins and implications for function. Curr Opin Struct Biol 2009; 19:3-7. [DOI: 10.1016/j.sbi.2008.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 12/04/2008] [Indexed: 10/21/2022]
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Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins. Proc Natl Acad Sci U S A 2008; 105:19241-6. [PMID: 19033470 DOI: 10.1073/pnas.0804774105] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The energy landscape theory provides a general framework for describing protein folding reactions. Because a large number of studies, however, have focused on two-state proteins with single well-defined folding pathways and without detectable intermediates, the extent to which free energy landscapes are shaped up by the native topology at the early stages of the folding process has not been fully characterized experimentally. To this end, we have investigated the folding mechanisms of two homologous three-state proteins, PTP-BL PDZ2 and PSD-95 PDZ3, and compared the early and late transition states on their folding pathways. Through a combination of Phi value analysis and molecular dynamics simulations we obtained atomic-level structures of the transition states of these homologous three-state proteins and found that the late transition states are much more structurally similar than the early ones. Our findings thus reveal that, while the native state topology defines essentially in a unique way the late stages of folding, it leaves significant freedom to the early events, a result that reflects the funneling of the free energy landscape toward the native state.
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Chi CN, Elfström L, Shi Y, Snäll T, Engström Å, Jemth P. Reassessing a sparse energetic network within a single protein domain. Proc Natl Acad Sci U S A 2008; 105:4679-84. [PMID: 18339805 PMCID: PMC2290805 DOI: 10.1073/pnas.0711732105] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Indexed: 11/18/2022] Open
Abstract
Understanding the molecular principles that govern allosteric communication is an important goal in protein science. One way allostery could be transmitted is via sparse energetic networks of residues, and one such evolutionary conserved network was identified in the PDZ domain family of proteins by multiple sequence alignment [Lockless SW, Ranganathan R (1999) Science 286:295-299]. We have reassessed the energetic coupling of these residues by double mutant cycles together with ligand binding and stability experiments and found that coupling is not a special property of the coevolved network of residues in PDZ domains. The observed coupling for ligand binding is better explained by a distance relationship, where residues close in space are more likely to couple than distal residues. Our study demonstrates that statistical coupling from sequence analysis is not necessarily a reporter of energetic coupling and allostery.
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Affiliation(s)
- Celestine N. Chi
- *Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical Centre, Box 582, SE-751 23 Uppsala, Sweden; and
| | - Lisa Elfström
- *Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical Centre, Box 582, SE-751 23 Uppsala, Sweden; and
| | - Yao Shi
- *Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical Centre, Box 582, SE-751 23 Uppsala, Sweden; and
| | - Tord Snäll
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, SE-750 07 Uppsala, Sweden
| | - Åke Engström
- *Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical Centre, Box 582, SE-751 23 Uppsala, Sweden; and
| | - Per Jemth
- *Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical Centre, Box 582, SE-751 23 Uppsala, Sweden; and
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Watson E, Matousek WM, Irimies EL, Alexandrescu AT. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 2007; 46:9484-94. [PMID: 17661445 PMCID: PMC2128864 DOI: 10.1021/bi700532j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have been interested in whether three proteins that share a five-stranded beta-barrel "OB-fold" structural motif but no detectable sequence homology fold by similar mechanisms. Here we describe native-state hydrogen exchange experiments as a function of urea for SN (staphylococcal nuclease), a protein with an OB-fold motif and additional nonconserved elements of structure. The regions of structure with the largest stability and unfolding cooperativity are contained within the conserved OB-fold portion of SN, consistent with previous results for CspA (cold shock protein A) and LysN (anticodon binding domain of lysyl tRNA synthetase). The OB-fold also has the subset of residues with the slowest unfolding rates in the three proteins, as determined by hydrogen exchange experiments in the EX1 limit. Although the protein folding hierarchy is maintained at the level of supersecondary structure, it is not evident for individual residues as might be expected if folding depended on obligatory nucleation sites. Rather, the site-specific stability profiles appear to be linked to sequence hydrophobicity and to the density of long-range contacts at each site in the three-dimensional structures of the proteins. We discuss the implications of the correlation between stability to unfolding and conservation of structure for mechanisms of protein structure evolution.
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Affiliation(s)
| | | | | | - Andrei T. Alexandrescu
- * To whom correspondence should be addressed: Department of Molecular and Cell Biology, University of Connecticut, 91 N,. Eagleville Rd., U-3125, Storrs, CT 06269–3125., Telephone: (860) 486–4414., Fax: (860) 486–4331., E-mail:
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Chi CN, Gianni S, Calosci N, Travaglini-Allocatelli C, Engström K, Jemth P. A conserved folding mechanism for PDZ domains. FEBS Lett 2007; 581:1109-13. [PMID: 17316619 DOI: 10.1016/j.febslet.2007.02.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 01/22/2007] [Accepted: 02/06/2007] [Indexed: 11/16/2022]
Abstract
An important question in protein folding is whether the folding mechanism is sequence dependent and conserved for homologous proteins. In this work we compared the kinetic folding mechanism of five postsynaptic density protein-95, disc-large tumor suppressor protein, zonula occludens-1 (PDZ) domains, sharing similar topology but having different primary structures. Investigation of the different proteins under various experimental conditions revealed that the folding kinetics of each member of the PDZ family can be described by a model with two transition states separated by an intermediate. Moreover, the positions of the two transition states along the reaction coordinate (as given by their beta(T)-values) are fairly constant for the five PDZ domains.
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Affiliation(s)
- Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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