1
|
Chen XR, Dixit K, Yang Y, McDermott MI, Imam HT, Bankaitis VA, Igumenova TI. A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated protein kinase C regulation. eLife 2024; 13:e92884. [PMID: 38687676 PMCID: PMC11060717 DOI: 10.7554/elife.92884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
Regulated hydrolysis of the phosphoinositide phosphatidylinositol(4,5)-bis-phosphate to diacylglycerol and inositol-1,4,5-P3 defines a major eukaryotic pathway for translation of extracellular cues to intracellular signaling circuits. Members of the lipid-activated protein kinase C isoenzyme family (PKCs) play central roles in this signaling circuit. One of the regulatory mechanisms employed to downregulate stimulated PKC activity is via a proteasome-dependent degradation pathway that is potentiated by peptidyl-prolyl isomerase Pin1. Here, we show that contrary to prevailing models, Pin1 does not regulate conventional PKC isoforms α and βII via a canonical cis-trans isomerization of the peptidyl-prolyl bond. Rather, Pin1 acts as a PKC binding partner that controls PKC activity via sequestration of the C-terminal tail of the kinase. The high-resolution structure of full-length Pin1 complexed to the C-terminal tail of PKCβII reveals that a novel bivalent interaction mode underlies the non-catalytic mode of Pin1 action. Specifically, Pin1 adopts a conformation in which it uses the WW and PPIase domains to engage two conserved phosphorylated PKC motifs, the turn motif and hydrophobic motif, respectively. Hydrophobic motif is a non-canonical Pin1-interacting element. The structural information combined with the results of extensive binding studies and experiments in cultured cells suggest that non-catalytic mechanisms represent unappreciated modes of Pin1-mediated regulation of AGC kinases and other key enzymes/substrates.
Collapse
Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Karuna Dixit
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Yuan Yang
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Mark I McDermott
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| | - Hasan Tanvir Imam
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Vytas A Bankaitis
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| | - Tatyana I Igumenova
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| |
Collapse
|
2
|
Katti SS, Igumenova TI. Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy. bioRxiv 2024:2023.11.03.565546. [PMID: 38405767 PMCID: PMC10888879 DOI: 10.1101/2023.11.03.565546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca 2+ and Zn 2+ . The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application of in-cell and lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intact E. coli cells and their lysates, revealed that Cd 2+ can profoundly affect the quinary interactions of its protein partners, and can replace Zn 2+ in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd 2+ can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α 3 DIV to sequester intracellular cadmium. Our data suggests that in-cell NMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents.
Collapse
|
3
|
Chen XR, Dixit K, Yang Y, McDermott MI, Imam HT, Bankaitis VA, Igumenova TI. A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated Protein Kinase C regulation. bioRxiv 2023:2023.09.18.558341. [PMID: 37781616 PMCID: PMC10541119 DOI: 10.1101/2023.09.18.558341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Regulated hydrolysis of the phosphoinositide phosphatidylinositol(4,5)-bis-phosphate to diacylglycerol and inositol-1,4,5-P3 defines a major eukaryotic pathway for translation of extracellular cues to intracellular signaling circuits. Members of the lipid-activated protein kinase C isoenzyme family (PKCs) play central roles in this signaling circuit. One of the regulatory mechanisms employed to downregulate stimulated PKC activity is via a proteasome-dependent degradation pathway that is potentiated by peptidyl-prolyl isomerase Pin1. Here, we show that contrary to prevailing models, Pin1 does not regulate conventional PKC isoforms α and βII via a canonical cis-trans isomerization of the peptidyl-prolyl bond. Rather, Pin1 acts as a PKC binding partner that controls PKC activity via sequestration of the C-terminal tail of the kinase. The high-resolution structure of Pin1 complexed to the C-terminal tail of PKCβII reveals that a novel bivalent interaction mode underlies the non-catalytic mode of Pin1 action. Specifically, Pin1 adopts a compact conformation in which it engages two conserved phosphorylated PKC motifs, the turn motif and hydrophobic motif, the latter being a non-canonical Pin1-interacting element. The structural information, combined with the results of extensive binding studies and in vivo experiments suggest that non-catalytic mechanisms represent unappreciated modes of Pin1-mediated regulation of AGC kinases and other key enzymes/substrates.
Collapse
|
4
|
Chen XR, Poudel L, Hong Z, Johnen P, Katti S, Tripathi A, Nile AH, Green SM, Khan D, Schaaf G, Bono F, Bankaitis VA, Igumenova TI. Mechanisms by which small molecules of diverse chemotypes arrest Sec14 lipid transfer activity. J Biol Chem 2023; 299:102861. [PMID: 36603766 PMCID: PMC9898755 DOI: 10.1016/j.jbc.2022.102861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Phosphatidylinositol (PtdIns) transfer proteins (PITPs) enhance the activities of PtdIns 4-OH kinases that generate signaling pools of PtdIns-4-phosphate. In that capacity, PITPs serve as key regulators of lipid signaling in eukaryotic cells. Although the PITP phospholipid exchange cycle is the engine that stimulates PtdIns 4-OH kinase activities, the underlying mechanism is not understood. Herein, we apply an integrative structural biology approach to investigate interactions of the yeast PITP Sec14 with small-molecule inhibitors (SMIs) of its phospholipid exchange cycle. Using a combination of X-ray crystallography, solution NMR spectroscopy, and atomistic MD simulations, we dissect how SMIs compete with native Sec14 phospholipid ligands and arrest phospholipid exchange. Moreover, as Sec14 PITPs represent new targets for the development of next-generation antifungal drugs, the structures of Sec14 bound to SMIs of diverse chemotypes reported in this study will provide critical information required for future structure-based design of next-generation lead compounds directed against Sec14 PITPs of virulent fungi.
Collapse
Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Lokendra Poudel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Zebin Hong
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Philipp Johnen
- Institute for Crop Science and Resource Conservation, Universität Bonn, Bonn, Germany
| | - Sachin Katti
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Ashutosh Tripathi
- Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA
| | - Aaron H Nile
- Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA
| | - Savana M Green
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA; Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA
| | - Danish Khan
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA
| | - Gabriel Schaaf
- Institute for Crop Science and Resource Conservation, Universität Bonn, Bonn, Germany
| | - Fulvia Bono
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Vytas A Bankaitis
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA; Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA.
| | - Tatyana I Igumenova
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA.
| |
Collapse
|
5
|
Chen XR, Igumenova TI. Regulation of eukaryotic protein kinases by Pin1, a peptidyl-prolyl isomerase. Adv Biol Regul 2023; 87:100938. [PMID: 36496344 PMCID: PMC9992314 DOI: 10.1016/j.jbior.2022.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The peptidyl-prolyl isomerase Pin1 cooperates with proline-directed kinases and phosphatases to regulate multiple oncogenic pathways. Pin1 specifically recognizes phosphorylated Ser/Thr-Pro motifs in proteins and catalyzes their cis-trans isomerization. The Pin1-catalyzed conformational changes determine the stability, activity, and subcellular localization of numerous protein substrates. We conducted a survey of eukaryotic protein kinases that are regulated by Pin1 and whose Pin1 binding sites have been identified. Our analyses reveal that Pin1 target sites in kinases do not fall exclusively within the intrinsically disordered regions of these enzymes. Rather, they fall into three groups based on their location: (i) within the catalytic kinase domain, (ii) in the C-terminal kinase region, and (iii) in regulatory domains. Some of the kinases downregulated by Pin1 activity are tumor-suppressing, and all kinases upregulated by Pin1 activity are functionally pro-oncogenic. These findings further reinforce the rationale for developing Pin1-specific inhibitors as attractive pharmaceuticals for cancer therapy.
Collapse
Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
6
|
Katti SS, Krieger IV, Ann J, Lee J, Sacchettini JC, Igumenova TI. Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists. Nat Commun 2022; 13:2695. [PMID: 35577811 PMCID: PMC9110374 DOI: 10.1038/s41467-022-30389-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/28/2022] [Indexed: 11/22/2022] Open
Abstract
Diacylglycerol (DAG) is a versatile lipid whose 1,2-sn-stereoisomer serves both as second messenger in signal transduction pathways that control vital cellular processes, and as metabolic precursor for downstream signaling lipids such as phosphatidic acid. Effector proteins translocate to available DAG pools in the membranes by using conserved homology 1 (C1) domains as DAG-sensing modules. Yet, how C1 domains recognize and capture DAG in the complex environment of a biological membrane has remained unresolved for the 40 years since the discovery of Protein Kinase C (PKC) as the first member of the DAG effector cohort. Herein, we report the high-resolution crystal structures of a C1 domain (C1B from PKCδ) complexed to DAG and to each of four potent PKC agonists that produce different biological readouts and that command intense therapeutic interest. This structural information details the mechanisms of stereospecific recognition of DAG by the C1 domains, the functional properties of the lipid-binding site, and the identities of the key residues required for the recognition and capture of DAG and exogenous agonists. Moreover, the structures of the five C1 domain complexes provide the high-resolution guides for the design of agents that modulate the activities of DAG effector proteins.
Collapse
Affiliation(s)
- Sachin S. Katti
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| | - Inna V. Krieger
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| | - Jihyae Ann
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Jeewoo Lee
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - James C. Sacchettini
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| | - Tatyana I. Igumenova
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| |
Collapse
|
7
|
Katti SS, Krieger IV, Sacchettini JC, Igumenova TI. Structural Basis of Agonist Capture by Regulatory C1 Domain of PKC. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l8086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sachin S. Katti
- Biochemistry & BiophysicsTexas A&M UniversityCollege StationTX
| | - Inna V. Krieger
- Biochemistry & BiophysicsTexas A&M UniversityCollege StationTX
| | | | | |
Collapse
|
8
|
Chen X, Igumenova TI. Detection of the Pin1‐ligand interactions using
19
F NMR spectroscopy. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l7818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
9
|
Bankaitis VA, Tripathi A, Chen XR, Igumenova TI. New strategies for combating fungal infections: Inhibiting inositol lipid signaling by targeting Sec14 phosphatidylinositol transfer proteins. Adv Biol Regul 2022; 84:100891. [PMID: 35240534 PMCID: PMC9149032 DOI: 10.1016/j.jbior.2022.100891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
Virulent fungi represent a particularly difficult problem in the infectious disease arena as these organisms are eukaryotes that share many orthologous activities with their human hosts. The fact that these activities are often catalyzed by conserved proteins places additional demands on development of pharmacological strategies for specifically inhibiting target fungal activities without imposing undesirable secondary effects on the host. While deployment of a limited set of anti-mycotics has to date satisfied the clinical needs for treatment of fungal infections, the recent emergence of multi-drug resistant fungal 'superbugs' now poses a serious global health threat with rapidly diminishing options for treatment. This escalating infectious disease problem emphasizes the urgent need for development of new classes of anti-mycotics. In that regard, Sec14 phosphatidylinositol transfer proteins offer interesting possibilities for interfering with fungal phosphoinositide signaling with exquisite specificity and without targeting the highly conserved lipid kinases responsible for phosphoinositide production. Herein, we review the establishment of proof-of-principle that demonstrates the feasibility of such an approach. We also describe the lead compounds of four chemotypes that directly target fungal Sec14 proteins. The rules that pertain to the mechanism(s) of Sec14 inhibition by validated small molecule inhibitors, and the open questions that remain, are discussed - as are the challenges that face development of next generation Sec14-directed inhibitors.
Collapse
Affiliation(s)
- Vytas A Bankaitis
- Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX, 77843-0014, USA; Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843-0014, USA.
| | - Ashutosh Tripathi
- Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX, 77843-0014, USA
| | - Xiao-Ru Chen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843-0014, USA
| | - Tatyana I Igumenova
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843-0014, USA
| |
Collapse
|
10
|
Cole TR, Igumenova TI. Reactivity of Thiol-Rich Zn Sites in Diacylglycerol-Sensing PKC C1 Domain Probed by NMR Spectroscopy. Front Mol Biosci 2021; 8:728711. [PMID: 34447788 PMCID: PMC8382798 DOI: 10.3389/fmolb.2021.728711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/27/2021] [Indexed: 11/13/2022] Open
Abstract
Conserved homology 1 (C1) domains are peripheral zinc finger domains that are responsible for recruiting their host signaling proteins, including Protein Kinase C (PKC) isoenzymes, to diacylglycerol-containing lipid membranes. In this work, we investigated the reactivity of the C1 structural zinc sites, using the cysteine-rich C1B regulatory region of the PKCα isoform as a paradigm. The choice of Cd2+ as a probe was prompted by previous findings that xenobiotic metal ions modulate PKC activity. Using solution NMR and UV-vis spectroscopy, we found that Cd2+ spontaneously replaced Zn2+ in both structural sites of the C1B domain, with the formation of all-Cd and mixed Zn/Cd protein species. The Cd2+ substitution for Zn2+ preserved the C1B fold and function, as probed by its ability to interact with a potent tumor-promoting agent. Both Cys3His metal-ion sites of C1B have higher affinity to Cd2+ than Zn2+, but are thermodynamically and kinetically inequivalent with respect to the metal ion replacement, despite the identical coordination spheres. We find that even in the presence of the oxygen-rich sites presented by the neighboring peripheral membrane-binding C2 domain, the thiol-rich sites can successfully compete for the available Cd2+. Our results indicate that Cd2+ can target the entire membrane-binding regulatory region of PKCs, and that the competition between the thiol- and oxygen-rich sites will likely determine the activation pattern of PKCs.
Collapse
Affiliation(s)
- Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| |
Collapse
|
11
|
Abstract
Munc13-1 is a presynaptic active zone protein that acts as a master regulator of synaptic vesicle priming and neurotransmitter release in the brain. It has been implicated in the pathophysiology of several neurodegenerative diseases. Diacylglycerol and phorbol ester activate Munc13-1 by binding to its C1 domain. The objective of this study is to identify the structural determinants of ligand binding activity of the Munc13-1 C1 domain. Molecular docking suggested that residues Trp-588, Ile-590, and Arg-592 of Munc13-1 are involved in ligand interactions. To elucidate the role of these three residues in ligand binding, we generated W588A, I590A, and R592A mutants in full-length Munc13-1, expressed them as GFP-tagged proteins in HT22 cells, and measured their ligand-induced membrane translocation by confocal microscopy and immunoblotting. The extent of 1,2-dioctanoyl-sn-glycerol (DOG)- and phorbol ester-induced membrane translocation decreased in the following order: wild type > I590A > W588A > R592A and wild type > W588A > I590A > R592A, respectively. To understand the effect of the mutations on ligand binding, we also measured the DOG binding affinity of the isolated wild-type C1 domain and its mutants in membrane-mimicking micelles using nuclear magnetic resonance methods. The DOG binding affinity decreased in the following order: wild type > I590A > R592A. No binding was detected for W588A with DOG in micelles. This study shows that Trp-588, Ile-590, and Arg-592 are essential determinants for the activity of Munc13-1 and the effects of the three residues on the activity are ligand-dependent. This study bears significance for the development of selective modulators of Munc13-1.
Collapse
Affiliation(s)
- Youngki You
- Department of Pharmacological & Pharmaceutical Sciences, College of Pharmacy, Health 2, University of Houston, Houston, Texas 77204, United States
| | - Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843, United States
| | - Binhan Yu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, Texas 77843, United States
| | - Joydip Das
- Department of Pharmacological & Pharmaceutical Sciences, College of Pharmacy, Health 2, University of Houston, Houston, Texas 77204, United States
| |
Collapse
|
12
|
Katti S, Igumenova TI. Structural insights into C1-ligand interactions: Filling the gaps by in silico methods. Adv Biol Regul 2021; 79:100784. [PMID: 33526356 DOI: 10.1016/j.jbior.2020.100784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023]
Abstract
Protein Kinase C isoenzymes (PKCs) are the key mediators of the phosphoinositide signaling pathway, which involves regulated hydrolysis of phosphatidylinositol (4,5)-bisphosphate to diacylglycerol (DAG) and inositol-1,4,5-trisphosphate. Dysregulation of PKCs is implicated in many human diseases making this class of enzymes an important therapeutic target. Specifically, the DAG-sensing cysteine-rich conserved homology-1 (C1) domains of PKCs have emerged as promising targets for pharmaceutical modulation. Despite significant progress, the rational design of the C1 modulators remains challenging due to difficulties associated with structure determination of the C1-ligand complexes. Given the dearth of experimental structural data, computationally derived models have been instrumental in providing atomistic insight into the interactions of the C1 domains with PKC agonists. In this review, we provide an overview of the in silico approaches for seven classes of C1 modulators and outline promising future directions.
Collapse
Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, United States.
| |
Collapse
|
13
|
Taylor JT, Mukherjee PK, Puckhaber LS, Dixit K, Igumenova TI, Suh C, Horwitz BA, Kenerley CM. Deletion of the Trichoderma virens NRPS, Tex7, induces accumulation of the anti-cancer compound heptelidic acid. Biochem Biophys Res Commun 2020; 529:672-677. [PMID: 32736691 DOI: 10.1016/j.bbrc.2020.06.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/08/2020] [Indexed: 01/26/2023]
Abstract
The anticancer antibiotic heptelidic acid is a sesquiterpene lactone produced by the beneficial plant fungus Trichoderma virens. This species has been separated into two strains, referred to as P and Q, based on its biosynthesis of secondary metabolites; notably, only P-strains were reported to produce heptelidic acid. While characterizing a Q-strain of T. virens containing a directed mutation in the non-ribosomal peptide synthetase encoding gene Tex7, the appearance of an unknown compound in anomalously large quantities was visualized by TLC. Using a combination of HPLC, LC-MS/MS, and NMR spectroscopy, this compound was identified as heptelidic acid. This discovery alters the strain classification structure of T. virens. Additionally, the Tex7 mutants inhibited growth of maize seedlings, while retaining the ability to induce systemic resistance against the foliar fungal pathogen, Cochliobolus heterostrophus.
Collapse
Affiliation(s)
- James T Taylor
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Lorraine S Puckhaber
- USDA, ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Karuna Dixit
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Charles Suh
- USDA, ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Benjamin A Horwitz
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
14
|
|
15
|
Abstract
Pb2+ is a xenobiotic metal ion that competes for Ca2+-binding sites in proteins. Using the peripheral Ca2+-sensing domains of Syt1, we show that the chelating pH buffer Bis-Tris enables identification and functional characterization of high-affinity Pb2+ sites that are likely to be targeted by bioavailable Pb2+.
Collapse
Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA.
| | | |
Collapse
|
16
|
Katti S, Nyenhuis SB, Her B, Cafiso DS, Igumenova TI. Partial Metal Ion Saturation of C2 Domains Primes Synaptotagmin 1-Membrane Interactions. Biophys J 2020; 118:1409-1423. [PMID: 32075747 DOI: 10.1016/j.bpj.2020.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/29/2022] Open
Abstract
Synaptotagmin 1 (Syt1) is an integral membrane protein whose phospholipid-binding tandem C2 domains, C2A and C2B, act as Ca2+ sensors of neurotransmitter release. Our objective was to understand the role of individual metal-ion binding sites of these domains in the membrane association process. We used Pb2+, a structural and functional surrogate of Ca2+, to generate the protein states with well-defined protein-metal ion stoichiometry. NMR experiments revealed that binding of one divalent metal ion per C2 domain results in loss of conformational plasticity of the loop regions, potentially pre-organizing them for additional metal-ion and membrane-binding events. In C2A, a divalent metal ion in site 1 is sufficient to drive its weak association with phosphatidylserine-containing membranes, whereas in C2B, it enhances the interactions with the signaling lipid phosphatidylinositol-4,5-bisphosphate. In full-length Syt1, both Pb2+-complexed C2 domains associate with phosphatidylserine-containing membranes. Electron paramagnetic resonance experiments show that the extent of membrane insertion correlates with the occupancy of the C2 metal ion sites. Together, our results indicate that upon partial metal ion saturation of the intra-loop region, Syt1 adopts a dynamic, partially membrane-bound state. The properties of this state, such as conformationally restricted loop regions and positioning of C2 domains in close proximity to anionic lipid headgroups, "prime" Syt1 for cooperative binding of a full complement of metal ions and deeper membrane insertion.
Collapse
Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Sarah B Nyenhuis
- Department of Chemistry and Biophysics Program, University of Virginia, Charlottesville, Virginia
| | - Bin Her
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - David S Cafiso
- Department of Chemistry and Biophysics Program, University of Virginia, Charlottesville, Virginia
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| |
Collapse
|
17
|
Yang Y, Shu C, Li P, Igumenova TI. Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail. Biophys J 2019; 114:1590-1603. [PMID: 29642029 DOI: 10.1016/j.bpj.2017.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/07/2017] [Accepted: 12/21/2017] [Indexed: 10/17/2022] Open
Abstract
Protein kinase C (PKC) isoenzymes are multi-modular proteins activated at the membrane surface to regulate signal transduction processes. When activated by second messengers, PKC undergoes a drastic conformational and spatial transition from the inactive cytosolic state to the activated membrane-bound state. The complete structure of either state of PKC remains elusive. We demonstrate, using NMR spectroscopy, that the isolated Ca2+-sensing membrane-binding C2 domain of the conventional PKCα interacts with a conserved hydrophobic motif of the kinase C-terminal region, and we report a structural model of the complex. Our data suggest that the C-terminal region plays a dual role in regulating the PKC activity: activating, through sensitization of PKC to intracellular Ca2+ oscillations; and auto-inhibitory, through its interaction with a conserved positively charged region of the C2 domain.
Collapse
Affiliation(s)
- Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Chang Shu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| |
Collapse
|
18
|
Cole TR, Erickson SG, Morales KA, Sung M, Holzenburg A, Igumenova TI. Cd(II)- and Pb(II)-Induced Self-Assembly of Peripheral Membrane Domains from Protein Kinase C. Biochemistry 2019; 58:509-513. [PMID: 30584764 DOI: 10.1021/acs.biochem.8b01235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cd2+ and Pb2+ are xenobiotic heavy metal ions that use ionic mimicry to interfere with the cellular function of biomacromolecules. Using a combination of SAXS, electron microscopy, FRET, and solution NMR spectroscopy, we demonstrate that treatment with Cd2+ and Pb2+ causes self-assembly of protein kinase C regulatory domains that peripherally associate with membranes. The self-assembly process successfully competes with ionic mimicry and is mediated by conserved protein regions that are distinct from the canonical Ca2+-binding motifs of protein kinase C. The ability of protein oligomers to interact with anionic membranes is enhanced compared to the monomeric species. Our findings suggest that metal-ion-dependent peripheral membrane domains can be utilized for generating protein-metal-ion nanoclusters and serve as biotemplates for the design of sequestration agents.
Collapse
Affiliation(s)
- Taylor R Cole
- Department of Biochemistry and Biophysics , Texas A&M University , 300 Olsen Boulevard , College Station , Texas 77843 , United States
| | - Samuel G Erickson
- Department of Biochemistry and Biophysics , Texas A&M University , 300 Olsen Boulevard , College Station , Texas 77843 , United States
| | - Krystal A Morales
- Department of Biochemistry and Biophysics , Texas A&M University , 300 Olsen Boulevard , College Station , Texas 77843 , United States
| | - MinWoo Sung
- Department of Biology , Texas A&M University , College Station , Texas 77843 , United States
| | - Andreas Holzenburg
- School of Medicine , University of Texas Rio Grande Valley , Harlingen , Texas 78550 , United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics , Texas A&M University , 300 Olsen Boulevard , College Station , Texas 77843 , United States
| |
Collapse
|
19
|
Abstract
Lead (Pb) is a potent neurotoxin that disrupts synaptic neurotransmission. We report that Synaptotagmin I (SytI), a key regulator of Ca2+-evoked neurotransmitter release, has two high-affinity Pb2+ binding sites that belong to its cytosolic C2A and C2B domains. The crystal structures of Pb2+-complexed C2 domains revealed that protein-bound Pb2+ ions have holodirected coordination geometries and all-oxygen coordination spheres. The on-rate constants of Pb2+ binding to the C2 domains of SytI are comparable to those of Ca2+ and are diffusion-limited. In contrast, the off-rate constants are at least two orders of magnitude smaller, indicating that Pb2+ can serve as both a thermodynamic and kinetic trap for the C2 domains. We demonstrate, using NMR spectroscopy, that population of these sites by Pb2+ ions inhibits further Ca2+ binding despite the existing coordination vacancies. Our work offers a unique insight into the bioinorganic chemistry of Pb(ii) and suggests a mechanism by which low concentrations of Pb2+ ions can interfere with the Ca2+-dependent function of SytI in the cell.
Collapse
Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA.
| | | | | | | | | | | |
Collapse
|
20
|
Igumenova TI, Cole TR, Katti S, Morales KA, Erickson SG, Woo Sung M, Nyenhuis SB, Taylor AB, Hart PJ, Holzenburg A, Cafiso DS. Not Just Ionic Mimicry: Biophysics of Toxic Metal Ion Interactions with Peripheral Membrane Targets. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
21
|
Morales KA, Yang Y, Cole TR, Igumenova TI. Dynamic Response of the C2 Domain of Protein Kinase Cα to Ca 2+ Binding. Biophys J 2017; 111:1655-1667. [PMID: 27760353 DOI: 10.1016/j.bpj.2016.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/04/2016] [Accepted: 09/07/2016] [Indexed: 11/28/2022] Open
Abstract
Ca2+-dependent conserved-region 2 (C2) domains target their host signaling proteins to anionic membranes. The Ca2+-binding event is a prerequisite for membrane association. Here, we investigate multiscale metal-ion-dependent dynamics of the C2 domain of protein kinase Cα (C2α) using NMR spectroscopy. Interactions with metal ions attenuate microsecond-timescale motions of the loop regions, indicating that preorganization of the metal-binding loops occurs before membrane insertion. Binding of a full complement of Ca2+ ions has a profound effect on the millisecond-timescale dynamics of the N- and C-terminal regions of C2α. We propose that Ca2+ binding allosterically destabilizes the terminal regions of C2α and thereby facilitates the conformational rearrangement necessary for full membrane insertion and activation of protein kinase Cα.
Collapse
Affiliation(s)
- Krystal A Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| |
Collapse
|
22
|
Katti S, Nyenhuis SB, Her B, Srivastava AK, Taylor AB, Hart PJ, Cafiso DS, Igumenova TI. Non-Native Metal Ion Reveals the Role of Electrostatics in Synaptotagmin 1-Membrane Interactions. Biochemistry 2017; 56:3283-3295. [PMID: 28574251 DOI: 10.1021/acs.biochem.7b00188] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
C2 domains are independently folded modules that often target their host proteins to anionic membranes in a Ca2+-dependent manner. In these cases, membrane association is triggered by Ca2+ binding to the negatively charged loop region of the C2 domain. Here, we used a non-native metal ion, Cd2+, in lieu of Ca2+ to gain insight into the contributions made by long-range Coulombic interactions and direct metal ion-lipid bridging to membrane binding. Using X-ray crystallography, NMR, Förster resonance energy transfer, and vesicle cosedimentation assays, we demonstrate that, although Cd2+ binds to the loop region of C2A/B domains of synaptotagmin 1 with high affinity, long-range Coulombic interactions are too weak to support membrane binding of individual domains. We attribute this behavior to two factors: the stoichiometry of Cd2+ binding to the loop regions of the C2A and C2B domains and the impaired ability of Cd2+ to directly coordinate the lipids. In contrast, electron paramagnetic resonance experiments revealed that Cd2+ does support membrane binding of the C2 domains in full-length synaptotagmin 1, where the high local lipid concentrations that result from membrane tethering can partially compensate for lack of a full complement of divalent metal ions and specific lipid coordination in Cd2+-complexed C2A/B domains. Our data suggest that long-range Coulombic interactions alone can drive the initial association of C2A/B with anionic membranes and that Ca2+ further augments membrane binding by the formation of metal ion-lipid coordination bonds and additional Ca2+ ion binding to the C2 domain loop regions.
Collapse
Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University , 300 Olsen Boulevard, College Station, Texas 77843, United States
| | - Sarah B Nyenhuis
- Department of Chemistry and Biophysics Program, University of Virginia , Charlottesville, Virginia 22904, United States
| | - Bin Her
- Department of Biochemistry and Biophysics, Texas A&M University , 300 Olsen Boulevard, College Station, Texas 77843, United States
| | - Atul K Srivastava
- Department of Biochemistry and Biophysics, Texas A&M University , 300 Olsen Boulevard, College Station, Texas 77843, United States
| | - Alexander B Taylor
- Department of Biochemistry and Structural Biology and the X-ray Crystallography Core Laboratory, University of Texas Health Science Center at San Antonio , San Antonio, Texas 78229, United States
| | - P John Hart
- Department of Biochemistry and Structural Biology and the X-ray Crystallography Core Laboratory, University of Texas Health Science Center at San Antonio , San Antonio, Texas 78229, United States
| | - David S Cafiso
- Department of Chemistry and Biophysics Program, University of Virginia , Charlottesville, Virginia 22904, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University , 300 Olsen Boulevard, College Station, Texas 77843, United States
| |
Collapse
|
23
|
Abstract
Conserved homology-1 (C1) domains are peripheral membrane domains that target their host proteins to diacylglycerol (DAG)-containing membranes. It has been previously shown that a conservative aromatic mutation of a single residue in the C1 domain has a profound effect on DAG affinity. We report that the "DAG-toggling" mutation changes the conformational dynamics of the loop region that forms the binding site for the C1 activators. Moreover, there is a correlation among the residue identity at the mutation site, DAG affinity, and loop dynamics in four C1 variants. We propose that "toggling" of DAG affinity may occur through modulation of both protein-membrane interactions and the geometry of the activator-binding cleft, with the loop dynamics being responsible for the latter.
Collapse
Affiliation(s)
- Mikaela D Stewart
- Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843, United States
| |
Collapse
|
24
|
Cole TR, Erickson SG, Woo Sung M, Holzenburg A, Igumenova TI. Toxic Metal Ions Promote Self-Association and Replace Structural Zinc Ions in the Regulatory Region of Protein Kinase C. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
25
|
Abstract
Protein kinase C (PKC) is a family of Ser/Thr kinases that regulate a multitude of cellular processes through participation in the phosphoinositide signaling pathway. Significant research efforts have been directed at understanding the structure, function, and regulatory modes of the enzyme since its discovery and identification as the first receptor for tumor-promoting phorbol esters. The activation of PKC involves a transition from the cytosolic autoinhibited latent form to the membrane-associated active form. The membrane recruitment step is accompanied by the conformational rearrangement of the enzyme, which relieves autoinhibitory interactions and thereby allows PKC to phosphorylate its targets. The multidomain structure and intrinsic flexibility of PKC present remarkable challenges and opportunities for the biophysical and structural biology studies of this class of enzymes and their interactions with membranes, the major focus of this Current Topic. I will highlight the recent advances in the field, outline the current challenges, and identify areas where biophysics and structural biology approaches can provide insight into the isoenzyme-specific regulation of PKC activity.
Collapse
|
26
|
Ghosh R, de Campos MKF, Huang J, Huh SK, Orlowski A, Yang Y, Tripathi A, Nile A, Lee HC, Dynowski M, Schäfer H, Róg T, Lete MG, Ahyayauch H, Alonso A, Vattulainen I, Igumenova TI, Schaaf G, Bankaitis VA. Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis. Mol Biol Cell 2015; 26:1764-81. [PMID: 25739452 PMCID: PMC4436786 DOI: 10.1091/mbc.e14-10-1475] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/26/2015] [Indexed: 12/12/2022] Open
Abstract
A Sec14-nodulin protein model is used to identify the nodulin domain as a novel phosphoinositide effector module with a role in controlling lateral organization of phosphoinositide. The domain organization of Sec14-nodulin proteins suggests a versatile principle for the bit mapping of membrane surfaces into high-definition lipid-signaling screens. Polarized membrane morphogenesis is a fundamental activity of eukaryotic cells. This process is essential for the biology of cells and tissues, and its execution demands exquisite temporal coordination of functionally diverse membrane signaling reactions with high spatial resolution. Moreover, mechanisms must exist to establish and preserve such organization in the face of randomizing forces that would diffuse it. Here we identify the conserved AtSfh1 Sec14-nodulin protein as a novel effector of phosphoinositide signaling in the extreme polarized membrane growth program exhibited by growing Arabidopsis root hairs. The data are consistent with Sec14-nodulin proteins controlling the lateral organization of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) landmarks for polarized membrane morphogenesis in plants. This patterning activity requires both the PtdIns(4,5)P2 binding and homo-oligomerization activities of the AtSfh1 nodulin domain and is an essential aspect of the polarity signaling program in root hairs. Finally, the data suggest a general principle for how the phosphoinositide signaling landscape is physically bit mapped so that eukaryotic cells are able to convert a membrane surface into a high-definition lipid-signaling screen.
Collapse
Affiliation(s)
- Ratna Ghosh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Marília K F de Campos
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Jin Huang
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Seong K Huh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Adam Orlowski
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Aaron Nile
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843
| | - Hsin-Chieh Lee
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Marek Dynowski
- Zentrum für Datenverarbeitung, Universität Tübingen, 72074 Tübingen, Germany
| | - Helen Schäfer
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Marta G Lete
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Hasna Ahyayauch
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain Institut de Formation aux Carrieres de Sante de Rabat, 10000 Rabat, Morocco
| | - Alicia Alonso
- Unidad de Biofísica (CSIC, UPV/EHU), Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Gabriel Schaaf
- Center for Plant Molecular Biology, Plant Physiology, Universität Tübingen, 72076 Tübingen, Germany
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843 Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 Department of Chemistry, Texas A&M University, College Station, TX 77843
| |
Collapse
|
27
|
Cole TR, Igumenova TI. Expression and purification of the N-terminal regulatory domain of Protein Kinase C for biophysical studies. Protein Expr Purif 2015; 110:14-21. [PMID: 25582765 DOI: 10.1016/j.pep.2014.12.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/20/2014] [Accepted: 12/25/2014] [Indexed: 11/25/2022]
Abstract
We report the protocol for heterologous expression and purification of the N-terminal regulatory region of two Protein Kinase C (PKC)(1) isozymes, one conventional and one novel. Previous studies of these domains relied almost exclusively on the fusion constructs with high-molecular-weight solubility fusion partners such as GST and MBP. We developed experimental procedures that enabled us to overcome challenges associated with the amphiphilic character of the regulatory domain and generate sufficient quantities of fusion partner-free proteins for biophysical work. The key features of the protocol are the identity of the cleavable fusion partner, expression conditions, growth medium additives, introduction of mutation/solubility tags, and incorporation of osmolytes. The protein yields are sufficient for cost-effective production of isotopically enriched proteins for NMR work and biophysical studies in general. Our work opens up an avenue for the structural studies of these challenging proteins with high amphiphilic character.
Collapse
Affiliation(s)
- Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA.
| |
Collapse
|
28
|
Stewart MD, Cole TR, Igumenova TI. Interfacial partitioning of a loop hinge residue contributes to diacylglycerol affinity of conserved region 1 domains. J Biol Chem 2014; 289:27653-64. [PMID: 25124034 DOI: 10.1074/jbc.m114.585570] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conventional and novel isoenzymes of PKC are activated by the membrane-embedded second messenger diacylglycerol (DAG) through its interactions with the C1 regulatory domain. The affinity of C1 domains to DAG varies considerably among PKCs. To gain insight into the origin of differential DAG affinities, we conducted high-resolution NMR studies of C1B domain from PKCδ (C1Bδ) and its W252Y variant. The W252Y mutation was previously shown to render C1Bδ less responsive to DAG (Dries, D. R., Gallegos, L. L., and Newton, A. C. (2007) A single residue in the C1 domain sensitizes novel protein kinase C isoforms to cellular diacylglycerol production. J. Biol. Chem. 282, 826-830) and thereby emulate the behavior of C1B domains from conventional PKCs that have a conserved Tyr at the equivalent position. Our data revealed that W252Y mutation did not perturb the conformation of C1Bδ in solution but significantly reduced its propensity to partition into a membrane-mimicking environment in the absence of DAG. Using detergent micelles doped with a paramagnetic lipid, we determined that both the residue identity at position 252 and complexation with diacylglycerol influence the geometry of C1Bδ-micelle interactions. In addition, we identified the C-terminal helix α1 of C1Bδ as an interaction site with the head groups of phosphatidylserine, a known activator of PKCδ. Taken together, our studies (i) reveal the identities of C1Bδ residues involved in interactions with membrane-mimicking environment, DAG, and phosphatidylserine, as well as the affinities associated with each event and (ii) suggest that the initial ligand-independent membrane recruitment of C1B domains, which is greatly facilitated by the interfacial partitioning of Trp-252, is responsible, at least in part, for the differential DAG affinities.
Collapse
Affiliation(s)
- Mikaela D Stewart
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Taylor R Cole
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Tatyana I Igumenova
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
29
|
Yang Y, Igumenova TI. The C-Terminal V5 Domain of Protein Kinase Cα is a Multi-Functional Intrinsically Disordered Protein Module. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
30
|
Morales KA, Stewart MD, Igumenova TI. NMR of Conditional Peripheral Membrane Proteins. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
31
|
Morales KA, Yang Y, Long Z, Li P, Taylor AB, Hart PJ, Igumenova TI. Cd2+ as a Ca2+ surrogate in protein-membrane interactions: isostructural but not isofunctional. J Am Chem Soc 2013; 135:12980-3. [PMID: 23937054 DOI: 10.1021/ja406958k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to its favorable spectroscopic properties, Cd(2+) is frequently used as a probe of Ca(2+) sites in proteins. We investigate the ability of Cd(2+) to act as a structural and functional surrogate of Ca(2+) in protein-membrane interactions. C2 domain from protein kinase Cα (C2α) was chosen as a paradigm for the Ca(2+)-dependent phosphatidylserine-binding peripheral membrane domains. We identified the Cd(2+)-binding sites of C2α using NMR spectroscopy, determined the 1.6 Å crystal structure of Cd(2+)-bound C2α, and characterized metal-ion-dependent interactions between C2α and phospholipid membranes using fluorescence spectroscopy and ultracentrifugation experiments. We show that Cd(2+) forms a tight complex with the membrane-binding loops of C2α but is unable to support its membrane-binding function. This is in sharp contrast with Pb(2+), which is almost as effective as Ca(2+) in driving the C2α-membrane association process. Our results provide the first direct evidence for the specific role of divalent metal ions in mediating protein-membrane interactions, have important implications for metal substitution studies in proteins, and illustrate the potential diversity of functional responses caused by toxic metal ions.
Collapse
Affiliation(s)
- Krystal A Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | | | | | | | | | | | | |
Collapse
|
32
|
Yang Y, Igumenova TI. The C-terminal V5 domain of Protein Kinase Cα is intrinsically disordered, with propensity to associate with a membrane mimetic. PLoS One 2013; 8:e65699. [PMID: 23762412 PMCID: PMC3675085 DOI: 10.1371/journal.pone.0065699] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/26/2013] [Indexed: 12/20/2022] Open
Abstract
The C-terminal V5 domain is one of the most variable domains in Protein Kinase C isoforms (PKCs). V5 confers isoform specificity on its parent enzyme through interactions with isoform-specific adaptor proteins and possibly through specific intra-molecular interactions with other PKC domains. The structural information about V5 domains in solution is sparse. The objective of this work was to determine the conformational preferences of the V5 domain from the α isoform of PKC (V5α) and evaluate its ability to associate with membrane mimetics. We show that V5α and its phosphorylation-mimicking variant, dmV5α, are intrinsically disordered protein domains. Phosphorylation-mimicking mutations do not alter the overall conformation of the polypeptide backbone, as evidenced by the local nature of chemical shift perturbations and the secondary structure propensity scores. However, the population of the “cis-trans” conformer of the Thr638-Pro639-Pro640 turn motif, which has been implicated in the down-regulation of PKCα via peptidyl-prolyl isomerase Pin1, increases in dmV5α, along with the conformational flexibility of the region between the turn and hydrophobic motifs. Both wild type and dmV5α associate with micelles made of a zwitterionic detergent, n-dodecylphosphocholine. Upon micelle binding, V5α acquires a higher propensity to form helical structures at the conserved “NFD” motif and the entire C-terminal third of the domain. The ability of V5α to partition into the hydrophobic micellar environment suggests that it may serve as a membrane anchor during the PKC maturation process.
Collapse
Affiliation(s)
- Yuan Yang
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America
| | | |
Collapse
|
33
|
Affiliation(s)
- Chang Shu
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | | | | | | | | | | |
Collapse
|
34
|
Abstract
Structural cysteine-rich Zn(2+) sites that stabilize protein folds are considered to be unreactive. In this article, we identified a reactive cysteine residue, Cys151, in a treble-clef zinc finger with a Cys(3)His coordination sphere. The protein in question is the C1B domain of Protein Kinase Cα (PKCα). Mass-tagging cysteine assays of several C1B variants were employed to ascertain the site specificity of the covalent modification. The reactivity of Cys151 in C1B also manifests itself in the structural dynamics of the Zn(2+) coordination sphere where the Sγ of Cys151 alternates between the Zn(2+)-bound thiolate and free thiol states. We used NMR-detected pH titrations, ZZ-exchange spectroscopy, and residual dipolar coupling (RDC)-driven structure refinement to characterize the two exchanging conformations of C1B that differ in zinc coordination. Our data suggest that Cys151 serves as an entry point for the reactive oxygen species that activate PKCα in a process involving Zn(2+) release.
Collapse
Affiliation(s)
- Mikaela D Stewart
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
| | | |
Collapse
|
35
|
Shu C, Sung MW, Stewart MD, Igumenova TI, Tan X, Li P. Cover Picture: The Structural Basis of Iron Sensing by the Human F-box Protein FBXL5 (ChemBioChem 6/2012). Chembiochem 2012. [DOI: 10.1002/cbic.201290018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
36
|
Morales KA, Igumenova TI. Synergistic effect of Pb(2+) and phosphatidylinositol 4,5-bisphosphate on C2 domain-membrane interactions. Biochemistry 2012; 51:3349-60. [PMID: 22475207 DOI: 10.1021/bi201850h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ca(2+)-responsive C2 domains are peripheral membrane modules that target their host proteins to anionic membranes upon binding Ca(2+) ions. Several C2 domain-containing proteins, such as protein kinase C isoenzymes (PKCs), have been identified as molecular targets of Pb(2+), a known environmental toxin. We demonstrated previously that the C2 domain from PKCα (C2α) binds Pb(2+) with high affinity and undergoes membrane insertion in the Pb(2+)-complexed form. The objective of this work was to determine the effect of phosphatidylinositol 4,5-bisphosphate (PIP(2)) on the C2α-Pb(2+) interactions. Using nuclear magnetic resonance (NMR) experiments, we show that Pb(2+) and PIP(2) synergistically enhance each other's affinity for C2α. Moreover, the affinity of C2α for PIP(2) increases upon progressive saturation of the metal-binding sites. Combining the NMR data with the results of protein-to-membrane Förster resonance energy transfer and vesicle sedimentation experiments, we demonstrate that PIP(2) can influence two aspects of C2α-Pb(2+)-membrane interactions: the affinity of C2α for Pb(2+) and the association of Pb(2+) with the anionic sites on the membrane. Both factors may contribute to the toxic effect of Pb(2+) resulting from the aberrant modulation of PKCα activity. Finally, we propose a mechanism for Pb(2+) outcompeting Ca(2+) from membrane-bound C2α.
Collapse
Affiliation(s)
- Krystal A Morales
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843-2128, USA
| | | |
Collapse
|
37
|
Morales KA, Lasagna M, Gribenko AV, Yoon Y, Reinhart GD, Lee JC, Cho W, Li P, Igumenova TI. Pb2+ as modulator of protein-membrane interactions. J Am Chem Soc 2011; 133:10599-611. [PMID: 21615172 DOI: 10.1021/ja2032772] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lead is a potent environmental toxin that mimics the effects of divalent metal ions, such as zinc and calcium, in the context of specific molecular targets and signaling processes. The molecular mechanism of lead toxicity remains poorly understood. The objective of this work was to characterize the effect of Pb(2+) on the structure and membrane-binding properties of C2α. C2α is a peripheral membrane-binding domain of Protein Kinase Cα (PKCα), which is a well-documented molecular target of lead. Using NMR and isothermal titration calorimetry (ITC) techniques, we established that C2α binds Pb(2+) with higher affinity than its natural cofactor, Ca(2+). To gain insight into the coordination geometry of protein-bound Pb(2+), we determined the crystal structures of apo and Pb(2+)-bound C2α at 1.9 and 1.5 Å resolution, respectively. A comparison of these structures revealed that the metal-binding site is not preorganized and that rotation of the oxygen-donating side chains is required for the metal coordination to occur. Remarkably, we found that holodirected and hemidirected coordination geometries for the two Pb(2+) ions coexist within a single protein molecule. Using protein-to-membrane Förster resonance energy transfer (FRET) spectroscopy, we demonstrated that Pb(2+) displaces Ca(2+) from C2α in the presence of lipid membranes through the high-affinity interaction with the membrane-unbound C2α. In addition, Pb(2+) associates with phosphatidylserine-containing membranes and thereby competes with C2α for the membrane-binding sites. This process can contribute to the inhibitory effect of Pb(2+) on the PKCα activity.
Collapse
Affiliation(s)
- Krystal A Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Stewart MD, Morgan B, Massi F, Igumenova TI. Probing the determinants of diacylglycerol binding affinity in the C1B domain of protein kinase Cα. J Mol Biol 2011; 408:949-70. [PMID: 21419781 DOI: 10.1016/j.jmb.2011.03.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/09/2011] [Accepted: 03/10/2011] [Indexed: 01/20/2023]
Abstract
C1 domains are independently folded modules that are responsible for targeting their parent proteins to lipid membranes containing diacylglycerol (DAG), a ubiquitous second messenger. The DAG binding affinities of C1 domains determine the threshold concentration of DAG required for the propagation of signaling response and the selectivity of this response among DAG receptors in the cell. The structural information currently available for C1 domains offers little insight into the molecular basis of their differential DAG binding affinities. In this work, we characterized the C1B domain of protein kinase Cα (C1Bα) and its diagnostic mutant, Y123W, using solution NMR methods and molecular dynamics simulations. The mutation did not perturb the C1Bα structure or the sub-nanosecond dynamics of the protein backbone, but resulted in a >100-fold increase in DAG binding affinity and a substantial change in microsecond timescale conformational dynamics, as quantified by NMR rotating-frame relaxation-dispersion methods. The differences in the conformational exchange behavior between wild type and Y123W C1Bα were localized to the hinge regions of ligand-binding loops. Molecular dynamics simulations provided insight into the identity of the exchanging conformers and revealed the significance of a particular residue (Gln128) in modulating the geometry of the ligand-binding site. Taken together with the results of binding studies, our findings suggest that the conformational dynamics and preferential partitioning of the tryptophan side chain into the water-lipid interface are important factors that modulate the DAG binding properties of the C1 domains.
Collapse
Affiliation(s)
- Mikaela D Stewart
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA
| | | | | | | |
Collapse
|
39
|
Affiliation(s)
- Tatyana I Igumenova
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | | | | | | |
Collapse
|
40
|
Abstract
The motion of the active site loop (loop 6) in triosephosphate isomerase is investigated in solution by TROSY NMR spin-relaxation experiments. The data show clear evidence for motion with an exchange rate constant (kex) of 9000 s-1, consistent with opening and closing of this loop being partially rate-limiting to catalytic throughput. Similar rate constants are observed for residues in both the N- and C-terminal regions of loop 6, suggesting motional coupling of the loop hinges. Mutation of tyrosine 208 to a phenylalanine (Y208F) eliminates a hydrogen bond in the closed loop conformation. NMR experiments with this mutant enzyme indicate an increase in the population of the open conformer and concomitant increase in the opening rate constant and a decrease in the rate of loop closure. The destabilization of the closed conformer by approximately 3 kJ/mol is consistent with a similar decrease in affinity of Y208F for ligand. The site-specific nature of these experiments leads to additional insight into loop 6 motion and the role of a conserved residue in modulating this motion.
Collapse
Affiliation(s)
- Rebecca B Berlow
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, USA
| | | | | |
Collapse
|
41
|
Igumenova TI, Palmer AG. Off-Resonance TROSY-Selected R1ρ Experiment with Improved Sensitivity for Medium- and High-Molecular-Weight Proteins. J Am Chem Soc 2006; 128:8110-1. [PMID: 16787055 DOI: 10.1021/ja061692f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NMR spin relaxation techniques that utilize relaxation interference phenomena (TROSY) enable chemical exchange processes to be characterized in high-molecular-weight proteins. A TROSY-selected (TS) approach for measuring off-resonance R1rho relaxation in the spin-locked rotating reference frame is developed using three principles: (i) deuteration of nonexchangeable 1H sites to minimize remote dipole-dipole interactions, (ii) selective excitation of the slowly relaxing 15N doublet component to obtain optimal initial conditions, and (iii) selective inversion of one of the 15N doublet components to suppress cross-relaxation during the spin-lock period. The method is validated using [90%-15N, 70%-2H] ubiquitin at 280 K. The TROSY-selected R1rho experiment enables characterization of backbone dynamics on the microsecond time scale in large proteins.
Collapse
Affiliation(s)
- Tatyana I Igumenova
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | | |
Collapse
|
42
|
Affiliation(s)
- Tatyana I Igumenova
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | |
Collapse
|
43
|
Abstract
The mechanism of long-range coupling of allosteric sites in calcium-saturated calmodulin (CaM) has been explored by characterizing structural and dynamics effects of mutants of calmodulin in complex with a peptide corresponding to the smooth muscle myosin light chain kinase calmodulin-binding domain (smMLCKp). Four CaM mutants were examined: D95N and D58N, located in Ca2+-binding loops; and M124L and E84K, located in the target domain-binding site of CaM. Three of these mutants have altered allosteric coupling either between Ca2+-binding sites (D58N and D95N) or between the target- and Ca2+-binding sites (E84K). The structure and dynamics of the mutant calmodulins in complex with smMLCKp were characterized using solution NMR. Analysis of chemical shift perturbations was employed to detect largely structural perturbations. 15N and 2H relaxation was employed to detect perturbations of the dynamics of the backbone and methyl-bearing side chains of calmodulin. The least median squares method was found to be robust in the detection of perturbed sites. The main chain dynamics of calmodulin are found to be largely unresponsive to the mutations. Three mutants show significantly perturbed dynamics of methyl-bearing side chains. Despite the pseudosymmetric location of Ca2+-binding loop mutations D58N and D95N, the dynamic response of CaM is asymmetric, producing long-range perturbation in D58N and almost none in D95N. The mutations located at the target domain-binding site have quite different effects. For M124L, a local perturbation of the methyl dynamics is observed, while the E84K mutation produces a long-range propagation of dynamic perturbations along the target domain-binding site.
Collapse
Affiliation(s)
- Tatyana I Igumenova
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
| | | | | |
Collapse
|
44
|
Igumenova TI, McDermott AE. Homo-nuclear 13C J-decoupling in uniformly 13C-enriched solid proteins. J Magn Reson 2005; 175:11-20. [PMID: 15949744 DOI: 10.1016/j.jmr.2005.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 02/28/2005] [Accepted: 03/09/2005] [Indexed: 05/02/2023]
Abstract
Recently, we reported an analysis of carbon lineshapes in high resolution solid-state NMR spectra of uniformly 13C-enriched amino acids. Application of a 13C J-decoupling protocol during the carbon chemical shift evolution period allowed us to separate the contribution of the second-order dipolar shift from that of the 13C-13C J-coupling interactions to carbon linewidths. In this work, we have extended this approach to microcrystalline proteins. We describe the performance of the J-decoupling sequence applied to remove homo-nuclear 13C J-couplings in the 13C spectra of ubiquitin. Analysis of the J-decoupling efficiency for C(alpha) and carbonyl protein sites showed that a significant gain in resolution can be achieved.
Collapse
Affiliation(s)
- Tatyana I Igumenova
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, NY 10027, USA
| | | |
Collapse
|
45
|
Wang T, Frederick KK, Igumenova TI, Wand AJ, Zuiderweg ERP. Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements. J Am Chem Soc 2005; 127:828-9. [PMID: 15656608 DOI: 10.1021/ja045743p] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fast dynamics of protein backbones are often investigated by nuclear magnetic relaxation experiments that report on the degree of spatial restriction of the amide bond vector. By comparing calmodulin in the peptide-bound and peptide-free states with these classical methods, we observe little difference in the dynamics of the polypeptide main chain (average order parameter decrease of 0.01 unit upon binding). However, when using NMR methods that monitor the mobility of the CO-Calpha bond vector, we reveal a significant reduction of dynamics of the protein main chain (average order parameter decrease of 0.048 units). Previous investigations have suggested that the side-chain dynamics is reduced by an average of 0.07 order parameter units upon ligand binding (Lee, A. L.; Kinnear, S. A.; Wand, A. J. Nat. Struct. Biol. 2000, 7, 72-77). The current findings suggest that the change of the CO-Calpha bond vector dynamics is intermediate between the changes in NH and side-chain dynamics and report a previously undetected loss of main-chain entropy. Weak site-to-site correlations between the different motional indicators are also observed.
Collapse
Affiliation(s)
- Tianzhi Wang
- Biophysics Research Division, Department of Biological Chemistry, The University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109-1055, USA
| | | | | | | | | |
Collapse
|
46
|
Abstract
Solid-state NMR 2D spectroscopy was used to correlate carbon backbone and side-chain chemical shifts for uniformly (13)C,(15)N-enriched microcrystalline ubiquitin. High applied field strengths, 800 MHz for protons, moderate proton decoupling fields, 80-100 kHz, and high magic angle sample spinning frequencies, 20 kHz, were used to narrow the most of the carbon line widths to 0.5-0.8 ppm. Homonuclear magnetization transfer was effected by matching the proton RF field to the spinning frequency, the so-called dipolar-assisted rotational resonance (DARR) (Takegoshi, K.; Nakamura, S.; Terao, T. Chem. Phys. Lett. 2001, 344, 631-637), and a mixing time of 20 ms was used to maximize the intensity of one-bond transfers between carbon atoms. This polarization transfer sequence resulted in roughly 14% transfer efficiencies for directly bonded carbon pairs and 4% transfer efficiencies for carbons separated by a third carbon. With this simple procedure, the majority of the one-bond correlations was observed with moderate transfer efficiencies, and many two-bond correlations were also observed with weaker intensities. Spin systems could be identified for more than half of the amino acid side chains, and site-specific assignments were readily possible via comparison with 400 MHz (15)N-(13)C-(13)C correlation spectroscopy (described separately).
Collapse
Affiliation(s)
- Tatyana I Igumenova
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, New York 10027, USA
| | | | | | | | | | | |
Collapse
|
47
|
Abstract
Site-specific assignments for the solid-state NMR spectra of uniformly 13C,15N-enriched ubiquitin are described. The assignments are derived from three three-dimensional 15N-13C-13C correlation spectra collected at 400 MHz on microcrystalline material. A few residues (the loop near Threonine 9 and the C-terminal fragment) were missing and correspond to regions previously reported to be mobile on the basis of X-ray crystallography and solution NMR studies. A few additional sites exhibit shifts that differ from previously reported solution NMR assignments. Nonetheless, these de novo assignments indicate close agreement between the chemical shifts observed in solution and those in microcrystalline or precipitated solids. The methods utilized are likely to be generally applicable for other noncrystalline, nonsoluble proteins.
Collapse
|
48
|
Igumenova TI, McDermott AE. Improvement of resolution in solid state NMR spectra with J-decoupling: an analysis of lineshape contributions in uniformly 13C-enriched amino acids and proteins. J Magn Reson 2003; 164:270-285. [PMID: 14511595 DOI: 10.1016/s1090-7807(03)00239-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In magic angle spinning (MAS) NMR spectra of highly and uniformly 13C,15N-enriched amino acids and proteins, homo-nuclear coupling interactions contribute significantly to the 13C linewidths, particularly for moderate applied magnetic field strengths and sample spinning frequencies. In this work, we attempted to dissect, analyze, and control the contributions of J-coupling and residual homo-nuclear dipolar coupling interactions to the linewidths of uniformly 13C,15N-enriched crystalline alanine; these studies were carried out at 9.4 T using a range of spinning frequencies from 5 to 15 kHz. The anisotropic second-order dipolar shifts and the J-splittings are comparable in their contribution to the linewidths, but behave very differently in terms of experimental protocols for line narrowing. In contrast to the J-coupling interactions, the second-order dipolar broadening cannot be refocused using selective pulses on the passively coupled spin. We carried out experiments to remove or refocus the 13C J-coupling interactions (omega1 J-decoupling) using a selective DANTE pulse in the center of the indirect evolution period. Inversion profiles and bandwidths of selective DANTE pulses acting on transverse magnetization, in the regime of moderate spinning frequencies, were characterized computationally and experimentally. A dramatic improvement in the resolution of the 2D spectrum was achieved when this decoupling protocol was employed.
Collapse
Affiliation(s)
- Tatyana I Igumenova
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113 New York, NY 10027, USA
| | | |
Collapse
|
49
|
Abstract
Recently, a new phase cycling scheme was introduced by this laboratory for use in biological solid-state NMR experiments involving multiple pi-pulses with characteristics that suggested it may enhance the sensitivity of these kind of experiments (Y. Li and J. N. S. Evans, 1995, Chem. Phys. Lett. 241, 79 and Erratum, 1995, ibid. 246, 527; Y. Li and J. N. S. Evans, 1996, J. Magn. Reson. B 111, 296). The new sequence followed the supercycled concept proposed a decade ago for heteronuclear decoupling experiments. In this paper, more detailed experiments demonstrate that the claim of enhanced sensitivity was unfounded, and in fact the supercycle proposed differs little from the established XY-8 and XY-16 based supercycles.
Collapse
Affiliation(s)
- T I Igumenova
- Department of Biochemistry and Biophysics, Washington State University, Pullman, Washington, 99164-4660, USA
| | | | | |
Collapse
|
50
|
Mitchell DJ, Jakeman DL, Igumenova TI, Shuttleworth WA, Miller KD, Evans JNS. Time-resolved solid-state REDOR-edited NMR detection of a transient enzyme–intermediate. Chem Commun (Camb) 1997. [DOI: 10.1039/a701926b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|