1
|
Wilkerson MD, Hupalo D, Gray JC, Zhang X, Wang J, Girgenti MJ, Alba C, Sukumar G, Lott NM, Naifeh JA, Aliaga P, Kessler RC, Turner C, Pollard HB, Dalgard CL, Ursano RJ, Stein MB. Uncommon Protein-Coding Variants Associated With Suicide Attempt in a Diverse Sample of U.S. Army Soldiers. Biol Psychiatry 2024; 96:15-25. [PMID: 38141912 DOI: 10.1016/j.biopsych.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/25/2023]
Abstract
BACKGROUND Suicide is a societal and public health concern of global scale. Identifying genetic risk factors for suicide attempt can characterize underlying biology and enable early interventions to prevent deaths. Recent studies have described common genetic variants for suicide-related behaviors. Here, we advance this search for genetic risk by analyzing the association between suicide attempt and uncommon variation exome-wide in a large, ancestrally diverse sample. METHODS We sequenced whole genomes of 13,584 soldiers from the Army STARRS (Army Study to Assess Risk and Resilience in Servicemembers), including 979 individuals with a history of suicide attempt. Uncommon, nonsilent protein-coding variants were analyzed exome-wide for association with suicide attempt using gene-collapsed and single-variant analyses. RESULTS We identified 19 genes with variants enriched in individuals with history of suicide attempt, either through gene-collapsed or single-variant analysis (Bonferroni padjusted < .05). These genes were CIB2, MLF1, HERC1, YWHAE, RCN2, VWA5B1, ATAD3A, NACA, EP400, ZNF585A, LYST, RC3H2, PSD3, STARD9, SGMS1, ACTR6, RGS7BP, DIRAS2, and KRTAP10-1. Most genes had variants across multiple genomic ancestry groups. Seventeen of these genes were expressed in healthy brain tissue, with 9 genes expressed at the highest levels in the brain versus other tissues. Brains from individuals deceased from suicide aberrantly expressed RGS7BP (padjusted = .035) in addition to nominally significant genes including YWHAE and ACTR6, all of which have reported associations with other mental disorders. CONCLUSIONS These results advance the molecular characterization of suicide attempt behavior and support the utility of whole-genome sequencing for complementing the findings of genome-wide association studies in suicide research.
Collapse
Affiliation(s)
- Matthew D Wilkerson
- Center for Military Precision Health, Uniformed Services University, Bethesda, Maryland; Department of Anatomy, Physiology, and Genetics, Uniformed Services University, Bethesda, Maryland
| | - Daniel Hupalo
- Center for Military Precision Health, Uniformed Services University, Bethesda, Maryland
| | - Joshua C Gray
- Department of Medical and Clinical Psychology, Uniformed Services University, Bethesda, Maryland
| | - Xijun Zhang
- Center for Military Precision Health, Uniformed Services University, Bethesda, Maryland
| | - Jiawei Wang
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Camille Alba
- Center for Military Precision Health, Uniformed Services University, Bethesda, Maryland
| | - Gauthaman Sukumar
- Center for Military Precision Health, Uniformed Services University, Bethesda, Maryland
| | - Nathaniel M Lott
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland
| | - James A Naifeh
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University, Bethesda, Maryland
| | - Pablo Aliaga
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University, Bethesda, Maryland
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, Massachusetts
| | - Clesson Turner
- Department of Pediatrics, Uniformed Services University, Bethesda, Maryland
| | - Harvey B Pollard
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, Bethesda, Maryland
| | - Clifton L Dalgard
- Center for Military Precision Health, Uniformed Services University, Bethesda, Maryland; Department of Anatomy, Physiology, and Genetics, Uniformed Services University, Bethesda, Maryland
| | - Robert J Ursano
- Center for the Study of Traumatic Stress, Department of Psychiatry, Uniformed Services University, Bethesda, Maryland
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, California; Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California; VA San Diego Healthcare System, San Diego, California.
| |
Collapse
|
2
|
Chakraborty G, Patra N. Elucidating the Molecular Basis of 14-3-3 Interaction with α-Synuclein: Insights from Molecular Dynamics Simulations and the Design of a Novel Protein-Protein Interaction Inhibitor. J Phys Chem B 2024. [PMID: 38857533 DOI: 10.1021/acs.jpcb.4c01743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Parkinson's disease is a widespread age-related neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain along with the appearance of protein aggregates, termed as "Lewy bodies" in the surviving neuronal cells. The components of Lewy bodies include proteins such as α-synuclein, 14-3-3, Parkin, and LRRK2, along with other cellular organelles, which, in their native state, perform a plethora of vital biological functions within the human biome. Formation of these aggregates renders these components inactive, thereby interfering with homeostasis. In this regard, the current study attempts to investigate the complexation behavior of all human-based 14-3-3 isoforms with α-synuclein via a combination of classical and enhanced sampling techniques and thereby determine the causality of these protein-protein interactions. The study indicated that upon complexation, the aggregation propensity of both 14-3-3 and α-synuclein increases, and this increment is propelled by the interfacial residues on either protein. Furthermore, mutagenesis studies revealed that Lys214 of 14-3-3 (henceforth termed K214A) is crucial for the formation of this binary complex. Principal component analysis combined with clustering studies unveiled the stability of these complexes in terms of their conformational distribution across the entire MD trajectory. For K214A, these clustered states were sparsely located, thereby making the transitions between them slightly difficult. Dynamic cross-correlation maps (DCCM) revealed the role of residues in the range 80-130 of 14-3-3 having a potential allosteric role in driving this complexation process. Finally, a novel peptide-based supramolecular inhibitor was designed, which exhibited higher proficiency in limiting the 14-3-3/α-synuclein interaction compared to the previous inhibitor model. It was also revealed that the presence of this inhibitor induces structural rigidity in α-synuclein, making changes in its conformations extremely difficult, as observed through Umbrella Sampling studies. Based on available information, the current study provides an insight into the molecular-level understanding of protein-protein interactions underlying Parkinson's disease and adds on to the methods of devising novel therapeutic approaches to treat the same.
Collapse
Affiliation(s)
- Gourav Chakraborty
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| |
Collapse
|
3
|
Li Z, Yang Y, Wu K, Li Y, Shi M. Myeloid leukemia factor 1: A "double-edged sword" in health and disease. Front Oncol 2023; 13:1124978. [PMID: 36814822 PMCID: PMC9939472 DOI: 10.3389/fonc.2023.1124978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/17/2023] [Indexed: 02/08/2023] Open
Abstract
The occurrence and development of malignancies are closely related to abnormal cell cycle regulation. Myeloid leukemia factor 1 (MLF1) is a small nucleocytoplasmic shuttling protein associated with cell cycle exit, apoptosis, and certain immune functions. Therefore, it is pertinent to explore the role of MLF1 in health and diseases. Studies to date have suggested that MLF1 could act as a double-edged sword, regulating biochemical activities directly or indirectly. In hematopoietic cells, it serves as a protective factor for the development of lineages, and in malignancies, it serves as an oncogenesis factor. The diversity of its functions depends on the binding partners, including tumor inhibitors, scaffolding molecules, mitochondrial membrane proteins, and transcription factors. Emerging evidence indicates that MLF1 influences immune responses as well. This paper reviews the structure, biological function, and research progress on MLF1 in health and diseases to provide new insights for future research.
Collapse
Affiliation(s)
- Zixuan Li
- Department of Hematology, the First Affiliated Hospital of Kunming Medical University, Kunming, China,Hematology Research Center of Yunnan Province, Kunming, China
| | - Yuanyuan Yang
- Department of Hematology, the First Affiliated Hospital of Kunming Medical University, Kunming, China,Hematology Research Center of Yunnan Province, Kunming, China
| | - Kun Wu
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuntao Li
- Department of Hematology, the First Affiliated Hospital of Kunming Medical University, Kunming, China,Hematology Research Center of Yunnan Province, Kunming, China
| | - Mingxia Shi
- Department of Hematology, the First Affiliated Hospital of Kunming Medical University, Kunming, China,Hematology Research Center of Yunnan Province, Kunming, China,*Correspondence: Mingxia Shi,
| |
Collapse
|
4
|
Mathivanan S, Chunchagatta Lakshman PK, Singh M, Giridharan S, Sathish K, Hurakadli MA, Bharatham K, Kamariah N. Structure of a 14-3-3ε:FOXO3a pS253 Phosphopeptide Complex Reveals 14-3-3 Isoform-Specific Binding of Forkhead Box Class O Transcription Factor (FOXO) Phosphoproteins. ACS OMEGA 2022; 7:24344-24352. [PMID: 35874228 PMCID: PMC9301721 DOI: 10.1021/acsomega.2c01700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The transcriptional activity of Forkhead Box O3 (FOXO3a) is inactivated by AKT-mediated phosphorylation on Serine 253 (S253), which enables FOXO3a binding to 14-3-3. Phosphorylated FOXO3a binding to 14-3-3 facilitates the nuclear exclusion of FOXO3a, causing cancer cell proliferation. The FOXO3a/14-3-3 interaction has, therefore, emerged as an important therapeutic target. Here, we report a comprehensive analysis using fluorescence polarization, isothermal titration calorimetry, small-angle X-ray scattering, X-ray crystallography, and molecular dynamics simulations to gain molecular-level insights into the interaction of FOXO3apS253 phosphopeptide with 14-3-3ε. A high-resolution structure of the fluorophore-labeled FOXO3apS253:14-3-3ε complex revealed a distinct mode of interaction compared to other 14-3-3 phosphopeptide complexes. FOXO3apS253 phosphopeptide showed significant structural difference in the positions of the -3 and -4 Arg residues relative to pSer, compared to that of a similar phosphopeptide, FOXO1pS256 bound to 14-3-3σ. Moreover, molecular dynamics studies show that the significant structural changes and molecular interactions noticed in the crystal structure of FOXO3apS253:14-3-3ε are preserved over the course of the simulation. Thus, this study reveals structural differences between the binding to 14-3-3 isoforms of FOXO1pS256 versus FOXO3apS253, providing a framework for the rational design of isoform-specific FOXO/14-3-3 protein-protein interaction inhibitors for therapy.
Collapse
|
5
|
Brink H, Riemens R, Thee S, Bieshuizen B, Da Costa Pereira D, Wijtmans M, De Esch IJP, Smit MJ, De Boer AH. Fragment screening yields a small-molecule stabilizer of 14-3-3 dimers that modulates client protein interactions. Chembiochem 2022; 23:e202200178. [PMID: 35767695 PMCID: PMC9543038 DOI: 10.1002/cbic.202200178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/28/2022] [Indexed: 11/30/2022]
Abstract
The development of protein‐protein interaction (PPI) inhibitors has been a successful strategy in drug development. However, the identification of PPI stabilizers has proven much more challenging. Here we report a fragment‐based drug screening approach using the regulatory hub‐protein 14‐3‐3 as a platform for identifying PPI stabilizers. A homogenous time‐resolved FRET assay was used to monitor stabilization of 14‐3‐3/peptide binding using the known interaction partner estrogen receptor alpha. Screening of an in‐house fragment library identified fragment 2 (VUF15640) as a putative PPI stabilizer capable of cooperatively stabilizing 14‐3‐3 PPIs in a cooperative fashion with Fusicoccin‐A. Mechanistically, fragment 2 appears to enhance 14‐3‐3 dimerization leading to increased client‐protein binding. Functionally, fragment 2 enhanced potency of 14‐3‐3 in a cell‐free system inhibiting the enzyme activity of the nitrate reductase. In conclusion, we identified a general PPI stabilizer targeting 14‐3‐3, which could be used as a tool compound for investigating 14‐3‐3 client protein interactions.
Collapse
Affiliation(s)
- Hendrik Brink
- Vrije Universiteit Amsterdam, Division of medicinal chemistry, faculty of life sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
| | - Rick Riemens
- Vrije Universiteit Amsterdam, Division of medicinal chemistry, faculty of life sciences, NETHERLANDS
| | - Stephanie Thee
- Vrije Universiteit Amsterdam, Division of Medicinal Chemistry, Faculty of Sciences, NETHERLANDS
| | - Berend Bieshuizen
- Vrije Universiteit Amsterdam, Division of medicinal chemistry, faculty of life sciences, NETHERLANDS
| | - Daniel Da Costa Pereira
- Vrije Universiteit Amsterdam, Division of Medicinal Chemistry, Faculty of Sciences, NETHERLANDS
| | - Maikel Wijtmans
- Vrije Universiteit Amsterdam, Division of medicinal chemistry, faculty of life sciences, NETHERLANDS
| | - Iwan J P De Esch
- Vrije Universiteit Amsterdam, Division of medicinal chemistry, faculty of life sciences, NETHERLANDS
| | - Martine J Smit
- Vrije Universiteit Amsterdam, Division of medicinal chemistry, faculty of life sciences, NETHERLANDS
| | - Albertus H De Boer
- Vrije Universiteit Amsterdam, Division of Medicinal Chemistry, De Boelelaan 1108, 1075GJ, Amsterdam, NETHERLANDS
| |
Collapse
|
6
|
Evans SR, West C, Klein-Seetharaman J. Similarity of the non-amyloid-β component and C-terminal tail of monomeric and tetrameric alpha-synuclein with 14-3-3 sigma. Comput Struct Biotechnol J 2021; 19:5348-5359. [PMID: 34667532 PMCID: PMC8495038 DOI: 10.1016/j.csbj.2021.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/28/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Alpha-synuclein (αSyn) is often described as a predominantly disordered protein that has a propensity to self-assemble into toxic oligomers that are found in patients with Parkinson's and Alzheimer's diseases. αSyn's chaperone behavior and tetrameric structure are proposed to be protective against toxic oligomerization. In this paper, we extended the previously proposed similarity between αSyn and 14-3-3 proteins to the α-helical tetrameric species of αSyn in detail. 14-3-3 proteins are a family of well-folded proteins with seven human isoforms, and function in signal transduction and as molecular chaperones. We investigated protein homology, using sequence alignment, amyloid, and disorder prediction, as well as three-dimensional visualization and protein-interaction networks. Our results show sequence homology and structural similarity between the aggregation-prone non-amyloid-β component (NAC) residues Val-52 to Gly-111 in αSyn and 14-3-3 sigma residues Leu-12 to Gly-78. We identified an additional region of sequence homology in the C-terminal region of αSyn (residues Ser-129 to Asp-135) and a C-terminal loop of 14-3-3 between helix αH and αI (residues Ser-209 to Asp-215). This data indicates αSyn shares conserved domain architecture with small heat shock proteins. We show predicted regions of high amyloidogenic propensity and intrinsic structural disorder in αSyn coincide with amyloidogenic and disordered predictions for 14-3-3 proteins. The homology in the NAC region aligns with residues involved in dimer- and tetramerization of the non-amyloidogenic 14-3-3 proteins. Because 14-3-3 proteins are generally not prone to misfolding, our results lend further support to the hypothesis that the NAC region is critical to the assembly of αSyn into the non-toxic tetrameric state.
Collapse
Key Words
- 14-3-3 proteins
- Alpha-synuclein
- BAD, BCL2 associated agonist of cell death gene name
- Homology
- IDP, Intrinsically disorder protein(s)
- MAPT, microtubule-associated protein tau gene name
- PPI, Protein-Protein interactions
- Prediction
- Protein structure
- SIP, shared interaction partner
- SNCA, alpha-synuclein gene name
- TH, tyrosine hydroxylase gene name
- Tetramer
- YWHAB, 14-3-3 protein beta isoform gene name
- YWHAE, 14-3-3 protein epsilon isoform gene name
- YWHAH, 14-3-3 protein eta isoform gene name
- pHSPB6, phosphorylated Heat Shock Protein beta-6
- sHSP, small heat shock protein
- αSyn, alpha-synuclein
Collapse
Affiliation(s)
- Sarah R. Evans
- Colorado School of Mines, Quantitative Biosciences and Engineering, 1012 14 St, Chemistry, Golden, CO 80401, USA
| | - Colista West
- Colorado School of Mines, Department of Chemistry, 1012 14 St, Chemistry, Golden, CO 80401, USA
| | - Judith Klein-Seetharaman
- Colorado School of Mines, Quantitative Biosciences and Engineering, 1012 14 St, Chemistry, Golden, CO 80401, USA
- Colorado School of Mines, Department of Chemistry, 1012 14 St, Chemistry, Golden, CO 80401, USA
| |
Collapse
|
7
|
14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains. Commun Biol 2021; 4:899. [PMID: 34294877 PMCID: PMC8298602 DOI: 10.1038/s42003-021-02419-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Neural precursor cell expressed developmentally down-regulated 4 ligase (Nedd4-2) is an E3 ubiquitin ligase that targets proteins for ubiquitination and endocytosis, thereby regulating numerous ion channels, membrane receptors and tumor suppressors. Nedd4-2 activity is regulated by autoinhibition, calcium binding, oxidative stress, substrate binding, phosphorylation and 14-3-3 protein binding. However, the structural basis of 14-3-3-mediated Nedd4-2 regulation remains poorly understood. Here, we combined several techniques of integrative structural biology to characterize Nedd4-2 and its complex with 14-3-3. We demonstrate that phosphorylated Ser342 and Ser448 are the key residues that facilitate 14-3-3 protein binding to Nedd4-2 and that 14-3-3 protein binding induces a structural rearrangement of Nedd4-2 by inhibiting interactions between its structured domains. Overall, our findings provide the structural glimpse into the 14-3-3-mediated Nedd4-2 regulation and highlight the potential of the Nedd4-2:14-3-3 complex as a pharmacological target for Nedd4-2-associated diseases such as hypertension, epilepsy, kidney disease and cancer. Pohl et al. investigated the structural basis of Nedd4-2 regulation by 14-3-3 and found that phosphorylated Ser342 and Ser448 are the main residues that facilitate 14-3-3 binding to Nedd4-2. The authors propose that the Nedd4-2:14-3-3 complex then stimulates a structural rearrangement of Nedd4-2 through inhibiting interaction of its structured domains.
Collapse
|
8
|
Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library. Cell Chem Biol 2021; 28:1602-1615.e9. [PMID: 34111400 PMCID: PMC8610377 DOI: 10.1016/j.chembiol.2021.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/03/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
Genetic screening technologies to identify and validate macromolecular interactions (MMIs) essential for complex pathways remain an important unmet need for systems biology and therapeutics development. Here, we use a library of peptides from diverse prokaryal genomes to screen MMIs promoting the nuclear relocalization of Forkhead Box O3 (FOXO3a), a tumor suppressor more frequently inactivated by post-translational modification than mutation. A hit peptide engages the 14-3-3 family of signal regulators through a phosphorylation-dependent interaction, modulates FOXO3a-mediated transcription, and suppresses cancer cell growth. In a crystal structure, the hit peptide occupies the phosphopeptide-binding groove of 14-3-3ε in a conformation distinct from its natural peptide substrates. A biophysical screen identifies drug-like small molecules that displace the hit peptide from 14-3-3ε, providing starting points for structure-guided development. Our findings exemplify “protein interference,” an approach using evolutionarily diverse, natural peptides to rapidly identify, validate, and develop chemical probes against MMIs essential for complex cellular phenotypes. We describe protein interference, an approach to identify and validate new drug targets A genetic screen identifies a protein interference probe inducing FOXO3a reactivation The probe defines a druggable binding site in the 14-3-3 signal regulator family We illustrate a workflow to parse complex cellular pathways for new drug targets
Collapse
|
9
|
Tugaeva KV, Hawkins DEDP, Smith JLR, Bayfield OW, Ker DS, Sysoev AA, Klychnikov OI, Antson AA, Sluchanko NN. The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins. J Mol Biol 2021; 433:166875. [PMID: 33556408 PMCID: PMC7863765 DOI: 10.1016/j.jmb.2021.166875] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association could regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, and could also hijack cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.
Collapse
Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
| |
Collapse
|
10
|
Holmes TR, Al Matouq J, Holmes M, Sioda N, Rudd JC, Bloom C, Nicola L, Palermo NY, Madson JG, Lovas S, Hansen LA. Targeting 14-3-3ε activates apoptotic signaling to prevent cutaneous squamous cell carcinoma. Carcinogenesis 2021; 42:232-242. [PMID: 32816038 PMCID: PMC7905839 DOI: 10.1093/carcin/bgaa091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
More than a million cases of cutaneous squamous cell carcinoma are diagnosed in the USA each year, and its incidence is increasing. Most of these malignancies arise from premalignant lesions, providing an opportunity for intervention before malignant progression. We previously documented how cytoplasmic mislocalization of CDC25A in premalignant and malignant skin cancers confers resistance to apoptotic cell death via a mechanism that depends on its interaction with 14-3-3ε. From these data, we hypothesized that 14-3-3ε overexpression drives skin tumor development and progression, such that targeting 14-3-3ε may be a useful strategy for skin cancer treatment. Like CDC25A, 14-3-3ε was overexpressed and mislocalized to the cytoplasm of both benign and malignant human skin cancer. Skin-targeted deletion of the 14-3-3ε gene reduced skin tumor development by 75% and blocked malignant progression. 14-3-3ε suppressed apoptosis through activation of Akt, leading to inhibition of BCL2 associated agonist of cell death and upregulation of Survivin. Using virtual tetrapeptide libraries, we developed a novel peptide that specifically blocked 14-3-3ε heterodimerization and thereby prevented its interaction with CDC25A. The peptide reduced prosurvival signaling, killed skin cancer cells and reduced skin tumor growth in xenograft. Normal skin keratinocytes were unaffected by inhibition or deletion of 14-3-3ε. Thus, targeting of 14-3-3ε dimerization is a promising strategy for the treatment of premalignant skin lesions.
Collapse
MESH Headings
- 14-3-3 Proteins/antagonists & inhibitors
- 14-3-3 Proteins/genetics
- 14-3-3 Proteins/metabolism
- 9,10-Dimethyl-1,2-benzanthracene/administration & dosage
- 9,10-Dimethyl-1,2-benzanthracene/toxicity
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Carcinogens/administration & dosage
- Carcinogens/toxicity
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cytoplasm/drug effects
- Cytoplasm/metabolism
- Female
- Humans
- Keratinocytes
- Male
- Mice
- Mice, Knockout
- Neoplasms, Experimental/chemically induced
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/pathology
- Protein Multimerization/drug effects
- Skin Neoplasms/drug therapy
- Skin Neoplasms/pathology
- Tetradecanoylphorbol Acetate/administration & dosage
- Tetradecanoylphorbol Acetate/analogs & derivatives
- Tetradecanoylphorbol Acetate/toxicity
- Xenograft Model Antitumor Assays
- cdc25 Phosphatases/metabolism
Collapse
Affiliation(s)
- Thomas R Holmes
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Jenan Al Matouq
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Matti Holmes
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Natasha Sioda
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Justin C Rudd
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Celia Bloom
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Lauren Nicola
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Nicholas Y Palermo
- Holland Computing Center, University of Nebraska–Lincoln, Lincoln, NE, USA
| | | | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Laura A Hansen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| |
Collapse
|
11
|
Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite. Biochem J 2020; 477:2153-2177. [PMID: 32484216 DOI: 10.1042/bcj20200145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022]
Abstract
Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs, and confer conformational changes leading to modulation of functional parameters of their target proteins. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have annotated and characterized PF3D7_0818200 as 14-3-3 isoform I in Plasmodium falciparum 3D7, and its interaction with one of the key kinases of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Molecular dynamics simulation studies indicated that CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The 14-3-3I/CDPK1 interaction was validated in vitro with ELISA and SPR, which confirmed that the interaction is phosphorylation dependent, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: Mode I-type ARSHpSYPA and Mode II-type RLYHpSLPA, by simulation studies and ITC. This interaction was found to marginally enhance CDPK1 functional activity. Furthermore, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy.
Collapse
|
12
|
Higo J, Kawabata T, Kusaka A, Kasahara K, Kamiya N, Fukuda I, Mori K, Hata Y, Fukunishi Y, Nakamura H. Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J Chem Inf Model 2020; 60:4867-4880. [PMID: 32910853 DOI: 10.1021/acs.jcim.0c00551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Enhanced conformational sampling, a genetic-algorithm-guided multidimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semistable complex structures and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spot are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding constant changes resulting from the alanine mutation experiment for the residues. We also performed a simulation of nonphosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.
Collapse
Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kentaro Mori
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Maizuru College, 234 Shiroya, Maizuru, Kyoto 625-8511 Japan
| | - Yutaka Hata
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
13
|
Ballone A, Lau RA, Zweipfenning FPA, Ottmann C. A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Acta Crystallogr F Struct Biol Commun 2020; 76:501-507. [PMID: 33006579 PMCID: PMC7531243 DOI: 10.1107/s2053230x2001122x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/16/2020] [Indexed: 11/29/2022] Open
Abstract
Interactions between a protein and a peptide motif of its protein partner are prevalent in nature. Often, a protein also has multiple interaction partners. X-ray protein crystallography is commonly used to examine these interactions in terms of bond distances and angles as well as to describe hotspots within protein complexes. However, the crystallization process presents a significant bottleneck in structure determination since it often requires notably time-consuming screening procedures, which involve testing a broad range of crystallization conditions via a trial-and-error approach. This difficulty is also increased as each protein-peptide complex does not necessarily crystallize under the same conditions. Here, a new co-crystallization/peptide-soaking method is presented which circumvents the need to return to the initial lengthy crystal screening and optimization processes for each consequent new complex. The 14-3-3σ protein, which has multiple interacting partners with specific peptidic motifs, was used as a case study. It was found that co-crystals of 14-3-3σ and a low-affinity peptide from one of its partners, c-Jun, could easily be soaked with another interacting peptide to quickly and easily generate new structures at high resolution. Not only does this significantly reduce the production time, but new 14-3-3-peptide structures that were previously not accessible with the 14-3-3σ isoform, despite screening hundreds of other different conditions, were now also able to be resolved. The findings achieved in this study may be considered as a supporting and practical guide to potentially enable the acceleration of the crystallization process of any protein-peptide system.
Collapse
Affiliation(s)
- Alice Ballone
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Roxanne A. Lau
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Fabian P. A. Zweipfenning
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| |
Collapse
|
14
|
Targeting 14-3-3ε-CDC25A interactions to trigger apoptotic cell death in skin cancer. Oncotarget 2020; 11:3267-3278. [PMID: 32934772 PMCID: PMC7476737 DOI: 10.18632/oncotarget.27700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 07/21/2020] [Indexed: 11/25/2022] Open
Abstract
Non-melanoma skin cancer is the most common form of cancer worldwide. We previously documented an anti-apoptotic role for CDC25A in cutaneous squamous cell carcinoma (SCC), an activity dependent on its association with 14-3-3 proteins. We hypothesized that targeting CDC25A-14-3-3ε interactions may be an effective strategy for inducing skin cancer cell apoptosis. Co-immunoprecipitation revealed that CDC25A associated with 14-3-3ε, 14-3-3γ and 14-3-3ζ in SCC cells but not normal keratinocytes. 14-3-3ε and CDC25A activated Akt/BAD/Survivin pro-survival signaling. To target the interaction of 14-3-3ε with CDC25A for cancer therapy, we developed two novel phospho-peptides, pS and pT, corresponding to each of the 14-3-3 binding sites of CDC25A, to specifically interfere with 14-3-3ε binding to CDC25A. Peptides pT (IC50 = 22.1 μM), and pS (IC50 = 29 μM) induced SCC cell death and blocked 14-3-3ε binding to CDC25A. pS or pT treatment of SCC xenografts increased apoptotic cell death and decreased pro-survival P-Akt (S473) and Survivin, demonstrating the effectiveness of the peptides in vivo. These findings lay a framework for the further development of peptides to target 14-3-3ε-CDC25A interactions for skin cancer treatment.
Collapse
|
15
|
Wolter M, Santo DL, Herman P, Ballone A, Centorrino F, Obsil T, Ottmann C. Interaction of an IκBα Peptide with 14-3-3. ACS OMEGA 2020; 5:5380-5388. [PMID: 32201828 PMCID: PMC7081424 DOI: 10.1021/acsomega.9b04413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Inflammatory responses mediated by the transcription factor nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB) play key roles in immunity, autoimmune diseases, and cancer. NF-κB is directly regulated through protein-protein interactions, including those with IκB and 14-3-3 proteins. These two important regulatory proteins have been reported to interact with each other, although little is known about this interaction. We analyzed the inhibitor of nuclear factor kappa B α (IκBα)/14-3-3σ interaction via a peptide/protein-based approach. Structural data were acquired via X-ray crystallography, while binding affinities were measured with fluorescence polarization assays and time-resolved tryptophan fluorescence. A high-resolution crystal structure (1.13 Å) of the uncommon 14-3-3 interaction motif of IκBα (IκBαpS63) in a complex with 14-3-3σ was evaluated. This motif harbors a tryptophan that makes this crystal structure the first one with such a residue visible in the electron density at that position. We used this tryptophan to determine the binding affinity of the unlabeled IκBα peptide to 14-3-3 via tryptophan fluorescence decay measurements.
Collapse
Affiliation(s)
- Madita Wolter
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Domenico Lentini Santo
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Petr Herman
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University, Prague 12116, Czech Republic
| | - Alice Ballone
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Federica Centorrino
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tomas Obsil
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Christian Ottmann
- Department
of Biomedical Engineering, Laboratory of Chemical Biology and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department
of Organic Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| |
Collapse
|
16
|
Kast DJ, Dominguez R. Mechanism of IRSp53 inhibition by 14-3-3. Nat Commun 2019; 10:483. [PMID: 30696821 PMCID: PMC6351565 DOI: 10.1038/s41467-019-08317-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 12/17/2018] [Indexed: 12/26/2022] Open
Abstract
Filopodia are precursors of dendritic spines and polarized cell migration. The I-BAR-domain protein IRSp53 is a key regulator of filopodia dynamics that couples Rho-GTPase signaling to cytoskeleton and membrane remodeling, playing essential roles in neuronal development and cell motility. Here, we describe the structural-functional basis for 14-3-3-dependent inhibition of IRSp53. Phosphoproteomics, quantitative binding and crystallographic studies demonstrate that 14-3-3 binds to two pairs of phosphorylation sites in IRSp53. Using bicistronic expression, we obtain an IRSp53 heterodimer in which only one subunit is phosphorylated, and show that each subunit of IRSp53 independently binds one 14-3-3 dimer. A FRET-sensor assay using natively phosphorylated IRSp53 reveals opposite conformational changes upon binding of activatory (Cdc42, Eps8) or inhibitory (14-3-3) inputs. Finally, we show that 14-3-3 inhibits IRSp53 binding to membranes. Collectively, our findings support a mechanism whereby phosphorylation-dependent inhibition of IRSp53 by 14-3-3 counters membrane binding and interactions with Cdc42 and downstream cytoskeletal effectors. IRSp53 is a key regulator of filopodia formation and cell migration. Here, the authors elucidate a mechanism of phosphorylation-dependent inhibition of IRSp53 by 14-3-3, which impedes the interactions of IRSp53 with membranes and downstream cytoskeletal effectors.
Collapse
Affiliation(s)
- David J Kast
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Cell Biology and Physiology, Washington University, St. Louis, MO, 63110, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
17
|
Cao J, Tan X. Comparative and evolutionary analysis of the 14-3-3 family genes in eleven fishes. Gene 2018; 662:76-82. [DOI: 10.1016/j.gene.2018.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/22/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
|
18
|
Luang S, Sornaraj P, Bazanova N, Jia W, Eini O, Hussain SS, Kovalchuk N, Agarwal PK, Hrmova M, Lopato S. The wheat TabZIP2 transcription factor is activated by the nutrient starvation-responsive SnRK3/CIPK protein kinase. PLANT MOLECULAR BIOLOGY 2018; 96:543-561. [PMID: 29564697 DOI: 10.1007/s11103-018-0713-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/23/2018] [Indexed: 05/09/2023]
Abstract
The understanding of roles of bZIP factors in biological processes during plant development and under abiotic stresses requires the detailed mechanistic knowledge of behaviour of TFs. Basic leucine zipper (bZIP) transcription factors (TFs) play key roles in the regulation of grain development and plant responses to abiotic stresses. We investigated the role and molecular mechanisms of function of the TabZIP2 gene isolated from drought-stressed wheat plants. Molecular characterisation of TabZIP2 and derived protein included analyses of gene expression and its target promoter, and the influence of interacting partners on the target promoter activation. Two interacting partners of TabZIP2, the 14-3-3 protein, TaWIN1 and the bZIP transcription factor TaABI5L, were identified in a Y2H screen. We established that under elevated ABA levels the activity of TabZIP2 was negatively regulated by the TaWIN1 protein and positively regulated by the SnRK3/CIPK protein kinase WPK4, reported previously to be responsive to nutrient starvation. The physical interaction between the TaWIN1 and the WPK4 was detected. We also compared the influence of homo- and hetero-dimerisation of TabZIP2 and TaABI5L on DNA binding. TabZIP2 gene functional analyses were performed using drought-inducible overexpression of TabZIP2 in transgenic wheat. Transgenic plants grown under moderate drought during flowering, were smaller than control plants, and had fewer spikes and seeds per plant. However, a single seed weight was increased compared to single seed weights of control plants in three of four evaluated transgenic lines. The observed phenotypes of transgenic plants and the regulation of TabZIP2 activity by nutrient starvation-responsive WPK4, suggest that the TabZIP2 could be the part of a signalling pathway, which controls the rearrangement of carbohydrate and nutrient flows in plant organs in response to drought.
Collapse
Affiliation(s)
- Sukanya Luang
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Pradeep Sornaraj
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Natalia Bazanova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Commonwealth Scientific and Industrial Research Organisation, Glen Osmond, SA, 5064, Australia
| | - Wei Jia
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Omid Eini
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Department of Plant Protection, School of Agriculture, University of Zanjan, Zanjan, Iran
| | - Syed Sarfraz Hussain
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Forman Christian College, Lahore, 54600, Pakistan
| | - Nataliya Kovalchuk
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Pradeep K Agarwal
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, India
| | - Maria Hrmova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia.
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
19
|
Centorrino F, Ballone A, Wolter M, Ottmann C. Biophysical and structural insight into the USP8/14‐3‐3 interaction. FEBS Lett 2018; 592:1211-1220. [DOI: 10.1002/1873-3468.13017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Federica Centorrino
- Laboratory of Chemical Biology Department of Biomedical Engineering Institute for Complex Molecular Systems Eindhoven University of Technology The Netherlands
| | - Alice Ballone
- Laboratory of Chemical Biology Department of Biomedical Engineering Institute for Complex Molecular Systems Eindhoven University of Technology The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology Department of Biomedical Engineering Institute for Complex Molecular Systems Eindhoven University of Technology The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical Engineering Institute for Complex Molecular Systems Eindhoven University of Technology The Netherlands
- Department of Chemistry University of Duisburg‐Essen Germany
| |
Collapse
|
20
|
Bier D, Mittal S, Bravo-Rodriguez K, Sowislok A, Guillory X, Briels J, Heid C, Bartel M, Wettig B, Brunsveld L, Sanchez-Garcia E, Schrader T, Ottmann C. The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface. J Am Chem Soc 2017; 139:16256-16263. [PMID: 29039919 PMCID: PMC5691318 DOI: 10.1021/jacs.7b07939] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 12/13/2022]
Abstract
Protein regions that are involved in protein-protein interactions (PPIs) very often display a high degree of intrinsic disorder, which is reduced during the recognition process. A prime example is binding of the rigid 14-3-3 adapter proteins to their numerous partner proteins, whose recognition motifs undergo an extensive disorder-to-order transition. In this context, it is highly desirable to control this entropy-costly process using tailored stabilizing agents. This study reveals how the molecular tweezer CLR01 tunes the 14-3-3/Cdc25CpS216 protein-protein interaction. Protein crystallography, biophysical affinity determination and biomolecular simulations unanimously deliver a remarkable finding: a supramolecular "Janus" ligand can bind simultaneously to a flexible peptidic PPI recognition motif and to a well-structured adapter protein. This binding fills a gap in the protein-protein interface, "freezes" one of the conformational states of the intrinsically disordered Cdc25C protein partner and enhances the apparent affinity of the interaction. This is the first structural and functional proof of a supramolecular ligand targeting a PPI interface and stabilizing the binding of an intrinsically disordered recognition motif to a rigid partner protein.
Collapse
Affiliation(s)
- David Bier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Sumit Mittal
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Kenny Bravo-Rodriguez
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Andrea Sowislok
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Xavier Guillory
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Jeroen Briels
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Christian Heid
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Maria Bartel
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Burkhard Wettig
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Elsa Sanchez-Garcia
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Schrader
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Department
of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
| |
Collapse
|
21
|
Sun Y, Chao JR, Xu W, Pourpak A, Boyd K, Moshiach S, Qi GY, Fu A, Shao HR, Pounds S, Morris SW. MLF1 is a proapoptotic antagonist of HOP complex-mediated survival. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:719-727. [PMID: 28137643 DOI: 10.1016/j.bbamcr.2017.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/16/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
In the HAX1/HtrA2-OMI/PARL (HOP) mitochondrial protein complex, anti-apoptotic signals are generated by cleavage and activation of the serine protease HtrA2/OMI by the rhomboid protease PARL upon recruitment of both proteases to inner mitochondrial membrane protein HAX1 (HS1-associated protein X-1). Here we report the negative regulation of the HOP complex by human leukemia-associated myeloid leukemia factor 1 (MLF1). We demonstrate that MLF1 physically and functionally associates with HAX1 and HtrA2. Increased interaction of MLF1 with HAX1 and HtrA2 displaces HtrA2 from the HOP complex and inhibits HtrA2 cleavage and activation, resulting in the apoptotic cell death. Conversely, over-expressed HAX1 neutralizes MLF1's effect and inhibits MLF1-induced apoptosis. Importantly, Mlf1 deletion reverses B- and T-cell lymphopenia and significantly ameliorates the progressive striatal and cerebellar neurodegeneration observed in Hax1-/- mice, with a doubling of the lifespan of Mlf1-/-/Hax1-/- animals compared to Hax1-/- animals. Collectively, these data indicate that MLF1 serves as a proapoptotic antagonist that interacts with the HOP mitochondrial complex to modulate cell survival.
Collapse
Affiliation(s)
- Yi Sun
- Department of Oncology, ShiJiaZhuangShi First Hospital, 36 FanXiLu, ShiJiaZhuangShi, Hebei 050011, PR China; Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA.
| | - Jyh-Rong Chao
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Alan Pourpak
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Kelli Boyd
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Simon Moshiach
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Guo-Yan Qi
- Department of Oncology, ShiJiaZhuangShi First Hospital, 36 FanXiLu, ShiJiaZhuangShi, Hebei 050011, PR China
| | - Amina Fu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Hua-Rong Shao
- Department of Orthopaedics, ShiJiaZhuangShi First Hospital, 36 FanXiLu, ShiJiaZhuangShi, Hebei 050011, PR China
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Stephan W Morris
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| |
Collapse
|
22
|
Parker CG, Galmozzi A, Wang Y, Correia BE, Sasaki K, Joslyn CM, Kim AS, Cavallaro CL, Lawrence RM, Johnson SR, Narvaiza I, Saez E, Cravatt BF. Ligand and Target Discovery by Fragment-Based Screening in Human Cells. Cell 2017; 168:527-541.e29. [PMID: 28111073 DOI: 10.1016/j.cell.2016.12.029] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/14/2016] [Accepted: 12/20/2016] [Indexed: 01/28/2023]
Abstract
Advances in the synthesis and screening of small-molecule libraries have accelerated the discovery of chemical probes for studying biological processes. Still, only a small fraction of the human proteome has chemical ligands. Here, we describe a platform that marries fragment-based ligand discovery with quantitative chemical proteomics to map thousands of reversible small molecule-protein interactions directly in human cells, many of which can be site-specifically determined. We show that fragment hits can be advanced to furnish selective ligands that affect the activity of proteins heretofore lacking chemical probes. We further combine fragment-based chemical proteomics with phenotypic screening to identify small molecules that promote adipocyte differentiation by engaging the poorly characterized membrane protein PGRMC2. Fragment-based screening in human cells thus provides an extensive proteome-wide map of protein ligandability and facilitates the coordinated discovery of bioactive small molecules and their molecular targets.
Collapse
Affiliation(s)
- Christopher G Parker
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Andrea Galmozzi
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yujia Wang
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruno E Correia
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Kenji Sasaki
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher M Joslyn
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Arthur S Kim
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cullen L Cavallaro
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08648, USA
| | - R Michael Lawrence
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08648, USA
| | - Stephen R Johnson
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08648, USA
| | - Iñigo Narvaiza
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Enrique Saez
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
23
|
Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR. Proc Natl Acad Sci U S A 2016; 113:E1152-61. [PMID: 26888287 DOI: 10.1073/pnas.1516631113] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cystic fibrosis is a fatal genetic disease, most frequently caused by the retention of the CFTR (cystic fibrosis transmembrane conductance regulator) mutant protein in the endoplasmic reticulum (ER). The binding of the 14-3-3 protein to the CFTR regulatory (R) domain has been found to enhance CFTR trafficking to the plasma membrane. To define the mechanism of action of this protein-protein interaction, we have examined the interaction in vitro. The disordered multiphosphorylated R domain contains nine different 14-3-3 binding motifs. Furthermore, the 14-3-3 protein forms a dimer containing two amphipathic grooves that can potentially bind these phosphorylated motifs. This results in a number of possible binding mechanisms between these two proteins. Using multiple biochemical assays and crystal structures, we show that the interaction between them is governed by two binding sites: The key binding site of CFTR (pS768) occupies one groove of the 14-3-3 dimer, and a weaker, secondary binding site occupies the other binding groove. We show that fusicoccin-A, a natural-product tool compound used in studies of 14-3-3 biology, can stabilize the interaction between 14-3-3 and CFTR by selectively interacting with a secondary binding motif of CFTR (pS753). The stabilization of this interaction stimulates the trafficking of mutant CFTR to the plasma membrane. This definition of the druggability of the 14-3-3-CFTR interface might offer an approach for cystic fibrosis therapeutics.
Collapse
|
24
|
Sun Y, Fu A, Xu W, Chao JR, Moshiach S, Morris SW. Myeloid leukemia factor 1 interfered with Bcl-XL to promote apoptosis and its function was regulated by 14-3-3. J Physiol Biochem 2015; 71:807-21. [DOI: 10.1007/s13105-015-0445-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 10/19/2015] [Indexed: 01/19/2023]
|
25
|
Babula JJ, Liu JY. Integrate Omics Data and Molecular Dynamics Simulations toward Better Understanding of Human 14-3-3 Interactomes and Better Drugs for Cancer Therapy. J Genet Genomics 2015; 42:531-547. [PMID: 26554908 DOI: 10.1016/j.jgg.2015.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/03/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
The 14-3-3 protein family is among the most extensively studied, yet still largely mysterious protein families in mammals to date. As they are well recognized for their roles in apoptosis, cell cycle regulation, and proliferation in healthy cells, aberrant 14-3-3 expression has unsurprisingly emerged as instrumental in the development of many cancers and in prognosis. Interestingly, while the seven known 14-3-3 isoforms in humans have many similar functions across cell types, evidence of isoform-specific functions and localization has been observed in both healthy and diseased cells. The strikingly high similarity among 14-3-3 isoforms has made it difficult to delineate isoform-specific functions and for isoform-specific targeting. Here, we review our knowledge of 14-3-3 interactome(s) generated by high-throughput techniques, bioinformatics, structural genomics and chemical genomics and point out that integrating the information with molecular dynamics (MD) simulations may bring us new opportunity to the design of isoform-specific inhibitors, which can not only be used as powerful research tools for delineating distinct interactomes of individual 14-3-3 isoforms, but also can serve as potential new anti-cancer drugs that selectively target aberrant 14-3-3 isoform.
Collapse
Affiliation(s)
- JoAnne J Babula
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202, USA
| | - Jing-Yuan Liu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202, USA; Department of Computer and Information Science, Indiana University Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, IN 46202, USA.
| |
Collapse
|
26
|
Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. CHEMISTRY & BIOLOGY 2015; 22:689-703. [PMID: 26091166 PMCID: PMC4518475 DOI: 10.1016/j.chembiol.2015.04.019] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.
Collapse
Affiliation(s)
- Luca Laraia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David J Huggins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| |
Collapse
|
27
|
Killoran RC, Fan J, Yang D, Shilton BH, Choy WY. Structural Analysis of the 14-3-3ζ/Chibby Interaction Involved in Wnt/β-Catenin Signaling. PLoS One 2015; 10:e0123934. [PMID: 25909186 PMCID: PMC4409382 DOI: 10.1371/journal.pone.0123934] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/09/2015] [Indexed: 12/26/2022] Open
Abstract
The partially disordered Chibby (Cby) is a conserved nuclear protein that antagonizes the Wnt/β-catenin signaling pathway. By competing with the Tcf/Lef family proteins for binding to β-catenin, Cby abrogates the β-catenin-mediated transcription of Wnt signaling genes. Additionally, upon phosphorylation on S20 by the kinase Akt, Cby forms a complex with 14-3-3 to facilitate the nuclear export of β-catenin, which represents another crucial mechanism for the regulation of Wnt signaling. To obtain a mechanistic understanding of the 14-3-3/Cby interaction, we have extensively characterized the complex using X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and isothermal titration calorimetry (ITC). The crystal structure of the human 14-3-3ζ/Cby protein-peptide complex reveals a canonical binding mode; however the residue at the +2 position from the phosphorylated serine is shown to be uniquely oriented relative to other solved structures of 14-3-3 complexes. Our ITC results illustrate that although the phosphorylation of S20 is essential for Cby to recognize 14-3-3, residues flanking the phosphorylation site also contribute to the binding affinity. However, as is commonly observed in other 14-3-3/phosphopeptide crystal structures, residues of Cby flanking the 14-3-3 binding motif lack observable electron density. To obtain a more detailed binding interface, we have completed the backbone NMR resonance assignment of 14-3-3ζ. NMR titration experiments reveal that residues outside of the 14-3-3 conserved binding cleft, namely a flexible loop consisting of residues 203-210, are also involved in binding Cby. By using a combined X-ray and NMR approach, we have dissected the molecular basis of the 14-3-3/Cby interaction.
Collapse
Affiliation(s)
- Ryan C Killoran
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Jingsong Fan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Brian H Shilton
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| |
Collapse
|
28
|
Teichmann A, Vargas DM, Monteiro KM, Meneghetti BV, Dutra CS, Paredes R, Galanti N, Zaha A, Ferreira HB. Characterization of 14-3-3 Isoforms Expressed in the Echinococcus granulosus Pathogenic Larval Stage. J Proteome Res 2015; 14:1700-15. [DOI: 10.1021/pr5010136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aline Teichmann
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| | - Daiani M. Vargas
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| | - Karina M. Monteiro
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| | - Bruna V. Meneghetti
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| | - Cristine S. Dutra
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| | - Rodolfo Paredes
- Escuela
de Medicina Veterinaria, Facultad de Ecologia y Recursos Naturales, Universidad Andrés Bello, 8370251 Santiago, Chile
| | - Norbel Galanti
- Programa
de Biología Celular y Molecular, Instituto de Ciencias Biomédicas,
Facultad de Medicina, Universidad de Chile, 8389100 Santiago, Chile
| | - Arnaldo Zaha
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| | - Henrique B. Ferreira
- Laboratório
de Genômica Estrutural e Funcional and Laboratório de
Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970 Porto
Alegre, RS, Brazil
| |
Collapse
|
29
|
Mori M, Vignaroli G, Botta M. Small molecules modulation of 14-3-3 protein-protein interactions. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 10:e541-7. [PMID: 24451646 DOI: 10.1016/j.ddtec.2012.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
14-3-3 is a family of highly conserved regulatory proteins which is attracting a significant interest due to its potential role as target for pharmacological intervention against cancer and neurodegenerative disorders. Although modulating protein-protein interactions (PPI) is still conceived as a challenging task in drug discovery, in past few years peptide inhibitors and small molecular modulators of 14-3-3 PPI have been described. Here we examine structural and biological features of 14-3-3 and propose an overview on techniques used for discovering small molecular inhibitors and stabilizers of 14-3-3 PPI.
Collapse
|
30
|
Milroy LG, Brunsveld L, Ottmann C. Stabilization and inhibition of protein-protein interactions: the 14-3-3 case study. ACS Chem Biol 2013; 8:27-35. [PMID: 23210482 DOI: 10.1021/cb300599t] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Small-molecule modulation of protein-protein interactions (PPIs) is one of the most exciting but also difficult fields in chemical biology and drug development. As one of the most important "hub" proteins with at least 200-300 interaction partners, the 14-3-3 proteins are an especially fruitful case for PPI intervention. Here, we summarize recent success stories in small-molecule modulation, both inhibition and stabilization, of 14-3-3 PPIs. The chemical breath of modulators includes natural products such as fusicoccin A and derivatives but also compounds identified via high-throughput and in silico screening, which has yielded a toolbox of useful inhibitors and stabilizers for this interesting class of adapter proteins. Protein-protein interactions (PPIs) are involved in almost all biological processes, with any given protein typically engaged in complexes with other proteins for the majority of its lifetime. Hence, proteins function not simply as single, isolated entities but display their roles by interacting with other cellular components. These different interaction patterns are presumably as important as the intrinsic biochemical activity status of the protein itself. The biological role of a protein is therefore decisively dependent on the underlying PPI network that furthermore can show great spatial and temporal variations. A thorough appreciation and understanding of this concept and its regulation mechanisms could help to develop new therapeutic agents and concepts.
Collapse
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory of Chemical
Biology,
Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech, 5612 AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical
Biology,
Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical
Biology,
Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech, 5612 AZ Eindhoven, The Netherlands
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße
15, 44227 Dortmund, Germany
| |
Collapse
|
31
|
Subcellular localization of full-length human myeloid leukemia factor 1 (MLF1) is independent of 14-3-3 proteins. Cell Mol Biol Lett 2012; 18:137-48. [PMID: 23271436 PMCID: PMC6275728 DOI: 10.2478/s11658-012-0044-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 12/17/2012] [Indexed: 12/30/2022] Open
Abstract
Myeloid leukemia factor 1 (MLF1) is associated with the development of leukemic diseases such as acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). However, information on the physiological function of MLF1 is limited and mostly derived from studies identifying MLF1 interaction partners like CSN3, MLF1IP, MADM, Manp and the 14-3-3 proteins. The 14-3-3-binding site surrounding S34 is one of the only known functional features of the MLF1 sequence, along with one nuclear export sequence (NES) and two nuclear localization sequences (NLS). It was recently shown that the subcellular localization of mouse MLF1 is dependent on 14-3-3 proteins. Based on these findings, we investigated whether the subcellular localization of human MLF1 was also directly 14-3-3-dependent. Live cell imaging with GFP-fused human MLF1 was used to study the effects of mutations and deletions on its subcellular localization. Surprisingly, we found that the subcellular localization of full-length human MLF1 is 14-3-3-independent, and is probably regulated by other as-yet-unknown proteins.
Collapse
|
32
|
Ottmann C. Small-molecule modulators of 14-3-3 protein-protein interactions. Bioorg Med Chem 2012; 21:4058-62. [PMID: 23266179 DOI: 10.1016/j.bmc.2012.11.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 11/17/2012] [Accepted: 11/20/2012] [Indexed: 01/07/2023]
Abstract
14-3-3 Proteins are eukaryotic adapter proteins that regulate a plethora of physiological processes by binding to several hundred partner proteins. They play a role in biological activities as diverse as signal transduction, cell cycle regulation, apoptosis, host-pathogen interactions and metabolic control. As such, 14-3-3s are implicated in disease areas like cancer, neurodegeneration, diabetes, pulmonary disease, and obesity. Targeted modulation of 14-3-3 protein-protein interactions (PPIs) by small molecules is therefore an attractive concept for disease intervention. In recent years a number of examples of inhibitors and stabilizers of 14-3-3 PPIs have been reported promising a vivid future in chemical biology and drug development for this remarkable class of proteins.
Collapse
Affiliation(s)
- Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.
| |
Collapse
|
33
|
Molzan M, Ottmann C. Synergistic binding of the phosphorylated S233- and S259-binding sites of C-RAF to one 14-3-3ζ dimer. J Mol Biol 2012; 423:486-95. [PMID: 22922483 DOI: 10.1016/j.jmb.2012.08.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/12/2012] [Accepted: 08/14/2012] [Indexed: 01/02/2023]
Abstract
C-RAF kinase is a central component of the Ras-RAF-MEK (mitogen-activated protein kinase/extracellular signal-regulated kinase)-ERK (extracellular signal-regulated kinase) pathway, which has been shown to be activated in 30% of human tumors. 14-3-3 proteins inactivate C-RAF by binding to the two N-terminal phosphorylation-dependent binding sites surrounding S233 and S259. 14-3-3 proteins can bind two target sequences located on one polypeptide chain simultaneously, thereby increasing binding affinity compared to single-site binding and possibly allowing regulated 14-3-3 binding through gatekeeper phosphorylation. To date, it was unclear whether 14-3-3 proteins can bind the two N-terminal phosphorylation-dependent binding sites of C-RAF simultaneously. Fluorescence polarization using phosphorylated peptides demonstrated that S233 is the low-affinity and S259 is the high-affinity binding site, while simultaneous engagement of both sites by 14-3-3ζ enhances affinity compared to single-site binding. Determination of a 1:1 stoichiometry for the di-phosphorylated peptide binding to one 14-3-3ζ dimer with isothermal titration calorimetry was supported by the crystal structure of the 14-3-3ζ/C-RAFpS233,pS259 complex. Cellular localization studies validate the significance of these sites for cytoplasmic retention of C-RAF, suggesting an extended mechanism of RAF regulation by 14-3-3 proteins.
Collapse
Affiliation(s)
- Manuela Molzan
- Chemical Genomics Centre of the Max-Planck-Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | | |
Collapse
|