1
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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] [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.
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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
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2
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Qiu C, Li Z, Leigh DA, Duan B, Stucky JE, Kim N, Xie G, Lu KP, Zhou XZ. The role of the Pin1- cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia. Front Cell Dev Biol 2024; 12:1343962. [PMID: 38628595 PMCID: PMC11019028 DOI: 10.3389/fcell.2024.1343962] [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: 11/24/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Tauopathies are neurodegenerative diseases characterized by deposits of abnormal Tau protein in the brain. Conventional tauopathies are often defined by a limited number of Tau epitopes, notably neurofibrillary tangles, but emerging evidence suggests structural heterogeneity among tauopathies. The prolyl isomerase Pin1 isomerizes cis P-tau to inhibit the development of oligomers, tangles and neurodegeneration in multiple neurodegenerative diseases such as Alzheimer's disease, traumatic brain injury, vascular contribution to cognitive impairment and dementia (VCID) and preeclampsia (PE). Thus, cis P-tau has emerged as an early etiological driver, blood marker and therapeutic target for multiple neurodegenerative diseases, with clinical trials ongoing. The discovery of cis P-tau and other tau pathologies in VCID and PE calls attention for simplistic classification of tauopathy in neurodegenerative diseases. These recent advances have revealed the exciting novel role of the Pin1-cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia.
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Affiliation(s)
- Chenxi Qiu
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Zhixiong Li
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry and Robarts Research Institute, Western University, London, ON, Canada
| | - David A. Leigh
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Joseph E. Stucky
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Nami Kim
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - George Xie
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry and Robarts Research Institute, Western University, London, ON, Canada
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry and Robarts Research Institute, Western University, London, ON, Canada
| | - Xiao Zhen Zhou
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry and Robarts Research Institute, Western University, London, ON, Canada
- Departments of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, and Lawson Health Research Institute, Western University, London, ON, Canada
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3
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Yao XQ, Hamelberg D. Dissecting the Allosteric Fine-Tuning of Enzyme Catalysis. JACS AU 2024; 4:837-846. [PMID: 38425926 PMCID: PMC10900222 DOI: 10.1021/jacsau.3c00806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Fully understanding the mechanism of allosteric regulation in biomolecules requires separating and examining all of the involved factors. In enzyme catalysis, allosteric effector binding shifts the structure and dynamics of the active site, leading to modified energetic (e.g., energy barrier) and dynamical (e.g., diffusion coefficient) factors underlying the catalyzed reaction rate. Such modifications can be subtle and dependent on the type of allosteric effector, representing a fine-tuning of protein function. The microscopic description of allosteric regulation at the level of function-dictating factors has prospective applications in fundamental and pharmaceutical sciences, which is, however, largely missing so far. Here, we characterize the allosteric fine-tuning of enzyme catalysis, using human Pin1 as an example, by performing more than half-millisecond all-atom molecular dynamics simulations. Changes of reaction kinetics and the dictating factors, including the free energy surface along the reaction coordinate and the diffusion coefficient of the reaction dynamics, under various enzyme and allosteric effector binding conditions are examined. Our results suggest equal importance of the energetic and dynamical factors, both of which can be modulated allosterically, and the combined effect determines the final allosteric output. We also reveal the potential dynamic basis for allosteric modulation using an advanced statistical technique to detect function-related conformational dynamics. Methods developed in this work can be applied to other allosteric systems.
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Affiliation(s)
- Xin-Qiu Yao
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Department
of Chemistry, University of Nebraska Omaha, Omaha, Nebraska 68182-0266, United
States
| | - Donald Hamelberg
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
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4
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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.
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5
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Chen J. A Specific pSer/Thr-Pro Motif Generates Interdomain Communication Bifurcations of Two Modes of Pin1 in Solution Nuclear Magnetic Resonance. Biochemistry 2022; 61:1167-1180. [PMID: 35648841 DOI: 10.1021/acs.biochem.2c00255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptides mediate the interdomain communication of Pin1 (peptidyl-prolyl cis-trans isomerase) and can regulate its conformation and biochemical functions, providing an idea for drug design using Pin1. Two template peptide sequences have been widely used in the extended or compact state of Pin1 (Cdc25C, E-Q-P-L-pT-P-V-T-D-L; Pintide, W-F-Y-pS-P-R). The way in which specific pSer/Thr-Pro peptides regulate interdomain communication to achieve the opposite state is not clear. In this study, we subdivided the sequence composition of eight types of modified peptides and investigated the interaction with Pin1 by solution nuclear magnetic resonance and molecular dynamics. Demonstrating sequence dependence on the pSer-Pro or pThr-Pro motif and different residues in anchoring the WW domain, the Pin peptide (Pintide, PintideT, Pin25C, and Pin25CT) transmits this concentration accumulation to the PPIase domain, thus exhibiting two anchoring tendencies. However, the Cdc peptide (Cdc25C, Cdc25CS, Cdctide, and CdctideS) has a low binding energy that makes it difficult for the conformation to reach a steady state. In addition, Pin1 is influenced by both compact and extended states, regulated precisely by the sequence as well as by threonine or serine. These results provide new insight into the interdomain communication of Pin1 via pSer/Thr-Pro peptide binding.
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Affiliation(s)
- Jingqiu Chen
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan
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6
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When Good Kinases Go Rogue: GSK3, p38 MAPK and CDKs as Therapeutic Targets for Alzheimer's and Huntington's Disease. Int J Mol Sci 2021; 22:ijms22115911. [PMID: 34072862 PMCID: PMC8199025 DOI: 10.3390/ijms22115911] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD) is a mostly sporadic brain disorder characterized by cognitive decline resulting from selective neurodegeneration in the hippocampus and cerebral cortex whereas Huntington's disease (HD) is a monogenic inherited disorder characterized by motor abnormalities and psychiatric disturbances resulting from selective neurodegeneration in the striatum. Although there have been numerous clinical trials for these diseases, they have been unsuccessful. Research conducted over the past three decades by a large number of laboratories has demonstrated that abnormal actions of common kinases play a key role in the pathogenesis of both AD and HD as well as several other neurodegenerative diseases. Prominent among these kinases are glycogen synthase kinase (GSK3), p38 mitogen-activated protein kinase (MAPK) and some of the cyclin-dependent kinases (CDKs). After a brief summary of the molecular and cell biology of AD and HD this review covers what is known about the role of these three groups of kinases in the brain and in the pathogenesis of the two neurodegenerative disorders. The potential of targeting GSK3, p38 MAPK and CDKS as effective therapeutics is also discussed as is a brief discussion on the utilization of recently developed drugs that simultaneously target two or all three of these groups of kinases. Multi-kinase inhibitors either by themselves or in combination with strategies currently being used such as immunotherapy or secretase inhibitors for AD and knockdown for HD could represent a more effective therapeutic approach for these fatal neurodegenerative diseases.
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7
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Namitz KEW, Zheng T, Canning AJ, Alicea-Velazquez NL, Castañeda CA, Cosgrove MS, Hanes SD. Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism. Commun Biol 2021; 4:398. [PMID: 33767358 PMCID: PMC7994582 DOI: 10.1038/s42003-021-01906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Accurate gene transcription in eukaryotes depends on isomerization of serine-proline bonds within the carboxy-terminal domain (CTD) of RNA polymerase II. Isomerization is part of the "CTD code" that regulates recruitment of proteins required for transcription and co-transcriptional RNA processing. Saccharomyces cerevisiae Ess1 and its human ortholog, Pin1, are prolyl isomerases that engage the long heptad repeat (YSPTSPS)26 of the CTD by an unknown mechanism. Here, we used an integrative structural approach to decipher Ess1 interactions with the CTD. Ess1 has a rigid linker between its WW and catalytic domains that enforces a distance constraint for bivalent interaction with the ends of long CTD substrates (≥4-5 heptad repeats). Our binding results suggest that the Ess1 WW domain anchors the proximal end of the CTD substrate during isomerization, and that linker divergence may underlie evolution of substrate specificity.
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Affiliation(s)
- Kevin E. W. Namitz
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.29857.310000 0001 2097 4281Present Address: Department of Chemistry, Pennsylvania State University, University Park, PA USA
| | - Tongyin Zheng
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Ashley J. Canning
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Nilda L. Alicea-Velazquez
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.247980.00000 0001 2184 3689Present Address: Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT USA
| | - Carlos A. Castañeda
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Michael S. Cosgrove
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Steven D. Hanes
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
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8
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Papin S, Paganetti P. Emerging Evidences for an Implication of the Neurodegeneration-Associated Protein TAU in Cancer. Brain Sci 2020; 10:brainsci10110862. [PMID: 33207722 PMCID: PMC7696480 DOI: 10.3390/brainsci10110862] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative disorders and cancer may appear unrelated illnesses. Yet, epidemiologic studies indicate an inverse correlation between their respective incidences for specific cancers. Possibly explaining these findings, increasing evidence indicates that common molecular pathways are involved, often in opposite manner, in the pathogenesis of both disease families. Genetic mutations in the MAPT gene encoding for TAU protein cause an inherited form of frontotemporal dementia, a neurodegenerative disorder, but also increase the risk of developing cancer. Assigning TAU at the interface between cancer and neurodegenerative disorders, two major aging-linked disease families, offers a possible clue for the epidemiological observation inversely correlating these human illnesses. In addition, the expression level of TAU is recognized as a prognostic marker for cancer, as well as a modifier of cancer resistance to chemotherapy. Because of its microtubule-binding properties, TAU may interfere with the mechanism of action of taxanes, a class of chemotherapeutic drugs designed to stabilize the microtubule network and impair cell division. Indeed, a low TAU expression is associated to a better response to taxanes. Although TAU main binding partners are microtubules, TAU is able to relocate to subcellular sites devoid of microtubules and is also able to bind to cancer-linked proteins, suggesting a role of TAU in modulating microtubule-independent cellular pathways associated to oncogenesis. This concept is strengthened by experimental evidence linking TAU to P53 signaling, DNA stability and protection, processes that protect against cancer. This review aims at collecting literature data supporting the association between TAU and cancer. We will first summarize the evidence linking neurodegenerative disorders and cancer, then published data supporting a role of TAU as a modifier of the efficacy of chemotherapies and of the oncogenic process. We will finish by addressing from a mechanistic point of view the role of TAU in de-regulating critical cancer pathways, including the interaction of TAU with cancer-associated proteins.
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Affiliation(s)
- Stéphanie Papin
- Neurodegeneration Research Group, Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Ente Ospedaliero Cantonale, Via ai Söi 24, CH-6807 Torricella-Taverne, Switzerland;
| | - Paolo Paganetti
- Neurodegeneration Research Group, Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Ente Ospedaliero Cantonale, Via ai Söi 24, CH-6807 Torricella-Taverne, Switzerland;
- Faculty of Biomedical Neurosciences, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
- Correspondence: ; Tel.: +41-91-811-7250
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9
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Schwarz DC, Williams SK, Dillenburg M, Wagner CR, Gestwicki JE. A Phosphoramidate Strategy Enables Membrane Permeability of a Non-nucleotide Inhibitor of the Prolyl Isomerase Pin1. ACS Med Chem Lett 2020; 11:1704-1710. [PMID: 32944137 PMCID: PMC7488286 DOI: 10.1021/acsmedchemlett.0c00170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
The membrane permeability of nucleotide-based drugs, such as sofosbuvir (Sovaldi), requires installation of phosphate-caging groups. One strategy, termed "ProTide", masks the anionic phosphate through an N-linked amino ester and an O-linked aromatic phospho-ester, such that release of the active drug requires consecutive enzymatic liberation by an esterase and then a phosphoramidase, such as Hint1. Because Hint1 is known to be selective for nucleotides, it was not clear if the ProTide approach could be deployed for non-nucleotides. Here, we demonstrate that caging of a phosphate-containing inhibitor of the prolyl isomerase Pin1 increases its permeability. Moreover, this compound was processed by both esterase and phosphoramidase activity, releasing the active molecule to bind and inhibit Pin1 in cells. Thus, Hint1 appears to recognize a broader set of substrates than previously appreciated. It seems possible that other potent, but impermeable, phosphate-containing inhibitors might likewise benefit from this approach.
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Affiliation(s)
- Daniel
M. C. Schwarz
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Sarah K. Williams
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Maxwell Dillenburg
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R. Wagner
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason E. Gestwicki
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
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10
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Wang L, Zhou Y, Chen D, Lee TH. Peptidyl-Prolyl Cis/Trans Isomerase Pin1 and Alzheimer's Disease. Front Cell Dev Biol 2020; 8:355. [PMID: 32500074 PMCID: PMC7243138 DOI: 10.3389/fcell.2020.00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of dementia with cognitive decline. The neuropathology of AD is characterized by intracellular aggregation of neurofibrillary tangles consisting of hyperphosphorylated tau and extracellular deposition of senile plaques composed of beta-amyloid peptides derived from amyloid precursor protein (APP). The peptidyl-prolyl cis/trans isomerase Pin1 binds to phosphorylated serine or threonine residues preceding proline and regulates the biological functions of its substrates. Although Pin1 is tightly regulated under physiological conditions, Pin1 deregulation in the brain contributes to the development of neurodegenerative diseases, including AD. In this review, we discuss the expression and regulatory mechanisms of Pin1 in AD. We also focus on the molecular mechanisms by which Pin1 controls two major proteins, tau and APP, after phosphorylation and their signaling cascades. Moreover, the major impact of Pin1 deregulation on the progression of AD in animal models is discussed. This information will lead to a better understanding of Pin1 signaling pathways in the brain and may provide therapeutic options for the treatment of AD.
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Affiliation(s)
- Long Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Ying Zhou
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases of Fujian Provincial Universities and Colleges, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Dongmei Chen
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Tae Ho Lee
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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11
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Delgado JY. An Alternative Pin1 Binding and Isomerization Site in the N-Terminus Domain of PSD-95. Front Mol Neurosci 2020; 13:31. [PMID: 32256312 PMCID: PMC7094161 DOI: 10.3389/fnmol.2020.00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/11/2020] [Indexed: 11/13/2022] Open
Abstract
Phosphorylation-dependent peptidyl-prolyl cis-trans isomerization plays key roles in cell cycle progression, the pathogenesis of cancer, and age-related neurodegeneration. Most of our knowledge about the role of phosphorylation-dependent peptidyl-prolyl cis-trans isomerization and the enzyme catalyzing this reaction, the peptidyl-prolyl isomerase (Pin1), is largely limited to proteins not present in neurons. Only a handful of examples have shown that phosphorylation-dependent peptidyl-prolyl cis-trans isomerization, Pin1 binding, or Pin1-mediated peptidyl-prolyl cis-trans isomerization regulate proteins present at excitatory synapses. In this work, I confirm previous findings showing that Pin1 binds postsynaptic density protein-95 (PSD-95) and identify an alternative binding site in the phosphorylated N-terminus of the PSD-95. Pin1 associates via its WW domain with phosphorylated threonine (T19) and serine (S25) in the N-terminus domain of PSD-95 and this association alters the local conformation of PSD-95. Most importantly, I show that proline-directed phosphorylation of the N-terminus domain of PSD-95 alters the local conformation of this region. Therefore, proline-directed phosphorylation of the N-terminus of PSD-95, Pin1 association, and peptidyl-prolyl cis-trans isomerization may all play a role in excitatory synaptic function and synapse development.
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Affiliation(s)
- Jary Y Delgado
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
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12
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Delgado JY, Nall D, Selvin PR. Pin1 Binding to Phosphorylated PSD-95 Regulates the Number of Functional Excitatory Synapses. Front Mol Neurosci 2020; 13:10. [PMID: 32231520 PMCID: PMC7082786 DOI: 10.3389/fnmol.2020.00010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
The post-synaptic density protein 95 (PSD-95) plays a central role in excitatory synapse development and synaptic plasticity. Phosphorylation of the N-terminus of PSD-95 at threonine 19 (T19) and serine 25 (S25) decreases PSD-95 stability at synapses; however, a molecular mechanism linking PSD-95 phosphorylation to altered synaptic stability is lacking. Here, we show that phosphorylation of T19/S25 recruits the phosphorylation-dependent peptidyl-prolyl cis-trans isomerase (Pin1) and reduces the palmitoylation of Cysteine 3 and Cysteine 5 in PSD-95. This reduction in PSD-95 palmitoylation accounts for the observed loss in the number of dendritic PSD-95 clusters, the increased AMPAR mobility, and the decreased number of functional excitatory synapses. We find the effects of Pin1 overexpression were all rescued by manipulations aimed at increasing the levels of PSD-95 palmitoylation. Therefore, Pin1 is a key signaling molecule that regulates the stability of excitatory synapses and may participate in the destabilization of PSD-95 following the induction of synaptic plasticity.
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Affiliation(s)
- Jary Y. Delgado
- Department of Neurobiology, The University of Chicago, Chicago, IL, United States
| | - Duncan Nall
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Paul R. Selvin
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Urbana, IL, United States
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13
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Yao XQ, Hamelberg D. Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis. Acc Chem Res 2019; 52:3455-3464. [PMID: 31793290 DOI: 10.1021/acs.accounts.9b00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances have made all-atom molecular dynamics (MD) a powerful tool to sample the conformational energy landscape. There are still however three major challenges in the application of MD to biological systems: accuracy of force field, time scale, and the analysis of simulation trajectories. Significant progress in addressing the first two challenges has been made and extensively reviewed previously. This Account focuses on strategies of analyzing simulation data of biomolecules that also covers ways to properly design simulations and validate simulation results. In particular, we examine an approach named comparative perturbed-ensembles analysis, which we developed to efficiently detect dynamics in protein MD simulations that can be linked to biological functions. In our recent studies, we implemented this approach to understand allosteric regulations in several disease-associated human proteins. The central task of a comparative perturbed-ensembles analysis is to compare two or more conformational ensembles of a system generated by MD simulations under distinct perturbation conditions. Perturbations can be different sequence variations, ligand-binding conditions, and other physical/chemical modifications of the system. Each simulation is long enough (e.g., microsecond-long) to ensure sufficient sampling of the local substate. Then, sophisticated bioinformatic and statistical tools are applied to extract function-related information from the simulation data, including principal component analysis, residue-residue contact analysis, difference contact network analysis (dCNA) based on the graph theory, and statistical analysis of side-chain conformations. Computational findings are further validated with experimental data. By comparing distinct conformational ensembles, functional micro- to millisecond dynamics can be inferred. In contrast, such a time scale is difficult to reach in a single simulation; even when reached for a single condition of a system, it is elusive as to what dynamical motions are related to functions without, for example, comparing free and substrate-bound proteins at the minimum. We illustrate our approach with three examples. First, we discuss using the approach to identify allosteric pathways in cyclophilin A (CypA), a member of a ubiquitous class of peptidyl-prolyl cis-trans isomerase enzymes. By comparing side-chain torsion-angle distributions of CypA in wild-type and mutant forms, we identified three pathways: two are consistent with recent nuclear magnetic resonance experiments, whereas the third is a novel pathway. Second, we show how the approach enables a dynamical-evolution analysis of the human cyclophilin family. In the analysis, both conserved and divergent conformational dynamics across three cyclophilin isoforms (CypA, CypD, and CypE) were summarized. The conserved dynamics led to the discovery of allosteric networks resembling those found in CypA. A residue wise determinant underlying the unique dynamics in CypD was also detected and validated with additional mutational MD simulations. In the third example, we applied the approach to elucidate a peptide sequence-dependent allosteric mechanism in human Pin 1, a phosphorylation-dependent peptidyl-prolyl isomerase. We finally present our outlook of future directions. Especially, we envisage how the approach could help open a new avenue in drug discovery.
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Affiliation(s)
- Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
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14
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Jinasena D, Simmons R, Gyamfi H, Fitzkee NC. Molecular Mechanism of the Pin1-Histone H1 Interaction. Biochemistry 2019; 58:788-798. [PMID: 30507159 DOI: 10.1021/acs.biochem.8b01036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pin1 is an essential peptidyl-prolyl isomerase (PPIase) that catalyzes cis-trans prolyl isomerization in proteins containing pSer/Thr-Pro motifs. It has an N-terminal WW domain that targets these motifs and a C-terminal PPIase domain that catalyzes isomerization. Recently, Pin1 was shown to modify the conformation of phosphorylated histone H1 and stabilize the chromatin-H1 interaction by increasing its residence time. This Pin1-histone H1 interaction plays a key role in pathogen response, in infection, and in cell cycle control; therefore, anti-Pin1 therapeutics are an important focus for treating infections as well as cancer. Each of the H1 histones (H1.0-H1.5) contains several potential Pin1 recognition pSer/pThr-Pro motifs. To understand the Pin1-histone H1 interaction fully, we investigated how both the isolated WW domain and full-length Pin1 interact with three H1 histone substrate peptide sequences that were previously identified as important binding partners (H1.1, H1.4, and H1.5). NMR spectroscopy was used to measure the binding affinities and the interdomain dynamics upon binding to these sequences. We observed different KD values depending on the histone binding site, suggesting that energetics play a role in guiding the Pin1-histone interaction. While interdomain interactions vary between the peptides, we find no evidence for allosteric activation for the histone H1 substrates.
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Affiliation(s)
- Dinusha Jinasena
- Department of Chemistry , Mississippi State University , Mississippi State , Mississippi 39762 , United States
| | - Robert Simmons
- Department of Chemistry , Mississippi State University , Mississippi State , Mississippi 39762 , United States
| | - Hawa Gyamfi
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Ontario N2l 3G1 , Canada
| | - Nicholas C Fitzkee
- Department of Chemistry , Mississippi State University , Mississippi State , Mississippi 39762 , United States
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15
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Danis C, Dupré E, Hanoulle X, Landrieu I, Lasorsa A, Neves JF, Schneider R, Smet-Nocca C. Nuclear Magnetic Resonance Spectroscopy Insights into Tau Structure in Solution: Impact of Post-translational Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1184:35-45. [PMID: 32096026 DOI: 10.1007/978-981-32-9358-8_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although Tau is an intrinsically disordered protein, some level of structure can still be defined, corresponding to short stretches of dynamic secondary structures and a preferential global fold described as an ensemble of conformations. These structures can be modified by Tau phosphorylation, and potentially other post-translational modifications. The analytical capacity of Nuclear Magnetic Resonance (NMR) spectroscopy provides the advantage of offering a residue-specific view of these modifications, allowing to link specific sites to a particular structure. The cis or trans conformation of X-Proline peptide bonds is an additional characteristic parameter of Tau structure that is targeted and modified by prolyl cis/trans isomerases. The challenge in molecular characterization of Tau lies in being able to link structural parameters to functional consequences in normal functions and dysfunctions of Tau, including potential misfolding on the path to aggregation and/or perturbation of the interactions of Tau with its many molecular partners. Phosphorylation of Ser and Thr residues has the potential to impact the local and global structure of Tau.
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Affiliation(s)
- Clément Danis
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Elian Dupré
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Xavier Hanoulle
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Isabelle Landrieu
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
| | - Alessia Lasorsa
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - João Filipe Neves
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Robert Schneider
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Caroline Smet-Nocca
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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16
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Ikura T, Tochio N, Kawasaki R, Matsuzaki M, Narita A, Kikumoto M, Utsunomiya‐Tate N, Tate S, Ito N. The
trans
isomer of Tau peptide is prone to aggregate, and the WW domain of Pin1 drastically decreases its aggregation. FEBS Lett 2018; 592:3082-3091. [DOI: 10.1002/1873-3468.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Teikichi Ikura
- Medical Research Institute Tokyo Medical and Dental University Japan
| | - Naoya Tochio
- Reseach Center for the Mathematics on Chromatin Live Dynamics (RcMcD) Hiroshima University Higashi‐Hiroshima Japan
- Faculty of Pharma‐Sciences Teikyo University Tokyo Japan
| | - Ryosuke Kawasaki
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Higashi‐Hiroshima Japan
| | - Mizuki Matsuzaki
- Structural Biology Research Center Graduate School of Science Nagoya University Japan
| | - Akihiro Narita
- Structural Biology Research Center Graduate School of Science Nagoya University Japan
| | - Mahito Kikumoto
- Structural Biology Research Center Graduate School of Science Nagoya University Japan
| | | | - Shin‐ichi Tate
- Reseach Center for the Mathematics on Chromatin Live Dynamics (RcMcD) Hiroshima University Higashi‐Hiroshima Japan
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Higashi‐Hiroshima Japan
| | - Nobutoshi Ito
- Medical Research Institute Tokyo Medical and Dental University Japan
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17
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Pin1 Modulation in Physiological Status and Neurodegeneration. Any Contribution to the Pathogenesis of Type 3 Diabetes? Int J Mol Sci 2018; 19:ijms19082319. [PMID: 30096758 PMCID: PMC6121450 DOI: 10.3390/ijms19082319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/29/2022] Open
Abstract
Prolyl isomerases (Peptidylprolyl isomerase, PPIases) are enzymes that catalyze the isomerization between the cis/trans Pro conformations. Three subclasses belong to the class: FKBP (FK506 binding protein family), Cyclophilin and Parvulin family (Pin1 and Par14). Among Prolyl isomerases, Pin1 presents as distinctive feature, the ability of binding to the motif pSer/pThr-Pro that is phosphorylated by kinases. Modulation of Pin1 is implicated in cellular processes such as mitosis, differentiation and metabolism: The enzyme is dysregulated in many diverse pathological conditions, i.e., cancer progression, neurodegenerative (i.e., Alzheimer’s diseases, AD) and metabolic disorders (i.e., type 2 diabetes, T2D). Indeed, Pin1 KO mice develop a complex phenotype of premature aging, cognitive impairment in elderly mice and neuronal degeneration resembling that of the AD in humans. In addition, since the molecule modulates glucose homeostasis in the brain and peripherally, Pin1 KO mice are resistant to diet-induced obesity, insulin resistance, peripheral glucose intolerance and diabetic vascular dysfunction. In this review, we revise first critically the role of Pin1 in neuronal development and differentiation and then focus on the in vivo studies that demonstrate its pivotal role in neurodegenerative processes and glucose homeostasis. We discuss evidence that enables us to speculate about the role of Pin1 as molecular link in the pathogenesis of type 3 diabetes i.e., the clinical association of dementia/AD and T2D.
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18
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Momin M, Yao XQ, Thor W, Hamelberg D. Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1. J Phys Chem B 2018; 122:6521-6527. [DOI: 10.1021/acs.jpcb.8b03819] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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The role of prostate tumor overexpressed 1 in cancer progression. Oncotarget 2017; 8:12451-12471. [PMID: 28029646 PMCID: PMC5355357 DOI: 10.18632/oncotarget.14104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/14/2016] [Indexed: 12/15/2022] Open
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20
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Vöhringer-Martinez E, Dörner C. Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1. J Phys Chem B 2016; 120:12444-12453. [DOI: 10.1021/acs.jpcb.6b09187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Esteban Vöhringer-Martinez
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
| | - Ciro Dörner
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
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21
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Rogals MJ, Greenwood AI, Kwon J, Lu KP, Nicholson LK. Neighboring phosphoSer-Pro motifs in the undefined domain of IRAK1 impart bivalent advantage for Pin1 binding. FEBS J 2016; 283:4528-4548. [PMID: 27790836 DOI: 10.1111/febs.13943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023]
Abstract
The peptidyl prolyl isomerase Pin1 has two domains that are considered to be its binding (WW) and catalytic (PPIase) domains, both of which interact with phosphorylated Ser/Thr-Pro motifs. This shared specificity might influence substrate selection, as many known Pin1 substrates have multiple sequentially close phosphoSer/Thr-Pro motifs, including the protein interleukin-1 receptor-associated kinase-1 (IRAK1). The IRAK1 undefined domain (UD) contains two sets of such neighboring motifs (Ser131/Ser144 and Ser163/Ser173), suggesting possible bivalent interactions with Pin1. Using a series of NMR titrations with 15N-labeled full-length Pin1 (Pin1-FL), PPIase, or WW domain and phosphopeptides representing the Ser131/Ser144 and Ser163/Ser173 regions of IRAK1-UD, bivalent interactions were investigated. Binding studies using singly phosphorylated peptides showed that individual motifs displayed weak affinities (> 100 μm) for Pin1-FL and each isolated domain. Analysis of dually phosphorylated peptides binding to Pin1-FL showed that inclusion of bivalent states was necessary to fit the data. The resulting complex model and fitted parameters were applied to predict the impact of bivalent states at low micromolar concentrations, demonstrating significant affinity enhancement for both dually phosphorylated peptides (3.5 and 24 μm for peptides based on the Ser131/Ser144 and Ser163/Ser173 regions, respectively). The complementary technique biolayer interferometry confirmed the predicted affinity enhancement for a representative set of singly and dually phosphorylated Ser131/Ser144 peptides at low micromolar concentrations, validating model predictions. These studies provide novel insights regarding the complexity of interactions between Pin1 and activated IRAK1, and more broadly suggest that phosphorylation of neighboring Ser/Thr-Pro motifs in proteins might provide competitive advantage at cellular concentrations for engaging with Pin1.
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Affiliation(s)
- Monique J Rogals
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Alexander I Greenwood
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, IL, USA
| | - Jeahoo Kwon
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Kun Ping Lu
- Division of Translational Therapeutics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
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22
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Dunyak BM, Gestwicki JE. Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds. J Med Chem 2016; 59:9622-9644. [PMID: 27409354 DOI: 10.1021/acs.jmedchem.6b00411] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptidyl-proline isomerases (PPIases) are a chaperone superfamily comprising the FK506-binding proteins (FKBPs), cyclophilins, and parvulins. PPIases catalyze the cis/trans isomerization of proline, acting as a regulatory switch during folding, activation, and/or degradation of many proteins. These "clients" include proteins with key roles in cancer, neurodegeneration, and psychiatric disorders, suggesting that PPIase inhibitors could be important therapeutics. However, the active site of PPIases is shallow, solvent-exposed, and well conserved between family members, making selective inhibitor design challenging. Despite these hurdles, macrocyclic natural products, including FK506, rapamycin, and cyclosporin, bind PPIases with nanomolar or better affinity. De novo attempts to derive new classes of inhibitors have been somewhat less successful, often showcasing the "undruggable" features of PPIases. Interestingly, the most potent of these next-generation molecules tend to integrate features of the natural products, including macrocyclization or proline mimicry strategies. Here, we review recent developments and ongoing challenges in the inhibition of PPIases, with a focus on how natural products might inform the creation of potent and selective inhibitors.
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Affiliation(s)
- Bryan M Dunyak
- Department of Biological Chemistry, University of Michigan Medical School , 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States.,Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
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