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Kober DL, Stuchell-Brereton MD, Kluender CE, Dean HB, Strickland MR, Steinberg DF, Nelson SS, Baban B, Holtzman DM, Frieden C, Alexander-Brett J, Roberson ED, Song Y, Brett TJ. Functional insights from biophysical study of TREM2 interactions with apoE and Aβ 1-42. Alzheimers Dement 2020; 17:10.1002/alz.12194. [PMID: 33090700 PMCID: PMC8026773 DOI: 10.1002/alz.12194] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Triggering receptor expressed on myeloid cells-2 (TREM2) is an immune receptor expressed on microglia that also can become soluble (sTREM2). How TREM2 engages different ligands remains poorly understood. METHODS We used comprehensive biolayer interferometry (BLI) analysis to investigate TREM2 and sTREM2 interactions with apolipoprotein E (apoE) and monomeric amyloid beta (Aβ) (mAβ42). RESULTS TREM2 engagement of apoE was protein mediated with little effect of lipidation, showing slight affinity differences between isoforms (E4 > E3 > E2). Another family member, TREML2, did not bind apoE. Disease-linked TREM2 variants within a "basic patch" minimally impact apoE binding. Instead, TREM2 uses a unique hydrophobic surface to bind apoE, which requires the apoE hinge region. TREM2 and sTREM2 directly bind mAβ42 and potently inhibit Aβ42 polymerization, suggesting a potential role for soluble sTREM2 in preventing AD pathogenesis. DISCUSSION These findings demonstrate that TREM2 has at least two ligand-binding surfaces that might be therapeutic targets and uncovers a potential function for sTREM2 in directly inhibiting Aβ polymerization.
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Affiliation(s)
- Daniel L. Kober
- Molecular Microbiology and Microbial Pathogenesis Program, Washington University School of Medicine, St. Louis, Missouri 63110
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Melissa D. Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Colin E. Kluender
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
- Biochemistry, Biophysics, and Structural Biology Program, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Hunter B. Dean
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer’s Disease Center, Departments of Neurology and Neurobiology, University of Alabama at Birmingham, AL 35294
- Department of Biomedical Engineering, University of Alabama at Birmingham, AL 35294
| | - Michael R. Strickland
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Deborah F. Steinberg
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Samantha S. Nelson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Berevan Baban
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - David M. Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, Missouri 63110
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jennifer Alexander-Brett
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Erik D. Roberson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer’s Disease Center, Departments of Neurology and Neurobiology, University of Alabama at Birmingham, AL 35294
| | - Yuhua Song
- Department of Biomedical Engineering, University of Alabama at Birmingham, AL 35294
| | - Tom J. Brett
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110
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Barton M, Santucci-Pereira J, Vaccaro OG, Nguyen T, Su Y, Russo J. BC200 overexpression contributes to luminal and triple negative breast cancer pathogenesis. BMC Cancer 2019; 19:994. [PMID: 31646972 PMCID: PMC6813071 DOI: 10.1186/s12885-019-6179-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/20/2019] [Indexed: 01/04/2023] Open
Abstract
Background Long non coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that are not translated into proteins, but regulate the transcription of genes involved in different cellular processes, including cancer. Epidemiological analyses have demonstrated that parous women have a decreased risk of developing breast cancer in postmenopausal years if they went through a full term pregnancy in their early twenties. We here provide evidence of the role of BC200 in breast cancer and, potentially, in pregnancy’s preventive effect in reducing the lifetime risk of developing breast cancer. Methods Transcriptome analysis of normal breast of parous and nulliparous postmenopausal women revealed that several lncRNAs are differentially expressed in the parous breast. RNA sequencing of healthy postmenopausal breast tissue biopsies from eight parous and eight nulliparous women showed that there are 42 novel lncRNAs differentially expressed between these two groups. Screening of several of these 42 lncRNAs by RT-qPCR in different breast cancer cell lines, provided evidence that one in particular, lncEPCAM (more commonly known as BC200), was a strong candidate involved in cancer progression. Proliferation, migration, invasion and xerograph studies confirmed this hypothesis. Results The poorly studied oncogenic BC200 was selected to be tested in vitro and in vivo to determine its relevance in breast cancer and also to provide us with an understanding of its role in the increased susceptibility of the nulliparous women to cancer. Our results show that BC200 is upregulated in nulliparous women, and breast cancer cells and tissue. The role of BC200 is not completely understood in any of the breast cancer subtypes. We here provide evidence that BC200 has a role in luminal breast cancer as well as in the triple negative breast cancer subtype. Conclusion When overexpressed in luminal and triple negative breast cancer cell lines, BC200 shows increased proliferation, migration, and invasion in vitro. In vivo, overexpression of BC200 increased tumor size. Although treatment for cancer using lncRNAs as targets is in its infancy, the advancement in knowledge and technology to study their relevance in disease could lead to the development of novel treatment and preventive strategies for breast cancer.
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Affiliation(s)
- Maria Barton
- Biochemistry Department, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA. .,The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA.
| | - Julia Santucci-Pereira
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Olivia G Vaccaro
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Theresa Nguyen
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Yanrong Su
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
| | - Jose Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
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Wang L, Holmes RP, Peng JB. Modeling the structural and dynamical changes of the epithelial calcium channel TRPV5 caused by the A563T variation based on the structure of TRPV6. J Biomol Struct Dyn 2018; 37:3506-3512. [PMID: 30175942 DOI: 10.1080/07391102.2018.1518790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
TRPV5, transient receptor potential cation channel vanilloid subfamily member 5, is an epithelial Ca2+ channel that plays a key role in the active Ca2+ reabsorption process in the kidney. A single nucleotide polymorphism (SNP) rs4252499 in the TRPV5 gene results in an A563T variation in the sixth transmembrane (TM) domain of TRPV5. Our previous study indicated that this variation increases the Ca2+ transport function of TRPV5. To understand the molecular mechanism, a model of TRPV5 was established based on the newly deposited structure of TRPV6 that has 83.1% amino acid identity with TRPV5 in the modeled region. Computational simulations were performed to study the structural and dynamical differences between the TRPV5 variants with A563 and T563. Consistent with the TRPV1-based simulation, the results indicate that the A563T variation increases the contacts between residues 563 and V540, which is one residue away from the key residue D542 in the Ca2+-selective filter. The variation enhanced the stability of the secondary structure of the pore region, decreased the fluctuation of residues around residue 563, and reduced correlated and anti-correlated motion between monomers. Furthermore, the variation increases the pore radius at the selective filter. These findings were confirmed using simulations based on the recently determined structure of rabbit TRPV5. The simulation results provide an explanation for the observation of enhanced Ca2+ influx in TRPV5 caused by the A563T variation. The A563T variation is an interesting example of how a residue distant from the Ca2+-selective filter influences the Ca2+ transport function of the TRPV5 channel. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lingyun Wang
- a Department of Medicine, Division of Nephrology , Nephrology Research and Training Center, University of Alabama at Birmingham , Birmingham , AL , USA
| | - Ross P Holmes
- b Department of Urology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Ji-Bin Peng
- a Department of Medicine, Division of Nephrology , Nephrology Research and Training Center, University of Alabama at Birmingham , Birmingham , AL , USA.,b Department of Urology , University of Alabama at Birmingham , Birmingham , AL , USA
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Bouillot S, Reboud E, Huber P. Functional Consequences of Calcium Influx Promoted by Bacterial Pore-Forming Toxins. Toxins (Basel) 2018; 10:toxins10100387. [PMID: 30257425 PMCID: PMC6215193 DOI: 10.3390/toxins10100387] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/14/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023] Open
Abstract
Bacterial pore-forming toxins induce a rapid and massive increase in cytosolic Ca2+ concentration due to the formation of pores in the plasma membrane and/or activation of Ca2+-channels. As Ca2+ is an essential messenger in cellular signaling, a sustained increase in Ca2+ concentration has dramatic consequences on cellular behavior, eventually leading to cell death. However, host cells have adapted mechanisms to protect against Ca2+ intoxication, such as Ca2+ efflux and membrane repair. The final outcome depends upon the nature and concentration of the toxin and on the cell type. This review highlights the repercussions of Ca2+ overload on the induction of cell death, repair mechanisms, cellular adhesive properties, and the inflammatory response.
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Affiliation(s)
- Stéphanie Bouillot
- Université Grenoble Alpes, CNRS ERL5261, CEA BIG-BCI, INSERM UMR1036, Grenoble 38054, France.
| | - Emeline Reboud
- Université Grenoble Alpes, CNRS ERL5261, CEA BIG-BCI, INSERM UMR1036, Grenoble 38054, France.
| | - Philippe Huber
- Université Grenoble Alpes, CNRS ERL5261, CEA BIG-BCI, INSERM UMR1036, Grenoble 38054, France.
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Wang L, Yan F. Trans and Cis Conformations of the Antihypertensive Drug Valsartan Respectively Lock the Inactive and Active-like States of Angiotensin II Type 1 Receptor: A Molecular Dynamics Study. J Chem Inf Model 2018; 58:2123-2130. [DOI: 10.1021/acs.jcim.8b00364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Feng Yan
- School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin 300387, People’s Republic of China
- State Key Laboratory of Separation Membranes and Membrane Processes, Tianjin Polytechnic University, Tianjin 300387, People’s Republic of China
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Fancy RM, Kim H, Napier T, Buchsbaum DJ, Zinn KR, Song Y. Calmodulin antagonist enhances DR5-mediated apoptotic signaling in TRA-8 resistant triple negative breast cancer cells. J Cell Biochem 2018; 119:6216-6230. [PMID: 29663486 DOI: 10.1002/jcb.26848] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 03/09/2018] [Indexed: 01/25/2023]
Abstract
Patients with triple negative breast cancer (TNBC) have no successful "targeted" treatment modality, which represents a priority for novel therapy strategies. Upregulated death receptor 5 (DR5) expression levels in breast cancer cells compared to normal cells enable TRA-8, a DR5 specific agonistic antibody, to specifically target malignant cells for apoptosis without inducing normal hepatocyte apoptosis. Drug resistance is a common obstacle in TRAIL-based therapy for TNBC. Calmodulin (CaM) is overexpressed in breast cancer. In this study, we characterized the novel function of CaM antagonist in enhancing TRA-8 induced cytotoxicity in TRA-8 resistant TNBC cells and its underlying molecular mechanisms. Results demonstrated that CaM antagonist(s) enhanced TRA-8 induced cytotoxicity in a concentration and time-dependent manner for TRA-8 resistant TNBC cells. CaM directly bound to DR5 in a Ca2+ dependent manner, and CaM siRNA promoted DR5 recruitment of FADD and caspase-8 for DISC formation and TRA-8 activated caspase cleavage for apoptosis in TRA-8 resistant TNBC cells. CaM antagonist, trifluoperazine, enhanced TRA-8 activated DR5 oligomerization, DR5-mediated DISC formation, and TRA-8 activated caspase cleavage for apoptosis, and decreased anti-apoptotic pERK, pAKT, XIAP, and cIAP-1 expression in TRA-8 resistant TNBC cells. These results suggest that CaM could be a key regulator to mediate DR5-mediated apoptotic signaling, and suggests a potential strategy for using CaM antagonists to overcome drug resistance of TRAIL-based therapy for TRA-8 resistant TNBC.
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Affiliation(s)
- Romone M Fancy
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Harrison Kim
- Department of Radiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tiara Napier
- Hospital, University of Alabama at Birmingham, Birmingham, Alabama
| | - Donald J Buchsbaum
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kurt R Zinn
- Department of Radiology, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Radiology and Biomedical Engineering, Michigan State University, East Lansing, Michigan
| | - Yuhua Song
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
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Wang L, Murphy-Ullrich JE, Song Y. Multiscale simulation of the interaction of calreticulin-thrombospondin-1 complex with a model membrane microdomain. J Biomol Struct Dyn 2018; 37:811-822. [PMID: 29380675 DOI: 10.1080/07391102.2018.1433065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell surface calreticulin (CRT) binding to thrombospondin-1 (TSP1), regulates cell adhesion, migration, anoikis resistance, and collagen production. Due to the essential role of membrane microdomains in CRT-mediated focal adhesion disassembly, we previously studied the effect of raft-like bilayers on TSP1-CRT interactions with all-atom molecular dynamics (AAMD) simulations. However, the simulated systems of protein on the surface of the bilayer(s) in the explicit solvent are too large for long timescale AAMD simulations due to computational expense. In this study, we adopted a multiscale modeling approach of combining AAMD, coarse-grained molecule dynamics (CGMD), and reversed AAMD (REV AAMD) simulations to investigate the interactions of single CRT or of the TSP1-CRT complex with a membrane microdomain at microsecond timescale. Results showed that CRT conformational stabilization by binding of TSP1 in AAMD simulation was undetectable in CGMD simulation, but it was recovered in REV AAMD simulation. Similarly, interactions of the CRT N-domain and TSP1 with the membrane microdomain were lost in CGMD simulations but they were re-gained in the REV AAMD simulations. There was the higher coordination of the CRT P-domain in the TSP1-CRT complex with the lipid components of membrane microdomain compared to that of single CRT, which could directly affect the conformation of CRT and further mediate CRT recruitment of LDL receptor-related protein for signaling events. This study provides structural and molecular insights into TSP1-CRT interactions in a membrane microdomain environment and demonstrates the feasibility of using multiscale simulations to investigate the interactions between protein and membrane microdomains at a long timescale.
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Affiliation(s)
- Lingyun Wang
- a Department of Biomedical Engineering , The University of Alabama at Birmingham , Birmingham 35294 , AL , USA
| | - Joanne E Murphy-Ullrich
- b Department of Pathology , The University of Alabama at Birmingham , Birmingham 35294 , AL , USA
| | - Yuhua Song
- a Department of Biomedical Engineering , The University of Alabama at Birmingham , Birmingham 35294 , AL , USA
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Molecular insights into the specific recognition between the RNA binding domain qRRM2 of hnRNP F and G-tract RNA: A molecular dynamics study. Biochem Biophys Res Commun 2017; 494:95-100. [PMID: 29050934 DOI: 10.1016/j.bbrc.2017.10.078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/15/2017] [Indexed: 01/21/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein F (hnRNP F) controls the expression of various genes through regulating the alternative splicing of pre-mRNAs in the nucleus. It uses three quasi-RNA recognition motifs (qRRMs) to recognize G-tract RNA which contains at least three consecutive guanines. The structures containing qRRMs of hnRNP F in complex with G-tract RNA have been determined by nuclear magnetic resonance (NMR) spectroscopy, shedding light on the recognition mechanism of qRRMs with G-tract RNA. However, knowledge of the recognition details is still lacking. To investigate how qRRMs specifically bind with G-tract RNA and how the mutations of any guanine to an adenine in the G-tract affect the binding, molecular dynamics simulations with binding free energy analysis were performed based on the NMR structure of qRRM2 in complex with G-tract RNA. Simulation results demonstrate that qRRM2 binds strongly with G-tract RNA, but any mutation of the G-tract leads to a drastic reduction of the binding free energy. Further comparisons of the energetic components reveal that van der Waals and non-polar interactions play essential roles in the binding between qRRM2 and G-tract RNA, but the interactions are weakened by the effect of RNA mutations. Structural and dynamical analyses indicate that when qRRM2 binds with G-tract RNA, both qRRM2 and G-tract maintain stabilized structures and dynamics; however, the stability is disrupted by the mutations of the G-tract. These results provide novel insights into the recognition mechanism of qRRM2 with G-tract RNA that are not elucidated by the NMR technique.
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Wang L, Holmes RP, Peng JB. The L530R variation associated with recurrent kidney stones impairs the structure and function of TRPV5. Biochem Biophys Res Commun 2017; 492:362-367. [PMID: 28847730 DOI: 10.1016/j.bbrc.2017.08.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/17/2023]
Abstract
TRPV5 is a Ca2+-selective channel that plays a key role in the reabsorption of Ca2+ ions in the kidney. Recently, a rare L530R variation (rs757494578) of TRPV5 was found to be associated with recurrent kidney stones in a founder population. However, it was unclear to what extent this variation alters the structure and function of TRPV5. To evaluate the function and expression of the TRPV5 variant, Ca2+ uptake in Xenopus oocytes and western blot analysis were performed. The L530R variation abolished the Ca2+ uptake activity of TRPV5 in Xenopus oocytes. The variant protein was expressed with drastic reduction in complex glycosylation. To assess the structural effects of this L530R variation, TRPV5 was modeled based on the crystal structure of TRPV6 and molecular dynamics simulations were carried out. Simulation results showed that the L530R variation disrupts the hydrophobic interaction between L530 and L502, damaging the secondary structure of transmembrane domain 5. The variation also alters its interaction with membrane lipid molecules. Compared to the electroneutral L530, the positively charged R530 residue shifts the surface electrostatic potential towards positive. R530 is attracted to the negatively charged phosphate group rather than the hydrophobic carbon atoms of membrane lipids. This shifts the pore helix where R530 is located and the D542 residue in the Ca2+-selective filter towards the surface of the membrane. These alterations may lead to misfolding of TRPV5, reduction in translocation of the channel to the plasma membrane and/or impaired Ca2+ transport function of the channel, and ultimately disrupt TRPV5-mediated Ca2+ reabsorption.
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Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ross P Holmes
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ji-Bin Peng
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Urology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Wang L, Yan F. Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: A molecular dynamics study. Protein Sci 2017; 26:2010-2020. [PMID: 28726316 DOI: 10.1002/pro.3239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/11/2017] [Accepted: 07/12/2017] [Indexed: 01/01/2023]
Abstract
Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn2+ ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn2+ ions and the other terminally coordinated with one of the Mn2+ ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn2+ ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor.
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Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Feng Yan
- School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin, 300387, P. R. China
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Wang L, Pan D, Yan Q, Song Y. Activation mechanisms of αVβ3 integrin by binding to fibronectin: A computational study. Protein Sci 2017; 26:1124-1137. [PMID: 28340512 PMCID: PMC5441423 DOI: 10.1002/pro.3163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/13/2017] [Accepted: 03/19/2017] [Indexed: 01/29/2023]
Abstract
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn2+ -bound integrin αVβ3 by binding to fibronectin with molecular dynamics simulations. Results showed that fibronectin binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3. The angle of Propeller domain with respect to the Calf-2 domain of αV subunit and the angle of Hybrid domain with respect to βA domain of β3 subunit significantly increased when integrin αVβ3 was bound to fibronectin. These changes could result in the conformational change tendency of αVβ3 from a bend conformation to an extended conformation and lead to the open swing of Hybrid domain relative to βA domain of β3 subunit, which have demonstrated their importance for αVβ3 activation. Fibronectin binding to integrin αVβ3 significantly decreased the relative position of α1 helix to βA domain and that to metal ion-dependent adhesion site, stabilized Mn2+ ions binding in integrin αVβ3 and changed fibronectin conformation, which are important for αVβ3 activation. Results from this study provide important molecular insight into the "outside-in" activation mechanism of integrin αVβ3 by binding to fibronectin.
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Affiliation(s)
- Lingyun Wang
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
| | - Di Pan
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
| | - Qi Yan
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
| | - Yuhua Song
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
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12
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Fancy RM, Kim H, Zhou T, Zinn KR, Buchsbaum DJ, Song Y. Calmodulin Binding to Death Receptor 5-mediated Death-Inducing Signaling Complex in Breast Cancer Cells. J Cell Biochem 2017; 118:2285-2294. [PMID: 28092099 DOI: 10.1002/jcb.25882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/16/2016] [Indexed: 01/01/2023]
Abstract
Activation of death receptor-5 (DR5) leads to the formation of death-inducing signaling complex (DISC) for apoptotic signaling. TRA-8, a DR5 specific agonistic antibody, has demonstrated significant cytotoxic activity in vitro and in vivo without inducing hepatotoxicity. Calmodulin (CaM) that is overexpressed in breast cancer plays a critical role in regulating DR5-mediated apoptosis. However, the mechanism of CaM in regulating DR5-mediated apoptotic signaling remains unknown. In this study, we characterized CaM binding to DR5-mediated DISC for apoptosis in TRA-8 sensitive breast cancer cell lines using co-immunoprecipitation, fluorescence microscopic imaging, caspase signaling analysis, and cell viability assay. Results show that upon DR5 activation, CaM was recruited into DR5-mediated DISC in a calcium dependent manner. CaM antagonist, trifluoperazine (TFP), inhibited CaM recruitment into the DISC and attenuated DISC formation. DR5 oligomerization is critical for DISC formation for apoptosis. TFP decreased TRA-8 activated DR5 oligomerization, which was consistent with TFP's effect on DR5-mediated DISC formation. TFP and Ca2+ chelator, EGTA, impeded TRA-8-activated caspase-dependent apoptotic signaling, and TFP decreased TRA-8-induced cell cytotoxicity. These results demonstrated CaM binding to DR5-mediated DISC in a calcium dependent manner and may identify CaM as a key regulator of DR5-mediated DISC formation for apoptosis in breast cancer. J. Cell. Biochem. 118: 2285-2294, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Romone M Fancy
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham 35294, Alabama
| | - Harrison Kim
- Department of Radiology, The University of Alabama at Birmingham, Birmingham 35294, Alabama
| | - Tong Zhou
- Department of Medicine, The University of Alabama at Birmingham, Birmingham 35294, Alabama
| | - Kurt R Zinn
- Department of Radiology, The University of Alabama at Birmingham, Birmingham 35294, Alabama
| | - Donald J Buchsbaum
- Department of Radiation Oncology, The University of Alabama at Birmingham, Birmingham 35294, Alabama
| | - Yuhua Song
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham 35294, Alabama
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Wang L, Peng JB. Phosphorylation of KLHL3 at serine 433 impairs its interaction with the acidic motif of WNK4: a molecular dynamics study. Protein Sci 2016; 26:163-173. [PMID: 27727489 DOI: 10.1002/pro.3063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/09/2016] [Accepted: 10/09/2016] [Indexed: 12/17/2022]
Abstract
Interaction between the acidic motif (AM) of protein kinase WNK4 and the Kelch domain of KLHL3 are involved in the pathogenesis of pseudohypoaldosteronism type II, a hereditary form of hypertension. This interaction is disrupted by some disease-causing mutations in either WNK4 or KLHL3, or by angiotensin II- and insulin-induced phosphorylation of KLHL3 at serine 433, which is also a site frequently mutated in patients. However, the mechanism by which this phosphorylation disrupts the interaction is unclear. In this study, we approached this problem using molecular dynamics simulation with structural, dynamical and energetic analyses. Results from independent simulations indicate that when S433 was phosphorylated, the electrostatic potential became more negative in the AM binding site of KLHL3 and therefore was unfavorable for binding with the negatively charged AM. In addition, the intermolecular hydrogen bond network that kept the AM stable in the binding site of KLHL3 was disrupted, and the forces for the hydrophobic interactions between the AM of WNK4 and KLHL3 were also reduced. As a result, the weakened interactions were no longer capable of holding the AM of WNK4 at its binding site in KLHL3. In conclusion, phosphorylation of KLHL3 at S433 disrupts the hydrogen bonds, hydrophobic and electrostatic interactions between the Kelch domain of KLHL3 and the AM of WNK4. This study provides a key molecular understanding of the KLHL3-mediated regulation of WNK4, which is an integrative regulator of electrolyte homeostasis and blood pressure regulation in the kidney. Significances Statement: WNK4 is an integrative regulator of electrolyte homeostasis, which is important in the blood pressure regulation by the kidney. Interaction between WNK4 and KLHL3 is a key physiological process that is impaired in a hereditary form of hypertension. This study provides substantial new insights into the role of phosphorylation of KLHL3 in regulating the interaction with WNK4, and therefore advances our understanding of molecular pathogenesis of hypertension and the mechanism of blood pressure regulation.
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Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL, 35294
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- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, AL, 35294.,Department of Urology, University of Alabama at Birmingham, Birmingham, AL, 35294
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