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Weninger G, Miotto MC, Tchagou C, Reiken S, Dridi H, Brandenburg S, Riedemann GC, Yuan Q, Liu Y, Chang A, Wronska A, Lehnart SE, Marks AR. Structural insights into the regulation of RyR1 by S100A1. Proc Natl Acad Sci U S A 2024; 121:e2400497121. [PMID: 38917010 DOI: 10.1073/pnas.2400497121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
S100A1, a small homodimeric EF-hand Ca2+-binding protein (~21 kDa), plays an important regulatory role in Ca2+ signaling pathways involved in various biological functions including Ca2+ cycling and contractile performance in skeletal and cardiac myocytes. One key target of the S100A1 interactome is the ryanodine receptor (RyR), a huge homotetrameric Ca2+ release channel (~2.3 MDa) of the sarcoplasmic reticulum. Here, we report cryoelectron microscopy structures of S100A1 bound to RyR1, the skeletal muscle isoform, in absence and presence of Ca2+. Ca2+-free apo-S100A1 binds beneath the bridging solenoid (BSol) and forms contacts with the junctional solenoid and the shell-core linker of RyR1. Upon Ca2+-binding, S100A1 undergoes a conformational change resulting in the exposure of the hydrophobic pocket known to serve as a major interaction site of S100A1. Through interactions of the hydrophobic pocket with RyR1, Ca2+-bound S100A1 intrudes deeper into the RyR1 structure beneath BSol than the apo-form and induces sideways motions of the C-terminal BSol region toward the adjacent RyR1 protomer resulting in tighter interprotomer contacts. Interestingly, the second hydrophobic pocket of the S100A1-dimer is largely exposed at the hydrophilic surface making it prone to interactions with the local environment, suggesting that S100A1 could be involved in forming larger heterocomplexes of RyRs with other protein partners. Since S100A1 interactions stabilizing BSol are implicated in the regulation of RyR-mediated Ca2+ release, the characterization of the S100A1 binding site conserved between RyR isoforms may provide the structural basis for the development of therapeutic strategies regarding treatments of RyR-related disorders.
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Affiliation(s)
- Gunnar Weninger
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Marco C Miotto
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Carl Tchagou
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Steven Reiken
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Haikel Dridi
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Sören Brandenburg
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37075 Göttingen, Germany
| | - Gabriel C Riedemann
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Qi Yuan
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Yang Liu
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Alexander Chang
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Anetta Wronska
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37075 Göttingen, Germany
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
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Wang Q, DiForte C, Aleshintsev A, Elci G, Bhattacharya S, Bongiorno A, Gupta R. Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins. Protein Sci 2024; 33:e4955. [PMID: 38501487 PMCID: PMC10949321 DOI: 10.1002/pro.4955] [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: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024]
Abstract
Structure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II loop is the principal trigger for the conformational switch between 'closed' apo to the 'open' Ca2+ -bound conformation of the protein. Elimination of binding in S100-specific EF-I loop has limited impact on the calcium binding affinity of the EF-II loop and the concomitant structural rearrangement. In contrast, deletion of binding in the EF-II loop significantly attenuates calcium affinity in the EF-I loop and the structure adopts a 'closed' apo-like conformation. Analysis of experimental amide nitrogen (15 N) relaxation rates (R1 , R2 , and 15 N-{1 H} NOE) and molecular dynamics (MD) simulations demonstrate that the calcium bound state is relatively floppy with pico-nanosecond motions induced in functionally relevant domains responsible for target recognition such as the hinge domain and the C-terminal residues. Experimental relaxation studies combined with MD simulations show that while calcium binding in the EF-I loop alone does not induce significant motions in the polypeptide chain, EF-I regulates fluctuations in the polypeptide in the presence of bound calcium in the EF-II loop. These results offer novel insights into the dynamic regulation of target recognition by calcium binding and unravels the role of cooperativity between the two calcium binding events in S100A12.
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Affiliation(s)
- Qian Wang
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
| | - Christopher DiForte
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Aleksey Aleshintsev
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Gianna Elci
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
| | | | - Angelo Bongiorno
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Rupal Gupta
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
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3
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Liang H, Li J, Zhang K. Pathogenic role of S100 proteins in psoriasis. Front Immunol 2023; 14:1191645. [PMID: 37346040 PMCID: PMC10279876 DOI: 10.3389/fimmu.2023.1191645] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Psoriasis is a chronic inflammatory skin disease. The histopathological features of psoriasis include excessive proliferation of keratinocytes and infiltration of immune cells. The S100 proteins are a group of EF-hand Ca2+-binding proteins, including S100A2, -A7, -A8/A9, -A12, -A15, which expression levels are markedly upregulated in psoriatic skin. These proteins exert numerous functions such as serving as intracellular Ca2+ sensors, transduction of Ca2+ signaling, response to extracellular stimuli, energy metabolism, and regulating cell proliferation and apoptosis. Evidence shows a crucial role of S100 proteins in the development and progress of inflammatory diseases, including psoriasis. S100 proteins can possibly be used as potential therapeutic target and diagnostic biomarkers. This review focuses on the pathogenic role of S100 proteins in psoriasis.
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Affiliation(s)
- Huifang Liang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, Taiyuan, China
- State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, Taiyuan, China
| | - Junqin Li
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, Taiyuan, China
- State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, Taiyuan, China
| | - Kaiming Zhang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, Taiyuan, China
- State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Center Hospital, Taiyuan, China
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4
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Mahmood F, Xu R, Awan MUN, Jia T, Zhang T, Shi W, Liu M, Han Q, Zhu Q, Zhang Q, Song Y, Xia X, Zhang J. Transcriptomics based identification of S100A3 as the key anti-hepatitis B virus factor of 16F16. Biomed Pharmacother 2023; 163:114904. [PMID: 37207431 DOI: 10.1016/j.biopha.2023.114904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023] Open
Abstract
More than 250 million people worldwide have chronic hepatitis B virus (HBV) infections, resulting in over 1 million annual fatalities because HBV cannot be adequately treated with current antivirals. Hepatocellular carcinoma (HCC) risk is elevated in the presence of the HBV. Novel and powerful medications that specifically target the persistent viral components are needed to remove infection. This study aimed to use HepG2.2.15 cells and the rAAV-HBV1.3 C57BL/6 mouse model established in our laboratory to examine the effects of 16F16 on HBV. The transcriptome analysis of the samples was performed to examine the impact of 16F16 therapy on host factors. We found that the HBsAg and HBeAg levels significantly decreased in a dose-dependent manner following the 16F16 treatment. 16F16 also showed significant anti-hepatitis B effects in vivo. The transcriptome analysis showed that 16F16 regulated the expression of several proteins in HBV-producing HepG2.2.15 cells. As one of the differentially expressed genes, the role of S100A3 in the anti-hepatitis B process of 16F16 was further investigated. The expression of the S100A3 protein significantly decreased following the 16F16 therapy. And upregulation of S100A3 caused an upregulation of HBV DNA, HBsAg, and HBeAg in HepG2.2.15 cells. Similarly, knockdown of S100A3 significantly reduced the levels of HBsAg, HBeAg, and HBV DNA. Our findings proved that S100A3 might be a new target for combating HBV pathogenesis. 16F16 can target several proteins involved in HBV pathogenesis, and may be a promising drug precursor molecule for the treatment of HBV.
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Affiliation(s)
- Faisal Mahmood
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Ruixian Xu
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Maher Un Nisa Awan
- Laboratory of Molecular Neurobiology, Medical Faculty, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Ting Jia
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Taoping Zhang
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Wengang Shi
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Min Liu
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Qinqin Han
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Qianhua Zhu
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Qilin Zhang
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Yuzhu Song
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China.
| | - Xueshan Xia
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China.
| | - Jinyang Zhang
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China.
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5
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Young BD, Cook ME, Costabile BK, Samanta R, Zhuang X, Sevdalis SE, Varney KM, Mancia F, Matysiak S, Lattman E, Weber DJ. Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery. J Mol Biol 2022; 434:167872. [PMID: 36354074 PMCID: PMC10871162 DOI: 10.1016/j.jmb.2022.167872] [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: 05/26/2022] [Revised: 09/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
EF-hand Ca2+-binding proteins (CBPs), such as S100 proteins (S100s) and calmodulin (CaM), are signaling proteins that undergo conformational changes upon increasing intracellular Ca2+. Upon binding Ca2+, S100 proteins and CaM interact with protein targets and induce important biological responses. The Ca2+-binding affinity of CaM and most S100s in the absence of target is weak (CaKD > 1 μM). However, upon effector protein binding, the Ca2+ affinity of these proteins increases via heterotropic allostery (CaKD < 1 μM). Because of the high number and micromolar concentrations of EF-hand CBPs in a cell, at any given time, allostery is required physiologically, allowing for (i) proper Ca2+ homeostasis and (ii) strict maintenance of Ca2+-signaling within a narrow dynamic range of free Ca2+ ion concentrations, [Ca2+]free. In this review, mechanisms of allostery are coalesced into an empirical "binding and functional folding (BFF)" physiological framework. At the molecular level, folding (F), binding and folding (BF), and BFF events include all atoms in the biomolecular complex under study. The BFF framework is introduced with two straightforward BFF types for proteins (type 1, concerted; type 2, stepwise) and considers how homologous and nonhomologous amino acid residues of CBPs and their effector protein(s) evolved to provide allosteric tightening of Ca2+ and simultaneously determine how specific and relatively promiscuous CBP-target complexes form as both are needed for proper cellular function.
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Affiliation(s)
- Brianna D Young
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mary E Cook
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Riya Samanta
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Xinhao Zhuang
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Spiridon E Sevdalis
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kristen M Varney
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Silvina Matysiak
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Eaton Lattman
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - David J Weber
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA.
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6
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Immadisetty K, Sun B, Kekenes-Huskey PM. Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins. J Phys Chem B 2021; 125:6390-6405. [PMID: 34115511 DOI: 10.1021/acs.jpcb.1c01269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Members of the parvalbumin (PV) family of calcium (Ca2+) binding proteins (CBPs) share a relatively high level of sequence similarity. However, their Ca2+ affinities and selectivities against competing ions like Mg2+ can widely vary. We conducted molecular dynamics simulations of several α-parvalbumin (αPV) constructs with micromolar to nanomolar Ca2+ affinities to identify structural and dynamic features that contribute to their binding of ions. Specifically, we examined a D94S/G98E construct with a lower Ca2+ affinity (≈-18 kcal/mol) relative to the wild type (WT) (≈-22 kcal/mol) and an S55D/E59D variant with enhanced affinity (≈-24 kcal/mol). Additionally, we also examined the binding of Mg2+ to these isoforms, which is much weaker than Ca2+. We used mean spherical approximation (MSA) theory to evaluate ion binding thermodynamics within the proteins' EF-hand domains to account for the impact of ions' finite sizes and the surrounding electrolyte composition. While the MSA scores differentiated Mg2+ from Ca2+, they did not indicate that Ca2+ binding affinities at the binding loop differed between the PV isoforms. Instead, molecular mechanics generalized Born surface area (MM/GBSA) approximation energies, which we used to quantify the thermodynamic cost of structural rearrangement of the proteins upon binding ions, indicated that S55D/E59D αPV favored Ca2+ binding by -20 kcal/mol relative to WT versus 30 kcal/mol for D94S/G98E αPV. Meanwhile, Mg2+ binding was favored for the S55D/E59D αPV and D94S/G98E αPV variants by -18.32 and -1.65 kcal/mol, respectively. These energies implicate significant contributions to ion binding beyond oxygen coordination at the binding loop, which stemmed from changes in α-helicity, β-sheet character, and hydrogen bonding. Hence, Ca2+ affinity and selectivity against Mg2+ are emergent properties stemming from both local effects within the proteins' ion binding sites as well as non-local contributions elsewhere. Our findings broaden our understanding of the molecular bases governing αPV ion binding that are likely shared by members of the broad family of CBPs.
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Affiliation(s)
| | - Bin Sun
- Stritch School of Medicine, Maywood, Illinois 60153, United States
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7
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The S100 Protein Family as Players and Therapeutic Targets in Pulmonary Diseases. Pulm Med 2021; 2021:5488591. [PMID: 34239729 PMCID: PMC8214497 DOI: 10.1155/2021/5488591] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
The S100 protein family consists of over 20 members in humans that are involved in many intracellular and extracellular processes, including proliferation, differentiation, apoptosis, Ca2+ homeostasis, energy metabolism, inflammation, tissue repair, and migration/invasion. Although there are structural similarities between each member, they are not functionally interchangeable. The S100 proteins function both as intracellular Ca2+ sensors and as extracellular factors. Dysregulated responses of multiple members of the S100 family are observed in several diseases, including the lungs (asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis, pulmonary hypertension, and lung cancer). To this degree, extensive research was undertaken to identify their roles in pulmonary disease pathogenesis and the identification of inhibitors for several S100 family members that have progressed to clinical trials in patients for nonpulmonary conditions. This review outlines the potential role of each S100 protein in pulmonary diseases, details the possible mechanisms observed in diseases, and outlines potential therapeutic strategies for treatment.
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Young BD, Yu W, Rodríguez DJV, Varney KM, MacKerell AD, Weber DJ. Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS). Molecules 2021; 26:E381. [PMID: 33450915 PMCID: PMC7828390 DOI: 10.3390/molecules26020381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/29/2022] Open
Abstract
S100B, a biomarker of malignant melanoma, interacts with the p53 protein and diminishes its tumor suppressor function, which makes this S100 family member a promising therapeutic target for treating malignant melanoma. However, it is a challenge to design inhibitors that are specific for S100B in melanoma versus other S100-family members that are important for normal cellular activities. For example, S100A1 is most similar in sequence and structure to S100B, and this S100 protein is important for normal skeletal and cardiac muscle function. Therefore, a combination of NMR and computer aided drug design (CADD) was used to initiate the design of specific S100B inhibitors. Fragment-based screening by NMR, also termed "SAR by NMR," is a well-established method, and was used to examine spectral perturbations in 2D [1H, 15N]-HSQC spectra of Ca2+-bound S100B and Ca2+-bound S100A1, side-by-side, and under identical conditions for comparison. Of the 1000 compounds screened, two were found to be specific for binding Ca2+-bound S100A1 and four were found to be specific for Ca2+-bound S100B, respectively. The NMR spectral perturbations observed in these six data sets were then used to model how each of these small molecule fragments showed specificity for one S100 versus the other using a CADD approach termed Site Identification by Ligand Competitive Saturation (SILCS). In summary, the combination of NMR and computational approaches provided insight into how S100A1 versus S100B bind small molecules specifically, which will enable improved drug design efforts to inhibit elevated S100B in melanoma. Such a fragment-based approach can be used generally to initiate the design of specific inhibitors for other highly homologous drug targets.
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Affiliation(s)
- Brianna D. Young
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
| | - Wenbo Yu
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - Darex J. Vera Rodríguez
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - Alexander D. MacKerell
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
| | - David J. Weber
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA; (B.D.Y.); (D.J.V.R.); (K.M.V.)
- Center for Biomolecular Therapeutics (CBT), Baltimore, MD 21201, USA; (W.Y.); (A.D.M.J.)
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA
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9
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Sun B, Kekenes-Huskey PM. Molecular Basis of S100A1 Activation and Target Regulation Within Physiological Cytosolic Ca 2+ Levels. Front Mol Biosci 2020; 7:77. [PMID: 32656226 PMCID: PMC7324869 DOI: 10.3389/fmolb.2020.00077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
The S100A1 protein regulates cardiomyocyte function through its binding of calcium (Ca2+) and target proteins, including titin, SERCA, and RyR. S100A1 presents two Ca2+ binding domains, a high-affinity canonical EF-hand (cEF) and a low-affinity pseudo EF-hand (pEF), that control S100A1 activation. For wild-type S100A1, both EF hands must be bound by Ca2+ to form the open state necessary for target peptide binding, which requires unphysiological high sub-millimolar Ca2+ levels. However, there is evidence that post-translational modifications at Cys85 may facilitate the formation of the open state at sub-saturating Ca2+ concentrations. Hence, post-translational modifications of S100A1 could potentially increase the Ca2+-sensitivity of binding protein targets, and thereby modulate corresponding signaling pathways. In this study, we examine the mechanism of S100A1 open-closed gating via molecular dynamics simulations to determine the extent to which Cys85 functionalization, namely via redox reactions, controls the relative population of open states at sub-saturating Ca2+ and capacity to bind peptides. We further characterize the protein's ability to bind a representative peptide target, TRKT12 and relate this propensity to published competition assay data. Our simulation results indicate that functionalization of Cys85 may stabilize the S100A1 open state at physiological, micromolar Ca2+ levels. Our conclusions support growing evidence that S100A1 serves as a signaling hub linking Ca2+ and redox signaling pathways.
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Affiliation(s)
- Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, United States
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, United States
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10
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Baudier J, Deloulme JC, Shaw GS. The Zn 2+ and Ca 2+ -binding S100B and S100A1 proteins: beyond the myths. Biol Rev Camb Philos Soc 2020; 95:738-758. [PMID: 32027773 DOI: 10.1111/brv.12585] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 01/06/2020] [Accepted: 01/20/2020] [Indexed: 12/17/2022]
Abstract
The S100 genes encode a conserved group of 21 vertebrate-specific EF-hand calcium-binding proteins. Since their discovery in 1965, S100 proteins have remained enigmatic in terms of their cellular functions. In this review, we summarize the calcium- and zinc-binding properties of the dimeric S100B and S100A1 proteins and highlight data that shed new light on the extracellular and intracellular regulation and functions of S100B. We point out that S100B and S100A1 homodimers are not functionally interchangeable and that in a S100A1/S100B heterodimer, S100A1 acts as a negative regulator for the ability of S100B to bind Zn2+ . The Ca2+ and Zn2+ -dependent interactions of S100B with a wide array of proteins form the basis of its activities and have led to the derivation of some initial rules for S100B recognition of protein targets. However, recent findings have strongly suggested that these rules need to be revisited. Here, we describe a new consensus S100B binding motif present in intracellular and extracellular vertebrate-specific proteins and propose a new model for stable interactions of S100B dimers with full-length target proteins. A chaperone-associated function for intracellular S100B in adaptive cellular stress responses is also discussed. This review may help guide future studies on the functions of S100 proteins in general.
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Affiliation(s)
- Jacques Baudier
- Institut de Biologie du Développement de Marseille-UMR CNRS 7288, Aix Marseille Université, 13288, Marseille Cedex 9, France
| | - Jean Christophe Deloulme
- Grenoble Institut des Neurosciences, INSERM U1216, Université Grenoble Alpes, 38000, Grenoble, France
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A5C1, Canada
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11
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Understanding Calcium-Dependent Conformational Changes in S100A1 Protein: A Combination of Molecular Dynamics and Gene Expression Study in Skeletal Muscle. Cells 2020; 9:cells9010181. [PMID: 31936886 PMCID: PMC7016722 DOI: 10.3390/cells9010181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
The S100A1 protein, involved in various physiological activities through the binding of calcium ions (Ca2+), participates in several protein-protein interaction (PPI) events after Ca2+-dependent activation. The present work investigates Ca2+-dependent conformational changes in the helix-EF hand-helix using the molecular dynamics (MD) simulation approach that facilitates the understanding of Ca2+-dependent structural and dynamic distinctions between the apo and holo forms of the protein. Furthermore, the process of ion binding by inserting Ca2+ into the bulk of the apo structure was simulated by molecular dynamics. Expectations of the simulation were demonstrated using cluster analysis and a variety of structural metrics, such as interhelical angle estimation, solvent accessible surface area, hydrogen bond analysis, and contact analysis. Ca2+ triggered a rise in the interhelical angles of S100A1 on the binding site and solvent accessible surface area. Significant configurational regulations were observed in the holo protein. The findings would contribute to understanding the molecular basis of the association of Ca2+ with the S100A1 protein, which may be an appropriate study to understand the Ca2+-mediated conformational changes in the protein target. In addition, we investigated the expression profile of S100A1 in myoblast differentiation and muscle regeneration. These data showed that S100A1 is expressed in skeletal muscles. However, the expression decreases with time during the process of myoblast differentiation.
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12
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Bresnick AR. S100 proteins as therapeutic targets. Biophys Rev 2018; 10:1617-1629. [PMID: 30382555 PMCID: PMC6297089 DOI: 10.1007/s12551-018-0471-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/21/2018] [Indexed: 12/13/2022] Open
Abstract
The human genome codes for 21 S100 protein family members, which exhibit cell- and tissue-specific expression patterns. Despite sharing a high degree of sequence and structural similarity, the S100 proteins bind a diverse range of protein targets and contribute to a broad array of intracellular and extracellular functions. Consequently, the S100 proteins regulate multiple cellular processes such as proliferation, migration and/or invasion, and differentiation, and play important roles in a variety of cancers, autoimmune diseases, and chronic inflammatory disorders. This review focuses on the development of S100 neutralizing antibodies and small molecule inhibitors and their potential therapeutic use in controlling disease progression and severity.
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Affiliation(s)
- Anne R Bresnick
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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13
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Chen B, Wang H, Wu Z, Duan B, Bai P, Zhang K, Li W, Zheng J, Xing J. Conformational stabilization of FOX-DNA complex architecture to sensitize prostate cancer chemotherapy. Amino Acids 2017; 49:1247-1254. [PMID: 28474127 DOI: 10.1007/s00726-017-2426-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/17/2017] [Indexed: 11/26/2022]
Abstract
The forkhead box (FOX) transcription factor is a family of tumor suppressors that negatively regulates the tumorigenesis activity of prostate cancer; stabilization of FOX-DNA complex architecture has been recognized as a new and promising strategy for sensitizing cancer chemotherapy. Here, we described a systematic method that combined in silico analysis and in vitro assay to investigate the intermolecular interaction between FOX DNA-binding domain (DBD) and its cognate DNA partner. The structural and energetic information harvested from the molecular investigation were used to guide high-throughput virtual screening against a structurally diverse, nonredundant library of natural product compounds, aiming at discovery of novel small-molecule medicines that can conformationally stabilize and promote FOX-DNA recognition and interaction. The screening identified a number of theoretically promising hits, which were then examined by using fluorescence anisotropy assay to determine their binding potency for FOX DBD domain. The antitumor activity of identified high-affinity compounds was also tested at cellular level. Structural dynamics analysis found that the small-molecule stabilizers can shift the conformational equilibrium of FOX DBD to DNA-bound state, thus promoting the protein domain to bind tightly with its DNA partner.
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Affiliation(s)
- Bin Chen
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Huiqiang Wang
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Zhun Wu
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Bo Duan
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Peide Bai
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Kaiyan Zhang
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Wei Li
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Jiaxin Zheng
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Jinchun Xing
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China.
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14
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Melville Z, Hernández-Ochoa EO, Pratt SJP, Liu Y, Pierce AD, Wilder PT, Adipietro KA, Breysse DH, Varney KM, Schneider MF, Weber DJ. The Activation of Protein Kinase A by the Calcium-Binding Protein S100A1 Is Independent of Cyclic AMP. Biochemistry 2017; 56:2328-2337. [PMID: 28409622 PMCID: PMC5415871 DOI: 10.1021/acs.biochem.7b00117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Biochemical
and structural studies demonstrate that S100A1 is involved
in a Ca2+-dependent interaction with the type 2α
and type 2β regulatory subunits of protein kinase A (PKA) (RIIα
and RIIβ) to activate holo-PKA. The interaction was specific
for S100A1 because other calcium-binding proteins (i.e., S100B and
calmodulin) had no effect. Likewise, a role for S100A1
in PKA-dependent signaling was established because the PKA-dependent
subcellular redistribution of HDAC4 was abolished in cells derived
from S100A1 knockout mice. Thus, the Ca2+-dependent interaction
between S100A1 and the type 2 regulatory subunits represents a novel
mechanism that provides a link between Ca2+ and PKA signaling,
which is important for the regulation of gene expression in skeletal
muscle via HDAC4 cytosolic–nuclear trafficking.
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Affiliation(s)
- Zephan Melville
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Erick O Hernández-Ochoa
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Stephen J P Pratt
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Yewei Liu
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Adam D Pierce
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Kaylin A Adipietro
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Daniel H Breysse
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Martin F Schneider
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - David J Weber
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
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15
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Tao R, Wang ZF, Qiu W, He YF, Yan WQ, Sun WY, Li HJ. Role of S100A3 in human hepatocellular carcinoma and the anticancer effect of sodium cantharidinate. Exp Ther Med 2017; 13:2812-2818. [PMID: 28588665 PMCID: PMC5450779 DOI: 10.3892/etm.2017.4294] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022] Open
Abstract
The fifth most common cancer worldwide is hepatocellular carcinoma (HCC), which has an annual mortality rate of ~800,000. Although surgical procedures for HCC, such as hepatic resection and liver transplantation, have progressed and the outcomes of patients have improved, HCC is still characterized by frequent recurrence, even after liver transplantation. In the present study the expression of the protein coding gene, S100 calcium binding protein A3 (S100A3), was observed in 62 HCC tissues and tumor-surrounding tissues. The present study indicated that S100A3 activation was involved in tumorigenesis and tumor aggressiveness. The protein and mRNA expression levels of S100A3 in the human HCC cell line (HepG2) were investigated using western blotting and reverse transcription-quantitative polymerase chain reaction analysis, respectively. The function of sodium cantharidinate in inducing HCC cell apoptosis was also investigated. Sodium cantharidinate inhibited the protein and gene expression of S100A3 in HepG2 cells in vitro. These data suggested that S100A3 has an important role in human HCC. The present study indicates that the functional properties of sodium cantharidinate are promising for the development of a novel drug that may control the expression of S100A3 and improve the treatment of human HCC in the near future.
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Affiliation(s)
- Ran Tao
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China.,Department of Clinical Pharmacy and Pharmaceutical Management, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Zhong-Feng Wang
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wei Qiu
- Department of Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yu-Fang He
- Institute of Phytochemistry, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin 130012, P.R. China
| | - Wei-Qun Yan
- Department of Clinical Pharmacy and Pharmaceutical Management, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wen-Yi Sun
- Department of Clinical Pharmacy and Pharmaceutical Management, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hai-Jun Li
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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16
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Melville Z, Aligholizadeh E, McKnight LE, Weber DJ, Pozharski E, Weber DJ. X-ray crystal structure of human calcium-bound S100A1. Acta Crystallogr F Struct Biol Commun 2017; 73:215-221. [PMID: 28368280 PMCID: PMC5379171 DOI: 10.1107/s2053230x17003983] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/11/2017] [Indexed: 01/02/2023] Open
Abstract
S100A1 is a member of the S100 family of Ca2+-binding proteins and regulates several cellular processes, including those involved in Ca2+ signaling and cardiac and skeletal muscle function. In Alzheimer's disease, brain S100A1 is overexpressed and gives rise to disease pathologies, making it a potential therapeutic target. The 2.25 Å resolution crystal structure of Ca2+-S100A1 is solved here and is compared with the structures of other S100 proteins, most notably S100B, which is a highly homologous S100-family member that is implicated in the progression of malignant melanoma. The observed structural differences in S100A1 versus S100B provide insights regarding target protein-binding specificity and for targeting these two S100 proteins in human diseases using structure-based drug-design approaches.
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Affiliation(s)
- Zephan Melville
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Ehson Aligholizadeh
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Laura E. McKnight
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Dylan J. Weber
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Edwin Pozharski
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
| | - David J. Weber
- Center for Biomolecular Therapeutics, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland Baltimore, 108 North Greene Street, Baltimore, MD 21201, USA
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17
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Molecular Basis of S100A1 Activation at Saturating and Subsaturating Calcium Concentrations. Biophys J 2016; 110:1052-63. [PMID: 26958883 DOI: 10.1016/j.bpj.2015.12.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022] Open
Abstract
The S100A1 protein mediates a wide variety of physiological processes through its binding of calcium (Ca(2+)) and endogenous target proteins. S100A1 presents two Ca(2+)-binding domains: a high-affinity "canonical" EF (cEF) hand and a low-affinity "pseudo" EF (pEF) hand. Accumulating evidence suggests that both Ca(2+)-binding sites must be saturated to stabilize an open state conducive to peptide recognition, yet the pEF hand's low affinity limits Ca(2+) binding at normal physiological concentrations. To understand the molecular basis of Ca(2+) binding and open-state stabilization, we performed 100 ns molecular dynamics simulations of S100A1 in the apo/holo (Ca(2+)-free/bound) states and a half-saturated state, for which only the cEF sites are Ca(2+)-bound. Our simulations indicate that the pattern of oxygen coordination about Ca(2+) in the cEF relative to the pEF site contributes to the former's higher affinity, whereas Ca(2+) binding strongly reshapes the protein's conformational dynamics by disrupting β-sheet coupling between EF hands. Moreover, modeling of the half-saturated configuration suggests that the open state is unstable and reverts toward a closed state in the absence of the pEF Ca(2+) ion. These findings indicate that Ca(2+) binding at the cEF site alone is insufficient to stabilize opening; thus, posttranslational modification of the protein may be required for target peptide binding at subsaturating intracellular Ca(2+) levels.
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18
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Subiaul F. What's Special about Human Imitation? A Comparison with Enculturated Apes. Behav Sci (Basel) 2016; 6:bs6030013. [PMID: 27399786 PMCID: PMC5039513 DOI: 10.3390/bs6030013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 06/25/2016] [Accepted: 06/28/2016] [Indexed: 12/04/2022] Open
Abstract
What, if anything, is special about human imitation? An evaluation of enculturated apes’ imitation skills, a “best case scenario” of non-human apes’ imitation performance, reveals important similarities and differences between this special population of apes and human children. Candidates for shared imitation mechanisms include the ability to imitate various familiar transitive responses and object–object actions that involve familiar tools. Candidates for uniquely derived imitation mechanisms include: imitating novel transitive actions and novel tool-using responses as well as imitating opaque or intransitive gestures, regardless of familiarity. While the evidence demonstrates that enculturated apes outperform non-enculturated apes and perform more like human children, all apes, regardless of rearing history, generally excel at imitating familiar, over-rehearsed responses and are poor, relative to human children, at imitating novel, opaque or intransitive responses. Given the similarities between the sensory and motor systems of preschool age human children and non-human apes, it is unlikely that differences in sensory input and/or motor-output alone explain the observed discontinuities in imitation performance. The special rearing history of enculturated apes—including imitation-specific training—further diminishes arguments suggesting that differences are experience-dependent. Here, it is argued that such differences are best explained by distinct, specialized mechanisms that have evolved for copying rules and responses in particular content domains. Uniquely derived social and imitation learning mechanisms may represent adaptations for learning novel communicative gestures and complex tool-use. Given our species’ dependence on both language and tools, mechanisms that accelerated learning in these domains are likely to have faced intense selective pressures, starting with the earliest of human ancestors.
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Affiliation(s)
- Francys Subiaul
- Department of Speech & Hearing Science, The George Washington University, 2115 G Street, NW # 204, Washington, DC 20052, USA.
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, 2115 G Street, NW # 204, Washington, DC 20052, USA.
- GW Institute for Neuroscience, The George Washington University, 2115 G Street, NW # 204, Washington, DC 20052, USA.
- Mind-Brain Institute, The George Washington University, 2115 G Street, NW # 204, Washington, DC 20052, USA.
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19
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Kucharski AN, Scott CE, Davis JP, Kekenes-Huskey PM. Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory. J Phys Chem B 2016; 120:8617-30. [PMID: 27267153 DOI: 10.1021/acs.jpcb.6b02666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of PV sequence homologues and EF-hand-containing, Ca(2+) binding proteins.
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Affiliation(s)
- Amir N Kucharski
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Caitlin E Scott
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, Ohio State University , Columbus, Ohio 43210, United States
| | - Peter M Kekenes-Huskey
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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20
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Abstract
In humans, the S100 protein family is composed of 21 members that exhibit a high degree of structural similarity, but are not functionally interchangeable. This family of proteins modulates cellular responses by functioning both as intracellular Ca(2+) sensors and as extracellular factors. Dysregulated expression of multiple members of the S100 family is a common feature of human cancers, with each type of cancer showing a unique S100 protein profile or signature. Emerging in vivo evidence indicates that the biology of most S100 proteins is complex and multifactorial, and that these proteins actively contribute to tumorigenic processes such as cell proliferation, metastasis, angiogenesis and immune evasion. Drug discovery efforts have identified leads for inhibiting several S100 family members, and two of the identified inhibitors have progressed to clinical trials in patients with cancer. This Review highlights new findings regarding the role of S100 family members in cancer diagnosis and treatment, the contribution of S100 signalling to tumour biology, and the discovery and development of S100 inhibitors for treating cancer.
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Affiliation(s)
- Anne R. Bresnick
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
| | - David J. Weber
- Center for Biomolecular Therapeutics and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, Maryland 20102, USA
| | - Danna B. Zimmer
- Center for Biomolecular Therapeutics and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, Maryland 20102, USA
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21
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Bresnick AR, Weber DJ, Zimmer DB. S100 proteins in cancer. Nat Rev Cancer 2015. [PMID: 25614008 DOI: 10.1038/nrc3893.s100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In humans, the S100 protein family is composed of 21 members that exhibit a high degree of structural similarity, but are not functionally interchangeable. This family of proteins modulates cellular responses by functioning both as intracellular Ca(2+) sensors and as extracellular factors. Dysregulated expression of multiple members of the S100 family is a common feature of human cancers, with each type of cancer showing a unique S100 protein profile or signature. Emerging in vivo evidence indicates that the biology of most S100 proteins is complex and multifactorial, and that these proteins actively contribute to tumorigenic processes such as cell proliferation, metastasis, angiogenesis and immune evasion. Drug discovery efforts have identified leads for inhibiting several S100 family members, and two of the identified inhibitors have progressed to clinical trials in patients with cancer. This Review highlights new findings regarding the role of S100 family members in cancer diagnosis and treatment, the contribution of S100 signalling to tumour biology, and the discovery and development of S100 inhibitors for treating cancer.
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Affiliation(s)
- Anne R Bresnick
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
| | - David J Weber
- Center for Biomolecular Therapeutics and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, Maryland 20102, USA
| | - Danna B Zimmer
- Center for Biomolecular Therapeutics and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, Maryland 20102, USA
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22
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Wafer LN, Tzul FO, Pandharipande PP, McCallum SA, Makhatadze GI. Structural and thermodynamic characterization of the recognition of the S100-binding peptides TRTK12 and p53 by calmodulin. Protein Sci 2014; 23:1247-61. [PMID: 24947426 DOI: 10.1002/pro.2506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/14/2014] [Accepted: 06/17/2014] [Indexed: 11/07/2022]
Abstract
Calmodulin (CaM) is a multifunctional messenger protein that activates a wide variety of signaling pathways in eukaryotic cells in a calcium-dependent manner. CaM has been proposed to be functionally distinct from the S100 proteins, a related family of eukaryotic calcium-binding proteins. Previously, it was demonstrated that peptides derived from the actin-capping protein, TRTK12, and the tumor-suppressor protein, p53, interact with multiple members of the S100 proteins. To test the specificity of these peptides, they were screened using isothermal titration calorimetry against 16 members of the human S100 protein family, as well as CaM, which served as a negative control. Interestingly, both the TRTK12 and p53 peptides were found to interact with CaM. These interactions were further confirmed by both fluorescence and nuclear magnetic resonance spectroscopies. These peptides have distinct sequences from the known CaM target sequences. The TRTK12 peptide was found to independently interact with both CaM domains and bind with a stoichiometry of 2:1 and dissociations constants Kd,C-term = 2 ± 1 µM and Kd,N-term = 14 ± 1 µM. In contrast, the p53 peptide was found to interact only with the C-terminal domain of CaM, Kd,C-term = 2 ± 1 µM, 25°C. Using NMR spectroscopy, the locations of the peptide binding sites were mapped onto the structure of CaM. The binding sites for both peptides were found to overlap with the binding interface for previously identified targets on both domains of CaM. This study demonstrates the plasticity of CaM in target binding and may suggest a possible overlap in target specificity between CaM and the S100 proteins.
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Affiliation(s)
- Lucas N Wafer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180
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Ramagopal UA, Dulyaninova NG, Varney KM, Wilder PT, Nallamsetty S, Brenowitz M, Weber DJ, Almo SC, Bresnick AR. Structure of the S100A4/myosin-IIA complex. BMC STRUCTURAL BIOLOGY 2013; 13:31. [PMID: 24252706 PMCID: PMC3924328 DOI: 10.1186/1472-6807-13-31] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/13/2013] [Indexed: 11/10/2022]
Abstract
Background S100A4, a member of the S100 family of Ca2+-binding proteins, modulates the motility of both non-transformed and cancer cells by regulating the localization and stability of cellular protrusions. Biochemical studies have demonstrated that S100A4 binds to the C-terminal end of the myosin-IIA heavy chain coiled-coil and disassembles myosin-IIA filaments; however, the mechanism by which S100A4 mediates myosin-IIA depolymerization is not well understood. Results We determined the X-ray crystal structure of the S100A4Δ8C/MIIA1908-1923 peptide complex, which showed an asymmetric binding mode for the myosin-IIA peptide across the S100A4 dimer interface. This asymmetric binding mode was confirmed in NMR studies using a spin-labeled myosin-IIA peptide. In addition, our NMR data indicate that S100A4Δ8C binds the MIIA1908-1923 peptide in an orientation very similar to that observed for wild-type S100A4. Studies of complex formation using a longer, dimeric myosin-IIA construct demonstrated that S100A4 binding dissociates the two myosin-IIA polypeptide chains to form a complex composed of one S100A4 dimer and a single myosin-IIA polypeptide chain. This interaction is mediated, in part, by the instability of the region of the myosin-IIA coiled-coil encompassing the S100A4 binding site. Conclusion The structure of the S100A4/MIIA1908-1923 peptide complex has revealed the overall architecture of this assembly and the detailed atomic interactions that mediate S100A4 binding to the myosin-IIA heavy chain. These structural studies support the idea that residues 1908–1923 of the myosin-IIA heavy chain represent a core sequence for the S100A4/myosin-IIA complex. In addition, biophysical studies suggest that structural fluctuations within the myosin-IIA coiled-coil may facilitate S100A4 docking onto a single myosin-IIA polypeptide chain.
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Affiliation(s)
- Udupi A Ramagopal
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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24
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Wafer LN, Tzul FO, Pandharipande PP, Makhatadze GI. Novel interactions of the TRTK12 peptide with S100 protein family members: specificity and thermodynamic characterization. Biochemistry 2013; 52:5844-56. [PMID: 23899389 DOI: 10.1021/bi400788s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The S100 protein family consists of small, dimeric proteins that exert their biological functions in response to changing calcium concentrations. S100B is the best-studied member and has been shown to interact with more than 20 binding partners in a calcium-dependent manner. The TRTK12 peptide, derived from the consensus binding sequence for S100B, has previously been found to interact with S100A1 and has been proposed to be a general binding partner of the S100 family. To test this hypothesis and gain a better understanding of the specificity of binding for the S100 proteins, 16 members of the human S100 family were screened against this peptide and its alanine variants. Novel interactions were found with only two family members, S100P and S100A2, indicating that TRTK12 selectively interacts with a small subset of the S100 proteins. Substantial promiscuity was observed in the binding site of S100B thereby accommodating variations in the peptide sequence, while S100A1, S100A2, and S100P exhibited larger differences in the binding constants for the TRTK12 alanine variants. This suggests that single-point substitutions can be used to selectively modulate the affinity of TRTK12 peptides for individual S100 proteins. This study has important implications for the rational drug design of inhibitors for the S100 proteins, which are involved in a variety of cancers and neurodegenerative diseases.
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Affiliation(s)
- Lucas N Wafer
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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25
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Nowakowski M, Ruszczyńska-Bartnik K, Budzińska M, Jaremko Ł, Jaremko M, Zdanowski K, Bierzyński A, Ejchart A. Impact of Calcium Binding and Thionylation of S100A1 Protein on Its Nuclear Magnetic Resonance-Derived Structure and Backbone Dynamics. Biochemistry 2013; 52:1149-59. [DOI: 10.1021/bi3015407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michał Nowakowski
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | | | - Monika Budzińska
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Łukasz Jaremko
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
- Faculty of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - Mariusz Jaremko
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Konrad Zdanowski
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
- Institute of Chemistry, University of Natural Sciences and Humanities, 3 Maja
54, 08-110 Siedlce, Poland
| | - Andrzej Bierzyński
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrzej Ejchart
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
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26
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Liriano MA, Varney KM, Wright NT, Hoffman CL, Toth EA, Ishima R, Weber DJ. Target binding to S100B reduces dynamic properties and increases Ca(2+)-binding affinity for wild type and EF-hand mutant proteins. J Mol Biol 2012; 423:365-85. [PMID: 22824086 PMCID: PMC3462298 DOI: 10.1016/j.jmb.2012.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/06/2012] [Accepted: 07/16/2012] [Indexed: 11/24/2022]
Abstract
Mutations in the second EF-hand (D61N, D63N, D65N, and E72A) of S100B were used to study its Ca(2+) binding and dynamic properties in the absence and presence of a bound target, TRTK-12. With (D63N)S100B as an exception ((D63N)K(D)=50±9 μM), Ca(2+) binding to EF2-hand mutants were reduced by more than 8-fold in the absence of TRTK-12 ((D61N)K(D)=412±67 μM, (D65N)K(D)=968±171 μM, and (E72A)K(D)=471±133 μM), when compared to wild-type protein ((WT)K(D)=56±9 μM). For the TRTK-12 complexes, the Ca(2+)-binding affinity to wild type ((WT+TRTK)K(D)=12±10 μM) and the EF2 mutants was increased by 5- to 14-fold versus in the absence of target ((D61N+TRTK)K(D)=29±1.2 μM, (D63N+TRTK)K(D)=10±2.2 μM, (D65N+TRTK)K(D)=73±4.4 μM, and (E72A+TRTK)K(D)=18±3.7 μM). In addition, R(ex), as measured using relaxation dispersion for side-chain (15)N resonances of Asn63 ((D63N)S100B), was reduced upon TRTK-12 binding when measured by NMR. Likewise, backbone motions on multiple timescales (picoseconds to milliseconds) throughout wild type, (D61N)S100B, (D63N)S100B, and (D65N)S100B were lowered upon binding TRTK-12. However, the X-ray structures of Ca(2+)-bound (2.0Å) and TRTK-bound (1.2Å) (D63N)S100B showed no change in Ca(2+) coordination; thus, these and analogous structural data for the wild-type protein could not be used to explain how target binding increased Ca(2+)-binding affinity in solution. Therefore, a model for how S100B-TRTK-12 complex formation increases Ca(2+) binding is discussed, which considers changes in protein dynamics upon binding the target TRTK-12.
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Affiliation(s)
- Melissa A. Liriano
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Nathan T. Wright
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Cassandra L. Hoffman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Eric A. Toth
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
| | - Rieko Ishima
- Department of Structural Biology, The University of Pittsburgh School of Medicine, 3501 5 Avenue N. Pittsburgh, PA 15260, USA
| | - David J. Weber
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St. Baltimore, MD 21201, USA
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Lenarčič Živković M, Zaręba-Kozioł M, Zhukova L, Poznański J, Zhukov I, Wysłouch-Cieszyńska A. Post-translational S-nitrosylation is an endogenous factor fine tuning the properties of human S100A1 protein. J Biol Chem 2012; 287:40457-70. [PMID: 22989881 DOI: 10.1074/jbc.m112.418392] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND S100A1 protein is a proposed target of molecule-guided therapy for heart failure. RESULTS S-Nitrosylation of S100A1 is present in cells, increases Ca(2+) binding, and tunes the overall protein conformation. CONCLUSION Thiol-aromatic molecular switch is responsible for NO-related modification of S100A1 properties. SIGNIFICANCE Post-translational S-nitrosylation may provide functional diversity and specificity to S100A1 and other S100 protein family members. S100A1 is a member of the Ca(2+)-binding S100 protein family. It is expressed in brain and heart tissue, where it plays a crucial role as a modulator of Ca(2+) homeostasis, energy metabolism, neurotransmitter release, and contractile performance. Biological effects of S100A1 have been attributed to its direct interaction with a variety of target proteins. The (patho)physiological relevance of S100A1 makes it an important molecular target for future therapeutic intervention. S-Nitrosylation is a post-translational modification of proteins, which plays a role in cellular signal transduction under physiological and pathological conditions. In this study, we confirmed that S100A1 protein is endogenously modified by Cys(85) S-nitrosylation in PC12 cells, which are a well established model system for studying S100A1 function. We used isothermal calorimetry to show that S-nitrosylation facilitates the formation of Ca(2+)-loaded S100A1 at physiological ionic strength conditions. To establish the unique influence of the S-nitroso group, our study describes high resolution three-dimensional structures of human apo-S100A1 protein with the Cys(85) thiol group in reduced and S-nitrosylated states. Solution structures of the proteins are based on NMR data obtained at physiological ionic strength. Comparative analysis shows that S-nitrosylation fine tunes the overall architecture of S100A1 protein. Although the typical S100 protein intersubunit four-helix bundle is conserved upon S-nitrosylation, the conformation of S100A1 protein is reorganized at the sites most important for target recognition (i.e. the C-terminal helix and the linker connecting two EF-hand domains). In summary, this study discloses cysteine S-nitrosylation as a new factor responsible for increasing functional diversity of S100A1 and helps explain the role of S100A1 as a Ca(2+) signal transmitter sensitive to NO/redox equilibrium within cells.
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Wafer LN, Streicher WW, McCallum SA, Makhatadze GI. Thermodynamic and kinetic analysis of peptides derived from CapZ, NDR, p53, HDM2, and HDM4 binding to human S100B. Biochemistry 2012; 51:7189-201. [PMID: 22913742 PMCID: PMC3448795 DOI: 10.1021/bi300865g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S100B is a member of the S100 subfamily of EF-hand proteins that has been implicated in malignant melanoma and neurodegenerative conditions such as Alzheimer's disease and Parkinson's disease. Calcium-induced conformational changes expose a hydrophobic binding cleft, facilitating interactions with a wide variety of nuclear, cytoplasmic, and extracellular target proteins. Previously, peptides derived from CapZ, p53, NDR, HDM2, and HDM4 have been shown to interact with S100B in a calcium-dependent manner. However, the thermodynamic and kinetic basis of these interactions remains largely unknown. To gain further insight, we screened these peptides against the S100B protein using isothermal titration calorimetry and nuclear magnetic resonance. All peptides were found to have binding affinities in the low micromolar to nanomolar range. Binding-induced changes in the line shapes of S100B backbone (1)H and (15)N resonances were monitored to obtain the dissociation constants and the kinetic binding parameters. The large microscopic K(on) rate constants observed in this study (≥1 × 10(7) M(-1) s(-1)) suggest that S100B utilizes a "fly casting mechanism" in the recognition of these peptide targets.
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Affiliation(s)
- Lucas N. Wafer
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | | | - Scott A. McCallum
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
| | - George I. Makhatadze
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA
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29
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Elliott PR, Irvine AF, Jung HS, Tozawa K, Pastok MW, Picone R, Badyal SK, Basran J, Rudland PS, Barraclough R, Lian LY, Bagshaw CR, Kriajevska M, Barsukov IL. Asymmetric mode of Ca²⁺-S100A4 interaction with nonmuscle myosin IIA generates nanomolar affinity required for filament remodeling. Structure 2012; 20:654-66. [PMID: 22483112 PMCID: PMC3343272 DOI: 10.1016/j.str.2012.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/31/2011] [Accepted: 02/09/2012] [Indexed: 01/01/2023]
Abstract
Filament assembly of nonmuscle myosin IIA (NMIIA) is selectively regulated by the small Ca2+-binding protein, S100A4, which causes enhanced cell migration and metastasis in certain cancers. Our NMR structure shows that an S100A4 dimer binds to a single myosin heavy chain in an asymmetrical configuration. NMIIA in the complex forms a continuous helix that stretches across the surface of S100A4 and engages the Ca2+-dependent binding sites of each subunit in the dimer. Synergy between these sites leads to a very tight association (KD ∼1 nM) that is unique in the S100 family. Single-residue mutations that remove this synergy weaken binding and ameliorate the effects of S100A4 on NMIIA filament assembly and cell spreading in A431 human epithelial carcinoma cells. We propose a model for NMIIA filament disassembly by S100A4 in which initial binding to the unstructured NMIIA tail initiates unzipping of the coiled coil and disruption of filament packing.
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Affiliation(s)
- Paul R Elliott
- Institute of Integrative Biology, BioSciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK
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30
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31
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Affiliation(s)
- Brian R Cannon
- University of Maryland, Baltimore, MD, USA (BRC, DJW); Texas A&M University, College Station, TX, USA (DBZ)
| | - Danna B Zimmer
- University of Maryland, Baltimore, MD, USA (BRC, DJW); Texas A&M University, College Station, TX, USA (DBZ)
| | - David J Weber
- University of Maryland, Baltimore, MD, USA (BRC, DJW); Texas A&M University, College Station, TX, USA (DBZ)
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32
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Dempsey BR, Shaw GS. Identification of calcium-independent and calcium-enhanced binding between S100B and the dopamine D2 receptor. Biochemistry 2011; 50:9056-65. [PMID: 21932834 PMCID: PMC3196243 DOI: 10.1021/bi201054x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
S100B is a dimeric EF-hand protein that undergoes a calcium-induced
conformational change and exposes a hydrophobic protein-binding surface.
Recently S100B was identified as a binding partner of the dopamine
D2 receptor in a bacterial two-hybrid screen involving the third intracellular
loop (IC3). The low in vivo calcium concentration
in bacteria (100–300 nM) suggests this interaction may occur
in the absence of calcium. In this work the calcium-sensitive ability
for S100B to recruit the IC3 of the dopamine D2 receptor was examined,
and regions in both proteins required for complex formation were identified.
Peptide array experiments identified the C-terminal 58 residues of
the IC3 (IC3-C58) as the major interacting site for S100B. These experiments
along with pull-down assays showed the IC3 interacts with S100B in
the absence and presence of calcium. 1H–15N HSQC experiments were used to identify residues, primarily in helices
III and IV, utilized in the IC3-C58 interaction. NMR titration data
indicated that although an interaction between apo-S100B and IC3-C58
occurs without calcium, the binding was enhanced more than 100-fold
upon calcium binding. Further, it was established that shorter regions
within IC3-C58 comprising its N- and C-terminal halves had diminished
binding to Ca2+-S100B and did not display any observable
affinity in the absence of calcium. This indicates that residue or
structural components within both regions are required for optimal
interaction with Ca2+-S100B. This work represents the first
example of an S100B target that interacts with both the apo- and calcium-saturated
forms of S100B.
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Affiliation(s)
- Brian R Dempsey
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
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Rezvanpour A, Santamaria-Kisiel L, Shaw GS. The S100A10-annexin A2 complex provides a novel asymmetric platform for membrane repair. J Biol Chem 2011; 286:40174-83. [PMID: 21949189 PMCID: PMC3220529 DOI: 10.1074/jbc.m111.244038] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Membrane repair is mediated by multiprotein complexes, such as that formed between the dimeric EF-hand protein S100A10, the calcium- and phospholipid-binding protein annexin A2, the enlargeosome protein AHNAK, and members of the transmembrane ferlin family. Although interactions between these proteins have been shown, little is known about their structural arrangement and mechanisms of formation. In this work, we used a non-covalent complex between S100A10 and the N terminus of annexin A2 (residues 1-15) and a designed hybrid protein (A10A2), where S100A10 is linked in tandem to the N-terminal region of annexin A2, to explore the binding region, stoichiometry, and affinity with a synthetic peptide from the C terminus of AHNAK. Using multiple biophysical methods, we identified a novel asymmetric arrangement between a single AHNAK peptide and the A10A2 dimer. The AHNAK peptide was shown to require the annexin A2 N terminus, indicating that the AHNAK binding site comprises regions on both S100A10 and annexin proteins. NMR spectroscopy was used to show that the AHNAK binding surface comprised residues from helix IV in S100A10 and the C-terminal portion from the annexin A2 peptide. This novel surface maps to the exposed side of helices IV and IV' of the S100 dimeric structure, a region not identified in any previous S100 target protein structures. The results provide the first structural details of the ternary S100A10 protein complex required for membrane repair.
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Affiliation(s)
- Atoosa Rezvanpour
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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34
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Dulyaninova NG, Hite KM, Zencheck WD, Scudiero DA, Almo SC, Shoemaker RH, Bresnick AR. Cysteine 81 is critical for the interaction of S100A4 and myosin-IIA. Biochemistry 2011; 50:7218-27. [PMID: 21749055 DOI: 10.1021/bi200853y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Overexpression of S100A4, a member of the S100 family of Ca(2+)-binding proteins, is associated with a number of human pathologies, including fibrosis, inflammatory disorders, and metastatic disease. The identification of small molecules that disrupt S100A4/target interactions provides a mechanism for inhibiting S100A4-mediated cellular activities and their associated pathologies. Using an anisotropy assay that monitors the Ca(2+)-dependent binding of myosin-IIA to S100A4, NSC 95397 was identified as an inhibitor that disrupts the S100A4/myosin-IIA interaction and inhibits S100A4-mediated depolymerization of myosin-IIA filaments. Mass spectrometry demonstrated that NSC 95397 forms covalent adducts with Cys81 and Cys86, which are located in the canonical target binding cleft. Mutagenesis studies showed that covalent modification of just Cys81 is sufficient to inhibit S100A4 function with respect to myosin-IIA binding and depolymerization. Remarkably, substitution of Cys81 with serine or alanine significantly impaired the ability of S100A4 to promote myosin-IIA filament disassembly. As reversible covalent cysteine modifications have been observed for several S100 proteins, we propose that modification of Cys81 may provide an additional regulatory mechanism for mediating the binding of S100A4 to myosin-IIA.
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Affiliation(s)
- Natalya G Dulyaninova
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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House RP, Pozzuto M, Patel P, Dulyaninova NG, Li ZH, Zencheck WD, Vitolo MI, Weber DJ, Bresnick AR. Two functional S100A4 monomers are necessary for regulating nonmuscle myosin-IIA and HCT116 cell invasion. Biochemistry 2011; 50:6920-32. [PMID: 21721535 DOI: 10.1021/bi200498q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
S100A4, a member of the Ca(2+)-activated S100 protein family, regulates the motility and invasiveness of cancer cells. Moreover, high S100A4 expression levels correlate with poor patient survival in several cancers. Although biochemical, biophysical, and structural data indicate that S100A4 is a noncovalent dimer, it is unknown if two functional S100A4 monomers are required for the productive recognition of protein targets and the promotion of cell invasion. To address this question, we created covalently linked S100A4 dimers using a glycine rich flexible linker. The single-chain S100A4 (sc-S100A4) proteins exhibited wild-type affinities for calcium and nonmuscle myosin-IIA, retained the ability to regulate nonmuscle myosin-IIA assembly, and promoted tumor cell invasion when expressed in S100A4-deficient colon carcinoma cells. Mutation of the two calcium-binding EF-hands in one monomer, while leaving the other monomer intact, caused a 30-60-fold reduction in binding affinity for nonmuscle myosin-IIA concomitant with a weakened ability to regulate the monomer-polymer equilibrium of nonmuscle myosin-IIA. Moreover, sc-S100A4 proteins with one monomer deficient in calcium responsiveness did not support S100A4-mediated colon carcinoma cell invasion. Cross-linking and titration data indicate that the S100A4 dimer binds a single myosin-IIA target peptide. These data are consistent with a model in which a single peptide forms interactions in the vicinity of the canonical target binding cleft of each monomer in such a manner that both target binding sites are required for the efficient interaction with myosin-IIA.
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Affiliation(s)
- Reniqua P House
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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36
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Fritz G, Botelho HM, Morozova-Roche LA, Gomes CM. Natural and amyloid self-assembly of S100 proteins: structural basis of functional diversity. FEBS J 2010; 277:4578-90. [PMID: 20977662 DOI: 10.1111/j.1742-4658.2010.07887.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The S100 proteins are 10-12 kDa EF-hand proteins that act as central regulators in a multitude of cellular processes including cell survival, proliferation, differentiation and motility. Consequently, many S100 proteins are implicated and display marked changes in their expression levels in many types of cancer, neurodegenerative disorders, inflammatory and autoimmune diseases. The structure and function of S100 proteins are modulated by metal ions via Ca(2+) binding through EF-hand motifs and binding of Zn(2+) and Cu(2+) at additional sites, usually at the homodimer interfaces. Ca(2+) binding modulates S100 conformational opening and thus promotes and affects the interaction with p53, the receptor for advanced glycation endproducts and Toll-like receptor 4, among many others. Structural plasticity also occurs at the quaternary level, where several S100 proteins self-assemble into multiple oligomeric states, many being functionally relevant. Recently, we have found that the S100A8/A9 proteins are involved in amyloidogenic processes in corpora amylacea of prostate cancer patients, and undergo metal-mediated amyloid oligomerization and fibrillation in vitro. Here we review the unique chemical and structural properties of S100 proteins that underlie the conformational changes resulting in their oligomerization upon metal ion binding and ultimately in functional control. The possibility that S100 proteins have intrinsic amyloid-forming capacity is also addressed, as well as the hypothesis that amyloid self-assemblies may, under particular physiological conditions, affect the S100 functions within the cellular milieu.
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Affiliation(s)
- Günter Fritz
- Department of Neuropathology, University of Freiburg, Freiburg, Germany
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The Calcium-Dependent Interaction of S100B with Its Protein Targets. Cardiovasc Psychiatry Neurol 2010; 2010. [PMID: 20827422 PMCID: PMC2933916 DOI: 10.1155/2010/728052] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/09/2010] [Indexed: 01/16/2023] Open
Abstract
S100B is a calcium signaling protein that is a member of the S100 protein family. An important feature of S100B and most other S100 proteins (S100s) is that they often bind Ca2+ ions relatively weakly in the absence of a protein target; upon binding their target proteins, Ca2+-binding then increases by as much as from 200- to 400-fold. This manuscript reviews the structural basis and physiological significance of increased Ca2+-binding affinity in the presence of protein targets. New information regarding redundancy among family members and the structural domains that mediate the interaction of S100B, and other S100s, with their targets is also presented. It is the diversity among individual S100s, the protein targets that they interact with, and the Ca2+ dependency of these protein-protein interactions that allow S100s to transduce changes in [Ca2+]intracellular levels into spatially and temporally unique biological responses.
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Charpentier TH, Thompson LE, Liriano MA, Varney KM, Wilder PT, Pozharski E, Toth EA, Weber DJ. The effects of CapZ peptide (TRTK-12) binding to S100B-Ca2+ as examined by NMR and X-ray crystallography. J Mol Biol 2010; 396:1227-43. [PMID: 20053360 DOI: 10.1016/j.jmb.2009.12.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/22/2009] [Accepted: 12/29/2009] [Indexed: 10/20/2022]
Abstract
Structure-based drug design is underway to inhibit the S100B-p53 interaction as a strategy for treating malignant melanoma. X-ray crystallography was used here to characterize an interaction between Ca(2)(+)-S100B and TRTK-12, a target that binds to the p53-binding site on S100B. The structures of Ca(2+)-S100B (1.5-A resolution) and S100B-Ca(2)(+)-TRTK-12 (2.0-A resolution) determined here indicate that the S100B-Ca(2+)-TRTK-12 complex is dominated by an interaction between Trp7 of TRTK-12 and a hydrophobic binding pocket exposed on Ca(2+)-S100B involving residues in helices 2 and 3 and loop 2. As with an S100B-Ca(2)(+)-p53 peptide complex, TRTK-12 binding to Ca(2+)-S100B was found to increase the protein's Ca(2)(+)-binding affinity. One explanation for this effect was that peptide binding introduced a structural change that increased the number of Ca(2+) ligands and/or improved the Ca(2+) coordination geometry of S100B. This possibility was ruled out when the structures of S100B-Ca(2+)-TRTK-12 and S100B-Ca(2+) were compared and calcium ion coordination by the protein was found to be nearly identical in both EF-hand calcium-binding domains (RMSD=0.19). On the other hand, B-factors for residues in EF2 of Ca(2+)-S100B were found to be significantly lowered with TRTK-12 bound. This result is consistent with NMR (15)N relaxation studies that showed that TRTK-12 binding eliminated dynamic properties observed in Ca(2+)-S100B. Such a loss of protein motion may also provide an explanation for how calcium-ion-binding affinity is increased upon binding a target. Lastly, it follows that any small-molecule inhibitor bound to Ca(2+)-S100B would also have to cause an increase in calcium-ion-binding affinity to be effective therapeutically inside a cell, so these data need to be considered in future drug design studies involving S100B.
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Affiliation(s)
- Thomas H Charpentier
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
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