1
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Samanta R, Zhuang X, Varney KM, Weber DJ, Matysiak S. Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator. J Chem Inf Model 2024; 64:3477-3487. [PMID: 38605537 DOI: 10.1021/acs.jcim.4c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Allostery is an essential biological phenomenon in which perturbation at one site in a biomolecule elicits a functional response at a distal location(s). It is integral to biological processes, such as cellular signaling, metabolism, and transcription regulation. Understanding allostery is also crucial for rational drug discovery. In this work, we focus on an allosteric S100B protein that belongs to the S100 class of EF-hand Ca2+-binding proteins. The Ca2+-binding affinity of S100B is modulated allosterically by TRTK-12 peptide binding 25 Å away from the Ca2+-binding site. We investigated S100B allostery by carrying out nuclear magnetic resonance (NMR) measurements along with microsecond-long molecular dynamics (MD) simulations on S100B/Ca2+ with/without TRTK-12 at different NaCl salt concentrations. NMR HSQC results show that TRTK-12 reorganizes how S100B/Ca2+ responds to different salt concentrations at both orthosteric and allosteric sites. The MD data suggest that TRTK-12 breaks the dynamic aromatic and hydrogen-bond interactions (not observed in X-ray crystallographic structures) between the hinge/helix and Ca2+-binding EF-hand loop of the two subunits in the homodimeric protein. This triggers rearrangement in the protein network architectures and leads to allosteric communication. Finally, computational studies of S100B at distinct ionic strengths suggest that ligand-bound species are more robust to the changing environment relative to the S100B/Ca2+ complex.
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Affiliation(s)
- Riya Samanta
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
| | - Xinhao Zhuang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland 20742, United States
| | - David J Weber
- IBBR, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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2
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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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Yoder MW, Wright NT, Borzok MA. Calpain Regulation and Dysregulation-Its Effects on the Intercalated Disk. Int J Mol Sci 2023; 24:11726. [PMID: 37511485 PMCID: PMC10380737 DOI: 10.3390/ijms241411726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The intercalated disk is a cardiac specific structure composed of three main protein complexes-adherens junctions, desmosomes, and gap junctions-that work in concert to provide mechanical stability and electrical synchronization to the heart. Each substructure is regulated through a variety of mechanisms including proteolysis. Calpain proteases, a class of cysteine proteases dependent on calcium for activation, have recently emerged as important regulators of individual intercalated disk components. In this review, we will examine how calcium homeostasis regulates normal calpain function. We will also explore how calpains modulate gap junctions, desmosomes, and adherens junctions activity by targeting specific proteins, and describe the molecular mechanisms of how calpain dysregulation leads to structural and signaling defects within the heart. We will then examine how changes in calpain activity affects cardiomyocytes, and how such changes underlie various heart diseases.
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Affiliation(s)
- Micah W Yoder
- Biochemistry, Chemistry, Engineering, and Physics Department, Commonwealth University of Pennsylvania, 31 Academy St., Mansfield, PA 16933, USA
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, USA
| | - Maegen A Borzok
- Biochemistry, Chemistry, Engineering, and Physics Department, Commonwealth University of Pennsylvania, 31 Academy St., Mansfield, PA 16933, USA
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4
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Smith M, Li P. Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. J Chem Inf Model 2023; 63:354-361. [PMID: 36507851 DOI: 10.1021/acs.jcim.2c01411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Calcium-binding proteins play critical roles in various biological processes such as signal transduction, cell growth, and transcription factor regulation. Ion binding and target binding of Ca2+-binding proteins are highly related. Therefore, understanding the ion binding mechanism will benefit the relevant inhibitor design toward the Ca2+-binding proteins. The EF-hand is the typical ion binding motif in Ca2+-binding proteins. Previous studies indicate that the ion binding affinity of the EF-hand increases with the peptide length, but this mechanism has not been fully understood. Herein, using molecular dynamics simulations, thermodynamic integration calculations, and molecular mechanics Poisson-Boltzmann surface area analysis, we systematically investigated four Ca2+-binding peptides containing the EF-hand loop in site III of rabbit skeletal troponin C. These four peptides have 13, 21, 26, and 34 residues. Our simulations reproduced the observed trend that the ion binding affinity increases with the peptide length. Our results implied that the E-helix motif preceding the EF-hand loop, likely the Phe99 residue in particular, plays a significant role in this regulation. The E-helix has a significant impact on the backbone and side-chain conformations of the Asp103 residue, rigidifying important hydrogen bonds in the EF-hand and decreasing the solvent exposure of the Ca2+ ion, hence leading to more favorable Ca2+ binding in longer peptides. The present study provides molecular insights into the ion binding in the EF-hand and establishes an important step toward elucidating the responses of Ca2+-binding proteins toward the ion and target availability.
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Affiliation(s)
- Madelyn Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, Illinois 60660, United States
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, Illinois 60660, United States
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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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Mendelman N, Meirovitch E. SRLS Analysis of 15N- 1H NMR Relaxation from the Protein S100A1: Dynamic Structure, Calcium Binding, and Related Changes in Conformational Entropy. J Phys Chem B 2021; 125:805-816. [PMID: 33449683 DOI: 10.1021/acs.jpcb.0c10124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report on amide (N-H) NMR relaxation from the protein S100A1 analyzed with the slowly relaxing local structure (SRLS) approach. S100A1 comprises two calcium-binding "EF-hands" (helix-loop-helix motifs) connected by a linker. The dynamic structure of this protein, in both calcium-free and calcium-bound form, is described as the restricted local N-H motion coupled to isotropic protein tumbling. The restrictions are given by a rhombic potential, u (∼10 kT), the local motion by a diffusion tensor with rate constant D2 (∼109 s-1), and principal axis tilted from the N-H bond at angle β (10-20°). This parameter combination provides a physically insightful picture of the dynamic structure of S100A1 from the N-H bond perspective. Calcium binding primarily affects the C-terminal EF-hand, among others slowing down the motion of helices III and IV approximately 10-fold. Overall, it brings about significant changes in the shape of the local potential, u, and the orientation of the local diffusion axis, β. Conformational entropy derived from u makes an unfavorable entropic contribution to the free energy of calcium binding estimated at 8.6 ± 0.5 kJ/mol. The N-terminal EF-hand undergoes moderate changes. These findings provide new insights into the calcium-binding process. The same data were analyzed previously with the extended model-free (EMF) method, which is a simple limit of SRLS. In that interpretation, the protein tumbles anisotropically. Locally, calcium binding increases ordering in the loops of S100A1 and conformational exchange (Rex) in the helices of its N-terminal EF-hand. These are very unusual features. We show that they most likely stem from problematic data-fitting, oversimplifications inherent in EMF, and experimental imperfections. Rex is shown to be mainly a fit parameter. By reanalyzing the experimental data with SRLS, which is largely free of these deficiencies, we obtain-as delineated above-physically-relevant structural, kinetic, geometric, and binding information.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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8
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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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9
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Xiao Y, Shaw GS, Konermann L. Calcium-Mediated Control of S100 Proteins: Allosteric Communication via an Agitator/Signal Blocking Mechanism. J Am Chem Soc 2017; 139:11460-11470. [PMID: 28758397 DOI: 10.1021/jacs.7b04380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Allosteric proteins possess dynamically coupled residues for the propagation of input signals to distant target binding sites. The input signals usually correspond to "effector is present" or "effector is not present". Many aspects of allosteric regulation remain incompletely understood. This work focused on S100A11, a dimeric EF-hand protein with two hydrophobic target binding sites. An annexin peptide (Ax) served as the target. Target binding is allosterically controlled by Ca2+ over a distance of ∼26 Å. Ca2+ promotes formation of a [Ca4 S100 Ax2] complex, where the Ax peptides are accommodated between helices III/IV and III'/IV'. Without Ca2+ these binding sites are closed, precluding interactions with Ax. The allosteric mechanism was probed by microsecond MD simulations in explicit water, complemented by hydrogen exchange mass spectrometry (HDX/MS). Consistent with experimental data, MD runs in the absence of Ca2+ and Ax culminated in target binding site closure. In simulations on [Ca4 S100] the target binding sites remained open. These results capture the essence of allosteric control, revealing how Ca2+ prevents binding site closure. Both HDX/MS and MD data showed that the metalation sites become more dynamic after Ca2+ loss. However, these enhanced dynamics do not represent the primary trigger of the allosteric cascade. Instead, a labile salt bridge acts as an incessantly active "agitator" that destabilizes the packing of adjacent residues, causing a domino chain of events that culminates in target binding site closure. This agitator represents the starting point of the allosteric signal propagation pathway. Ca2+ binding rigidifies elements along this pathway, thereby blocking signal transmission. This blocking mechanism does not conform to the commonly held view that allosteric communication pathways generally originate at the sites where effectors interact with the protein.
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Affiliation(s)
- Yiming Xiao
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Gary S Shaw
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
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10
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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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11
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Pálfy G, Kiss B, Nyitray L, Bodor A. Multilevel Changes in Protein Dynamics upon Complex Formation of the Calcium-Loaded S100A4 with a Nonmuscle Myosin IIA Tail Fragment. Chembiochem 2016; 17:1829-1838. [PMID: 27418229 DOI: 10.1002/cbic.201600280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 11/11/2022]
Abstract
Dysregulation of Ca2+ -binding S100 proteins plays important role in various diseases. The asymmetric complex of Ca2+ -bound S100A4 with nonmuscle myosin IIA has high stability and highly increased Ca2+ affinity. Here we investigated the possible causes of this allosteric effect by NMR spectroscopy. Chemical shift-based secondary-structure analysis did not show substantial changes for the complex. Backbone dynamics revealed slow-timescale local motions in the H1 helices of homodimeric S100A4; these were less pronounced in the complex form and might be accompanied by an increase in dimer stability. Different mobilities in the Ca2+ -coordinating EF-hand sites indicate that they communicate by an allosteric mechanism operating through changes in protein dynamics; this must be responsible for the elevated Ca2+ affinity. These multilevel changes in protein dynamics as conformational adaptation allow S100A4 fine-tuning of its protein-protein interactions inside the cell during Ca2+ signaling.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1 A, 1117, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1 A, 1117, Budapest, Hungary.
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12
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Cavalier MC, Ansari MI, Pierce AD, Wilder PT, McKnight LE, Raman EP, Neau DB, Bezawada P, Alasady MJ, Charpentier TH, Varney KM, Toth EA, MacKerell AD, Coop A, Weber DJ. Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. J Med Chem 2016; 59:592-608. [PMID: 26727270 DOI: 10.1021/acs.jmedchem.5b01369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The drug pentamidine inhibits calcium-dependent complex formation with p53 ((Ca)S100B·p53) in malignant melanoma (MM) and restores p53 tumor suppressor activity in vivo. However, off-target effects associated with this drug were problematic in MM patients. Structure-activity relationship (SAR) studies were therefore completed here with 23 pentamidine analogues, and X-ray structures of (Ca)S100B·inhibitor complexes revealed that the C-terminus of S100B adopts two different conformations, with location of Phe87 and Phe88 being the distinguishing feature and termed the "FF-gate". For symmetric pentamidine analogues ((Ca)S100B·5a, (Ca)S100B·6b) a channel between sites 1 and 2 on S100B was occluded by residue Phe88, but for an asymmetric pentamidine analogue ((Ca)S100B·17), this same channel was open. The (Ca)S100B·17 structure illustrates, for the first time, a pentamidine analog capable of binding the "open" form of the "FF-gate" and provides a means to block all three "hot spots" on (Ca)S100B, which will impact next generation (Ca)S100B·p53 inhibitor design.
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Affiliation(s)
- Michael C Cavalier
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Mohd Imran Ansari
- Computer Aided Drug Design Center, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Adam D Pierce
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Laura E McKnight
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - E Prabhu Raman
- Computer Aided Drug Design Center, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | | | - Padmavani Bezawada
- Computer Aided Drug Design Center, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Milad J Alasady
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Thomas H Charpentier
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Eric A Toth
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Alexander D MacKerell
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Computer Aided Drug Design Center, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Andrew Coop
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Computer Aided Drug Design Center, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - David J Weber
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine , Baltimore, Maryland 21201, United States.,Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
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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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Hartman KG, Vitolo MI, Pierce AD, Fox JM, Shapiro P, Martin SS, Wilder PT, Weber DJ. Complex formation between S100B protein and the p90 ribosomal S6 kinase (RSK) in malignant melanoma is calcium-dependent and inhibits extracellular signal-regulated kinase (ERK)-mediated phosphorylation of RSK. J Biol Chem 2014; 289:12886-95. [PMID: 24627490 DOI: 10.1074/jbc.m114.561613] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
S100B is a prognostic marker for malignant melanoma. Increasing S100B levels are predictive of advancing disease stage, increased recurrence, and low overall survival in malignant melanoma patients. Using S100B overexpression and shRNA(S100B) knockdown studies in melanoma cell lines, elevated S100B was found to enhance cell viability and modulate MAPK signaling by binding directly to the p90 ribosomal S6 kinase (RSK). S100B-RSK complex formation was shown to be Ca(2+)-dependent and to block ERK-dependent phosphorylation of RSK, at Thr-573, in its C-terminal kinase domain. Additionally, the overexpression of S100B sequesters RSK into the cytosol and prevents it from acting on nuclear targets. Thus, elevated S100B contributes to abnormal ERK/RSK signaling and increased cell survival in malignant melanoma.
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Affiliation(s)
- Kira G Hartman
- From the Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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15
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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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16
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Smith FJ, Pau VP, Cingolani G, Rothberg BS. Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain. Nat Commun 2013; 4:2621. [DOI: 10.1038/ncomms3621] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/16/2013] [Indexed: 12/24/2022] Open
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17
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The evolution of S100B inhibitors for the treatment of malignant melanoma. Future Med Chem 2013; 5:97-109. [PMID: 23256816 DOI: 10.4155/fmc.12.191] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Malignant melanoma continues to be an extremely fatal cancer due to a lack of viable treatment options for patients. The calcium-binding protein S100B has long been used as a clinical biomarker, aiding in malignant melanoma staging and patient prognosis. However, the discovery of p53 as a S100B target and the consequent impact on cell apoptosis redirected research efforts towards the development of inhibitors of this S100B-p53 interaction. Several approaches, including computer-aided drug design, fluorescence polarization competition assays, NMR, x-ray crystallography and cell-based screens have been performed to identify compounds that block the S100B-p53 association, reactivate p53 transcriptional activities and induce cancer cell death. Eight promising compounds, including pentamidine, are presented in this review and the potential for future modifications is discussed. Synthesis of compound derivatives will likely exhibit increased S100B affinity and mimic important S100B-target dynamic properties that will result in high specificity.
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