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Heid LF, Agerschou ED, Orr AA, Kupreichyk T, Schneider W, Wördehoff MM, Schwarten M, Willbold D, Tamamis P, Stoldt M, Hoyer W. Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation. Comput Struct Biotechnol J 2024; 23:417-430. [PMID: 38223341 PMCID: PMC10787225 DOI: 10.1016/j.csbj.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
β-Structure-rich amyloid fibrils are hallmarks of several diseases, including Alzheimer's (AD), Parkinson's (PD), and type 2 diabetes (T2D). While amyloid fibrils typically consist of parallel β-sheets, the anti-parallel β-hairpin is a structural motif accessible to amyloidogenic proteins in their monomeric and oligomeric states. Here, to investigate implications of β-hairpins in amyloid formation, potential β-hairpin-forming amyloidogenic segments in the human proteome were predicted based on sequence similarity with β-hairpins previously observed in Aβ, α-synuclein, and islet amyloid polypeptide, amyloidogenic proteins associated with AD, PD, and T2D, respectively. These three β-hairpins, established upon binding to the engineered binding protein β-wrapin AS10, are characterized by proximity of two sequence segments rich in hydrophobic and aromatic amino acids, with high β-aggregation scores according to the TANGO algorithm. Using these criteria, 2505 potential β-hairpin-forming amyloidogenic segments in 2098 human proteins were identified. Characterization of a test set of eight protein segments showed that seven assembled into Thioflavin T-positive aggregates and four formed β-hairpins in complex with AS10 according to NMR. One of those is a segment of prostatic acid phosphatase (PAP) comprising amino acids 185-208. PAP is naturally cleaved into fragments, including PAP(248-286) which forms functional amyloid in semen. We find that PAP(185-208) strongly decreases the protein concentrations required for fibril formation of PAP(248-286) and of another semen amyloid peptide, SEM1(86-107), indicating that it promotes nucleation of semen amyloids. In conclusion, β-hairpin-forming amyloidogenic protein segments could be identified in the human proteome with potential roles in functional or disease-related amyloid formation.
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Affiliation(s)
- Laetitia F. Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Emil Dandanell Agerschou
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, United States
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Walfried Schneider
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Michael M. Wördehoff
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Melanie Schwarten
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3033, United States
| | - Matthias Stoldt
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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2
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Heid LF, Kupreichyk T, Schützmann MP, Schneider W, Stoldt M, Hoyer W. Nucleation of α-Synuclein Amyloid Fibrils Induced by Cross-Interaction with β-Hairpin Peptides Derived from Immunoglobulin Light Chains. Int J Mol Sci 2023; 24:16132. [PMID: 38003322 PMCID: PMC10671648 DOI: 10.3390/ijms242216132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Heterologous interactions between different amyloid-forming proteins, also called cross-interactions, may have a critical impact on disease-related amyloid formation. β-hairpin conformers of amyloid-forming proteins have been shown to affect homologous interactions in the amyloid self-assembly process. Here, we applied two β-hairpin-forming peptides derived from immunoglobulin light chains as models to test how heterologous β-hairpins modulate the fibril formation of Parkinson's disease-associated protein α-synuclein (αSyn). The peptides SMAhp and LENhp comprise β-strands C and C' of the κ4 antibodies SMA and LEN, which are associated with light chain amyloidosis and multiple myeloma, respectively. SMAhp and LENhp bind with high affinity to the β-hairpin-binding protein β-wrapin AS10 according to isothermal titration calorimetry and NMR spectroscopy. The addition of SMAhp and LENhp affects the kinetics of αSyn aggregation monitored by Thioflavin T (ThT) fluorescence, with the effect depending on assay conditions, salt concentration, and the applied β-hairpin peptide. In the absence of agitation, substoichiometric concentrations of the hairpin peptides strongly reduce the lag time of αSyn aggregation, suggesting that they support the nucleation of αSyn amyloid fibrils. The effect is also observed for the aggregation of αSyn fragments lacking the N-terminus or the C-terminus, indicating that the promotion of nucleation involves the interaction of hairpin peptides with the hydrophobic non-amyloid-β component (NAC) region.
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Affiliation(s)
- Laetitia F. Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marie P. Schützmann
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Walfried Schneider
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Matthias Stoldt
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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3
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Hu J, Zhao Y, Li Y. Rationally designed amyloid inhibitors based on amyloid-related structural studies. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Orr AA, Kuhlmann SK, Tamamis P. Computational design of a β-wrapin's N-terminal domain with canonical and non-canonical amino acid modifications mimicking curcumin's proposed inhibitory function. Biophys Chem 2022; 286:106805. [DOI: 10.1016/j.bpc.2022.106805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/14/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
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Abstract
The concept of engineering robust protein scaffolds for novel binding functions emerged 20 years ago, one decade after the advent of recombinant antibody technology. Early examples were the Affibody, Monobody (Adnectin), and Anticalin proteins, which were derived from fragments of streptococcal protein A, from the tenth type III domain of human fibronectin, and from natural lipocalin proteins, respectively. Since then, this concept has expanded considerably, including many other protein templates. In fact, engineered protein scaffolds with useful binding specificities, mostly directed against targets of biomedical relevance, constitute an area of active research today, which has yielded versatile reagents as laboratory tools. However, despite strong interest from basic science, only a handful of those protein scaffolds have undergone biopharmaceutical development up to the clinical stage. This includes the abovementioned pioneering examples as well as designed ankyrin repeat proteins (DARPins). Here we review the current state and clinical validation of these next-generation therapeutics.
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Affiliation(s)
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany;
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6
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Saini RK, Goyal D, Goyal B. Targeting Human Islet Amyloid Polypeptide Aggregation and Toxicity in Type 2 Diabetes: An Overview of Peptide-Based Inhibitors. Chem Res Toxicol 2020; 33:2719-2738. [PMID: 33124419 DOI: 10.1021/acs.chemrestox.0c00416] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Type 2 diabetes (T2D) is a chronic metabolic disease characterized by insulin resistance and a progressive loss of pancreatic islet β-cell mass, which leads to insufficient secretion of insulin and hyperglycemia. Emerging evidence suggests that toxic oligomers and fibrils of human islet amyloid polypeptide (hIAPP) contribute to the death of β-cells and lead to T2D pathogenesis. These observations have opened new avenues for the development of islet amyloid therapies for the treatment of T2D. The peptide-based inhibitors are of great value as therapeutic agents against hIAPP aggregation in T2D owing to their biocompatibility, feasibility of synthesis and modification, high specificity, low toxicity, proteolytic stability (modified peptides), and weak immunogenicity as well as the large size of involved interfaces during self-aggregation of hIAPP. An understanding of what has been done and achieved will provide key insights into T2D pathology and assist in the discovery of more potent drug candidates for the treatment of T2D. In this article, we review various peptide-based inhibitors of hIAPP aggregation, including those derived from the hIAPP sequence and those not based on the sequence, consisting of both natural as well as unnatural amino acids and their derivatives. The present review will be beneficial in advancing the field of peptide medicine for the treatment of T2D.
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Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab India
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7
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Frame NM, Kumanan M, Wales TE, Bandara A, Fändrich M, Straub JE, Engen JR, Gursky O. Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A. J Mol Biol 2020; 432:1978-1995. [PMID: 32035904 PMCID: PMC7225066 DOI: 10.1016/j.jmb.2020.01.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/28/2023]
Abstract
Serum amyloid A (SAA) is a plasma protein that transports lipids during inflammation. To explore SAA solution conformations and lipid-binding mechanism, we used hydrogen-deuterium exchange mass spectrometry, lipoprotein reconstitution, amino acid sequence analysis, and molecular dynamics simulations. Solution conformations of lipid-bound and lipid-free mSAA1 at pH~7.4 agreed in details with the crystal structures but also showed important differences. The results revealed that amphipathic α-helices h1 and h3 comprise a lipid-binding site that is partially pre-formed in solution, is stabilized upon binding lipids, and shows lipid-induced folding of h3. This site sequesters apolar ligands via a concave hydrophobic surface in SAA oligomers. The largely disordered/dynamic C-terminal region is conjectured to mediate the promiscuous binding of other ligands. The h1-h2 linker region is predicted to form an unexpected β-hairpin that may represent an early amyloidogenic intermediate. The results help establish structural underpinnings for understanding SAA interactions with its key functional ligands, its evolutional conservation, and its transition to amyloid.
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Affiliation(s)
- Nicholas M Frame
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, United States
| | - Meera Kumanan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Asanga Bandara
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, United States
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, 89081, Germany
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, United States.
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States.
| | - Olga Gursky
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, United States; Amyloidosis Treatment and Research Center, Boston University School of Medicine, Boston, MA, 02118, United States.
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8
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Gonzalez-Rivera JC, Orr AA, Engels SM, Jakubowski JM, Sherman MW, O'Connor KN, Matteson T, Woodcock BC, Contreras LM, Tamamis P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Comput Struct Biotechnol J 2020; 18:137-152. [PMID: 31988703 PMCID: PMC6965710 DOI: 10.1016/j.csbj.2019.12.003] [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: 08/24/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/02/2022] Open
Abstract
The oxidation of RNA has been implicated in the development of many diseases. Among the four ribonucleotides, guanosine is the most susceptible to oxidation, resulting in the formation of 8-oxo-7,8-dihydroguanosine (8-oxoG). Despite the limited knowledge about how cells regulate the detrimental effects of oxidized RNA, cellular factors involved in its regulation have begun to be identified. One of these factors is polynucleotide phosphorylase (PNPase), a multifunctional enzyme implicated in RNA turnover. In the present study, we have examined the interaction of PNPase with 8-oxoG in atomic detail to provide insights into the mechanism of 8-oxoG discrimination. We hypothesized that PNPase subunits cooperate to form a binding site using the dynamic SFF loop within the central channel of the PNPase homotrimer. We evolved this site using a novel approach that initially screened mutants from a library of beneficial mutations and assessed their interactions using multi-nanosecond Molecular Dynamics simulations. We found that evolving this single site resulted in a fold change increase in 8-oxoG affinity between 1.2 and 1.5 and/or selectivity between 1.5 and 1.9. In addition to the improvement in 8-oxoG binding, complementation of K12 Δpnp with plasmids expressing mutant PNPases caused increased cell tolerance to H2O2. This observation provides a clear link between molecular discrimination of RNA oxidation and cell survival. Moreover, this study provides a framework for the manipulation of modified-RNA protein readers, which has potential application in synthetic biology and epitranscriptomics.
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Affiliation(s)
- Juan C. Gonzalez-Rivera
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Sean M. Engels
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Joseph M. Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Mark W. Sherman
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
| | - Katherine N. O'Connor
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Tomas Matteson
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
| | - Brendan C. Woodcock
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
- Corresponding authors at: McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States (L.M. Contreras).
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
- Corresponding authors at: McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States (L.M. Contreras).
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9
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Jakubowski J, Orr AA, Le DA, Tamamis P. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:289-305. [PMID: 31809572 PMCID: PMC7732148 DOI: 10.1021/acs.jcim.9b00561] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 12/24/2022]
Abstract
The aggregation of amyloid-β (Aβ) peptides into senile plaques is a hallmark of Alzheimer's disease (AD) and is hypothesized to be the primary cause of AD related neurodegeneration. Previous studies have shown the ability of curcumin to both inhibit the aggregation of Aβ peptides into oligomers or fibrils and reduce amyloids in vivo. Despite the promise of curcumin and its derivatives to serve as diagnostic, preventative, and potentially therapeutic AD molecules, the mechanism by which curcumin and its derivatives bind to and inhibit Aβ fibrils' formation remains elusive. Here, we investigated curcumin and a set of curcumin derivatives in complex with a hexamer peptide model of the Aβ1-42 fibril using nearly exhaustive docking, followed by multi-ns molecular dynamics simulations, to provide atomistic-detail insights into the molecules' binding and inhibitory properties. In the vast majority of the simulations, curcumin and its derivatives remain firmly bound in complex with the fibril through primarily three different principle binding modes, in which the molecules interact with residue domain 17LVFFA21, in line with previous experiments. In a small subset of these simulations, the molecules partly dissociate the outermost peptide of the Aβ1-42 fibril by disrupting β-sheets within the residue domain 12VHHQKLVFF20. A comparison between binding modes leading or not leading to partial dissociation of the outermost peptide suggests that the latter is attributed to a few subtle key structural and energetic interaction-based differences. Interestingly, partial dissociation appears to be either an outcome of high affinity interactions or a cause leading to high affinity interactions between the molecules and the fibril, which could partly serve as a compensation for the energy loss in the fibril due to partial dissociation. In conjunction with this, we suggest a potential inhibition mechanism of Αβ1-42 aggregation by the molecules, where the partially dissociated 16KLVFF20 domain of the outermost peptide could either remain unstructured or wrap around to form intramolecular interactions with the same peptide's 29GAIIG33 domain, while the molecules could additionally act as a patch against the external edge of the second outermost peptide's 16KLVFF20 domain. Thereby, individually or concurrently, these could prohibit fibril elongation.
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Affiliation(s)
| | | | - Doan A. Le
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Phanourios Tamamis
- Artie McFerrin Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
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10
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Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J 2019; 118:492-504. [PMID: 31839263 DOI: 10.1016/j.bpj.2019.11.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
The attractant chemotaxis response of Escherichia coli to norepinephrine requires that it be converted to 3,4-dihydroxymandelic acid (DHMA) by the monoamine oxidase TynA and the aromatic aldehyde dehydrogenase FeaB. DHMA is sensed by the serine chemoreceptor Tsr, and the attractant response requires that at least one subunit of the periplasmic domain of the Tsr homodimer (pTsr) has an intact serine-binding site. DHMA that is generated in vivo by E. coli is expected to be a racemic mixture of the (R) and (S) enantiomers, so it has been unclear whether one or both chiral forms are active. Here, we used a combination of state-of-the-art tools in molecular docking and simulations, including an in-house simulation-based docking protocol, to investigate the binding properties of (R)-DHMA and (S)-DHMA to E. coli pTsr. Our studies computationally predicted that (R)-DHMA should promote a stronger attractant response than (S)-DHMA because of a consistently greater-magnitude piston-like pushdown of the pTsr α-helix 4 toward the membrane upon binding of (R)-DHMA than upon binding of (S)-DHMA. This displacement is caused primarily by interaction of DHMA with Tsr residue Thr156, which has been shown by genetic studies to be critical for the attractant response to L-serine and DHMA. These findings led us to separate the two chiral species and test their effectiveness as chemoattractants. Both the tethered cell and motility migration coefficient assays validated the prediction that (R)-DHMA is a stronger attractant than (S)-DHMA. Our study demonstrates that refined computational docking and simulation studies combined with experiments can be used to investigate situations in which subtle differences between ligands may lead to diverse chemotactic responses.
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Affiliation(s)
- Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Jingyun Yang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Nitesh Sule
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Michael D Manson
- Department of Biology, Texas A&M University, College Station, Texas.
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.
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11
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Activation of COUP-TFI by a Novel Diindolylmethane Derivative. Cells 2019; 8:cells8030220. [PMID: 30866413 PMCID: PMC6468570 DOI: 10.3390/cells8030220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI) is an orphan receptor and member of the nuclear receptor superfamily. Among a series of methylene substituted diindolylmethanes (C-DIMs) containing substituted phenyl and heteroaromatic groups, we identified 1,1-bis(3'-indolyl)-1-(4-pyridyl)-methane (DIM-C-Pyr-4) as an activator of COUP-TFI. Structure activity studies with structurally diverse heteroaromatic C-DIMs showed that the pyridyl substituted compound was active and the 4-pyridyl substituent was more potent than the 2- or 3-pyridyl analogs in transactivation assays in breast cancer cells. The DIM-C-Pyr-4 activated chimeric GAL4-COUP-TFI constructs containing full length, C- or N-terminal deletions, and transactivation was inhibited by phosphatidylinositol-3-kinase and protein kinase A inhibitors. However, DIM-C-Pyr-4 also induced transactivation and interactions of COUP-TFI and steroid receptor coactivators-1 and -2 in mammalian two-hybrid assays, and ligand-induced interactions of the C-terminal region of COUP-TFI were not affected by kinase inhibitors. We also showed that DIM-C-Pyr-4 activated COUP-TFI-dependent early growth response 1 (Egr-1) expression and this response primarily involved COUP-TFI interactions with Sp3 and to a lesser extent Sp1 bound to the proximal region of the Egr-1 promoter. Modeling studies showed interactions of DIM-C-Pyr-4 within the ligand binding domain of COUP-TFI. This report is the first to identify a COUP-TFI agonist and demonstrate activation of COUP-TFI-dependent Egr-1 expression.
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12
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Cell Responses to Extracellular α-Synuclein. Molecules 2019; 24:molecules24020305. [PMID: 30650656 PMCID: PMC6359176 DOI: 10.3390/molecules24020305] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/25/2022] Open
Abstract
Synucleins are small naturally unfolded proteins involved in neurodegenerative diseases and cancer. The family contains three members: α-, β-, and -synuclein. α-Synuclein is the most thoroughly investigated because of its close association with Parkinson's disease (PD), dementia with Lewy bodies and multiple system atrophy. Until recently, the synuclein's research was mainly focused on their intracellular forms. However, new studies highlighted the important role of extracellular synucleins. Extracellular forms of synucleins propagate between various types of cells, bind to cell surface receptors and transmit signals, regulating numerous intracellular processes. Here we give an update of the latest results about the mechanisms of action of extracellular synucleins, their binding to cell surface receptors, effect on biochemical pathways and the role in neurodegeneration and neuroinflammation.
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13
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Jonnalagadda SVR, Kokotidou C, Orr AA, Fotopoulou E, Henderson KJ, Choi CH, Lim WT, Choi SJ, Jeong HK, Mitraki A, Tamamis P. Computational Design of Functional Amyloid Materials with Cesium Binding, Deposition, and Capture Properties. J Phys Chem B 2018; 122:7555-7568. [DOI: 10.1021/acs.jpcb.8b04103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
| | | | - Emmanouela Fotopoulou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
| | | | | | - Woo Taik Lim
- Department of Applied Chemistry, Andong National University, Andong 36729, Republic of Korea
| | - Sang June Choi
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
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