1
|
Dwivedi N, Patra B, Mentink-Vigier F, Wi S, Sinha N. Unveiling Charge-Pair Salt-Bridge Interaction Between GAGs and Collagen Protein in Cartilage: Atomic Evidence from DNP-Enhanced ssNMR at Natural Isotopic Abundance. J Am Chem Soc 2024. [PMID: 38980938 DOI: 10.1021/jacs.4c05539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The interactions between glycosaminoglycans (GAGs) and proteins are essential in numerous biochemical processes that involve ion-pair interactions. However, there is no evidence of direct and specific interactions between GAGs and collagen proteins in native cartilage. The resolution of solid-state NMR (ssNMR) can offer such information but the detection of GAG interactions in cartilage is limited by the sensitivity of the experiments when 13C and 15N isotopes are at natural abundance. In this communication, this limitation is overcome by taking advantage of dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) experiments to obtain two-dimensional (2D) 15N-13C and 13C-13C correlations on native samples at natural abundance. These experiments unveiled inter-residue correlations in the aliphatic regions of the collagen protein previously unobserved. Additionally, our findings provide direct evidence of charge-pair salt-bridge interactions between negatively charged GAGs and positively charged arginine (Arg) residues of collagen protein. We also identified potential hydrogen bonding interactions between hydroxyproline (Hyp) and GAGs, offering atomic insights into the biochemical interactions within the extracellular matrix of native cartilage. Our approach may provide a new avenue for the structural characterization of other native systems.
Collapse
Affiliation(s)
- Navneet Dwivedi
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, India
| | - Bijaylaxmi Patra
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Sungsool Wi
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
2
|
Yosefi G, Kass I, Rapaport H, Bitton R. Decoupling Charge and Side Chain Effects in Hierarchical Organization of Cationic PFX Peptide and Alginate. Biomacromolecules 2024; 25:4168-4176. [PMID: 38902961 DOI: 10.1021/acs.biomac.4c00278] [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: 06/22/2024]
Abstract
We have successfully created self-assembled membranes by combining positively charged (Pro-X-(Phe-X)5-Pro) PFX peptides with negatively charged alginate. These PFX/alginate membranes were formed by three different peptides that contain either X = Arginine (R), Histidine (H), or Ornithine (O) as their charged amino acid. The assemblies were compared to membranes that were previously reported by us composed of X = lysine (K). This study enabled us to elucidate the impact of amino acids' specific interactions on membrane formation. SEM, SAXS, and cryo-TEM measurements show that although K, R, H, and O may have a similar net charge, the specific traits of the charged amino acid is an essential factor in determining the hierarchical structure of alginate/PFX self-assembled membranes.
Collapse
Affiliation(s)
- Gal Yosefi
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Itamar Kass
- Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Hanna Rapaport
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ronit Bitton
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| |
Collapse
|
3
|
Messina JM, Luo M, Hossan MS, Gadelrab HA, Yang X, John A, Wilmore JR, Luo J. Unveiling cytokine charge disparity as a potential mechanism for immune regulation. Cytokine Growth Factor Rev 2024; 77:1-14. [PMID: 38184374 DOI: 10.1016/j.cytogfr.2023.12.002] [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: 11/20/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
Cytokines are small signaling proteins that regulate the immune responses to infection and tissue damage. Surface charges of cytokines determine their in vivo fate in immune regulation, e.g., half-life and distribution. The overall negative charges in the extracellular microenvironment and the acidosis during inflammation and infection may differentially impact cytokines with different surface charges for fine-tuned immune regulation via controlling tissue residential properties. However, the trend and role of cytokine surface charges has yet to be elucidated in the literature. Interestingly, we have observed that most pro-inflammatory cytokines have a negative charge, while most anti-inflammatory cytokines and chemokines have a positive charge. In this review, we extensively examined the surface charges of all cytokines and chemokines, summarized the pharmacokinetics and tissue adhesion of major cytokines, and analyzed the link of surface charge with cytokine biodistribution, activation, and function in immune regulation. Additionally, we identified that the general trend of charge disparity between pro- and anti-inflammatory cytokines represents a unique opportunity to develop precise immune modulation approaches, which can be applied to many inflammation-associated diseases including solid tumors, chronic wounds, infection, and sepsis.
Collapse
Affiliation(s)
- Jennifer M Messina
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States
| | - Minghao Luo
- Department of Clinical Medicine, 2nd Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Md Shanewaz Hossan
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States
| | - Hadil A Gadelrab
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States
| | - Xiguang Yang
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States
| | - Anna John
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States
| | - Joel R Wilmore
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States; Upstate Sepsis Interdisciplinary Research Center, State University of New York Upstate Medical University, Syracuse, NY 13210, United States
| | - Juntao Luo
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States; Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY 13210, United States; Department of Surgery, State University of New York Upstate Medical University, Syracuse, NY 13210, United States; Upstate Cancer Center, State University of New York Upstate Medical University, Syracuse, NY 13210, United States; Upstate Sepsis Interdisciplinary Research Center, State University of New York Upstate Medical University, Syracuse, NY 13210, United States.
| |
Collapse
|
4
|
Shen H, Zhang C, Li S, Liang Y, Lee LT, Aggarwal N, Wun KS, Liu J, Nadarajan SP, Weng C, Ling H, Tay JK, Wang DY, Yao SQ, Hwang IY, Lee YS, Chang MW. Prodrug-conjugated tumor-seeking commensals for targeted cancer therapy. Nat Commun 2024; 15:4343. [PMID: 38773197 PMCID: PMC11109227 DOI: 10.1038/s41467-024-48661-y] [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: 09/25/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Prodrugs have been explored as an alternative to conventional chemotherapy; however, their target specificity remains limited. The tumor microenvironment harbors a range of microorganisms that potentially serve as tumor-targeting vectors for delivering prodrugs. In this study, we harness bacteria-cancer interactions native to the tumor microbiome to achieve high target specificity for prodrug delivery. We identify an oral commensal strain of Lactobacillus plantarum with an intrinsic cancer-binding mechanism and engineer the strain to enable the surface loading of anticancer prodrugs, with nasopharyngeal carcinoma (NPC) as a model cancer. The engineered commensals show specific binding to NPC via OppA-mediated recognition of surface heparan sulfate, and the loaded prodrugs are activated by tumor-associated biosignals to release SN-38, a chemotherapy compound, near NPC. In vitro experiments demonstrate that the prodrug-loaded microbes significantly increase the potency of SN-38 against NPC cell lines, up to 10-fold. In a mouse xenograft model, intravenous injection of the engineered L. plantarum leads to bacterial colonization in NPC tumors and a 67% inhibition in tumor growth, enhancing the efficacy of SN-38 by 54%.
Collapse
Affiliation(s)
- Haosheng Shen
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
| | - Changyu Zhang
- Ningbo Institute of Dalian University of Technology, Ningbo, China
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Shengjie Li
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Li Ting Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
| | - Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
| | - Kwok Soon Wun
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National Centre for Engineering Biology (NCEB), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jing Liu
- Department of Otolaryngology, Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Saravanan Prabhu Nadarajan
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cheng Weng
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Wilmar International Limited, Singapore, Singapore
| | - Joshua K Tay
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - De Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Food, Chemical and Biotechnology, Singapore Institute of Technology, Singapore, Singapore.
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- National Centre for Engineering Biology (NCEB), Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
5
|
Li M, Xue Y, Chi L, Jin L. Heparin Oligosaccharides as Vasoactive Intestinal Peptide Inhibitors via their Binding Process Characterization. Curr Protein Pept Sci 2024; 25:480-491. [PMID: 38284716 DOI: 10.2174/0113892037287189240122110819] [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: 11/09/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND It has been proven that vasoactive intestinal peptide (VIP) was involved in the pathogenesis of prostate cancer. Cardin et al. found that by an alanine scan, the heparin- binding site on VIP was exactly the same sequence in VIP and its receptor. Therefore, heparin could competitively block the binding of VIP and its receptor. However, the structure-activity relationship between heparin and VIP has not been reported, especially in terms of the sequence and sulfation patterns of heparin oligosaccharides upon binding to VIP. OBJECTIVE A variety of experiments were designed to study the binding process and structure-activity relationship between heparin oligosaccharides and VIP. METHODS Heparin was enzymatically digested and purified to produce heparin oligosaccharides, and the structures were characterized by NMR. The binding capacity between heparin oligosaccharides and VIP was analyzed by GMSA and ITC experiments. The binding between heparin oligosaccharides and VIP was simulated using a molecular docking program to show the complex. ELISA assay was used to investigate the effect of non-anticoagulant heparin oligosaccharides on the VIP-mediated cAMP/PKA signaling pathway in vitro. RESULTS The results indicated that both the length and the sulfation pattern of heparin oligosaccharides affected its binding to VIP. VIP could induce the expression of cAMP at a higher level in PC3 cells, which could be regulated by the interaction of heparin oligosaccharides and VIP. CONCLUSION The binding between heparin oligosaccharides and VIP could block the binding between VIP and its receptor on tumor cells. Downloading the regulation of the expression level of cAMP could possibly further affect the subsequent activation of PKA. These non-anticoagulant heparin oligosaccharides may block the VIP-mediated cAMP/PKA signaling pathway and thus exert their antitumor activity.
Collapse
Affiliation(s)
- Meixin Li
- National Glycoengineering Research Center, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate- based Medicine, Shandong University, Qingdao, Shandong, 266237, China
| | - Yaqi Xue
- National Glycoengineering Research Center, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate- based Medicine, Shandong University, Qingdao, Shandong, 266237, China
| | - Lianli Chi
- National Glycoengineering Research Center, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate- based Medicine, Shandong University, Qingdao, Shandong, 266237, China
| | - Lan Jin
- National Glycoengineering Research Center, NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate- based Medicine, Shandong University, Qingdao, Shandong, 266237, China
| |
Collapse
|
6
|
Yosefi G, Eliraz N, Kolusheva S, Rapaport H, Bitton R. Self-assembly at the interface of λ-carrageenan and amphiphilic and cationic peptides: More than meets the eye. J Colloid Interface Sci 2023; 652:1897-1907. [PMID: 37690297 DOI: 10.1016/j.jcis.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/27/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Self-assembly of macroscopic membranes at the interface between self-assembling peptides and aqueous polymer solutions of opposite charge has been explored mostly due to the membranes' unique hierarchical structure of three distinct regions, including a layer of perpendicular fibers. We report here on the formation and characterization of self-assembled membranes made with λ-carrageenan and the cationic β-sheet peptides, Pro-Lys-(Phe-Lys)5-Pro (PFK). Using SAXS, SEM, ITC, and rheology, we compared these membranes' morphology and physical properties to membranes made with alginate. We recognized that the polysaccharide's single chain conformation, its solution's viscosity, the potential of hydrogen bonding and electrostatic interactions between the polysaccharides and the peptides charged groups, and the strength of these interactions all affect the properties of the resulting membranes. As a result, we identified that an interplay between the polymer-peptide strength of interactions and the stiffness of the polysaccharide's single chain could be used as a route to control the structure-function relationship of the membranes. These results provide valuable information for creating guidelines to design self-assembly membranes with specific properties.
Collapse
Affiliation(s)
- Gal Yosefi
- Department of Chemical Engineering Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nitsan Eliraz
- Department of Chemical Engineering Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Hanna Rapaport
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ronit Bitton
- Department of Chemical Engineering Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology (IKI), Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| |
Collapse
|
7
|
Schulze C, Danielsson A, Liwo A, Huster D, Samsonov SA, Penk A. Ligand binding of interleukin-8: a comparison of glycosaminoglycans and acidic peptides. Phys Chem Chem Phys 2023; 25:24930-24947. [PMID: 37694394 DOI: 10.1039/d3cp02457a] [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: 09/12/2023]
Abstract
Recognition and binding of regulatory proteins to glycosaminoglycans (GAGs) from the extracellular matrix is a process of high biological importance. The interaction between negatively charged sulfate or carboxyl groups of the GAGs and clusters of basic amino acids on the protein is crucial in this binding process and it is believed that electrostatics represent the key factor for this interaction. However, given the rather undirected nature of electrostatics, it is important to achieve a clear understanding of its role in protein-GAG interactions and how specificity and selectivity in these systems can be achieved, when the classical key-lock binding motif is not applicable. Here, we compare protein binding of a highly charged heparin (HP) hexasaccharide with four de novo designed decapeptides of varying negative net charge. The charge density of these peptides was comparable to typical GAGs of the extracellular matrix. We used the regulatory protein interleukin-8 (IL-8) because its interactions with GAGs are well described. All four peptide ligands bind to the same epitope of IL-8 but show much weaker binding affinity as revealed in 1H-15N HSQC NMR titration experiments. Complementary molecular docking and molecular dynamics simulations revealed further atomistic details of the interaction mode of GAG versus peptide ligands. Overall, similar contributions to the binding energy and hydrogen bond formation are determined for HP and the highly charged peptides, suggesting that the entropic loss of the peptides upon binding likely account for the remarkably different affinity of GAG versus peptide ligands to IL-8.
Collapse
Affiliation(s)
- Christian Schulze
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Anja Penk
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| |
Collapse
|
8
|
Schäffler M, Samantray S, Strodel B. Transition Networks Unveil Disorder-to-Order Transformations in A β Caused by Glycosaminoglycans or Lipids. Int J Mol Sci 2023; 24:11238. [PMID: 37510997 PMCID: PMC10380057 DOI: 10.3390/ijms241411238] [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: 05/23/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The aggregation of amyloid-β (Aβ) peptides, particularly of Aβ1-42, has been linked to the pathogenesis of Alzheimer's disease. In this study, we focus on the conformational change of Aβ1-42 in the presence of glycosaminoglycans (GAGs) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids using molecular dynamics simulations. We analyze the conformational changes that occur in Aβ by extracting the key structural features that are then used to generate transition networks. Using the same three features per network highlights the transitions from intrinsically disordered states ubiquitous in Aβ1-42 in solution to more compact states arising from stable β-hairpin formation when Aβ1-42 is in the vicinity of a GAG molecule, and even more compact states characterized by a α-helix or β-sheet structures when Aβ1-42 interacts with a POPC lipid cluster. We show that the molecular mechanisms underlying these transitions from disorder to order are different for the Aβ1-42/GAG and Aβ1-42/POPC systems. While in the latter the hydrophobicity provided by the lipid tails facilitates the folding of Aβ1-42, in the case of GAG there are hardly any intermolecular Aβ1-42-GAG interactions. Instead, GAG removes sodium ions from the peptide, allowing stronger electrostatic interactions within the peptide that stabilize a β-hairpin. Our results contribute to the growing knowledge of the role of GAGs and lipids in the conformational preferences of the Aβ peptide, which in turn influences its aggregation into toxic oligomers and amyloid fibrils.
Collapse
Affiliation(s)
- Moritz Schäffler
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Suman Samantray
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
9
|
Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
Collapse
Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| |
Collapse
|
10
|
Hogwood J, Mulloy B, Lever R, Gray E, Page CP. Pharmacology of Heparin and Related Drugs: An Update. Pharmacol Rev 2023; 75:328-379. [PMID: 36792365 DOI: 10.1124/pharmrev.122.000684] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/17/2023] Open
Abstract
Heparin has been used extensively as an antithrombotic and anticoagulant for close to 100 years. This anticoagulant activity is attributed mainly to the pentasaccharide sequence, which potentiates the inhibitory action of antithrombin, a major inhibitor of the coagulation cascade. More recently it has been elucidated that heparin exhibits anti-inflammatory effect via interference of the formation of neutrophil extracellular traps and this may also contribute to heparin's antithrombotic activity. This illustrates that heparin interacts with a broad range of biomolecules, exerting both anticoagulant and nonanticoagulant actions. Since our previous review, there has been an increased interest in these nonanticoagulant effects of heparin, with the beneficial role in patients infected with SARS2-coronavirus a highly topical example. This article provides an update on our previous review with more recent developments and observations made for these novel uses of heparin and an overview of the development status of heparin-based drugs. SIGNIFICANCE STATEMENT: This state-of-the-art review covers recent developments in the use of heparin and heparin-like materials as anticoagulant, now including immunothrombosis observations, and as nonanticoagulant including a role in the treatment of SARS-coronavirus and inflammatory conditions.
Collapse
Affiliation(s)
- John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Rebeca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| |
Collapse
|
11
|
Pągielska M, Samsonov SA. Molecular Dynamics-Based Comparative Analysis of Chondroitin and Dermatan Sulfates. Biomolecules 2023; 13:biom13020247. [PMID: 36830616 PMCID: PMC9953526 DOI: 10.3390/biom13020247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Glycosaminoglycans (GAGs) are a class of linear anionic periodic polysaccharides containing disaccharide repetitive units. These molecules interact with a variety of proteins in the extracellular matrix and so participate in biochemically crucial processes such as cell signalling affecting tissue regeneration as well as the onset of cancer, Alzheimer's or Parkinson's diseases. Due to their flexibility, periodicity and chemical heterogeneity, often termed "sulfation code", GAGs are challenging molecules both for experiments and computation. One of the key questions in the GAG research is the specificity of their intermolecular interactions. In this study, we make a step forward to deciphering the "sulfation code" of chondroitin sulfates-4,6 (CS4, CS6, where the numbers correspond to the position of sulfation in NAcGal residue) and dermatan sulfate (DS), which is different from CSs by the presence of IdoA acid instead of GlcA. We rigorously investigate two sets of these GAGs in dimeric, tetrameric and hexameric forms with molecular dynamics-based descriptors. Our data clearly suggest that CS4, CS6 and DS are substantially different in terms of their structural, conformational and dynamic properties, which contributes to the understanding of how these molecules can be different when they bind proteins, which could have practical implications for the GAG-based drug design strategies in the regenerative medicine.
Collapse
|
12
|
Pomin VH, Rajarathnam K. NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions. Methods Mol Biol 2023; 2597:143-157. [PMID: 36374420 DOI: 10.1007/978-1-0716-2835-5_12] [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] [Indexed: 06/16/2023]
Abstract
Humans express around 50 chemokines that play crucial roles in human pathophysiology from combating infection to immune surveillance by directing and trafficking leukocytes to the target tissue. Glycosaminoglycans (GAGs) regulate chemokine function by tuning monomer/dimer levels, chemotactic/haptotactic gradients, and how they are presented to their receptors. Knowledge of the structural features of the chemokine-GAG complexes and GAG properties that define chemokine interactions is essential not only to understand chemokine function, but also for developing drugs that disrupt chemokine-GAG crosstalk and thereby impart protection against dysregulated host defense. Nuclear magnetic resonance (NMR) spectroscopy has proven to be quite useful for providing residue-specific interactions, binding geometry and models, specificity, and affinity. Multiple NMR methods have been used including (1) chemical shift perturbation (CSP), (2) saturation transfer difference (STD), and (3) paramagnetic relaxation enhancement (PRE) techniques. In this chapter, we describe how NMR CSP, STD, and PRE can be best used for characterizing chemokine-GAG interactions.
Collapse
Affiliation(s)
- Vitor H Pomin
- Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USA.
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, Department of Microbiology and Immunology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| |
Collapse
|
13
|
O'Connor A, Jurado‐Martín I, Mysior MM, Manzira AL, Drabinska J, Simpson JC, Lucey M, Schaffer K, Berisio R, McClean S. A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis. Microbiologyopen 2022; 12:e1311. [PMID: 36825886 PMCID: PMC9733578 DOI: 10.1002/mbo3.1311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δusp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.
Collapse
Affiliation(s)
- Andrew O'Connor
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
| | - Irene Jurado‐Martín
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Margaritha M. Mysior
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland,Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Anotidaishe L. Manzira
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Jeremy C. Simpson
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland,Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Mary Lucey
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Kirsten Schaffer
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| |
Collapse
|
14
|
Guvench O. Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes. Molecules 2022; 27:7276. [PMID: 36364098 PMCID: PMC9658939 DOI: 10.3390/molecules27217276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2023] Open
Abstract
This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.
Collapse
Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Avenue, Portland, ME 04103, USA
| |
Collapse
|
15
|
Chapman AVE, Elmore JM, McReynolds M, Walley JW, Wise RP. SGT1-Specific Domain Mutations Impair Interactions with the Barley MLA6 Immune Receptor in Association with Loss of NLR Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:274-289. [PMID: 34889653 DOI: 10.1094/mpmi-08-21-0217-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Mla (Mildew resistance locus a) of barley (Hordeum vulgare L.) is an effective model for cereal immunity against fungal pathogens. Like many resistance proteins, variants of the MLA coiled-coil nucleotide-binding leucine-rich repeat (CC-NLR) receptor often require the HRS complex (HSP90, RAR1, and SGT1) to function. However, functional analysis of Sgt1 has been particularly difficult, as deletions are often lethal. Recently, we identified rar3 (required for Mla6 resistance 3), an in-frame Sgt1ΔKL308-309 mutation in the SGT1-specific domain, that alters resistance conferred by MLA but without lethality. Here, we use autoactive MLA6 and recombinant yeast-two-hybrid strains with stably integrated HvRar1 and HvHsp90 to determine that this mutation weakens but does not entirely disrupt the interaction between SGT1 and MLA. This causes a concomitant reduction in MLA6 protein accumulation below the apparent threshold required for effective resistance. The ΔKL308-309 deletion had a lesser effect on intramolecular interactions than alanine or arginine substitutions, and MLA variants that display diminished interactions with SGT1 appear to be disproportionately affected by the SGT1ΔKL308-309 mutation. We hypothesize that those dimeric plant CC-NLRs that appear unaffected by Sgt1 silencing are those with the strongest intermolecular interactions with it. Combining our data with recent work in CC-NLRs, we propose a cyclical model of the MLA-HRS resistosome interactions.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
Collapse
Affiliation(s)
- Antony V E Chapman
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - J Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Maxwell McReynolds
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, U.S.A
| | - Justin W Walley
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, U.S.A
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, U.S.A
| |
Collapse
|
16
|
Joseph PRB, Sepuru KM, Poluri KM, Rajarathnam K. Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions. Methods Mol Biol 2022; 2303:13-23. [PMID: 34626366 DOI: 10.1007/978-1-0716-1398-6_2] [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] [Indexed: 06/13/2023]
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy and, in particular, chemical shift perturbation (CSP) titration experiments are ideally suited for mapping and characterizing the binding interface of macromolecular complexes. 1H-15N-HSQC-based CSP studies have become the method of choice due to their simplicity, short-time requirements, and minimal working knowledge of NMR. CSP studies for characterizing protein-glycosaminoglycan (GAG) interactions can be challenging due to binding-induced aggregation/precipitation and/or poor quality data. In this chapter, we discuss how optimizing experimental conditions such as protein concentration, choice of buffer pH, ionic strength, and GAG size, as well as sensitivity of NMR instrumentation can overcome these roadblocks to obtain meaningful structural insights into protein-GAG interactions.
Collapse
Affiliation(s)
- Prem Raj B Joseph
- Departments of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Mohan Sepuru
- Departments of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Krishna Rajarathnam
- Departments of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
17
|
Cao S, Liu M, Sehrawat TS, Shah VH. Regulation and functional roles of chemokines in liver diseases. Nat Rev Gastroenterol Hepatol 2021; 18:630-647. [PMID: 33976393 PMCID: PMC9036964 DOI: 10.1038/s41575-021-00444-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2021] [Indexed: 02/03/2023]
Abstract
Inflammation is a major contributor to the pathogenesis of almost all liver diseases. Low-molecular-weight proteins called chemokines are the main drivers of liver infiltration by immune cells such as macrophages, neutrophils and others during an inflammatory response. During the past 25 years, tremendous progress has been made in understanding the regulation and functions of chemokines in the liver. This Review summarizes three main aspects of the latest advances in the study of chemokine function in liver diseases. First, we provide an overview of chemokine biology, with a particular focus on the genetic and epigenetic regulation of chemokine transcription as well as on the cell type-specific production of chemokines by liver cells and liver-associated immune cells. Second, we highlight the functional roles of chemokines in liver homeostasis and their involvement in progression to disease in both human and animal models. Third, we discuss the therapeutic opportunities targeting chemokine production and signalling in the treatment of liver diseases, such as alcohol-associated liver disease and nonalcoholic steatohepatitis, including the relevant preclinical studies and ongoing clinical trials.
Collapse
|
18
|
Tiwari N, Wi S, Mentink-Vigier F, Sinha N. Mechanistic Insights into the Structural Stability of Collagen-Containing Biomaterials Such as Bones and Cartilage. J Phys Chem B 2021; 125:4757-4766. [PMID: 33929847 PMCID: PMC8151626 DOI: 10.1021/acs.jpcb.1c01431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural stability of various collagen-containing biomaterials such as bones and cartilage is still a mystery. Despite the spectroscopic development of several decades, the detailed mechanism of collagen interaction with citrate in bones and glycosaminoglycans (GAGs) in the cartilage extracellular matrix (ECM) in its native state is unobservable. We present a significant advancement to probe the collagen interactions with citrate and GAGs in the ECM of native bones and cartilage along with specific/non-specific interactions inside the collagen assembly at the nanoscopic level through natural-abundance dynamic nuclear polarization-based solid-state nuclear magnetic resonance spectroscopy. The detected molecular-level interactions between citrate-collagen and GAG-collagen inside the native bone and cartilage matrices and other backbone and side-chain interactions in the collagen assembly are responsible for the structural stability and other biomechanical properties of these important classes of biomaterials.
Collapse
Affiliation(s)
- Nidhi Tiwari
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow – 226014, INDIA
- Department of Chemistry, Institute of Sciences, Banaras Hindu University, Varanasi – 221005, INDIA
| | - Sungsool Wi
- National High Magnetic Field Laboratory, Tallahassee, Florida 32304, USA
| | | | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow – 226014, INDIA
| |
Collapse
|
19
|
Rajarathnam K, Desai UR. Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges. Front Immunol 2020; 11:660. [PMID: 32391006 PMCID: PMC7193095 DOI: 10.3389/fimmu.2020.00660] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/23/2020] [Indexed: 01/01/2023] Open
Abstract
Proteoglycans (PGs), present in diverse environments, such as the cell membrane surface, extracellular milieu, and intracellular granules, are fundamental to life. Sulfated glycosaminoglycans (GAGs) are covalently attached to the core protein of proteoglycans. PGs are complex structures, and are diverse in terms of amino acid sequence, size, shape, and in the nature and number of attached GAG chains, and this diversity is further compounded by the phenomenal diversity in GAG structures. Chemokines play vital roles in human pathophysiology, from combating infection and cancer to leukocyte trafficking, immune surveillance, and neurobiology. Chemokines mediate their function by activating receptors that belong to the GPCR class, and receptor interactions are regulated by how, when, and where chemokines bind GAGs. GAGs fine-tune chemokine function by regulating monomer/dimer levels and chemotactic/haptotactic gradients, which are also coupled to how they are presented to their receptors. Despite their small size and similar structures, chemokines show a range of GAG-binding geometries, affinities, and specificities, indicating that chemokines have evolved to exploit the repertoire of chemical and structural features of GAGs. In this review, we summarize the current status of research on how GAG interactions regulate ELR-chemokine activation of CXCR1 and CXCR2 receptors, and discuss knowledge gaps that must be overcome to establish causal relationships governing the impact of GAG interactions on chemokine function in human health and disease.
Collapse
Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| |
Collapse
|
20
|
Sepuru KM, Rajarathnam K. Structural basis of chemokine interactions with heparan sulfate, chondroitin sulfate, and dermatan sulfate. J Biol Chem 2019; 294:15650-15661. [PMID: 31455633 DOI: 10.1074/jbc.ra119.009879] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Indexed: 11/06/2022] Open
Abstract
Chemokines play diverse roles in human pathophysiology, ranging from trafficking leukocytes and immunosurveillance to the regulation of metabolism and neural function. Chemokine function is intimately coupled to binding tissue glycosaminoglycans (GAGs), heparan sulfate (HS), chondroitin sulfate (CS), and dermatan sulfate (DS). Currently, very little is known about how the structural features and sequences of a given chemokine, the structure and sulfation pattern of a given GAG, and structural differences among GAGs and among chemokines impact binding interactions. In this study, we used solution NMR spectroscopy to characterize the binding interactions of two related neutrophil-activating chemokines, CXCL1 and CXCL5, with HS, CS, and DS. For both chemokines, the dimer bound all three GAGs with higher affinity than did the monomer, and affinities of the chemokines for CS and DS were lower than for HS. NMR-based structural models reveal diverse binding geometries and show that the binding surfaces for each of the three GAGs were different between the two chemokines. However, a given chemokine had similar binding interactions with CS and DS that were different from HS. Considering the fact that CXCL1 and CXCL5 activate the same CXCR2 receptor, we conclude that GAG interactions play a role in determining the nature of chemokine gradients, levels of free chemokine available for receptor activation, how chemokines bind their receptors, and that differences in these interactions determine chemokine-specific function.
Collapse
Affiliation(s)
- Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1055
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055 .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1055.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1055
| |
Collapse
|
21
|
Hall L, Donovan E, Araya M, Idowa E, Jiminez-Segovia I, Folck A, Wells CD, Kimble-Hill AC. Identification of Specific Lysines and Arginines That Mediate Angiomotin Membrane Association. ACS OMEGA 2019; 4:6726-6736. [PMID: 31179409 PMCID: PMC6547806 DOI: 10.1021/acsomega.9b00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/28/2019] [Indexed: 05/17/2023]
Abstract
The family of Angiomotin (Amot) proteins regulate several biological pathways associated with cellular differentiation, proliferation, and migration. These adaptor proteins target proteins to the apical membrane, actin fibers, or the nucleus. A major function of the Amot coiled-coil homology (ACCH) domain is to initiate protein interactions with the cellular membrane, particularly those containing phosphatidylinositol lipids. The work presented in this article uses several ACCH domain lysine/arginine mutants to probe the relative importance of individual residues for lipid binding. This identified four lysine and three arginine residues that mediate full lipid binding. Based on these findings, three of these residues were mutated to glutamates in the Angiomotin 80 kDa splice form and were incorporated into human mammary cell lines. Results show that mutating three of these residues in the context of full-length Angiomotin reduced the residence of the protein at the apical membrane. These findings provide new insight into how the ACCH domain mediates lipid binding to enable Amot proteins to control epithelial cell growth.
Collapse
Affiliation(s)
- Le’Celia Hall
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Emily Donovan
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Michael Araya
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Eniola Idowa
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ilse Jiminez-Segovia
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Anthony Folck
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Clark D. Wells
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ann C. Kimble-Hill
- Department of Biochemistry
and Molecular Biology, Indiana University
School of Medicine, Room MS 4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| |
Collapse
|