1
|
Yu D, Lu Z, Chong Y. Integrins as a bridge between bacteria and cells: key targets for therapeutic wound healing. BURNS & TRAUMA 2024; 12:tkae022. [PMID: 39015251 PMCID: PMC11250365 DOI: 10.1093/burnst/tkae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 12/17/2023] [Accepted: 04/22/2024] [Indexed: 07/18/2024]
Abstract
Integrins are heterodimers composed of α and β subunits that are bonded through non-covalent interactions. Integrins mediate the dynamic connection between extracellular adhesion molecules and the intracellular actin cytoskeleton. Integrins are present in various tissues and organs where these heterodimers participate in diverse physiological and pathological responses at the molecular level in living organisms. Wound healing is a crucial process in the recovery from traumatic diseases and comprises three overlapping phases: inflammation, proliferation and remodeling. Integrins are regulated during the entire wound healing process to enhance processes such as inflammation, angiogenesis and re-epithelialization. Prolonged inflammation may result in failure of wound healing, leading to conditions such as chronic wounds. Bacterial colonization of a wound is one of the primary causes of chronic wounds. Integrins facilitate the infectious effects of bacteria on the host organism, leading to chronic inflammation, bacterial colonization, and ultimately, the failure of wound healing. The present study investigated the role of integrins as bridges for bacteria-cell interactions during wound healing, evaluated the role of integrins as nodes for bacterial inhibition during chronic wound formation, and discussed the challenges and prospects of using integrins as therapeutic targets in wound healing.
Collapse
Affiliation(s)
- Dong Yu
- Department of Traditional Chinese Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368 Hanjiang Middle Road, Yangzhou 225000, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368 Hanjiang Middle Road, Yangzhou 225000, Jiangsu, China
| | - Zhaoyu Lu
- Department of Traditional Chinese Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368 Hanjiang Middle Road, Yangzhou 225000, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368 Hanjiang Middle Road, Yangzhou 225000, Jiangsu, China
| | - Yang Chong
- Department of Traditional Chinese Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368 Hanjiang Middle Road, Yangzhou 225000, Jiangsu, China
- Department of General Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, No. 368 Hanjiang Middle Road, Yangzhou 225000, Jiangsu, China
| |
Collapse
|
2
|
Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol 2024; 20:751-760. [PMID: 38480980 PMCID: PMC11142920 DOI: 10.1038/s41589-024-01562-z] [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: 02/14/2023] [Accepted: 01/25/2024] [Indexed: 05/30/2024]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.
Collapse
Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Li He
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Huong T Kratochvil
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Sarah E Nick
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Weiya Bai
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Anne Edwards
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, New Haven, CT, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
| |
Collapse
|
3
|
Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
Collapse
|
4
|
Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
Collapse
Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
5
|
Bassereau P. Concluding remarks: peptide-membrane interactions. Faraday Discuss 2021; 232:482-493. [PMID: 34825682 DOI: 10.1039/d1fd00077b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article is based on the concluding remarks lecture given at the Faraday Discussion meeting on peptide-membrane interactions, held online, 8-10th September 2021.
Collapse
Affiliation(s)
- Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France.
| |
Collapse
|
6
|
Michael M, Parsons M. New perspectives on integrin-dependent adhesions. Curr Opin Cell Biol 2020; 63:31-37. [PMID: 31945690 PMCID: PMC7262580 DOI: 10.1016/j.ceb.2019.12.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/04/2019] [Accepted: 12/14/2019] [Indexed: 01/12/2023]
Abstract
Integrins are heterodimeric transmembrane receptors that connect the extracellular matrix environment to the actin cytoskeleton via adaptor molecules through assembly of a range of adhesion structures. Recent advances in biochemical, imaging and biophysical methods have enabled a deeper understanding of integrin signalling and their associated regulatory processes. The identification of the consensus integrin-based 'adhesomes' within the last 5 years has defined common core components of adhesion complexes and associated partners. These approaches have also uncovered unexpected adhesion protein behaviour and molecules recruited to adhesion sites that have expanded our understanding of the molecular and physical control of integrin signalling.
Collapse
Affiliation(s)
- Magdalene Michael
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Cam, London, SE1 1UL, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunts House, Guys Cam, London, SE1 1UL, UK.
| |
Collapse
|
7
|
Zheng Y, Leftheris K. Insights into Protein–Ligand Interactions in Integrin Complexes: Advances in Structure Determinations. J Med Chem 2020; 63:5675-5696. [DOI: 10.1021/acs.jmedchem.9b01869] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yajun Zheng
- Pliant Therapeutics, South San Francisco, California 94080, United States
| | - Katerina Leftheris
- Pliant Therapeutics, South San Francisco, California 94080, United States
| |
Collapse
|
8
|
McKay MJ, Fu R, Greathouse DV, Koeppe RE. Breaking the Backbone: Central Arginine Residues Induce Membrane Exit and Helix Distortions within a Dynamic Membrane Peptide. J Phys Chem B 2019; 123:8034-8047. [PMID: 31483653 DOI: 10.1021/acs.jpcb.9b06034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane domains of membrane proteins sometimes contain conserved charged or ionizable residues which may be essential for protein function and regulation. This work examines the molecular interactions of single Arg residues within a highly dynamic transmembrane peptide helix. To this end, we have modified the GW4,20ALP23 (acetyl-GGAW4(AL)7AW20AGA-amide) model peptide framework to incorporate Arg residues near the center of the peptide. Peptide helix formation, orientation and dynamics were analyzed by means of solid-state NMR spectroscopy to monitor specific 2H- or 15N-labeled residues. GW4,20ALP23 itself adopts a tilted orientation within lipid bilayer membranes. Nevertheless, the GW4,20ALP23 helix exhibits moderate to high dynamic averaging of NMR observables, such as 2H quadrupolar splittings or 15N-1H dipolar couplings, due to competition between the interfacial Trp residues on opposing helix faces. Here we examine how the helix dynamics are impacted by the introduction of a single Arg residue at position 12 or 14. Residue R14 restricts the helix to low dynamic averaging and a well-defined tilt that varies inversely with the lipid bilayer thickness. To compensate for the dominance of R14, the competing Trp residues cause partial unwinding of the helix at the C-terminal. By contrast, R12GW4,20ALP23 exits the DOPC bilayer to an interfacial surface-bound location. Interestingly, multiple orientations are exhibited by a single residue, Ala-9. Quadrupolar splittings generated by 2H-labeled residues A3, A5, A7, and A9 do not fit to the α-helical quadrupolar wave plot defined by residues A11, A13, A15, A17, A19, and A21. The discontinuity at residue A9 implicates a helical swivel distortion and an apparent 310-helix involving the N-terminal residues preceding A11. These molecular features suggest that, while arginine residues are prominent factors controlling transmembrane helix dynamics, the influence of interfacial tryptophan residues cannot be ignored.
Collapse
Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University , Tallahassee , Florida 32310 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| |
Collapse
|