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Serra R, Rallo V, Steri M, Olla S, Piras MG, Marongiu M, Gorospe M, Schlessinger D, Pinna A, Fiorillo E, Cucca F, Angius A. A large-scale screening identified in USH2A gene the P3272L founder pathogenic variant explaining familial Usher syndrome in Sardinia, Italy. BMC Ophthalmol 2024; 24:306. [PMID: 39044131 PMCID: PMC11265335 DOI: 10.1186/s12886-024-03578-4] [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: 05/24/2023] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Usher syndrome (USH) encompasses a group of disorders characterized by congenital sensorineural hearing loss (SNHL) and retinitis pigmentosa (RP). We described the clinical findings, natural history, and molecular analyses of USH patients identified during a large-scale screening to identify quantitative traits related to ocular disorders in the SardiNIA project cohort. METHODS We identified 3 USH-affected families out of a cohort of 6,148 healthy subjects. 9 subjects presented a pathological phenotype, with SNHL and RP. All patients and their family members underwent a complete ophthalmic examination including best-corrected visual acuity, slit-lamp biomicroscopy, fundoscopy, fundus autofluorescence, spectral-domain optical coherence tomography, and electrophysiological testing. Audiological evaluation was performed with a clinical audiometer. Genotyping was performed using several arrays integrated with whole genome sequence data providing approximately 22 million markers equally distributed for each subject analyzed. Molecular diagnostics focused on analysis of the following candidate genes: MYO7A, USH1C, CDH23, PCDH15, USH1G, CIB2, USH2A, GPR98, DFNB31, CLRN1, and PDZD7. RESULTS A single missense causal variant in USH2A gene was identified in homozygous status in all patients and in heterozygous status in unaffected parents. The presence of multiple homozygous patients with the same phenotypic severity of the syndromic form suggests that the Sardinian USH phenotype is the result of a founder effect on a specific pathogenic variant related haplotype. The frequency of heterozygotes in general Sardinian population is 1.89. Additionally, to provide new insights into the structure of usherin and the pathological mechanisms caused by small pathogenic in-frame variants, like p.Pro3272Leu, molecular dynamics simulations of native and mutant protein-protein and protein-ligand complexes were performed that predicted a destabilization of the protein with a decrease in the free energy change. CONCLUSIONS Our results suggest that our approach is effective for the genetic diagnosis of USH. Based on the heterozygous frequency, targeted screening of this variant in the general population and in families at risk or with familial USH can be suggested. This can lead to more accurate molecular diagnosis, better genetic counseling, and improved molecular epidemiology data that are critical for future intervention plans. TRIAL REGISTRATION We did not perform any health-related interventions for the participants.
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Affiliation(s)
- Rita Serra
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Vincenzo Rallo
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
| | - Maristella Steri
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
| | - Stefania Olla
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
| | - Maria Grazia Piras
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
| | - Michele Marongiu
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute On Aging, Baltimore, MD, USA
| | - David Schlessinger
- Laboratory of Genetics and Genomics, National Institute On Aging, Baltimore, MD, USA
| | - Antonio Pinna
- Department of Medicine, Surgery and Pharmacy Ophthalmology Unit, University of Sassari, Sassari, Italy
| | - Edoardo Fiorillo
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy
| | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Andrea Angius
- Institute of Genetic and Biomedical Research, National Research Council (CNR), Cittadella Universitaria Di Cagliari, C/O S.S 554 Bivio Per Sestu Km 4, 500, 09042, Monserrato, CA, Italy.
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2
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Paulus J, Sewald N. Small molecule- and peptide-drug conjugates addressing integrins: A story of targeted cancer treatment. J Pept Sci 2024; 30:e3561. [PMID: 38382900 DOI: 10.1002/psc.3561] [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: 09/20/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 02/23/2024]
Abstract
Targeted cancer treatment should avoid side effects and damage to healthy cells commonly encountered during traditional chemotherapy. By combining small molecule or peptidic ligands as homing devices with cytotoxic drugs connected by a cleavable or non-cleavable linker in peptide-drug conjugates (PDCs) or small molecule-drug conjugates (SMDCs), cancer cells and tumours can be selectively targeted. The development of highly affine, selective peptides and small molecules in recent years has allowed PDCs and SMDCs to increasingly compete with antibody-drug conjugates (ADCs). Integrins represent an excellent target for conjugates because they are overexpressed by most cancer cells and because of the broad knowledge about native binding partners as well as the multitude of small-molecule and peptidic ligands that have been developed over the last 30 years. In particular, integrin αVβ3 has been addressed using a variety of different PDCs and SMDCs over the last two decades, following various strategies. This review summarises and describes integrin-addressing PDCs and SMDCs while highlighting points of great interest.
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Affiliation(s)
- Jannik Paulus
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
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3
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Ding S, Chen Y, Huang C, Song L, Liang Z, Wei B. Perception and response of skeleton to mechanical stress. Phys Life Rev 2024; 49:77-94. [PMID: 38564907 DOI: 10.1016/j.plrev.2024.03.011] [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: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Mechanical stress stands as a fundamental factor in the intricate processes governing the growth, development, morphological shaping, and maintenance of skeletal mass. The profound influence of stress in shaping the skeletal framework prompts the assertion that stress essentially births the skeleton. Despite this acknowledgment, the mechanisms by which the skeleton perceives and responds to mechanical stress remain enigmatic. In this comprehensive review, our scrutiny focuses on the structural composition and characteristics of sclerotin, leading us to posit that it serves as the primary structure within the skeleton responsible for bearing and perceiving mechanical stress. Furthermore, we propose that osteocytes within the sclerotin emerge as the principal mechanical-sensitive cells, finely attuned to perceive mechanical stress. And a detailed analysis was conducted on the possible transmission pathways of mechanical stress from the extracellular matrix to the nucleus.
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Affiliation(s)
- Sicheng Ding
- Department of Minimally invasive spine surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Yiren Chen
- Department of Minimally invasive spine surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Chengshuo Huang
- Department of Minimally invasive spine surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Lijun Song
- Reproductive Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Zhen Liang
- Department of Minimally invasive spine surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.
| | - Bo Wei
- Department of Minimally invasive spine surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.
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4
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Li J, Jo MH, Yan J, Hall T, Lee J, López-Sánchez U, Yan S, Ha T, Springer TA. Ligand binding initiates single-molecule integrin conformational activation. Cell 2024; 187:2990-3005.e17. [PMID: 38772370 PMCID: PMC11162317 DOI: 10.1016/j.cell.2024.04.049] [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: 10/27/2023] [Revised: 02/21/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Integrins link the extracellular environment to the actin cytoskeleton in cell migration and adhesiveness. Rapid coordination between events outside and inside the cell is essential. Single-molecule fluorescence dynamics show that ligand binding to the bent-closed integrin conformation, which predominates on cell surfaces, is followed within milliseconds by two concerted changes, leg extension and headpiece opening, to give the high-affinity integrin conformation. The extended-closed integrin conformation is not an intermediate but can be directly accessed from the extended-open conformation and provides a pathway for ligand dissociation. In contrast to ligand, talin, which links the integrin β-subunit cytoplasmic domain to the actin cytoskeleton, modestly stabilizes but does not induce extension or opening. Integrin activation is thus initiated by outside-in signaling and followed by inside-out signaling. Our results further imply that talin binding is insufficient for inside-out integrin activation and that tensile force transmission through the ligand-integrin-talin-actin cytoskeleton complex is required.
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Affiliation(s)
- Jing Li
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Myung Hyun Jo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jiabin Yan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Taylor Hall
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joon Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Uriel López-Sánchez
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sophia Yan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Newton South High School, Newton, MA 02459, USA
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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5
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Belyaev AV, Fedotova IV. Molecular mechanisms of catch bonds and their implications for platelet hemostasis. Biophys Rev 2023; 15:1233-1256. [PMID: 37974999 PMCID: PMC10643804 DOI: 10.1007/s12551-023-01144-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/07/2023] [Indexed: 11/19/2023] Open
Abstract
Adhesive molecular bonds between blood cells are essential for thrombosis and hemostasis as they provide means for platelet adhesion, aggregation, and signaling in flowing blood. According to the nowadays conventional definition, a "catch" bond is a type of non-covalent bio-molecular bridge, whose dissociation lifetime counter-intuitively increases with applied tensile force. Following recent experimental findings, such receptor-ligand protein bonds are vital to the blood cells involved in the prevention of bleeding (hemostatic response) and infection (immunity). In this review, we examine the up-to-date experimental discoveries and theoretical insights about catch bonds between the blood cells, their biomechanical principles at the molecular level, and their role in platelet thrombosis and hemostasis.
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Affiliation(s)
- Aleksey V. Belyaev
- Faculty of Physics, M.V.Lomonosov Moscow State University, 1, Leninskiye Gory, build.2, Moscow, 119991 Russia
| | - Irina V. Fedotova
- Faculty of Physics, M.V.Lomonosov Moscow State University, 1, Leninskiye Gory, build.2, Moscow, 119991 Russia
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6
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Zhang H, Zhu DS, Zhu J. Family-wide analysis of integrin structures predicted by AlphaFold2. Comput Struct Biotechnol J 2023; 21:4497-4507. [PMID: 37753178 PMCID: PMC10518446 DOI: 10.1016/j.csbj.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/17/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023] Open
Abstract
Recent advances in protein structure prediction using AlphaFold2, known for its high efficiency and accuracy, have opened new avenues for comprehensive analysis of all structures within a single protein family. In this study, we evaluated the capabilities of AphaFold2 in analyzing integrin structures. Integrins are heterodimeric cell surface receptors composed of a combination of 18 α and 8 β subunits, resulting in a family of 24 different members. Both α and β subunits consist of a large extracellular domain, a short transmembrane domain, and typically, a short cytoplasmic tail. Integrins play a pivotal role in a wide range of cellular functions by recognizing diverse ligands. Despite significant advances in integrin structural studies in recent decades, high-resolution structures have only been determined for a limited subsets of integrin members, thus limiting our understanding of the entire integrin family. Here, we first analyzed the single-chain structures of 18 α and 8 β integrins in the AlphaFold2 protein structure database. We then employed the newly developed AlphaFold2-multimer program to predict the α/β heterodimer structures of all 24 human integrins. The predicted structures show a high level of accuracy for the subdomains of both α and β subunits, offering high-resolution structure insights for all integrin heterodimers. Our comprehensive structural analysis of the entire integrin family unveils a potentially diverse range of conformations among the 24 members, providing a valuable structure database for studies related to integrin structure and function. We further discussed the potential applications and limitations of the AlphaFold2-derived integrin structures.
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Affiliation(s)
- Heng Zhang
- Versiti Blood Research Institute, Milwaukee, WI, USA
| | - Daniel S. Zhu
- Versiti Blood Research Institute, Milwaukee, WI, USA
| | - Jieqing Zhu
- Versiti Blood Research Institute, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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7
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Zhang H, Zhu DS, Zhu J. Family-wide analysis of integrin structures predicted by AlphaFold2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539023. [PMID: 37205578 PMCID: PMC10187181 DOI: 10.1101/2023.05.02.539023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent advances in protein structure prediction using AlphaFold2, known for its high efficiency and accuracy, have opened new avenues for comprehensive analysis of all structures within a single protein family. In this study, we evaluated the capabilities of AphaFold2 in analyzing integrin structures. Integrins are heterodimeric cell surface receptors composed of a combination of 18 α and 8 β subunits, resulting in a family of 24 different members. Both α and β subunits consist of a large extracellular domain, a short transmembrane domain, and typically, a short cytoplasmic tail. Integrins play a pivotal role in a wide range of cellular functions by recognizing diverse ligands. Despite significant advances in integrin structural studies in recent decades, high-resolution structures have only been determined for a limited subsets of integrin members, thus limiting our understanding of the entire integrin family. Here, we first analyzed the single-chain structures of 18 α and 8 β integrins in the AlphaFold2 protein structure database. We then employed the newly developed AlphaFold2-multimer program to predict the α/β heterodimer structures of all 24 human integrins. The predicted structures show a high level of accuracy for the subdomains of both α and β subunits, offering high-resolution structure insights for all integrin heterodimers. Our comprehensive structural analysis of the entire integrin family unveils a potentially diverse range of conformations among the 24 members, providing a valuable structure database for studies related to integrin structure and function. We further discussed the potential applications and limitations of the AlphaFold2-derived integrin structures.
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Affiliation(s)
- Heng Zhang
- Versiti Blood Research Institute, Milwaukee, WI, USA
| | - Daniel S. Zhu
- Versiti Blood Research Institute, Milwaukee, WI, USA
| | - Jieqing Zhu
- Versiti Blood Research Institute, Milwaukee, WI, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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8
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Gu Y, Dong B, He X, Qiu Z, Zhang J, Zhang M, Liu H, Pang X, Cui Y. The challenges and opportunities of αvβ3-based therapeutics in cancer: From bench to clinical trials. Pharmacol Res 2023; 189:106694. [PMID: 36775082 DOI: 10.1016/j.phrs.2023.106694] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]
Abstract
Integrins are main cell adhesion receptors serving as linker attaching cells to extracellular matrix (ECM) and bidirectional hubs transmitting biochemical and mechanical signals between cells and their environment. Integrin αvβ3 is a critical family member of integrins and interacts with ECM proteins containing RGD tripeptide sequence. Accumulating evidence indicated that the abnormal expression of integrin αvβ3 was associated with various tumor progressions, including tumor initiation, sustained tumor growth, distant metastasis, drug resistance development, maintenance of stemness in cancer cells. Therefore, αvβ3 has been explored as a therapeutic target in various types of cancers, but there is no αvβ3 antagonist approved for human therapy. Targeting-integrin αvβ3 therapeutics has been a challenge, but lessons from the past are valuable to the development of innovative targeting approaches. This review systematically summarized the structure, signal transduction, regulatory role in cancer, and drug development history of integrin αvβ3, and also provided new insights into αvβ3-based therapeutics in cancer from bench to clinical trials, which would contribute to developing effective targeting αvβ3 agents for cancer treatment.
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Affiliation(s)
- Yanlun Gu
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China; Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China; Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Bingqi Dong
- Department of General Surgery, Peking University First Hospital, Xishiku street, Xicheng District, 100034 Beijing, China
| | - Xu He
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China; Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Zhiwei Qiu
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China; Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Juqi Zhang
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China; Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Mo Zhang
- Department of traditional Chinese and Western medicine,Peking University Of First Hospital, Xishiku street 8th,Xicheng District,10034 Beijing, China
| | - Haitao Liu
- Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China
| | - Xiaocong Pang
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China; Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China.
| | - Yimin Cui
- Department of Pharmacy, Peking University First Hospital, Xishiku Street, Xicheng District, 100034 Beijing, China; Institute of Clinical Pharmacology, Peking University First Hospital, Xueyuan Road 38, Haidian District, 100191 Beijing, China; Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191 Beijing, China.
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9
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Tvaroška I, Kozmon S, Kóňa J. Molecular Modeling Insights into the Structure and Behavior of Integrins: A Review. Cells 2023; 12:cells12020324. [PMID: 36672259 PMCID: PMC9856412 DOI: 10.3390/cells12020324] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Integrins are heterodimeric glycoproteins crucial to the physiology and pathology of many biological functions. As adhesion molecules, they mediate immune cell trafficking, migration, and immunological synapse formation during inflammation and cancer. The recognition of the vital roles of integrins in various diseases revealed their therapeutic potential. Despite the great effort in the last thirty years, up to now, only seven integrin-based drugs have entered the market. Recent progress in deciphering integrin functions, signaling, and interactions with ligands, along with advancement in rational drug design strategies, provide an opportunity to exploit their therapeutic potential and discover novel agents. This review will discuss the molecular modeling methods used in determining integrins' dynamic properties and in providing information toward understanding their properties and function at the atomic level. Then, we will survey the relevant contributions and the current understanding of integrin structure, activation, the binding of essential ligands, and the role of molecular modeling methods in the rational design of antagonists. We will emphasize the role played by molecular modeling methods in progress in these areas and the designing of integrin antagonists.
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Affiliation(s)
- Igor Tvaroška
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovakia
- Correspondence:
| | - Stanislav Kozmon
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovakia
- Medical Vision o. z., Záhradnícka 4837/55, 821 08 Bratislava, Slovakia
| | - Juraj Kóňa
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovakia
- Medical Vision o. z., Záhradnícka 4837/55, 821 08 Bratislava, Slovakia
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10
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Huet-Calderwood C, Rivera-Molina F, Toomre D, Calderwood DA. Use of Ecto-Tagged Integrins to Monitor Integrin Exocytosis and Endocytosis. Methods Mol Biol 2023; 2608:17-38. [PMID: 36653699 PMCID: PMC9999384 DOI: 10.1007/978-1-0716-2887-4_2] [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] [Indexed: 01/19/2023]
Abstract
Controlled exocytosis and endocytosis of integrin adhesion receptors is required for normal cell adhesion, migration, and signaling. In this chapter, we describe the design of functional β1 integrins carrying extracellular fluorescent or chemically traceable tags (ecto-tag) and methods for their use to image β1 integrin trafficking in cells. We provide approaches to generate cells in which endogenous β1 integrins are replaced by ecto-tagged integrins containing a pH-sensitive fluorophore pHluorin or a HaloTag and describe strategies using photobleaching, selective extracellular/intracellular labeling, and chase, quenching, and blocking to reveal β1 integrin exocytosis, endocytosis, and recycling by live total internal reflection fluorescence (TIRF) microscopy.
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Affiliation(s)
- Clotilde Huet-Calderwood
- Departments of Pharmacology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Felix Rivera-Molina
- Departments of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Derek Toomre
- Departments of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - David A Calderwood
- Departments of Pharmacology, Yale University School of Medicine, Yale University, New Haven, CT, USA.
- Departments of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT, USA.
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11
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Wang A, Yue K, Wei Y, Zhong W, Zhang G. Temperature‐induced structural change of integrin αvβ3 receptor and its interaction with the
RGD
peptide ligand. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anqi Wang
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Kai Yue
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Yiang Wei
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
| | - Weishen Zhong
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Genpei Zhang
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
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12
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Integrin Conformational Dynamics and Mechanotransduction. Cells 2022; 11:cells11223584. [PMID: 36429013 PMCID: PMC9688440 DOI: 10.3390/cells11223584] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
The function of the integrin family of receptors as central mediators of cell-extracellular matrix (ECM) and cell-cell adhesion requires a remarkable convergence of interactions and influences. Integrins must be anchored to the cytoskeleton and bound to extracellular ligands in order to provide firm adhesion, with force transmission across this linkage conferring tissue integrity. Integrin affinity to ligands is highly regulated by cell signaling pathways, altering affinity constants by 1000-fold or more, via a series of long-range conformational transitions. In this review, we first summarize basic, well-known features of integrin conformational states and then focus on new information concerning the impact of mechanical forces on these states and interstate transitions. We also discuss how these effects may impact mechansensitive cell functions and identify unanswered questions for future studies.
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13
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Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2. Cell Rep 2022; 40:111254. [PMID: 36001965 PMCID: PMC9440770 DOI: 10.1016/j.celrep.2022.111254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 05/23/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Allosteric activation and silencing of leukocyte β2-integrins transpire through cation-dependent structural changes, which mediate integrin biosynthesis and recycling, and are essential to designing leukocyte-specific drugs. Stepwise addition of Mg2+ reveals two mutually coupled events for the αXβ2 ligand-binding domain-the αX I-domain-corresponding to allostery establishment and affinity maturation. Electrostatic alterations in the Mg2+-binding site establish long-range couplings, leading to both pH- and Mg2+-occupancy-dependent biphasic stability change in the αX I-domain fold. The ligand-binding sensorgrams show composite affinity events for the αX I-domain accounting for the multiplicity of the αX I-domain conformational states existing in the solution. On cell surfaces, increasing Mg2+ concentration enhanced adhesiveness of αXβ2. This work highlights how intrinsically flexible pH- and cation-sensitive architecture endows a unique dynamic continuum to the αI-domain structure on the intact integrin, thereby revealing the importance of allostery establishment and affinity maturation in both extracellular and intracellular integrin events.
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14
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Multitarget-Based Virtual Screening for Identification of Herbal Substances toward Potential Osteoclastic Targets. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Osteoporosis is a complex bone disease indicating porous bone with low bone mass density and fragility. Cathepsin K, V-ATPase, and αVβ3 integrin are exhibited as novel targets for osteoporosis treatment. Our preliminary study uses a state-of-the-art method, including target-based virtual screening and clustering methods to determine promising candidates with multitarget properties. Phytochemicals with osteoprotective properties from the literature are used to elucidate the molecular interactions toward three targets. The binding scores of compounds are normalized and rescored. The K-means and hierarchical clustering methods are applied to filter and define the promising compounds, and the silhouette analysis is supposed to validate the clustering method. We explore 108 herbal compounds by virtual screening and the cluster approach, and find that rutin, sagittatoside A, icariin, and kaempferitrin showed strong binding affinities against Cathepsin K, V-ATPase, and αVβ3 integrin. Dockings of candidates toward three targets also provide the protein-ligand interactions and crucial amino acids for binding. Our study provides a straightforward and less time-consuming approach to exploring the new multitarget candidates for further investigations, using a combination of in silico methods.
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15
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Analysis of Integrin α IIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains. Int J Mol Sci 2022; 23:ijms23020858. [PMID: 35055046 PMCID: PMC8776176 DOI: 10.3390/ijms23020858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/23/2021] [Accepted: 12/30/2021] [Indexed: 11/17/2022] Open
Abstract
Integrin αIIbβ3, a glycoprotein complex expressed at the platelet surface, is involved in platelet aggregation and contributes to primary haemostasis. Several integrin αIIbβ3 polymorphisms prevent the aggregation that causes haemorrhagic syndromes, such as Glanzmann thrombasthenia (GT). Access to 3D structure allows understanding the structural effects of polymorphisms related to GT. In a previous analysis using Molecular Dynamics (MD) simulations of αIIbCalf-1 domain structure, it was observed that GT associated with single amino acid variation affects distant loops, but not the mutated position. In this study, experiments are extended to Calf-1, Thigh, and Calf-2 domains. Two loops in Calf-2 are unstructured and therefore are modelled expertly using biophysical restraints. Surprisingly, MD revealed the presence of rigid zones in these loops. Detailed analysis with structural alphabet, the Proteins Blocks (PBs), allowed observing local changes in highly flexible regions. The variant P741R located at C-terminal of Calf-1 revealed that the Calf-2 presence did not affect the results obtained with isolated Calf-1 domain. Simulations for Calf-1 + Calf-2, and Thigh + Calf-1 variant systems are designed to comprehend the impact of five single amino acid variations in these domains. Distant conformational changes are observed, thus highlighting the potential role of allostery in the structural basis of GT.
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16
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Kadir SR, Lilja A, Gunn N, Strong C, Hughes RT, Bailey BJ, Rae J, Parton RG, McGhee J. Nanoscape, a data-driven 3D real-time interactive virtual cell environment. eLife 2021; 10:64047. [PMID: 34191720 PMCID: PMC8245131 DOI: 10.7554/elife.64047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Our understanding of cellular and structural biology has reached unprecedented levels of detail, and computer visualisation techniques can be used to create three-dimensional (3D) representations of cells and their environment that are useful in both teaching and research. However, extracting and integrating the relevant scientific data, and then presenting them in an effective way, can pose substantial computational and aesthetic challenges. Here we report how computer artists, experts in computer graphics and cell biologists have collaborated to produce a tool called Nanoscape that allows users to explore and interact with 3D representations of cells and their environment that are both scientifically accurate and visually appealing. We believe that using Nanoscape as an immersive learning application will lead to an improved understanding of the complexities of cellular scales, densities and interactions compared with traditional learning modalities.
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Affiliation(s)
- Shereen R Kadir
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Andrew Lilja
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Nick Gunn
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Campbell Strong
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Rowan T Hughes
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Benjamin J Bailey
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - James Rae
- Institute for Molecular Bioscience, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia
| | - John McGhee
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
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17
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Tomassi S, D’Amore VM, Di Leva FS, Vannini A, Quilici G, Weinmüller M, Reichart F, Amato J, Romano B, Izzo AA, Di Maro S, Novellino E, Musco G, Gianni T, Kessler H, Marinelli L. Halting the Spread of Herpes Simplex Virus-1: The Discovery of an Effective Dual αvβ6/αvβ8 Integrin Ligand. J Med Chem 2021; 64:6972-6984. [PMID: 33961417 PMCID: PMC8279406 DOI: 10.1021/acs.jmedchem.1c00533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 02/08/2023]
Abstract
Over recent years, αvβ6 and αvβ8 Arg-Gly-Asp (RGD) integrins have risen to prominence as interchangeable co-receptors for the cellular entry of herpes simplex virus-1 (HSV-1). In fact, the employment of subtype-specific integrin-neutralizing antibodies or gene-silencing siRNAs has emerged as a valuable strategy for impairing HSV infectivity. Here, we shift the focus to a more affordable pharmaceutical approach based on small RGD-containing cyclic pentapeptides. Starting from our recently developed αvβ6-preferential peptide [RGD-Chg-E]-CONH2 (1), a small library of N-methylated derivatives (2-6) was indeed synthesized in the attempt to increase its affinity toward αvβ8. Among the novel compounds, [RGD-Chg-(NMe)E]-CONH2 (6) turned out to be a potent αvβ6/αvβ8 binder and a promising inhibitor of HSV entry through an integrin-dependent mechanism. Furthermore, the renewed selectivity profile of 6 was fully rationalized by a NMR/molecular modeling combined approach, providing novel valuable hints for the design of RGD integrin ligands with the desired specificity profile.
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Affiliation(s)
- Stefano Tomassi
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Vincenzo Maria D’Amore
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Francesco Saverio Di Leva
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Andrea Vannini
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Giacomo Quilici
- Biomolecular
NMR Unit c/o IRCCS S. Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Michael Weinmüller
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Florian Reichart
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Jussara Amato
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Barbara Romano
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Angelo Antonio Izzo
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania
“Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
- Facoltà
di Medicina e Chirurgia, Università
Cattolica del Sacro Cuore, Largo Francesco Vito, 1, 00168 Roma, Italy
| | - Giovanna Musco
- Biomolecular
NMR Unit c/o IRCCS S. Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Tatiana Gianni
- Department
of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
| | - Horst Kessler
- Institute
for Advanced Study, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Luciana Marinelli
- Dipartimento
di Farmacia, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
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18
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Song G, Luo BH. Effects of the association of the α v β 8 lower legs on integrin ligand binding. J Cell Biochem 2021; 122:801-813. [PMID: 33619784 DOI: 10.1002/jcb.29912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/18/2022]
Abstract
Many integrins transmit signals through global conformational changes. However, it is unclear whether integrin αv β8 adopts a similar mechanism during integrin activation and signaling on the cell surface. Here, we showed that disulfide-bonded mutants, which prevented integrin αv β8 lower leg dissociation, bound ligands with similar level as the wild-type protein, suggesting that αv β8 ligand binding did not require lower leg disassociation. We further showed that the N-glycosylation mutant at the interface between the β I and hybrid domains did not affect ligand binding, suggesting that the αv β8 open headpiece was not present on the cell surface. We proposed that αv β8 integrin may adopt only one state, that is, the extended conformation with a closed headpiece. Our results showed that two lower legs retained heterodimeric interfaces, and this association might be important for stabilizing integrin in the extended conformation. Therefore, αv β8 may not transmit bidirectional signals across the plasma membrane but instead may serve as an anchoring site with high affinity and high accessibility for extracellular ligands.
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Affiliation(s)
- Guannan Song
- Department of Life Science, University of Louisiana State University, Baton Rouge, Louisiana, USA
| | - Bing-Hao Luo
- Department of Life Science, University of Louisiana State University, Baton Rouge, Louisiana, USA
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19
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Dynamics and Physics of Integrin Activation in Tumor Cells by Nano-Sized Extracellular Ligands and Electromagnetic Fields. Methods Mol Biol 2021; 2217:197-233. [PMID: 33215383 DOI: 10.1007/978-1-0716-0962-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Integrins are stress-sensing proteins expressed on the surface of cells. They regulate bidirectional signal transduction during cell-cell or cell-extracellular matrix (ECM) contacts. Integrins link the ECM with the cytoplasm through interaction with their ligands. Biophysically, such interactions can be understood as changes in stress fields at specific integrin stress-sensing domains, such as the MIDAS and ADMIDAS domains. Stress changes between ligands and cytoskeletal structures are involved in cancer cell growth by altering signal transduction pathways dependent on integrin activation. In this chapter, previous results regarding integrin activation and tumor cell growth using nanoparticles (NPs) of different materials, sizes and shapes are placed within a framework of polarized NPs in the ECM by external electromagnetic fields, in which the synergic action between polarized NPs and electromagnetic fields activates the integrins. Small size NPs activate integrins via the polar component of the dipole force between NPs and integrin sensing stress sites, while large size NPs exercise a similar action via the radial component. A quantum electrodynamic model also accounts for ECM overstressing by electromagnetic mode trapping between coherent symmetric and antisymmetric quantum states.
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20
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Kleynhans J, Kruger HG, Cloete T, Zeevaart JR, Ebenhan T. In Silico Modelling in the Development of Novel Radiolabelled Peptide Probes. Curr Med Chem 2020; 27:7048-7063. [DOI: 10.2174/0929867327666200504082256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
Abstract
This review describes the usefulness of in silico design approaches in the design of
new radiopharmaceuticals, especially peptide-based radiotracers (including peptidomimetics).
Although not part of the standard arsenal utilized during radiopharmaceutical design, the use
of in silico strategies is steadily increasing in the field of radiochemistry as it contributes to a
more rational and scientific approach. The development of new peptide-based radiopharmaceuticals
as well as a short introduction to suitable computational approaches are provided in
this review. The first section comprises a concise overview of the three most useful computeraided
drug design strategies used, namely i) a Ligand-based Approach (LBDD) using pharmacophore
modelling, ii) a Structure-based Design Approach (SBDD) using molecular docking
strategies and iii) Absorption-Distribution-Metabolism-Excretion-Toxicity (ADMET)
predictions. The second section summarizes the challenges connected to these computer-aided
techniques and discusses successful applications of in silico radiopharmaceutical design in
peptide-based radiopharmaceutical development, thereby improving the clinical procedure in
Nuclear Medicine. Finally, the advances and future potential of in silico modelling as a design
strategy is highlighted.
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Affiliation(s)
- Janke Kleynhans
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
| | | | - Theunis Cloete
- Center of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
| | - Thomas Ebenhan
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
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21
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Yu D, Zou J, Chen Q, Zhu T, Sui R, Yang J. Structural modeling, mutation analysis, and in vitro expression of usherin, a major protein in inherited retinal degeneration and hearing loss. Comput Struct Biotechnol J 2020; 18:1363-1382. [PMID: 32637036 PMCID: PMC7317166 DOI: 10.1016/j.csbj.2020.05.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/15/2022] Open
Abstract
Usherin is the most common causative protein associated with autosomal recessive retinitis pigmentosa (RP) and Usher syndrome (USH), which are characterized by retinal degeneration alone and in combination with hearing loss, respectively. Usherin is essential for photoreceptor survival and hair cell bundle integrity. However, the molecular mechanism underlying usherin function in normal and disease conditions is unclear. In this study, we investigated structural models of usherin domains and localization of usherin pathogenic small in-frame mutations, mainly homozygous missense mutations. We found that usherin fibronectin III (FN3) domains and most laminin-related domains have a β-sandwich structure. Some FN3 domains are predicted to interact with each other and with laminin-related domains. The usherin protein may bend at some FN3 linker regions. RP- and USH-associated small in-frame mutations are differentially located in usherin domains. Most of them are located at the periphery of β-sandwiches, with some at the interface between interacting domains. The usherin laminin epidermal growth factor repeats adopt a rod-shaped structure, which is maintained by disulfide bonds. Most missense mutations and deletion of exon 13 in this region disrupt the disulfide bonds and may affect local protein folding. Despite low expression of the recombinant entire protein and protein fragments in mammalian cell culture, usherin FN3 fragments are more robustly expressed and secreted than its laminin-related fragments. Our findings provide new insights into the usherin structure and the disease mechanisms caused by pathogenic small in-frame mutations, which will help inform future experimental research on diagnosis, disease mechanisms, and therapeutic approaches.
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Key Words
- Cell adhesion
- DCC, deleted in colorectal cancer
- FN3, fibronectin III
- GMQE, global quality estimation score
- HGMD, Human Gene Mutation Database
- Hair cell
- I-TASSER, Iterative Threading ASSEmbly Refinement
- LE, laminin EGF
- LG, laminin globular
- LGL, laminin globular-like
- LN, laminin N-terminal
- Membrane protein
- NCBI, National Center for Biotechnology Information
- Photoreceptor
- Protein folding
- QMEAN, qualitative model energy analysis score
- QSQE, Quaternary Structure Quality Estimation
- RMSD, root mean square deviation
- RP, retinitis pigmentosa
- Recombinant protein expression
- Retinitis pigmentosa
- SMTL, SWISS-MODEL template library
- Structural model
- TM-score, template modeling score
- USH, Usher syndrome
- Usher syndrome
- hFc, human Fc fragment
- mFc, mouse Fc fragment
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Affiliation(s)
- Dongmei Yu
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Junhuang Zou
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Qian Chen
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jun Yang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
- Division of Otolaryngology, Department of Surgery, University of Utah, Salt Lake City, UT, United States
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22
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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
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23
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Wu HB, Wang ZW, Shi F, Ren ZL, Li LC, Hu XP, Hu R, Li BW. Av β3 Single-Stranded DNA Aptamer Attenuates Vascular Smooth Muscle Cell Proliferation and Migration via Ras-PI3K/MAPK Pathway. Cardiovasc Ther 2020; 2020:6869856. [PMID: 32042311 PMCID: PMC6995496 DOI: 10.1155/2020/6869856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/15/2019] [Accepted: 11/05/2019] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES To observe the effect of avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. BACKGROUND Percutaneous transluminal coronary angioplasty (PTCA) is currently the preferred method for the treatment of coronary heart disease. However, vascular restenosis still occurs after PTCA treatment, severely affecting the clinical efficacy of PTCA. Integrin avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. METHODS In this experiment, we used systematic evolution of ligands by exponential enrichment (SELEX) to screen out avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. RESULTS In the present study, we found that avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. P < 0.05). Avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. P < 0.05). AvP < 0.05). Av. CONCLUSIONS The findings suggest that avβ3 ssDNA inhibited the proliferation and migration of VSMCs by suppressing the activation of Ras-PI3K/MAPK signaling.β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism.
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MESH Headings
- Animals
- Apoptosis
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Cell Movement
- Cell Proliferation
- Cells, Cultured
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Focal Adhesion Kinase 1/genetics
- Focal Adhesion Kinase 1/metabolism
- Gene Expression Regulation
- Integrin alphaVbeta3/genetics
- Integrin alphaVbeta3/metabolism
- Mitogen-Activated Protein Kinases/genetics
- Mitogen-Activated Protein Kinases/metabolism
- Muscle, Smooth, Vascular/enzymology
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/enzymology
- Myocytes, Smooth Muscle/pathology
- Osteopontin/genetics
- Osteopontin/metabolism
- Phosphatidylinositol 3-Kinases/genetics
- Phosphatidylinositol 3-Kinases/metabolism
- Phosphorylation
- Rats, Sprague-Dawley
- Signal Transduction
- ras Proteins/genetics
- ras Proteins/metabolism
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Affiliation(s)
- Hong-Bing Wu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhi-Wei Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng Shi
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zong-Li Ren
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Luo-Cheng Li
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiao-Ping Hu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rui Hu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bo-Wen Li
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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24
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Regulation of cell adhesion: a collaborative effort of integrins, their ligands, cytoplasmic actors, and phosphorylation. Q Rev Biophys 2019; 52:e10. [PMID: 31709962 DOI: 10.1017/s0033583519000088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrins are large heterodimeric type 1 membrane proteins expressed in all nucleated mammalian cells. Eighteen α-chains and eight β-chains can combine to form 24 different integrins. They are cell adhesion proteins, which bind to a large variety of cellular and extracellular ligands. Integrins are required for cell migration, hemostasis, translocation of cells out from the blood stream and further movement into tissues, but also for the immune response and tissue morphogenesis. Importantly, integrins are not usually active as such, but need activation to become adhesive. Integrins are activated by outside-in activation through integrin ligand binding, or by inside-out activation through intracellular signaling. An important question is how integrin activity is regulated, and this topic has recently drawn much attention. Changes in integrin affinity for ligand binding are due to allosteric structural alterations, but equally important are avidity changes due to integrin clustering in the plane of the plasma membrane. Recent studies have partially solved how integrin cell surface structures change during activation. The integrin cytoplasmic domains are relatively short, but by interacting with a variety of cytoplasmic proteins in a regulated manner, the integrins acquire a number of properties important not only for cell adhesion and movement, but also for cellular signaling. Recent work has shown that specific integrin phosphorylations play pivotal roles in the regulation of integrin activity. Our purpose in this review is to integrate the present knowledge to enable an understanding of how cell adhesion is dynamically regulated.
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25
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Kulke M, Langel W. Molecular dynamics simulations to the bidirectional adhesion signaling pathway of integrin α V β 3. Proteins 2019; 88:679-688. [PMID: 31693219 DOI: 10.1002/prot.25849] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/10/2019] [Accepted: 11/03/2019] [Indexed: 12/27/2022]
Abstract
The bidirectional force transmission process of integrin through the cell membrane is still not well understood. Several possible mechanisms have been discussed in literature on the basis of experimental data, and in this study, we investigate these mechanisms by free and steered molecular dynamics simulations. For the first time, constant velocity pulling on the complete integrin molecule inside a dipalmitoyl-phosphatidylcholine membrane is conducted. From the results, the most likely mechanism for inside-out and outside-in signaling is the switchblade model with further separation of the transmembrane helices.
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Affiliation(s)
- Martin Kulke
- Institut für Biochemie, Universität Greifswald, Greifswald, Germany
| | - Walter Langel
- Institut für Biochemie, Universität Greifswald, Greifswald, Germany
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26
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Chakraborty S, Banerjee S, Raina M, Haldar S. Force-Directed “Mechanointeractome” of Talin–Integrin. Biochemistry 2019; 58:4677-4695. [DOI: 10.1021/acs.biochem.9b00442] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Manasven Raina
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
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27
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Gocheva G, Ivanova A. A Look at Receptor–Ligand Pairs for Active-Targeting Drug Delivery from Crystallographic and Molecular Dynamics Perspectives. Mol Pharm 2019; 16:3293-3321. [DOI: 10.1021/acs.molpharmaceut.9b00250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gergana Gocheva
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Anela Ivanova
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
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28
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Baaske J, Mühlhäuser WWD, Yousefi OS, Zanner S, Radziwill G, Hörner M, Schamel WWA, Weber W. Optogenetic control of integrin-matrix interaction. Commun Biol 2019; 2:15. [PMID: 30652127 PMCID: PMC6325061 DOI: 10.1038/s42003-018-0264-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Abstract
Optogenetic approaches have gathered momentum in precisely modulating and interrogating cellular signalling and gene expression. The use of optogenetics on the outer cell surface to interrogate how cells receive stimuli from their environment, however, has so far not reached its full potential. Here we demonstrate the development of an optogenetically regulated membrane receptor-ligand pair exemplified by the optically responsive interaction of an integrin receptor with the extracellular matrix. The system is based on an integrin engineered with a phytochrome-interacting factor domain (OptoIntegrin) and a red light-switchable phytochrome B-functionalized matrix (OptoMatrix). This optogenetic receptor-ligand pair enables light-inducible and -reversible cell-matrix interaction, as well as the controlled activation of downstream mechanosensory signalling pathways. Pioneering the application of optogenetic switches in the extracellular environment of cells, this OptoMatrix-OptoIntegrin system may serve as a blueprint for rendering matrix-receptor interactions amendable to precise control with light.
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Affiliation(s)
- Julia Baaske
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Wignand W. D. Mühlhäuser
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - O. Sascha Yousefi
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian Zanner
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Maximilian Hörner
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
| | - Wolfgang W. A. Schamel
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
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29
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Hall ER, Slack RJ. The effect of divalent metal cations on the αv integrin binding site is ligand and integrin specific. Biomed Pharmacother 2018; 110:362-370. [PMID: 30529769 DOI: 10.1016/j.biopha.2018.11.130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022] Open
Abstract
The binding of orthosteric ligands to integrins requires the presence of divalent metal cations bound to metal ion-binding sites located in the I domains of the integrin α and β subunits. In this study the influence of the type and concentration of divalent metal cation present was investigated on a single arginyl-glycinyl-aspartic acid (RGD) ligand across the αv integrin sub-family and single αv integrin (αvβ6) with different ligands. These relationships were determined using radioligand binding studies completed with [3H] ligands and purified αv integrin protein preparations. The binding of [3H]compound 1 to the RGD site on individual αv integrins demonstrated a unique profile in relation to the type and concentration of divalent metal cation present. The use of physiological concentrations of Mg2+ and Ca2+ in simulated lung fluid altered the αv integrin selectivity profile of [3H]compound 1 in terms of affinity and the level of receptor occupancy. In addition, different RGD ligands for the αvβ6 integrin behaved differently under the same divalent metal cation conditions. In conclusion, this study demonstrates the need to determine the individual relationship between RGD ligands and the integrins they may engage in vivo, especially when determining selectivity profiles for potential RGD-mimetic small molecule therapeutics, with organ and disease state also considered.
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Affiliation(s)
- Eleanor R Hall
- Fibrosis Discovery Performance Unit, Respiratory TAU, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, UK
| | - Robert J Slack
- Fibrosis Discovery Performance Unit, Respiratory TAU, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, UK.
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30
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Semashko VV, Pudovkin MS, Cefalas AC, Zelenikhin PV, Gavriil VE, Nizamutdinov AS, Kollia Z, Ferraro A, Sarantopoulou E. Tiny Rare-Earth Fluoride Nanoparticles Activate Tumour Cell Growth via Electrical Polar Interactions. NANOSCALE RESEARCH LETTERS 2018; 13:370. [PMID: 30465280 PMCID: PMC6249154 DOI: 10.1186/s11671-018-2775-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 06/09/2023]
Abstract
Localised extracellular interactions between nanoparticles and transmembrane signal receptors may well activate cancer cell growth. Herein, tiny LaF3 and PrF3 nanoparticles in DMEM+FBS suspensions stimulated tumour cell growth in three different human cell lines (A549, SW837 and MCF7). Size distribution of nanoparticles, activation of AKT and ERK signalling pathways and viability tests pointed to mechanical stimulation of ligand adhesion binding sites of integrins and EGFR via a synergistic action of an ensemble of tiny size nanoparticles (< 10 nm). While tiny size nanoparticles may be well associated with the activation of EGFR, integrin interplay with nanoparticles remains a multifaceted issue. A theoretical motif shows that, within the requisite pN force scale, each ligand adhesion binding site can be activated by a tiny size dielectric nanoparticle via electrical dipole interaction. The size of the active nanoparticle stayed specified by the amount of the surface charges on the ligand adhesion binding site and the nanoparticle, and also by the separating distance between them. The polar component of the electrical dipole force remained inversely proportional to the second power of nanoparticle's size, evincing that only tiny size dielectric nanoparticles might stimulate cancer cell growth via electrical dipole interactions. The work contributes towards recognising different cytoskeletal stressing modes of cancer cells.
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Affiliation(s)
- Vadim V. Semashko
- Institute of Physics, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
| | - Maksim S. Pudovkin
- Institute of Physics, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
| | - Alkiviadis-Constantinos Cefalas
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
- Institute of Physics, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
| | - Pavel V. Zelenikhin
- Department of Microbiology, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
| | - Vassilios E. Gavriil
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Alexei S. Nizamutdinov
- Institute of Physics, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
| | - Zoe Kollia
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Angelo Ferraro
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
- Institute of Physics, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
| | - Evangelia Sarantopoulou
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
- Institute of Physics, Kazan Federal University, 18 Kremljovskaja str, Kazan, 420008 Russia
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31
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Autonomous conformational regulation of β 3 integrin and the conformation-dependent property of HPA-1a alloantibodies. Proc Natl Acad Sci U S A 2018; 115:E9105-E9114. [PMID: 30209215 DOI: 10.1073/pnas.1806205115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Integrin α/β heterodimer adopts a compact bent conformation in the resting state, and upon activation undergoes a large-scale conformational rearrangement. During the inside-out activation, signals impinging on the cytoplasmic tail of β subunit induce the α/β separation at the transmembrane and cytoplasmic domains, leading to the extended conformation of the ectodomain with the separated leg and the opening headpiece that is required for the high-affinity ligand binding. It remains enigmatic which integrin subunit drives the bent-to-extended conformational rearrangement in the inside-out activation. The β3 integrins, including αIIbβ3 and αVβ3, are the prototypes for understanding integrin structural regulation. The Leu33Pro polymorphism located at the β3 PSI domain defines the human platelet-specific alloantigen (HPA) 1a/b, which provokes the alloimmune response leading to clinically important bleeding disorders. Some, but not all, anti-HPA-1a alloantibodies can distinguish the αIIbβ3 from αVβ3 and affect their functions with unknown mechanisms. Here we designed a single-chain β3 subunit that mimics a separation of α/β heterodimer on inside-out activation. Our crystallographic and functional studies show that the single-chain β3 integrin folds into a bent conformation in solution but spontaneously extends on the cell surface. This demonstrates that the β3 subunit autonomously drives the membrane-dependent conformational rearrangement during integrin activation. Using the single-chain β3 integrin, we identified the conformation-dependent property of anti-HPA-1a alloantibodies, which enables them to differently recognize the β3 in the bent state vs. the extended state and in the complex with αIIb vs. αV This study provides deeper understandings of integrin conformational activation on the cell surface.
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32
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Zhou D, Thinn AMM, Zhao Y, Wang Z, Zhu J. Structure of an extended β 3 integrin. Blood 2018; 132:962-972. [PMID: 30018079 PMCID: PMC6117741 DOI: 10.1182/blood-2018-01-829572] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/10/2018] [Indexed: 12/23/2022] Open
Abstract
Cells use adhesion receptor integrins to communicate with their surroundings. Integrin activation and cellular signaling are coupled with change from bent to extended conformation. β3 integrins, including αIIbβ3, which is essential for the function of platelets in hemostasis and thrombosis, and αVβ3, which plays multiple roles in diverse cell types, have been prototypes in understanding integrin structure and function. Despite extensive structural studies, a high-resolution integrin structure in an extended conformation remains to be determined. The human β3 Leu33Pro polymorphism, located at the PSI domain, defines human platelet-specific alloantigens 1a and 1b (HPA-1a/b), immune response to which is a cause of posttransfusion purpura and fetal/neonatal alloimmune thrombocytopenia. Leu33Pro substitution has also been suggested to be a risk factor for thrombosis. Here we report the crystal structure of the β3 headpiece in either Leu33 or Pro33 form, both of which reveal intermediate and fully extended conformations coexisting in 1 crystal. These were used to build high-resolution structures of full-length β3 integrin in the intermediate and fully extended states, agreeing well with the corresponding conformations observed by electron microscopy. Our structures reveal how β3 integrin becomes extended at its β-knee region and how the flexibility of β-leg domains is determined. In addition, our structures reveal conformational changes of the PSI and I-EGF1 domains upon β3 extension, which may affect the binding of conformation-dependent anti-HPA-1a alloantibodies. Our structural and functional data show that Leu33Pro substitution does not directly alter the conformation or ligand binding of β3 integrin.
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Affiliation(s)
- Dongwen Zhou
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
| | - Aye Myat Myat Thinn
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI; and
| | - Yan Zhao
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
- Department of Physiology, School of Basic Medical Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhengli Wang
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
| | - Jieqing Zhu
- Blood Research Institute, BloodCenter of Wisconsin, part of Versiti, Milwaukee, WI
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI; and
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33
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Martín-Moldes Z, Ebrahimi D, Plowright R, Dinjaski N, Perry CC, Buehler MJ, Kaplan DL. Intracellular Pathways Involved in Bone Regeneration Triggered by Recombinant Silk-silica Chimeras. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1702570. [PMID: 30140193 PMCID: PMC6101667 DOI: 10.1002/adfm.201702570] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Biomineralization at the organic-inorganic interface is critical to many biology material functions in vitro and in vivo. Recombinant silk-silica fusion peptides are organic-inorganic hybrid material systems that can be effectively used to study and control biologically-mediated mineralization due to the genetic basis of sequence control. However, to date, the mechanisms by which these functionalized silk-silica proteins trigger the differentiation of human mesenchymal stem cells (hMSCs) to osteoblasts remain unknown. To address this challenge, we analyzed silk-silica surfaces for silica-hMSC receptor binding and activation, and the intracellular pathways involved in the induction of osteogenesis on these bioengineered biomaterials. The induction of gene expression of αVβ3 integrin, all three Mitogen-activated Protein Kinsases (MAPKs) as well as c-Jun, Runt-related Transcription Factor 2 (Runx2) and osteoblast marker genes was demonstrated upon growth of the hMSCs on the silk-silica materials. This induction of key markers of osteogenesis correlated with the content of silica on the materials. Moreover, computational simulations were performed for silk/silica-integrin binding which showed activation of αVβ3 integrin in contact with silica. This integrated computational and experimental approach provides insight into interactions that regulate osteogenesis towards more efficient biomaterial designs.
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Affiliation(s)
- Zaira Martín-Moldes
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Davoud Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Robyn Plowright
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Nina Dinjaski
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
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34
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Hu P, Luo B. The interface between the EGF1 and EGF2 domains is critical in integrin affinity regulation. J Cell Biochem 2018; 119:7264-7273. [DOI: 10.1002/jcb.26921] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/04/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Ping Hu
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginia
| | - Bing‐Hao Luo
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
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35
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Pagani G, Gohlke H. On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation. Sci Rep 2018; 8:5733. [PMID: 29636500 PMCID: PMC5893634 DOI: 10.1038/s41598-018-23778-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/20/2018] [Indexed: 12/20/2022] Open
Abstract
Integrins are α/β heterodimeric transmembrane adhesion receptors. Evidence exists that their transmembrane domain (TMD) separates upon activation. Subunit-specific differences in activation sensitivity of integrins were reported. However, whether sequence variations in the TMD lead to differential TMD association has remained elusive. Here, we show by molecular dynamics simulations and association free energy calculations on TMDs of integrin αIIbβ3, αvβ3, and α5β1 that αIIbβ3 TMD is most stably associated; this difference is related to interaction differences across the TMDs. The order of TMD association stability is paralleled by the basal activity of these integrins, which suggests that TMD differences can have a decisive effect on integrin conformational free energies. We also identified a specific order of clasp disintegration upon TMD dissociation, which suggests that the closed state of integrins may comprise several microstates. Our results provide unprecedented insights into a possibly contributing role of TMD towards subunit-specific sensitivity of integrin activation.
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Affiliation(s)
- Giulia Pagani
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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36
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High integrin α Vβ 6 affinity reached by hybrid domain deletion slows ligand-binding on-rate. Proc Natl Acad Sci U S A 2018; 115:E1429-E1436. [PMID: 29378937 DOI: 10.1073/pnas.1718662115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of the hybrid domain in integrin affinity regulation is unknown, as is whether the kinetics of ligand binding is modulated by integrin affinity state. Here, we compare cell surface and soluble integrin αVβ6 truncation mutants for ligand-binding affinity, kinetics, and thermodynamics. Removal of the integrin transmembrane/cytoplasmic domains or lower legs has little effect on αVβ6 affinity, in contrast to β1 integrins. In integrin opening, rearrangement at the interface between the βI and hybrid domains is linked to remodeling at the ligand-binding site at the opposite end of the βI domain, which greatly increases in affinity in the open conformation. The larger size of the βI-hybrid interface in the closed state suggests that the hybrid domain stabilizes closing. In agreement, deletion of the hybrid domain raised affinity by 50-fold. Surface plasmon resonance and isothermal titration calorimetry gave similar results and the latter revealed tradeoffs between enthalpy and entropy not apparent from affinity. At extremely high affinity reached in Mn2+ with hybrid domain truncation, αVβ6 on-rate for both pro-TGF-β1 and fibronectin declined. The results suggest that the open conformation of αVβ6 has lower on-rate than the closed conformation, correlate with constriction of the ligand-binding pocket in open αVβ6 structures, and suggest that the extended-closed conformation is kinetically selected for ligand binding. Subsequent transition to the extended-open conformation is stabilized by its much higher affinity for ligand and would also be stabilized by force exerted across ligand-bound integrins by the actin cytoskeleton.
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37
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Hanein D, Volkmann N. Conformational Equilibrium of Human Platelet Integrin Investigated by Three-Dimensional Electron Cryo-Microscopy. Subcell Biochem 2018; 87:353-363. [PMID: 29464566 DOI: 10.1007/978-981-10-7757-9_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Integrins are bidirectional transmembrane receptors that play central roles in hemostasis and arterial thrombosis. They have been subject to structural studies for many years, in particular using X-ray crystallography, nuclear magnetic resonance spectroscopy, and two-dimensional negative stain electron microscopy. Despite considerable progress, a full consensus on the molecular mechanism of integrin activation is still lacking. Three-dimensional reconstructions of full-length human platelet integrin αIIbβ3 in lipid-bilayer nanodiscs obtained by electron cryo-microscopy and single-particle reconstruction have shed new light on the activation process. These studies show that integrin αIIbβ3 exists in a continuous conformational equilibrium ranging from a compact nodular conformation similar to that obtained in crystal structures to a fully extended state with the leg domains separated. This equilibrium is shifted towards the extended conformation when extracellular ligands, cytosolic activators and lipid-bilayer nanodiscs are added. Addition of cytosolic activators and extracellular ligands in the absense of nanodiscs produces significantly less dramatic shifts, emphasizing the importance of the membrane bilayer in the activation process.
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Affiliation(s)
- Dorit Hanein
- Bioinformatics and Structural Biology Program, Sanford-Burnham-Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Niels Volkmann
- Bioinformatics and Structural Biology Program, Sanford-Burnham-Prebys Medical Discovery Institute, San Diego, CA, USA.
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38
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Huet-Calderwood C, Rivera-Molina F, Iwamoto DV, Kromann EB, Toomre D, Calderwood DA. Novel ecto-tagged integrins reveal their trafficking in live cells. Nat Commun 2017; 8:570. [PMID: 28924207 PMCID: PMC5603536 DOI: 10.1038/s41467-017-00646-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 07/16/2017] [Indexed: 12/22/2022] Open
Abstract
Integrins are abundant heterodimeric cell-surface adhesion receptors essential in multicellular organisms. Integrin function is dynamically modulated by endo-exocytic trafficking, however, major mysteries remain about where, when, and how this occurs in living cells. To address this, here we report the generation of functional recombinant β1 integrins with traceable tags inserted in an extracellular loop. We demonstrate that these ‘ecto-tagged’ integrins are cell-surface expressed, localize to adhesions, exhibit normal integrin activation, and restore adhesion in β1 integrin knockout fibroblasts. Importantly, β1 integrins containing an extracellular pH-sensitive pHluorin tag allow direct visualization of integrin exocytosis in live cells and revealed targeted delivery of integrin vesicles to focal adhesions. Further, using β1 integrins containing a HaloTag in combination with membrane-permeant and -impermeant Halo dyes allows imaging of integrin endocytosis and recycling. Thus, ecto-tagged integrins provide novel powerful tools to characterize integrin function and trafficking. Integrins are cell-surface adhesion receptors that are modulated by endo-exocytic trafficking, but existing tools to study this process can interfere with function. Here the authors develop β1 integrins carrying traceable tags in the extracellular domain; a pH-sensitive pHlourin tag or a HaloTag to facilitate dye attachment.
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Affiliation(s)
- Clotilde Huet-Calderwood
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA
| | - Felix Rivera-Molina
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA
| | - Daniel V Iwamoto
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA
| | - Emil B Kromann
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA.,Department of Biomedical Engineering, Yale University, 333 Cedar Street, New Haven, Connecticut, 06520, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA.
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA. .,Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut, 06520, USA.
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39
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Dissecting intrinsic and ligand-induced structural communication in the β3 headpiece of integrins. Biochim Biophys Acta Gen Subj 2017; 1861:2367-2381. [DOI: 10.1016/j.bbagen.2017.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 12/15/2022]
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40
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The importance of N-glycosylation on β 3 integrin ligand binding and conformational regulation. Sci Rep 2017; 7:4656. [PMID: 28680094 PMCID: PMC5498496 DOI: 10.1038/s41598-017-04844-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/19/2017] [Indexed: 11/25/2022] Open
Abstract
N-glycosylations can regulate the adhesive function of integrins. Great variations in both the number and distribution of N-glycosylation sites are found in the 18 α and 8 β integrin subunits. Crystal structures of αIIbβ3 and αVβ3 have resolved the precise structural location of each N-glycan site, but the structural consequences of individual N-glycan site on integrin activation remain unclear. By site-directed mutagenesis and structure-guided analyses, we dissected the function of individual N-glycan sites in β3 integrin activation. We found that the N-glycan site, β3-N320 at the headpiece and leg domain interface positively regulates αIIbβ3 but not αVβ3 activation. The β3-N559 N-glycan at the β3-I-EGF3 and αIIb-calf-1 domain interface, and the β3-N654 N-glycan at the β3-β-tail and αIIb-calf-2 domain interface positively regulate the activation of both αIIbβ3 and αVβ3 integrins. In contrast, removal of the β3-N371 N-glycan near the β3 hybrid and I-EGF3 interface, or the β3-N452 N-glycan at the I-EGF1 domain rendered β3 integrin more active than the wild type. We identified one unique N-glycan at the βI domain of β1 subunit that negatively regulates α5β1 activation. Our study suggests that the bulky N-glycans influence the large-scale conformational rearrangement by potentially stabilizing or destabilizing the domain interfaces of integrin.
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41
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Wang L, Pan D, Yan Q, Song Y. Activation mechanisms of αVβ3 integrin by binding to fibronectin: A computational study. Protein Sci 2017; 26:1124-1137. [PMID: 28340512 PMCID: PMC5441423 DOI: 10.1002/pro.3163] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/13/2017] [Accepted: 03/19/2017] [Indexed: 01/29/2023]
Abstract
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn2+ -bound integrin αVβ3 by binding to fibronectin with molecular dynamics simulations. Results showed that fibronectin binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3. The angle of Propeller domain with respect to the Calf-2 domain of αV subunit and the angle of Hybrid domain with respect to βA domain of β3 subunit significantly increased when integrin αVβ3 was bound to fibronectin. These changes could result in the conformational change tendency of αVβ3 from a bend conformation to an extended conformation and lead to the open swing of Hybrid domain relative to βA domain of β3 subunit, which have demonstrated their importance for αVβ3 activation. Fibronectin binding to integrin αVβ3 significantly decreased the relative position of α1 helix to βA domain and that to metal ion-dependent adhesion site, stabilized Mn2+ ions binding in integrin αVβ3 and changed fibronectin conformation, which are important for αVβ3 activation. Results from this study provide important molecular insight into the "outside-in" activation mechanism of integrin αVβ3 by binding to fibronectin.
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Affiliation(s)
- Lingyun Wang
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
| | - Di Pan
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
| | - Qi Yan
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
| | - Yuhua Song
- Department of Biomedical EngineeringThe University of Alabama at BirminghamBirminghamAlabama35294
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42
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Hu P, Luo BH. Integrin αv
β8
Adopts a High Affinity State for Soluble Ligands Under Physiological Conditions. J Cell Biochem 2017; 118:2044-2052. [DOI: 10.1002/jcb.25780] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/01/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Ping Hu
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
| | - Bing-Hao Luo
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
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43
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High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design. PLoS Comput Biol 2017; 13:e1005334. [PMID: 28114375 PMCID: PMC5293283 DOI: 10.1371/journal.pcbi.1005334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 02/06/2017] [Accepted: 12/23/2016] [Indexed: 11/19/2022] Open
Abstract
Understanding how binding events modulate functional motions of multidomain proteins is a major issue in chemical biology. We address several aspects of this problem by analyzing the differential dynamics of αvβ3 integrin bound to wild type (wtFN10, agonist) or high affinity (hFN10, antagonist) mutants of fibronectin. We compare the dynamics of complexes from large-scale domain motions to inter-residue coordinated fluctuations to characterize the distinctive traits of conformational evolution and shed light on the determinants of differential αvβ3 activation induced by different FN sequences. We propose an allosteric model for ligand-based integrin modulation: the conserved integrin binding pocket anchors the ligand, while different residues on the two FN10's act as the drivers that reorganize relevant interaction networks, guiding the shift towards inactive (hFN10-bound) or active states (wtFN10-bound). We discuss the implications of results for the design of integrin inhibitors.
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44
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Zhang B, Song W, Pang P, Zhao Y, Zhang P, Csabai I, Vattay G, Lindsay S. Observation of Giant Conductance Fluctuations in a Protein. NANO FUTURES 2017; 1:035002. [PMID: 29552645 PMCID: PMC5851656 DOI: 10.1088/2399-1984/aa8f91] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Proteins are insulating molecular solids, yet even those containing easily reduced or oxidized centers can have single-molecule electronic conductances that are too large to account for with conventional transport theories. Here, we report the observation of remarkably high electronic conductance states in an electrochemically-inactive protein, the ~200 kD αVβ3 extracelluar domain of human integrin. Large current pulses (up to nA) were observed for long durations (many ms, corresponding to many pC of charge transfer) at large gap (>5nm) distances in an STM when the protein was bound specifically by a small peptide ligand attached to the electrodes. The effect is greatly reduced when a homologous, weakly-binding protein (α4β1) is used as a control. In order to overcome the limitations of the STM, the time- and voltage-dependence of the conductance were further explored using a fixed-gap (5 nm) tunneling junction device that was small enough to trap a single protein molecule at any one time. Transitions to a high conductance (~ nS) state were observed, the protein being "on" for times from ms to tenths of a second. The high-conductance states only occur above ~ 100mV applied bias, and thus are not an equilibrium property of the protein. Nanoamp two-level signals indicate the specific capture of a single molecule in an electrode gap functionalized with the ligand. This offers a new approach to label-free electronic detection of single protein molecules. Electronic structure calculations yield a distribution of energy level spacings that is consistent with a recently proposed quantum-critical state for proteins, in which small fluctuations can drive transitions between localized and band-like electronic states.
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Affiliation(s)
- Bintian Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Pei Pang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yanan Zhao
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Pázmány P. s. 1/A, Hungary
| | - Gábor Vattay
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Pázmány P. s. 1/A, Hungary
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- To whom correspondence should be addressed:
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45
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Dalton AC, Shlamkovitch T, Papo N, Barton WA. Constitutive Association of Tie1 and Tie2 with Endothelial Integrins is Functionally Modulated by Angiopoietin-1 and Fibronectin. PLoS One 2016; 11:e0163732. [PMID: 27695111 PMCID: PMC5047623 DOI: 10.1371/journal.pone.0163732] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/13/2016] [Indexed: 12/29/2022] Open
Abstract
Functional cross-talk between Tie2 and Integrin signaling pathways is essential to coordinate endothelial cell adhesion and migration in response to the extracellular matrix, yet the mechanisms behind this phenomenon are unclear. Here, we examine the possibility that receptor cross-talk is driven through uncharacterized Tie-integrin interactions on the endothelial surface. Using a live cell FRET-based proximity assay, we monitor Tie-integrin receptor recognition and demonstrate that both Tie1 and Tie2 readily associate with integrins α5ß1 and αVß3 through their respective ectodomains. Although not required, Tie2-integrin association is significantly enhanced in the presence of the extracellular component and integrin ligand fibronectin. In vitro binding assays with purified components reveal that Tie-integrin recognition is direct, and further demonstrate that the receptor binding domain of the Tie2 ligand Ang-1, but not the receptor binding domain of Ang-2, can independently associate with α5ß1 or αVß3. Finally, we reveal that cooperative Tie/integrin interactions selectively stimulate ERK/MAPK signaling in the presence of both Ang-1 and fibronectin, suggesting a molecular mechanism to sensitize Tie2 to extracellular matrix. We provide a mechanistic model highlighting the role of receptor localization and association in regulating distinct signaling cascades and in turn, the angiogenic switch.
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Affiliation(s)
- Annamarie C. Dalton
- Virginia Commonwealth University, Department of Biochemistry and Molecular Biology, Richmond, Virginia, 23298, United States of America
| | - Tomer Shlamkovitch
- Ben-Gurion University of the Negev, Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Beer-Sheva, 8410501, Israel
| | - Niv Papo
- Ben-Gurion University of the Negev, Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Beer-Sheva, 8410501, Israel
| | - William A. Barton
- Virginia Commonwealth University, Department of Biochemistry and Molecular Biology, Richmond, Virginia, 23298, United States of America
- * E-mail:
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46
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Schmidt T, Ye F, Situ AJ, An W, Ginsberg MH, Ulmer TS. A Conserved Ectodomain-Transmembrane Domain Linker Motif Tunes the Allosteric Regulation of Cell Surface Receptors. J Biol Chem 2016; 291:17536-46. [PMID: 27365391 PMCID: PMC5016151 DOI: 10.1074/jbc.m116.733683] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/09/2016] [Indexed: 11/06/2022] Open
Abstract
In many families of cell surface receptors, a single transmembrane (TM) α-helix separates ecto- and cytosolic domains. A defined coupling of ecto- and TM domains must be essential to allosteric receptor regulation but remains little understood. Here, we characterize the linker structure, dynamics, and resulting ecto-TM domain coupling of integrin αIIb in model constructs and relate it to other integrin α subunits by mutagenesis. Cellular integrin activation assays subsequently validate the findings in intact receptors. Our results indicate a flexible yet carefully tuned ecto-TM coupling that modulates the signaling threshold of integrin receptors. Interestingly, a proline at the N-terminal TM helix border, termed NBP, is critical to linker flexibility in integrins. NBP is further predicted in 21% of human single-pass TM proteins and validated in cytokine receptors by the TM domain structure of the cytokine receptor common subunit β and its P441A-substituted variant. Thus, NBP is a conserved uncoupling motif of the ecto-TM domain transition and the degree of ecto-TM domain coupling represents an important parameter in the allosteric regulation of diverse cell surface receptors.
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Affiliation(s)
- Thomas Schmidt
- From the Department of Biochemistry & Molecular Biology and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Feng Ye
- the Department of Medicine, University of California San Diego, La Jolla, California 92093, and
| | - Alan J Situ
- From the Department of Biochemistry & Molecular Biology and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Woojin An
- the Department of Biochemistry & Molecular Biology and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033
| | - Mark H Ginsberg
- the Department of Medicine, University of California San Diego, La Jolla, California 92093, and
| | - Tobias S Ulmer
- From the Department of Biochemistry & Molecular Biology and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033,
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47
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Abstract
Whether β1 integrin ectodomains visit conformational states similarly to β2 and β3 integrins has not been characterized. Furthermore, despite a wealth of activating and inhibitory antibodies to β1 integrins, the conformational states that these antibodies stabilize, and the relation of these conformations to function, remain incompletely characterized. Using negative-stain electron microscopy, we show that the integrin α5β1 ectodomain adopts extended-closed and extended-open conformations as well as a bent conformation. Antibodies SNAKA51, 8E3, N29, and 9EG7 bind to different domains in the α5 or β1 legs, activate, and stabilize extended ectodomain conformations. Antibodies 12G10 and HUTS-4 bind to the β1 βI domain and hybrid domains, respectively, activate, and stabilize the open headpiece conformation. Antibody TS2/16 binds a similar epitope as 12G10, activates, and appears to stabilize an open βI domain conformation without requiring extension or hybrid domain swing-out. mAb13 and SG/19 bind to the βI domain and βI-hybrid domain interface, respectively, inhibit, and stabilize the closed conformation of the headpiece. The effects of the antibodies on cell adhesion to fibronectin substrates suggest that the extended-open conformation of α5β1 is adhesive and that the extended-closed and bent-closed conformations are nonadhesive. The functional effects and binding sites of antibodies and fibronectin were consistent with their ability in binding to α5β1 on cell surfaces to cross-enhance or inhibit one another by competitive or noncompetitive (allosteric) mechanisms.
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48
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Mas-Moruno C, Fraioli R, Rechenmacher F, Neubauer S, Kapp TG, Kessler H. αvβ3- or α5β1-Integrin-Selective Peptidomimetics for Surface Coating. Angew Chem Int Ed Engl 2016; 55:7048-67. [PMID: 27258759 DOI: 10.1002/anie.201509782] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 12/21/2022]
Abstract
Engineering biomaterials with integrin-binding activity is a very powerful approach to promote cell adhesion, modulate cell behavior, and induce specific biological responses at the surface level. The aim of this Review is to illustrate the evolution of surface-coating molecules in this field: from peptides and proteins with relatively low integrin-binding activity and receptor selectivity to highly active and selective peptidomimetic ligands. In particular, we will bring into focus the difficult challenge of achieving selectivity between the two closely related integrin subtypes αvβ3 and α5β1. The functionalization of surfaces with such peptidomimetics opens the way for a new generation of highly specific cell-instructive surfaces to dissect the biological role of integrin subtypes and for application in tissue engineering and regenerative medicine.
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Affiliation(s)
- Carlos Mas-Moruno
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering and Centre for Research in NanoEngineering, Universitat Politècnica de Catalunya (UPC), Diagonal 647, 08028, Barcelona, Spain.
| | - Roberta Fraioli
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering and Centre for Research in NanoEngineering, Universitat Politècnica de Catalunya (UPC), Diagonal 647, 08028, Barcelona, Spain
| | - Florian Rechenmacher
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Stefanie Neubauer
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Tobias G Kapp
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Horst Kessler
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany.
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49
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Mas-Moruno C, Fraioli R, Rechenmacher F, Neubauer S, Kapp TG, Kessler H. αvβ3- oder α5β1-Integrin-selektive Peptidmimetika für die Oberflächenbeschichtung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509782] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Carlos Mas-Moruno
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering and Centre for Research in NanoEngineering; Universitat Politècnica de Catalunya (UPC); Diagonal 647 08028 Barcelona Spanien
| | - Roberta Fraioli
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Metallurgical Engineering and Centre for Research in NanoEngineering; Universitat Politècnica de Catalunya (UPC); Diagonal 647 08028 Barcelona Spanien
| | - Florian Rechenmacher
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM); Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Stefanie Neubauer
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM); Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Tobias G. Kapp
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM); Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Horst Kessler
- Institute for Advanced Study at the Department Chemie und Center of Integrated Protein Science München (CIPSM); Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
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50
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Ozawa A, Sato Y, Imabayashi T, Uemura T, Takagi J, Sekiguchi K. Molecular Basis of the Ligand Binding Specificity of αvβ8 Integrin. J Biol Chem 2016; 291:11551-65. [PMID: 27033701 DOI: 10.1074/jbc.m116.719138] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 11/06/2022] Open
Abstract
αvβ8 is an integrin that recognizes an Arg-Gly-Asp (RGD) motif and interacts with fibronectin, vitronectin, and latent TGF-β1. We comprehensively determined the binding activity of the αvβ8 integrin toward 25 secreted proteins having an RGD motif. The αvβ8 integrin strongly bound to latent TGF-β1 but showed marginal activity for other RGD-containing proteins, including fibronectin and vitronectin. Site-directed mutagenesis of latent TGF-β1 demonstrated that the high affinity binding of αvβ8 integrin to latent TGF-β1 was defined by Leu-218 immediately following the RGD motif within the latency-associated peptide of TGF-β1. Consistent with the critical role of Leu-218 in latent TGF-β1 recognition by αvβ8 integrin, a 9-mer synthetic peptide containing an RGDL sequence strongly inhibited interactions of latent TGF-β1 with αvβ8 integrin, whereas a 9-mer peptide with an RGDA sequence was ∼60-fold less inhibitory. Because αvβ3 integrin did not exhibit strong binding to latent TGF-β1 or distinguish between RGDL- and RGDA-containing peptides, we explored the mechanism by which the integrin β8 subunit defines the high affinity binding of latent TGF-β1 by αvβ8 integrin. Production of a series of swap mutants of integrin β8 and β3 subunits indicated that the high affinity binding of αvβ8 integrin with latent TGF-β1 was ensured by interactions between the Leu-218 residue and the β8 I-like domain, with the former serving as an auxiliary recognition residue defining the restricted ligand specificity of αvβ8 integrin toward latent TGF-β1. In support of this conclusion, high affinity binding toward the αvβ8 integrin was conferred on fibronectin by substitution of its RGDS motif with an RGDL sequence.
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Affiliation(s)
- Akio Ozawa
- From the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuya Sato
- From the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsukasa Imabayashi
- From the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshihiko Uemura
- From the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junichi Takagi
- From the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kiyotoshi Sekiguchi
- From the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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