1
|
Li Z. A molecular arm: the molecular bending-unbending mechanism of integrin. Biomech Model Mechanobiol 2024; 23:781-792. [PMID: 38308770 DOI: 10.1007/s10237-023-01805-3] [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: 07/18/2023] [Accepted: 12/13/2023] [Indexed: 02/05/2024]
Abstract
The balance of integrin activation and deactivation regulates its function and mediates cell behaviors. Mechanical force triggers the unbending and activation of integrin. However, how an activated and extended integrin spontaneously bends back is unclear. I performed all-atom molecular dynamics simulations on an integrin or its subunits to reveal the bending-unbending mechanism of integrin. According to the simulations, the integrin structure works like a human arm. The integrin α subunit serves as the bones, while the β leg serves as the bicep. The integrin extension results in the stretching of the β leg, and the extended integrin spontaneously bends as a consequence of the contraction of the β leg. This study provides new insights into the mechanism of how the integrin secures in the bent inactivated state and sheds light on how the integrin could achieve a stable extended state.
Collapse
Affiliation(s)
- Zhenhai Li
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai, 200072, China.
| |
Collapse
|
2
|
Adair BD, Xiong JP, Yeager M, Arnaout MA. Cryo-EM structures of full-length integrin αIIbβ3 in native lipids. Nat Commun 2023; 14:4168. [PMID: 37443315 PMCID: PMC10345127 DOI: 10.1038/s41467-023-39763-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Platelet integrin αIIbβ3 is maintained in a bent inactive state (low affinity to physiologic ligand), but can rapidly switch to a ligand-competent (high-affinity) state in response to intracellular signals ("inside-out" activation). Once bound, ligands drive proadhesive "outside-in" signaling. Anti-αIIbβ3 drugs like eptifibatide can engage the inactive integrin directly, inhibiting thrombosis but inadvertently impairing αIIbβ3 hemostatic functions. Bidirectional αIIbβ3 signaling is mediated by reorganization of the associated αIIb and β3 transmembrane α-helices, but the underlying changes remain poorly defined absent the structure of the full-length receptor. We now report the cryo-EM structures of full-length αIIbβ3 in its apo and eptifibatide-bound states in native cell-membrane nanoparticles at near-atomic resolution. The apo form adopts the bent inactive state but with separated transmembrane α-helices, and a fully accessible ligand-binding site that challenges the model that this site is occluded by the plasma membrane. Bound eptifibatide triggers dramatic conformational changes that may account for impaired hemostasis. These results advance our understanding of integrin structure and function and may guide development of safer inhibitors.
Collapse
Affiliation(s)
- Brian D Adair
- Leukocyte Biology and Inflammation Laboratory, Structural Biology Program, Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Jian-Ping Xiong
- Leukocyte Biology and Inflammation Laboratory, Structural Biology Program, Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Chemistry, School of Arts and Sciences, University of Miami, Coral Gables, FL 33146, University of Miami, Miami, FL, 33146, USA
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - M Amin Arnaout
- Leukocyte Biology and Inflammation Laboratory, Structural Biology Program, Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
3
|
Bidone TC, Odde DJ. Multiscale models of integrins and cellular adhesions. Curr Opin Struct Biol 2023; 80:102576. [PMID: 36947952 PMCID: PMC10238663 DOI: 10.1016/j.sbi.2023.102576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Computational models of integrin-based adhesion complexes have revealed important insights into the mechanisms by which cells establish connections with their external environment. However, how changes in conformation and function of individual adhesion proteins regulate the dynamics of whole adhesion complexes remains largely elusive. This is because of the large separation in time and length scales between the dynamics of individual adhesion proteins (nanoseconds and nanometers) and the emergent dynamics of the whole adhesion complex (seconds and micrometers), and the limitations of molecular simulation approaches in extracting accurate free energies, conformational transitions, reaction mechanisms, and kinetic rates, that can inform mechanisms at the larger scales. In this review, we discuss models of integrin-based adhesion complexes and highlight their main findings regarding: (i) the conformational transitions of integrins at the molecular and macromolecular scales and (ii) the molecular clutch mechanism at the mesoscale. Lastly, we present unanswered questions in the field of modeling adhesions and propose new ideas for future exciting modeling opportunities.
Collapse
Affiliation(s)
- Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA.
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA. https://twitter.com/davidodde
| |
Collapse
|
4
|
Nakagawa H, Saio T, Nagao M, Inoue R, Sugiyama M, Ajito S, Tominaga T, Kawakita Y. Conformational dynamics of a multidomain protein by neutron scattering and computational analysis. Biophys J 2021; 120:3341-3354. [PMID: 34242590 PMCID: PMC8391080 DOI: 10.1016/j.bpj.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/07/2021] [Accepted: 07/01/2021] [Indexed: 11/25/2022] Open
Abstract
The flexible conformations of a multidomain protein are responsible for its biological functions. Although MurD, a 47-kDa protein that consists of three domains, sequentially changes its domain conformation from an open form to a closed form through a semiclosed form in its enzymatic reaction, the domain dynamics in each conformation remains unclear. In this study, we verify the conformational dynamics of MurD in the corresponding three states (apo and ATP- and inhibitor-bound states) with a combination of small-angle x-ray and neutron scattering (SAXS and SANS), dynamic light scattering (DLS), neutron backscattering (NBS), neutron spin echo (NSE) spectroscopy, and molecular dynamics (MD) simulations. Applying principal component analysis of the MD trajectories, twisting and open-closed domain modes are identified as the major collective coordinates. The deviations of the experimental SAXS profiles from the theoretical calculations based on the known crystal structures become smaller in the ATP-bound state than in the apo state, and a further decrease is evident upon inhibitor binding. These results suggest that domain motions of the protein are suppressed step by step of each ligand binding. The DLS and NBS data yield collective and self-translational diffusion constants, respectively, and we used them to extract collective domain motions in nanometer and nanosecond scales from the NSE data. In the apo state, MurD shows both twisting and open-closed domain modes, whereas an ATP binding suppresses twisting domain motions, and a further reduction of open-closed mode is seen in the inhibitor-binding state. These observations are consistent with the structure modifications measured by the small-angle scattering as well as the MD simulations. Such changes in the domain dynamics associated with the sequential enzymatic reactions should be related to the affinity and reaction efficiency with a ligand that binds specifically to each reaction state.
Collapse
Affiliation(s)
- Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan; 2 J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Michihiro Nagao
- NIST Centre for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland; Department of Materials Science and Engineering, University of Maryland, College Park, Maryland; Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Rintaro Inoue
- Institute for Integrative Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, Japan
| | - Masaaki Sugiyama
- Institute for Integrative Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, Japan
| | - Satoshi Ajito
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Taiki Tominaga
- Neutron Science and Technology Center, CROSS, Tokai, Ibaraki, Japan
| | | |
Collapse
|
5
|
Gaetani R, Zizzi EA, Deriu MA, Morbiducci U, Pesce M, Messina E. When Stiffness Matters: Mechanosensing in Heart Development and Disease. Front Cell Dev Biol 2020; 8:334. [PMID: 32671058 PMCID: PMC7326078 DOI: 10.3389/fcell.2020.00334] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
During embryonic morphogenesis, the heart undergoes a complex series of cellular phenotypic maturations (e.g., transition of myocytes from proliferative to quiescent or maturation of the contractile apparatus), and this involves stiffening of the extracellular matrix (ECM) acting in concert with morphogenetic signals. The maladaptive remodeling of the myocardium, one of the processes involved in determination of heart failure, also involves mechanical cues, with a progressive stiffening of the tissue that produces cellular mechanical damage, inflammation, and ultimately myocardial fibrosis. The assessment of the biomechanical dependence of the molecular machinery (in myocardial and non-myocardial cells) is therefore essential to contextualize the maturation of the cardiac tissue at early stages and understand its pathologic evolution in aging. Because systems to perform multiscale modeling of cellular and tissue mechanics have been developed, it appears particularly novel to design integrated mechano-molecular models of heart development and disease to be tested in ex vivo reconstituted cells/tissue-mimicking conditions. In the present contribution, we will discuss the latest implication of mechanosensing in heart development and pathology, describe the most recent models of cell/tissue mechanics, and delineate novel strategies to target the consequences of heart failure with personalized approaches based on tissue engineering and induced pluripotent stem cell (iPSC) technologies.
Collapse
Affiliation(s)
- Roberto Gaetani
- Department of Molecular Medicine, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy.,Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, CA, United States
| | - Eric Adriano Zizzi
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Umberto Morbiducci
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Maurizio Pesce
- Tissue Engineering Research Unit, "Centro Cardiologico Monzino," IRCCS, Milan, Italy
| | - Elisa Messina
- Department of Maternal, Infantile, and Urological Sciences, "Umberto I" Hospital, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
6
|
2DHybrid Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 30617830 DOI: 10.1007/978-981-13-2200-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
We have developed an approach termed '2D hybrid analysis' for building three-dimensional (3D) structures from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by the approach in which 3DEM maps are reconstructed. In the proposed approach, a large number of atomic models with different conformations are first built by computer simulation. Then, simulated EM images are produced from each atomic model. Finally, these images are compared with an experimental EM image to identify the best-fitting atomic model. Two kinds of models are used to simulate the EM images: the negative-stain model and the simple projection model. Although the former is more realistic, the latter permits faster computation. We applied this approach to the averaged EM images of integrin. Although many of these were reproduced well by the best-fitting atomic models, others did not closely resemble any of the simulated EM images. However, the latter group were well reproduced by averaging multiple simulated EM images originating from atomic models with rather different conformations or orientations. This indicated that our approach is capable of detecting mixtures of conformations in the averaged EM images, which should assist in their correct interpretation.
Collapse
|
7
|
2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching. Sci Rep 2017; 7:377. [PMID: 28336911 PMCID: PMC5428313 DOI: 10.1038/s41598-017-00337-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/21/2017] [Indexed: 01/20/2023] Open
Abstract
In this study, we develop an approach termed “2D hybrid analysis” for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.
Collapse
|
8
|
Suzuki Y, Yura K. Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state. Biophys Physicobiol 2016; 13:127-134. [PMID: 27924266 PMCID: PMC5042161 DOI: 10.2142/biophysico.13.0_127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 01/12/2016] [Indexed: 01/11/2023] Open
Abstract
We investigated the effect of ATP binding to GroEL and elucidated a role of ATP in the conformational change of GroEL. GroEL is a tetradecamer chaperonin that helps protein folding by undergoing a conformational change from a closed state to an open state. This conformational change requires ATP, but does not require the hydrolysis of the ATP. The following three types of conformations are crystalized and the atomic coordinates are available; closed state without ATP, closed state with ATP and open state with ADP. We conducted simulations of the conformational change using Elastic Network Model from the closed state without ATP targeting at the open state, and from the closed state with ATP targeting at the open state. The simulations emphasizing the lowest normal mode showed that the one started with the closed state with ATP, rather than the one without ATP, reached a conformation closer to the open state. This difference was mainly caused by the changes in the positions of residues in the initial structure rather than the changes in "connectivity" of residues within the subunit. Our results suggest that ATP should behave as an insulator to induce conformation population shift in the closed state to the conformation that has a pathway leading to the open state.
Collapse
Affiliation(s)
- Yuka Suzuki
- Department of Biology, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan; Center for Informational Biology, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan; National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
9
|
Giant cadherins Fat and Dachsous self-bend to organize properly spaced intercellular junctions. Proc Natl Acad Sci U S A 2014; 111:16011-6. [PMID: 25355906 DOI: 10.1073/pnas.1418990111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cadherins Fat and Dachsous regulate cell polarity and proliferation via their heterophilic interactions at intercellular junctions. Their ectodomains are unusually large because of repetitive extracellular cadherin (EC) domains, which raises the question of how they fit in regular intercellular spaces. Cadherins typically exhibit a linear topology through the binding of Ca(2+) to the linker between the EC domains. Our electron-microscopic observations of mammalian Fat4 and Dachsous1 ectodomains, however, revealed that, although their N-terminal regions exhibit a linear configuration, the C-terminal regions are kinked with multiple hairpin-like bends. Notably, certain EC-EC linkers in Fat4 and Dachsous1 lost Ca(2+)-binding amino acids. When such non-Ca(2+)-binding linkers were substituted for a normal linker in E-cadherin, the mutant E-cadherins deformed more extensively than the wild-type molecule. To simulate cadherin structures with non-Ca(2+)-binding linkers, we used an elastic network model and confirmed that bent configurations can be generated by deformation of non-Ca(2+)-binding linkers. These findings suggest that Fat and Dachsous self-bend due to the loss of Ca(2+)-binding amino acids from specific EC-EC linkers, and can therefore adapt to confined spaces.
Collapse
|
10
|
Dong X, Mi LZ, Zhu J, Wang W, Hu P, Luo BH, Springer TA. α(V)β(3) integrin crystal structures and their functional implications. Biochemistry 2012; 51:8814-28. [PMID: 23106217 PMCID: PMC3495331 DOI: 10.1021/bi300734n] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many questions about the significance of structural features of integrin α(V)β(3) with respect to its mechanism of activation remain. We have determined and re-refined crystal structures of the α(V)β(3) ectodomain linked to C-terminal coiled coils (α(V)β(3)-AB) and four transmembrane (TM) residues in each subunit (α(V)β(3)-1TM), respectively. The α(V) and β(3) subunits with four and eight extracellular domains, respectively, are bent at knees between the integrin headpiece and lower legs, and the headpiece has the closed, low-affinity conformation. The structures differ in the occupancy of three metal-binding sites in the βI domain. Occupancy appears to be related to the pH of crystallization, rather than to the physiologic regulation of ligand binding at the central, metal ion-dependent adhesion site. No electron density was observed for TM residues and much of the α(V) linker. α(V)β(3)-AB and α(V)β(3)-1TM demonstrate flexibility in the linker between their extracellular and TM domains, rather than the previously proposed rigid linkage. A previously postulated interface between the α(V) and β(3) subunits at their knees was also not supported, because it lacks high-quality density, required rebuilding in α(V)β(3)-1TM, and differed markedly between α(V)β(3)-1TM and α(V)β(3)-AB. Together with the variation in domain-domain orientation within their bent ectodomains between α(V)β(3)-AB and α(V)β(3)-1TM, these findings are compatible with the requirement for large structural changes, such as extension at the knees and headpiece opening, in conveying activation signals between the extracellular ligand-binding site and the cytoplasm.
Collapse
Affiliation(s)
- Xianchi Dong
- Immune Disease Institute, Children's Hospital Boston and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115
| | - Li-Zhi Mi
- Immune Disease Institute, Children's Hospital Boston and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115
| | - Jianghai Zhu
- Immune Disease Institute, Children's Hospital Boston and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115
| | - Wei Wang
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803
| | - Ping Hu
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803
| | - Bing-Hao Luo
- Immune Disease Institute, Children's Hospital Boston and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803
| | - Timothy A. Springer
- Immune Disease Institute, Children's Hospital Boston and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115
| |
Collapse
|
11
|
Besya AB, Mobasheri H, Ejtehadi MR. Gating and conduction of nano-channel forming proteins: a computational approach. J Biomol Struct Dyn 2012; 31:818-28. [PMID: 22928968 DOI: 10.1080/07391102.2012.712460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used to measure the possible amplitude of vibration in channel forming proteins. The current approach complements theoretical and experimental techniques including HOLE, Molecular Dynamics (MD), and voltage clamp used to address the channel's structure and dynamics and provides the means to conduct a theoretical simultaneous study of the structure and function of the channel. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:3.
Collapse
Affiliation(s)
- A B Besya
- Institute for Nano Science and Technology, Sharif University of Technology, P.O. Box 14588-89694, Tehran, Iran
| | | | | |
Collapse
|
12
|
Kendall T, Mukai L, Jannuzi AL, Bunch TA. Identification of integrin beta subunit mutations that alter affinity for extracellular matrix ligand. J Biol Chem 2011; 286:30981-30993. [PMID: 21757698 DOI: 10.1074/jbc.m111.254797] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We examined over 50 mutations in the Drosophila βPS integrin subunit that alter integrin function in situ for their ability to bind a soluble monovalent ligand, TWOW-1. Surprisingly, very few of the mutations, which were selected for conditional lethality in the fly, reduce the ligand binding ability of the integrin. The most prevalent class of mutations activates the integrin heterodimer. These findings emphasize the importance of integrin affinity regulation and point out how molecular interactions throughout the integrin molecule are important in keeping the integrin in a low affinity state. Mutations strongly support the controversial deadbolt hypothesis, where the CD loop in the β tail domain acts to restrain the I domain in the inactive, bent conformation. Site-directed mutations in the cytoplasmic domains of βPS and αPS2C reveal different effects on ligand binding from those observed for αIIbβ3 integrins and identify for the first time a cytoplasmic cysteine residue, conserved in three human integrins, as being important in affinity regulation. In the fly, we find that genetic interactions of the βPS mutations with reduction in talin function are consistent with the integrin affinity differences measured in cells. Additionally, these genetic interactions report on increased and decreased integrin functions that do not result in affinity changes in the PS2C integrin measured in cultured cells.
Collapse
Affiliation(s)
- Timmy Kendall
- Department of Molecular and Cellular Biology, Arizona Cancer Center, Tucson, Arizona 85724
| | - Leona Mukai
- Department of Molecular and Cellular Biology, Arizona Cancer Center, Tucson, Arizona 85724
| | - Alison L Jannuzi
- Department of Molecular and Cellular Biology, Arizona Cancer Center, Tucson, Arizona 85724
| | - Thomas A Bunch
- Department of Molecular and Cellular Biology, Arizona Cancer Center, Tucson, Arizona 85724.
| |
Collapse
|
13
|
Fuchigami S, Fujisaki H, Matsunaga Y, Kidera A. Protein Functional Motions: Basic Concepts and Computational Methodologies. ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS 2011. [DOI: 10.1002/9781118087817.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
14
|
Molecular dynamics simulations of forced unbending of integrin α(v)β₃. PLoS Comput Biol 2011; 7:e1001086. [PMID: 21379327 PMCID: PMC3040657 DOI: 10.1371/journal.pcbi.1001086] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 01/18/2011] [Indexed: 11/24/2022] Open
Abstract
Integrins may undergo large conformational changes during activation, but the dynamic processes and pathways remain poorly understood. We used molecular dynamics to simulate forced unbending of a complete integrin αVβ3 ectodomain in both unliganded and liganded forms. Pulling the head of the integrin readily induced changes in the integrin from a bent to an extended conformation. Pulling at a cyclic RGD ligand bound to the integrin head also extended the integrin, suggesting that force can activate integrins. Interactions at the interfaces between the hybrid and β tail domains and between the hybrid and epidermal growth factor 4 domains formed the major energy barrier along the unbending pathway, which could be overcome spontaneously in ∼1 µs to yield a partially-extended conformation that tended to rebend. By comparison, a fully-extended conformation was stable. A newly-formed coordination between the αV Asp457 and the α-genu metal ion might contribute to the stability of the fully-extended conformation. These results reveal the dynamic processes and pathways of integrin conformational changes with atomic details and provide new insights into the structural mechanisms of integrin activation. Proteins can regulate their functions via conformational changes. One example is integrins, which are transmembrane receptors mediating cell-cell and cell-matrix adhesions. Inactive integrins may assume a bent conformation with low affinities for ligands unable to support adhesions. Intracellular or extracellular stimuli induce large scale changes from the bent to an extended conformation, resulting in active integrins with high affinities for ligands to mediate strong adhesions. We used molecular dynamics simulations to reveal the dynamics and pathways of integrin unbending in atomic details. Critical interactions in this process were identified. This study not only sheds light on the structural mechanisms of integrin activation, but also exemplifies allosteric regulations of protein functions.
Collapse
|
15
|
Kamata T, Handa M, Ito S, Sato Y, Ohtani T, Kawai Y, Ikeda Y, Aiso S. Structural requirements for activation in alphaIIb beta3 integrin. J Biol Chem 2010; 285:38428-37. [PMID: 20884611 DOI: 10.1074/jbc.m110.139667] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Integrins are postulated to undergo structural rearrangement from a low affinity bent conformer to a high affinity extended conformer upon activation. However, some reports have shown that a bent conformer is capable of binding a ligand, whereas another report has shown that integrin extension does not absolutely lead to activation. To clarify whether integrin affinity is indeed regulated by the so-called switchblade-like movement, we have engineered a series of mutant αIIbβ3 integrins that are constrained specifically in either a bent or an extended conformation. These mutant αIIbβ3 integrins were expressed in mammalian cells, and fibrinogen binding to these cells was examined. The bent integrins were created through the introduction of artificial disulfide bridges in the β-head/β-tail interface. Cells expressing bent integrins all failed to bind fibrinogen unless pretreated with DTT to disrupt the disulfide bridges. The extended integrins were created by introducing N-glycosylation sites in amino acid residues located close to the α-genu, where the integrin legs fold backward. Among these mutants, activation was maximized in one integrin with an N-glycosylation site located behind the α-genu. This extension-induced activation was completely blocked when the swing-out of the hybrid domain was prevented. These results suggest that the bent and extended conformers represent low affinity and high affinity conformers, respectively, and that extension-induced activation depends on the swing-out of the hybrid domain. Taken together, these results are consistent with the current hypothesis that integrin affinity is regulated by the switchblade-like movement of the integrin legs.
Collapse
Affiliation(s)
- Tetsuji Kamata
- Department of Anatomy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Landau M, Rosenberg N. Molecular insight into human platelet antigens: structural and evolutionary conservation analyses offer new perspective to immunogenic disorders. Transfusion 2010; 51:558-69. [PMID: 20804530 PMCID: PMC3084503 DOI: 10.1111/j.1537-2995.2010.02862.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Human platelet antigens (HPAs) are polymorphisms in platelet membrane glycoproteins (GPs) that can stimulate production of alloantibodies once exposed to foreign platelets (PLTs) with different HPAs. These antibodies can cause neonatal alloimmune thrombocytopenia, posttransfusion purpura, and PLT transfusion refractoriness. Most HPAs are localized on the main PLT receptors: 1) integrin αIIbβ3, known as the fibrinogen receptor; 2) the GPIb-IX-V complex that functions as the receptor for von Willebrand factor; and 3) integrin α2β1, which functions as the collagen receptor. STUDY DESIGN AND METHODS We analyzed the structural location and the evolutionary conservation of the residues associated with the HPAs to characterize the features that induce immunologic responses but do not cause inherited diseases. RESULTS We found that all HPAs reside in positions located on the protein surface, apart from the ligand-binding site, and are evolutionary variable. CONCLUSION Disease-causing mutations often reside in highly conserved and buried positions. In contrast, the HPAs affect residues on the protein surface that were not conserved throughout evolution; this explains their naive effect on the protein function. Nonetheless, the HPAs involve substitutions of solvent-exposed positions that lead to altered interfaces on the surface of the protein and might present epitopes foreign to the immune system.
Collapse
Affiliation(s)
- Meytal Landau
- Amalia Biron Research Institute of Thrombosis and Hemostasis, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | |
Collapse
|
17
|
Provasi D, Murcia M, Coller BS, Filizola M. Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing-out in beta3 integrins. Proteins 2009; 77:477-89. [PMID: 19455709 DOI: 10.1002/prot.22463] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The beta3 integrin family members alphaIIbeta3 and alphaVbeta3 signal bidirectionally through long-range allosteric changes, including a transition from a bent unliganded-closed low-affinity state to an extended liganded-open high-affinity state. To obtain an atomic-level description of this transition in an explicit solvent, we carried out targeted molecular dynamics simulations of the headpieces of alphaIIbeta3 and alphaVbeta3 integrins. Although minor differences were observed between these receptors, our results suggest a common transition pathway in which the hybrid domain swing-out is accompanied by conformational changes within the beta3 betaA (I-like) domain that propagate through the alpha7 helix C-terminus, and are followed by the alpha7 helix downward motion and the opening of the beta6-alpha7 loop. Breaking of contact interactions between the beta6-alpha7 loop and the alpha1 helix N-terminus results in helix straightening, internal rearrangements of the specificity determining loop (SDL), movement of the beta1-alpha1 loop toward the metal ion dependent adhesion site (MIDAS), and final changes at the interfaces between the beta3 betaA (I-like) domain and either the hybrid or the alpha beta-propeller domains. Taken together, our results suggest novel testable hypotheses of intradomain and interdomain interactions responsible for beta3 integrin activation.
Collapse
Affiliation(s)
- Davide Provasi
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029-6574, USA
| | | | | | | |
Collapse
|
18
|
Xiong JP, Mahalingham B, Alonso JL, Borrelli LA, Rui X, Anand S, Hyman BT, Rysiok T, Müller-Pompalla D, Goodman SL, Arnaout MA. Crystal structure of the complete integrin alphaVbeta3 ectodomain plus an alpha/beta transmembrane fragment. J Cell Biol 2009; 186:589-600. [PMID: 19704023 PMCID: PMC2733745 DOI: 10.1083/jcb.200905085] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 07/16/2009] [Indexed: 11/22/2022] Open
Abstract
We determined the crystal structure of 1TM-alphaVbeta3, which represents the complete unconstrained ectodomain plus short C-terminal transmembrane stretches of the alphaV and beta3 subunits. 1TM-alphaVbeta3 is more compact and less active in solution when compared with DeltaTM-alphaVbeta3, which lacks the short C-terminal stretches. The structure reveals a bent conformation and defines the alpha-beta interface between IE2 (EGF-like 2) and the thigh domains. Modifying this interface by site-directed mutagenesis leads to robust integrin activation. Fluorescent lifetime imaging microscopy of inactive full-length alphaVbeta3 on live cells yields a donor-membrane acceptor distance, which is consistent with the bent conformation and does not change in the activated integrin. These data are the first direct demonstration of conformational coupling of the integrin leg and head domains, identify the IE2-thigh interface as a critical steric barrier in integrin activation, and suggest that inside-out activation in intact cells may involve conformational changes other than the postulated switch to a genu-linear state.
Collapse
Affiliation(s)
- Jian-Ping Xiong
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Bhuvaneshwari Mahalingham
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Jose Luis Alonso
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Laura Ann Borrelli
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Xianliang Rui
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Saurabh Anand
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Bradley T. Hyman
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| | - Thomas Rysiok
- Biologicals: Protein and Cell Science, Biologicals: Protein Purification, and Therapeutic Area Oncology: Biochemistry and Cellular Pharmacology, Merck-Serono Research, 64293 Darmstadt, Germany
| | - Dirk Müller-Pompalla
- Biologicals: Protein and Cell Science, Biologicals: Protein Purification, and Therapeutic Area Oncology: Biochemistry and Cellular Pharmacology, Merck-Serono Research, 64293 Darmstadt, Germany
| | - Simon L. Goodman
- Biologicals: Protein and Cell Science, Biologicals: Protein Purification, and Therapeutic Area Oncology: Biochemistry and Cellular Pharmacology, Merck-Serono Research, 64293 Darmstadt, Germany
| | - M. Amin Arnaout
- Program in Leukocyte Biology and Inflammation and Program in Structural Biology, Nephrology Division, Department of Medicine and Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129
| |
Collapse
|
19
|
Poornam GP, Matsumoto A, Ishida H, Hayward S. A method for the analysis of domain movements in large biomolecular complexes. Proteins 2009; 76:201-12. [PMID: 19137621 DOI: 10.1002/prot.22339] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a "rotation space" and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alcohol dehydrogenase, S-Adenosylhomocysteine hydrolase, aspartate transcarbamylase, and the 70S ribosome. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. Of particular interest is the allosteric mechanism in some of these molecules. Results indicate that common boundaries between subunits and domains are good regions to focus on as movement in one subunit can be transmitted to another subunit through such interfaces.
Collapse
Affiliation(s)
- Guru Prasad Poornam
- School of Computing Sciences and School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | | | | |
Collapse
|