1
|
Fang L, Zhao Y, Guo P, Fang Y, Wu J. MD Simulation Reveals Regulation of Mechanical Force and Extracellular Domain 2 on Binding of DNAM-1 to CD155. Molecules 2023; 28:molecules28062847. [PMID: 36985819 PMCID: PMC10053669 DOI: 10.3390/molecules28062847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Two extracellular domains of the adhesive receptor DNAM-1 are involved in various cellular biological processes through binding to ligand CD155, usually under a mechano-microenvironment. The first extracellular domain (D1) plays a key role in recognition, but the function of the second extracellular domain (D2) and effects of force on the interaction of DNAM-1 with CD155 remain unclear. We herein studied the interaction of DNAM-1 with CD155 by performing steered molecular dynamics (MD) simulations, and observed the roles of tensile force and D2 on the affinity of DNAM-1 to CD155. The results showed that D2 improved DNAM-1 affinity to CD155; the DNAM-1/CD155 complex had a high mechanical strength and a better mechanical stability for its conformational conservation either at pulling with constant velocity or under constant tensile force (≤100 pN); the catch-slip bond transition governed CD155 dissociation from DNAM-1; and, together with the newly assigned key residues in the binding site, force-induced conformation changes should be responsible for the mechanical regulation of DNAM-1's affinity to CD155. This work provided a novel insight in understanding the mechanical regulation mechanism and D2 function in the interaction of DNAM-1 with CD155, as well as their molecular basis, relevant transmembrane signaling, and cellular immune responses under a mechano-microenvironment.
Collapse
Affiliation(s)
- Liping Fang
- Institute of Biomechanics, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yang Zhao
- Institute of Biomechanics, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Pei Guo
- Institute of Biomechanics, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Fang
- Institute of Biomechanics, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jianhua Wu
- Institute of Biomechanics, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| |
Collapse
|
2
|
Sun X, Huang B, Pan Y, Fang J, Wang H, Ji Y, Ling Y, Guo P, Lin J, Li Q, Fang Y, Wu J. Spatiotemporal characteristics of P-selectin-induced β 2 integrin activation of human neutrophils under flow. Front Immunol 2022; 13:1023865. [PMID: 36439190 PMCID: PMC9692129 DOI: 10.3389/fimmu.2022.1023865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2023] Open
Abstract
Activation of integrins is crucial for recruitment of flowing leukocytes to inflammatory or injured vascular sites, but their spatiotemporal characteristics are incompletely understood. We discovered that β2-integrin activation over the entire surface of neutrophils on immobilized P-selectin occurred via mitogen-activated protein kinase (MAPK) or non-MAPK signaling with a minute-level timescale in a force-dependent manner. In flow, MAPK signaling required intracellular Ca2+ release to activate integrin within 2 min. Integrin activation via non-MAPK signaling occurred first locally in the vicinity of ligated P-selectin glycoprotein ligand-1 (PSGL-1) within sub-seconds, and then over the entire cell surface within 1 min in an extracellular Ca2+ influx-dependent manner. The transition from a local (but rapid) to global (but slow) activation mode was triggered by ligating the freshly activated integrin. Lipid rafts, moesin, actin, and talin were involved in non-MAPK signaling. Fluid loads had a slight effect on local integrin activation with a second-level timescale, but served as enhancers of global integrin activation.
Collapse
Affiliation(s)
- Xiaoxi Sun
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Bing Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuping Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jinhua Fang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hefeng Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yanru Ji
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yingchen Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Pei Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiangguo Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Research Center of Medical Sciences, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Quhuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Fang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianhua Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
3
|
Su S, Ling Y, Fang Y, Wu J. Force-enhanced biophysical connectivity of platelet β3 integrin signaling through Talin is predicted by steered molecular dynamics simulations. Sci Rep 2022; 12:4605. [PMID: 35301368 PMCID: PMC8931153 DOI: 10.1038/s41598-022-08554-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Platelet β3-integrin signaling through Talin is crucial in platelet transmembrane signaling, activation, adhesion, spreading and aggregation, and remains unclear in mechano-microenvironments. In order to examine Talin-β3 integrin biophysical connectivity, a series of “ramp-clamp” steered molecular dynamics (SMD) simulations were performed on complex of F3 domain of Talin and cytoplasmic tail of β3 integrin to imitate different force-loads in platelet. Pull-induced allostery of the hydrophobic pocket in F3 domain might markedly enhance complex rupture-force (> 150pN) and slow down breakage of the complex; the complex should mechano-stable for its conformational conservation under loads (≤ 80pN); increasing force below 60pN would decrease the complex dissociation probability, and force-induced extension of β5 strand on Talin and binding site residues, ASP740 and ALA742 as well as Asn744, on β3-integrin were responsible for the force-enhanced linkage of the Talin-β3 integrin. Force might enhance biophysical connectivity of β3-integrin signaling through Talin by a catch bond mechanism, which be mediated by the force-induced allostery of complex at clamped stage. This work provides a novel insight into the force-regulated transmembrane β3-integrin signaling and its molecular basis for platelet activation, and exhibited a potential power of the present computer strategy in predicting mechanical regulation on ligand-receptor interaction under loads.
Collapse
Affiliation(s)
- Shuixiu Su
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yingchen Ling
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ying Fang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Jianhua Wu
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| |
Collapse
|
4
|
Yang J, Wu Z, Xie X, Liu G, Fang Y, Wu J, Lin J. Characterization of the interactions of ADAMTS13 CUB1 domain to WT- and GOF-Spacer domain by molecular dynamics simulation. J Mol Graph Model 2021; 109:108029. [PMID: 34517169 DOI: 10.1016/j.jmgm.2021.108029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/22/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Metalloprotease ADAMTS13 specifically cleaves VWF (von Willebrand Factor) to prevent excessive platelet aggregation and thrombus formation at the sites of vascular injury. To avoid non-specific cleavage, ADAMTS13 has the auto-inhibition effect in which the Spacer domain in N-terminal interacts with the CUB1 domain in C-terminal, resulting in decreased proteolytic activity. Previous studies reported that exosite-3 in the Spacer domain was a key binding site in the Spacer-CUB1 interaction. When exosite-3 was mutated (R660K/F592Y/R568K/Y661F/Y665F, GOF), the auto-inhibition of ADAMTS13 was disrupted and the enzymatic activity was markedly increased. However, the characteristics of the Spacer-CUB1 interaction is not fully understood. Here, we constructed the model of Spacer-CUB1 complex by homologous modeling and molecular docking to characterize the Spacer-CUB1 binding and predict key amino acid residues via molecular dynamics simulation. Our data showed that G607-S610 was a non-reported potential binding site in the Spacer domain; GOF mutation attenuated the formation of hydrogen bond between exosite-3 and the CUB1 domain; Residues E1231, R1251, L1258, D1259 and T1261 in the CUB1 domain might play an important role in the Spacer-CUB1 interaction. Our study advances the understanding of the structural basis of the auto-inhibition of ADAMTS13 and provides information about the key residues in the binding interface.
Collapse
Affiliation(s)
- Junxian Yang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Zhiwei Wu
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Xubin Xie
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Guangjian Liu
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Ying Fang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jianhua Wu
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jiangguo Lin
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| |
Collapse
|
5
|
Jiang X, Sun X, Lin J, Ling Y, Fang Y, Wu J. MD Simulations on a Well-Built Docking Model Reveal Fine Mechanical Stability and Force-Dependent Dissociation of Mac-1/GPIbα Complex. Front Mol Biosci 2021; 8:638396. [PMID: 33968982 PMCID: PMC8100526 DOI: 10.3389/fmolb.2021.638396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/12/2021] [Indexed: 12/20/2022] Open
Abstract
Interaction of leukocyte integrin macrophage-1 antigen (Mac-1) to platelet glycoprotein Ibα (GPIbα) is critical for platelet-leukocyte crosstalk in hemostasis and inflammatory responses to vessel injuries under hemodynamic environments. The mechano-regulation and its molecular basis for binding of Mac-1 to GPIbα remain unclear, mainly coming from the lack of crystal structure of the Mac-1/GPIbα complex. We herein built a Mac-1/GPIbα complex model through a novel computer strategy, which included a flexible molecular docking and system equilibrium followed by a "force-ramp + snapback" molecular dynamics (MD) simulation. With this model, a series of "ramp-clamp" steered molecular dynamics (SMD) simulations were performed to examine the GPIbα-Mac-1 interaction under various loads. The results demonstrated that the complex was mechano-stable for both the high rupture force (>250 pN) at a pulling velocity of 3 Å/ns and the conformational conservation under various constant tensile forces (≤75 pN); a catch-slip bond transition was predicted through the dissociation probability, examined with single molecular AFM measurements, reflected by the interaction energy and the interface H-bond number, and related to the force-induced allostery of the complex; besides the mutation-identified residues D222 and R218, the residues were also dominant in the binding of Mac-1 to GPIbα. This study recommended a valid computer strategy for building a likely wild-type docking model of a complex, provided a novel insight into the mechanical regulation mechanism and its molecular basis for the interaction of Mac-1 with GPIbα, and would be helpful for understanding the platelet-leukocyte interaction in hemostasis and inflammatory responses under mechano-microenvironments.
Collapse
Affiliation(s)
- Xiaoyan Jiang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoxi Sun
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiangguo Lin
- Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yingchen Ling
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Fang
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianhua Wu
- Institute of Biomechanics/School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|