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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [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: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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Zhao Y, Fang L, Guo P, Fang Y, Wu J. A MD Simulation Prediction for Regulation of N-Terminal Modification on Binding of CD47 to CD172a in a Force-Dependent Manner. Molecules 2023; 28:molecules28104224. [PMID: 37241964 DOI: 10.3390/molecules28104224] [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: 04/16/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Cancer cells can evade immune surveillance through binding of its transmembrane receptor CD47 to CD172a on myeloid cells. CD47 is recognized as a promising immune checkpoint for cancer immunotherapy inhibiting macrophage phagocytosis. N-terminal post-translated modification (PTM) via glutaminyl cyclase is a landmark event in CD47 function maturation, but the molecular mechanism underlying the mechano-chemical regulation of the modification on CD47/CD172a remains unclear. Here, we performed so-called "ramp-clamp" steered molecular dynamics (SMD) simulations, and found that the N-terminal PTM enhanced interaction of CD172a with CD47 by inducing a dynamics-driven contraction of the binding pocket of the bound CD172a, an additional constraint on CYS15 on CD47 significantly improved the tensile strength of the complex with or without PTM, and a catch bond phenomenon would occur in complex dissociation under tensile force of 25 pN in a PTM-independent manner too. The residues GLN52 and SER66 on CD172a reinforced the H-bonding with their partners on CD47 in responding to PTM, while ARG69 on CD172 with its partner on CD47 might be crucial in the structural stability of the complex. This work might serve as molecular basis for the PTM-induced function improvement of CD47, should be helpful for deeply understanding CD47-relevant immune response and cancer development, and provides a novel insight in developing of new strategies of immunotherapy targeting this molecule interaction.
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Affiliation(s)
- Yang Zhao
- Institute of Biomechanics, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Liping Fang
- 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
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Du R, Li L, Ji J, Fan Y. Receptor-Ligand Binding: Effect of Mechanical Factors. Int J Mol Sci 2023; 24:ijms24109062. [PMID: 37240408 DOI: 10.3390/ijms24109062] [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: 03/22/2023] [Revised: 04/20/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Gaining insight into the in situ receptor-ligand binding is pivotal for revealing the molecular mechanisms underlying the physiological and pathological processes and will contribute to drug discovery and biomedical application. An important issue involved is how the receptor-ligand binding responds to mechanical stimuli. This review aims to provide an overview of the current understanding of the effect of several representative mechanical factors, such as tension, shear stress, stretch, compression, and substrate stiffness on receptor-ligand binding, wherein the biomedical implications are focused. In addition, we highlight the importance of synergistic development of experimental and computational methods for fully understanding the in situ receptor-ligand binding, and further studies should focus on the coupling effects of these mechanical factors.
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Affiliation(s)
- Ruotian Du
- Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Long Li
- State Key Laboratory of Nonlinear Mechanics, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jing Ji
- Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yubo Fan
- Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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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.
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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
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Residues R1075, D1090, R1095, and C1130 Are Critical in ADAMTS13 TSP8-Spacer Interaction Predicted by Molecular Dynamics Simulation. Molecules 2021; 26:molecules26247525. [PMID: 34946607 PMCID: PMC8703438 DOI: 10.3390/molecules26247525] [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: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
ADAMTS13 (A Disintegrin and Metalloprotease with Thrombospondin type 1 repeats, member 13) cleaves von Willebrand Factor (VWF) multimers to limit the prothrombotic function of VWF. The deficiency of ADAMTS13 causes a lethal thrombotic microvascular disease, thrombotic thrombocytopenic purpura (TTP). ADAMTS13 circulates in a “closed” conformation with the distal domain associating the Spacer domain to avoid off-target proteolysis or recognition by auto-antibodies. However, the interactions of the distal TSP8 domain and the Spacer domain remain elusive. Here, we constructed the TSP8-Spacer complex by a combination of homology modelling and flexible docking. Molecular dynamics simulation was applied to map the binding sites on the TSP8 or Spacer domain. The results predicted that R1075, D1090, R1095, and C1130 on the TSP8 domain were key residues that interacted with the Spacer domain. R1075 and R1095 bound exosite-4 tightly, D1090 formed multiple hydrogen bonds and salt bridges with exosite-3, and C1130 interacted with both exosite-3 and exosite-4. Specific mutations of exosite-3 (R568K/F592Y/R660K/Y661F/Y665F) or the four key residues (R1075A/D1090A/R1095A/C1130A) impaired the binding of the TSP8 domain to the Spacer domain. These results shed new light on the understanding of the auto-inhibition of ADAMTS13.
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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.
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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.
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