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Baksi A, Zerze H, Agrawal A, Karim A, Zerze GH. The molecular picture of the local environment in a stable model coacervate. Commun Chem 2024; 7:222. [PMID: 39349768 PMCID: PMC11442467 DOI: 10.1038/s42004-024-01304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
Complex coacervates play essential roles in various biological processes and applications. Although substantial progress has been made in understanding the molecular interactions driving complex coacervation, the mechanisms stabilizing coacervates against coalescence remain experimentally challenging and not fully elucidated. We recently showed that polydiallyldimethylammonium chloride (PDDA) and adenosine triphosphate (ATP) coacervates stabilize upon their transfer to deionized (DI) water. Here, we perform molecular dynamics simulations of PDDA-ATP coacervates in supernatant and DI water, to understand the ion dynamics and structure within stable coacervates. We found that transferring the coacervates to DI water results in an immediate ejection of a significant fraction of small ions (Na+ and Cl-) from the surface of the coacervates to DI water. We also observed a notable reduction in the mobility of these counterions in coacervates when in DI water, both in the cluster-forming and slab simulations, together with a lowered displacement of PDDA and ATP. These results suggest that the initial ejection of the ions from the coacervates in DI water may induce an interfacial skin layer formation, inhibiting further mobility of ions in the skin layer.
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Affiliation(s)
- Atanu Baksi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Hasan Zerze
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Aman Agrawal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
- Department of Chemistry and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Alamgir Karim
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Gül H Zerze
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA.
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2
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Varma SG, Mitra A, Sarkar S. Self-diffusion is temperature independent on active membranes. Phys Chem Chem Phys 2024; 26:23348-23362. [PMID: 39211961 DOI: 10.1039/d4cp02470b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling. Temperature variations in thermal equilibrium rapidly change molecular transport properties. The coefficient of lipid self-diffusion increases exponentially with temperature in thermal equilibrium, for example. Hence, maintaining cellular homeostasis through molecular transport is hard in thermal equilibrium in the noisy cellular environment, where temperatures can fluctuate widely due to local heat generation. In this paper, using both molecular and lattice-based modeling of membrane transport, we show that the presence of active transport originating from the cell's cytoskeleton can make the self-diffusion of the molecules on the membrane robust to temperature fluctuations. The resultant temperature-independence of self-diffusion keeps the precision of cellular signaling invariant over a broad range of ambient temperatures, allowing cells to make robust decisions. We have also found that the Kawasaki algorithm, the widely used model of lipid transport on lattices, predicts incorrect temperature dependence of lipid self-diffusion in equilibrium. We propose a new algorithm that correctly captures the equilibrium properties of lipid self-diffusion and reproduces experimental observations.
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Affiliation(s)
- Saurav G Varma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| | - Argha Mitra
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| | - Sumantra Sarkar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
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3
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Skeens A, Markle JM, Petipas G, Frey SL, Legleiter J. Divalent cations promote huntingtin fibril formation on endoplasmic reticulum derived and model membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184339. [PMID: 38763270 DOI: 10.1016/j.bbamem.2024.184339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Huntington's Disease (HD) is caused by an abnormal expansion of the polyglutamine (polyQ) domain within the first exon of the huntingtin protein (htt). This expansion promotes disease-related htt aggregation into amyloid fibrils and the formation of proteinaceous inclusion bodies within neurons. Fibril formation is a complex heterogenous process involving an array of aggregate species such as oligomers, protofibrils, and fibrils. In HD, structural abnormalities of membranes of several organelles develop. In particular, the accumulation of htt fibrils near the endoplasmic reticulum (ER) impinges upon the membrane, resulting in ER damage, altered dynamics, and leakage of Ca2+. Here, the aggregation of htt at a bilayer interface assembled from ER-derived liposomes was investigated, and fibril formation directly on these membranes was enhanced. Based on these observations, simplified model systems were used to investigate mechanisms associated with htt aggregation on ER membranes. As the ER-derived liposome fractions contained residual Ca2+, the role of divalent cations was also investigated. In the absence of lipids, divalent cations had minimal impact on htt structure and aggregation. However, the presence of Ca2+ or Mg2+ played a key role in promoting fibril formation on lipid membranes despite reduced htt insertion into and association with lipid interfaces, suggesting that the ability of divalent cations to promote fibril formation on membranes is mediated by induced changes to the lipid membrane physicochemical properties. With enhanced concentrations of intracellular calcium being a hallmark of HD, the ability of divalent cations to influence htt aggregation at lipid membranes may play a role in aggregation events that lead to organelle abnormalities associated with disease.
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Affiliation(s)
- Adam Skeens
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Jordyn M Markle
- The Department of Chemistry, Gettysburg College, 300 N. Washington Street, Gettysburg, PA 17325, USA
| | - Gabriella Petipas
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Shelli L Frey
- The Department of Chemistry, Gettysburg College, 300 N. Washington Street, Gettysburg, PA 17325, USA.
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA; Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, USA; Department of Neuroscience, West Virginia University, 1 Medical Center Dr., P.O. Box 9303, Morgantown, WV 26505, USA.
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4
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Brown CM, Marrink SJ. Modeling membranes in situ. Curr Opin Struct Biol 2024; 87:102837. [PMID: 38744147 DOI: 10.1016/j.sbi.2024.102837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, in situ, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.
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Affiliation(s)
- Chelsea M Brown
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. https://twitter.com/chelseabrowncg
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. s.j.marrinkrug.nl
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5
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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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6
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Borges-Araújo L, Pereira GP, Valério M, Souza PCT. Assessing the Martini 3 protein model: A review of its path and potential. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141014. [PMID: 38670324 DOI: 10.1016/j.bbapap.2024.141014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field - Martini 3 - a new iteration of its protein model was also made available. The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short time since its release, many of which would not have been possible before. Furthermore, we discuss reported limitations, potential directions for model improvement and comment on what the likely future development and application avenues are.
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Affiliation(s)
- Luís Borges-Araújo
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Gilberto P Pereira
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Mariana Valério
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Paulo C T Souza
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France; Centre Blaise Pascal de Simulation et de Modélisation Numérique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France.
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7
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Zhu Q, Wu Y, Luo R. Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine. Phys Chem Chem Phys 2024; 26:10568-10578. [PMID: 38512104 PMCID: PMC11056285 DOI: 10.1039/d4cp00761a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Liquid-liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The electrostatic interaction between oligolysine and ATP is of great importance in forming LLPS. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of α-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases.
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Affiliation(s)
- Qiang Zhu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| | - Yongxian Wu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
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8
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Waechtler BE, Jayasankar R, Morin EP, Robinson DN. Benefits and challenges of reconstituting the actin cortex. Cytoskeleton (Hoboken) 2024:10.1002/cm.21855. [PMID: 38520148 PMCID: PMC11417134 DOI: 10.1002/cm.21855] [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: 12/05/2023] [Revised: 02/21/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
The cell's ability to change shape is a central feature in many cellular processes, including cytokinesis, motility, migration, and tissue formation. The cell constructs a network of contractile proteins underneath the cell membrane to form the cortex, and the reorganization of these components directly contributes to cellular shape changes. The desire to mimic these cell shape changes to aid in the creation of a synthetic cell has been increasing. Therefore, membrane-based reconstitution experiments have flourished, furthering our understanding of the minimal components the cell uses throughout these processes. Although biochemical approaches increased our understanding of actin, myosin II, and actin-associated proteins, using membrane-based reconstituted systems has further expanded our understanding of actin structures and functions because membrane-cortex interactions can be analyzed. In this review, we highlight the recent developments in membrane-based reconstitution techniques. We examine the current findings on the minimal components needed to recapitulate distinct actin structures and functions and how they relate to the cortex's impact on cellular mechanical properties. We also explore how co-processing of computational models with wet-lab experiments enhances our understanding of these properties. Finally, we emphasize the benefits and challenges inherent to membrane-based, reconstitution assays, ranging from the advantage of precise control over the system to the difficulty of integrating these findings into the complex cellular environment.
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Affiliation(s)
- Brooke E. Waechtler
- Department of Cell Biology, Johns Hopkins University, School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205
| | - Rajan Jayasankar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Whiting School of Engineering, 725 N Wolfe Street, Baltimore, MD 21205
| | - Emma P. Morin
- Department of Cell Biology, Johns Hopkins University, School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205
| | - Douglas N. Robinson
- Department of Cell Biology, Johns Hopkins University, School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Whiting School of Engineering, 725 N Wolfe Street, Baltimore, MD 21205
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205
- Department of Medicine, Johns Hopkins University, School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205
- Department of Oncology, Johns Hopkins University, School of Medicine, 725 N Wolfe Street, Baltimore, MD 21205
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9
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Yao X, Yin Q, Tian X, Zheng Y, Li H, Fu S, Lian Z, Zhang Y, Li F, Zhang W, He Y, Wang R, Wu B, Nie K, Xu S, Cheng J, Li X, Wang H, Liang G. Human and animal exposure to newly discovered sand fly viruses, China. Front Cell Infect Microbiol 2024; 13:1291937. [PMID: 38235489 PMCID: PMC10791927 DOI: 10.3389/fcimb.2023.1291937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/24/2023] [Indexed: 01/19/2024] Open
Abstract
Introduction The Hedi virus (HEDV) and Wuxiang virus (WUXV) are newly discovered Bunyaviruses transmitted by sandflies. The geographical distribution of isolation of these two viruses continues to expand and it has been reported that WUXV causes neurological symptoms and even death in suckling mice. However, little is known about the prevalence of the two viruses in mammalian infections. Methods In order to understand the infection status of HEDV and WUXV in humans and animals from regions where the viruses have been isolated, this study used Western blotting to detect the positive rates of HEDV and WUXV IgG antibodies in serum samples from febrile patients, dogs, and chickens in the forementioned regions. Results The results showed that of the 29 human serum samples, 17.24% (5/29) tested positive for HEDV, while 68.96% (20/29) were positive for WUXV. In the 31 dog serum samples, 87.10% (27/31) were positive for HEDV and 70.97% (22/31) were positive for WUXV, while in the 36 chicken serum samples, 47.22% (17/36) were positive for HEDV, and 52.78% (19/36) were positive for WUXV. Discussion These findings suggest there are widespread infections of HEDV and WUXV in mammals (dogs, chickens) and humans from the regions where these viruses have been isolated. Moreover, the positive rate of HEDV infections was higher in local animals compared to that measured in human specimens. This is the first seroepidemiological study of these two sandfly-transmitted viruses. The findings of the study have practical implications for vector-borne viral infections and related zoonotic infections in China, as well as providing an important reference for studies on the relationship between sandfly-transmitted viruses and zoonotic infections outside of China.
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Affiliation(s)
- Xiaohui Yao
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Qikai Yin
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaodong Tian
- Department of Vector Biology, Shanxi Province Center for Disease Control and Prevention, Taiyuan, Shanxi, China
| | - Yuke Zheng
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongyan Li
- Yangquan Center for Disease Control and Prevention, Yangquan, Shanxi, China
| | - Shihong Fu
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhengmin Lian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yijia Zhang
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fan Li
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weijia Zhang
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying He
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruichen Wang
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bin Wu
- Yangquan Center for Disease Control and Prevention, Yangquan, Shanxi, China
| | - Kai Nie
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Songtao Xu
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingxia Cheng
- Department of Vector Biology, Shanxi Province Center for Disease Control and Prevention, Taiyuan, Shanxi, China
| | - Xiangdong Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Huanyu Wang
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guodong Liang
- Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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10
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Bandyopadhyay S, Gurjar D, Saha B, Bodhale N. Decoding the contextual duality of CD40 functions. Hum Immunol 2023; 84:590-599. [PMID: 37596136 DOI: 10.1016/j.humimm.2023.08.142] [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: 05/20/2023] [Revised: 07/13/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
Previously, we established that as a function of its mode of interaction with its ligand or cellular conditions such as membrane lipids, preexisting signaling intermediates activation status, a transmembrane receptor, as represented here with CD40, can induce counteractive cellular responses. Using CD40-binding peptides, recombinant mutated CD40-ligands, and an agonistic antibody, we have established the functional duality of CD40. CD40 builds up two constitutionally different signalosomes on lipid raft and non-raft membrane domains initiating two different signaling pathways. Although this initial signaling may be modified by the pre-existing signaling conditions downstream and may be subjected to feed-forward or negative signaling effects, the initial CD40-CD40L interaction plays a crucial role in the functional outcome of CD40. Herein, we have reviewed the influence of interaction between the CD40-CD40L evoking the functional duality of CD40 contingent upon different physiological states of the cells.
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Affiliation(s)
| | - Dhiraj Gurjar
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Neelam Bodhale
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
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11
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Arnold DP, Gubbala A, Takatori SC. Active Surface Flows Accelerate the Coarsening of Lipid Membrane Domains. PHYSICAL REVIEW LETTERS 2023; 131:128402. [PMID: 37802933 DOI: 10.1103/physrevlett.131.128402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/24/2023] [Indexed: 10/08/2023]
Abstract
Phase separation of multicomponent lipid membranes is characterized by the nucleation and coarsening of circular membrane domains that grow slowly in time as ∼t^{1/3}, following classical theories of coalescence and Ostwald ripening. In this Letter, we study the coarsening kinetics of phase-separating lipid membranes subjected to nonequilibrium forces and flows transmitted by motor-driven gliding actin filaments. We experimentally observe that the activity-induced surface flows trigger rapid coarsening of noncircular membrane domains that grow as ∼t^{2/3}, a 2x acceleration in the growth exponent compared to passive coalescence and Ostwald ripening. We analyze these results by developing analytical theories based on the Smoluchowski coagulation model and the phase field model to predict the domain growth in the presence of active flows. Our Letter demonstrates that active matter forces may be used to control the growth and morphology of membrane domains driven out of equilibrium.
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Affiliation(s)
- Daniel P Arnold
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Aakanksha Gubbala
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Sho C Takatori
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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12
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Stoops EH, Ferrin MA, Jorgens DM, Drubin DG. Self-organizing actin networks drive sequential endocytic protein recruitment and vesicle release on synthetic lipid bilayers. Proc Natl Acad Sci U S A 2023; 120:e2302622120. [PMID: 37216532 PMCID: PMC10235984 DOI: 10.1073/pnas.2302622120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Forces generated by actin assembly assist membrane invagination during clathrin-mediated endocytosis (CME). The sequential recruitment of core endocytic proteins and regulatory proteins, and assembly of the actin network, are well documented in live cells and are highly conserved from yeasts to humans. However, understanding of CME protein self-organization, as well as the biochemical and mechanical principles that underlie actin's role in CME, is lacking. Here, we show that supported lipid bilayers coated with purified yeast Wiskott Aldrich Syndrome Protein (WASP), an endocytic actin assembly regulator, and incubated in cytoplasmic yeast extracts, recruit downstream endocytic proteins and assemble actin networks. Time-lapse imaging of WASP-coated bilayers revealed sequential recruitment of proteins from different endocytic modules, faithfully replicating in vivo behavior. Reconstituted actin networks assemble in a WASP-dependent manner and deform lipid bilayers, as seen by electron microscopy. Time-lapse imaging revealed that vesicles are released from the lipid bilayers with a burst of actin assembly. Actin networks pushing on membranes have previously been reconstituted; here, we have reconstituted a biologically important variation of these actin networks that self-organize on bilayers and produce pulling forces sufficient to bud off membrane vesicles. We propose that actin-driven vesicle generation may represent an ancient evolutionary precursor to diverse vesicle forming processes adapted for a wide array of cellular environments and applications.
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Affiliation(s)
- Emily H. Stoops
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Michael A. Ferrin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | | | - David G. Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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13
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Liebe NL, Mey I, Vuong L, Shikho F, Geil B, Janshoff A, Steinem C. Bioinspired Membrane Interfaces: Controlling Actomyosin Architecture and Contractility. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11586-11598. [PMID: 36848241 PMCID: PMC9999349 DOI: 10.1021/acsami.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The creation of biologically inspired artificial lipid bilayers on planar supports provides a unique platform to study membrane-confined processes in a well-controlled setting. At the plasma membrane of mammalian cells, the linkage of the filamentous (F)-actin network is of pivotal importance leading to cell-specific and dynamic F-actin architectures, which are essential for the cell's shape, mechanical resilience, and biological function. These networks are established through the coordinated action of diverse actin-binding proteins and the presence of the plasma membrane. Here, we established phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P2)-doped supported planar lipid bilayers to which contractile actomyosin networks were bound via the membrane-actin linker ezrin. This membrane system, amenable to high-resolution fluorescence microscopy, enabled us to analyze the connectivity and contractility of the actomyosin network. We found that the network architecture and dynamics are not only a function of the PtdIns[4,5]P2 concentration but also depend on the presence of negatively charged phosphatidylserine (PS). PS drives the attached network into a regime, where low but physiologically relevant connectivity to the membrane results in strong contractility of the actomyosin network, emphasizing the importance of the lipid composition of the membrane interface.
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Affiliation(s)
- Nils L. Liebe
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Ingo Mey
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Loan Vuong
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Fadi Shikho
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Burkhard Geil
- Institut
für Physikalische Chemie, Georg-August
Universität, Tammannstr. 6, Göttingen 37077, Germany
| | - Andreas Janshoff
- Institut
für Physikalische Chemie, Georg-August
Universität, Tammannstr. 6, Göttingen 37077, Germany
| | - Claudia Steinem
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
- Max-Planck-Institut
für Dynamik und Selbstorganisation, Am Fassberg 17, Göttingen 37077, Germany
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14
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Stoops EH, Ferrin MA, Jorgens DM, Drubin DG. Self-organizing actin networks drive sequential endocytic protein recruitment and vesicle release on synthetic lipid bilayers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528546. [PMID: 36824809 PMCID: PMC9949000 DOI: 10.1101/2023.02.14.528546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Forces generated by actin assembly assist membrane invagination during clathrin-mediated endocytosis (CME). The sequential recruitment of core endocytic proteins and regulatory proteins, and assembly of the actin network, are well documented in live cells and are highly conserved from yeasts to humans. However, understanding of CME protein self-organization, as well as the biochemical and mechanical principles that underlie actin’s role in CME, is lacking. Here, we show that supported lipid bilayers coated with purified yeast WASP, an endocytic actin assembly regulator, and incubated in cytoplasmic yeast extracts, recruit downstream endocytic proteins and assemble actin tails. Time-lapse imaging of WASP-coated bilayers revealed sequential recruitment of proteins from different endocytic modules, faithfully replicating in vivo behavior. Reconstituted actin networks assemble in a WASP-dependent manner and deform lipid bilayers, as seen by electron microscopy. Time-lapse imaging revealed that vesicles are released from the lipid bilayers with a burst of actin assembly. Actin networks pushing on membranes have previously been reconstituted; here, we have reconstituted a biologically important variation of these actin networks that self-organize on bilayers and produce pulling forces sufficient to bud off membrane vesicles. We propose that actin-driven vesicle generation may represent an ancient evolutionary precursor to diverse vesicle forming processes adapted for a wide array of cellular environments and applications. Significance Statement Actin filament assembly participates in many vesicle-forming processes. However, the underlying principles for how assembly is initiated and organized to effectively harness assembly forces remain elusive. To address this gap, we report a novel reconstitution of actin-driven vesicle release from supported lipid bilayers. Using real-time imaging, we observe sequential recruitment of endocytic proteins and, following a burst of actin assembly, vesicle release from bilayers. Given the absence of cargo or upstream endocytic regulatory proteins on the bilayers, and the participation of actin in many vesicle-forming processes, we posit that this mode of vesicle formation represents an early evolutionary precursor for multiple trafficking pathways. We expect that this assay will be of great use for future investigations of actin-mediated vesicle-forming processes.
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Affiliation(s)
- Emily H. Stoops
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Michael A. Ferrin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Danielle M. Jorgens
- Electron Microscope Laboratory, University of California, Berkeley, Berkeley, CA
| | - David G. Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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15
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Prakash S, Krishna A, Sengupta D. Cofilin-Membrane Interactions: Electrostatic Effects in Phosphoinositide Lipid Binding. Chemphyschem 2023; 24:e202200509. [PMID: 36200760 DOI: 10.1002/cphc.202200509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/06/2022] [Indexed: 02/04/2023]
Abstract
The actin cytoskeleton interacts with the cell membrane primarily through the indirect interactions of actin-binding proteins such as cofilin-1. The molecular mechanisms underlying the specific interactions of cofilin-1 with membrane lipids are still unclear. Here, we performed coarse-grain molecular dynamics simulations of cofilin-1 with complex lipid bilayers to analyze the specificity of protein-lipid interactions. We observed the maximal interactions with phosphoinositide (PIP) lipids, especially PIP2 and PIP3 lipids. A good match was observed between the residues predicted to interact and previous experimental studies. The clustering of PIP lipids around the membrane bound protein leads to an overall lipid demixing and gives rise to persistent membrane curvature. Further, through a series of control simulations, we observe that both electrostatics and geometry are critical for specificity of lipid binding. Our current study is a step towards understanding the physico-chemical basis of cofilin-PIP lipid interactions.
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Affiliation(s)
- Shikha Prakash
- CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Anjali Krishna
- CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Current Address: School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Durba Sengupta
- CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
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16
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Liu Y, Wang X, Wan Z, Ngai T, Tse YLS. Capturing coacervate formation and protein partition by molecular dynamics simulation. Chem Sci 2023; 14:1168-1175. [PMID: 36756326 PMCID: PMC9891350 DOI: 10.1039/d2sc01164f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
Biomolecules localize and function in microenvironments where their local concentration, spatial organization, and biochemical reactivity are regulated. To compartmentalize and control the local properties of the native microenvironment, cellular mimics and artificial bioreactors have been developed to study the properties of membraneless organelles or mimic the bio-environment for life origin. Here, we carried out molecular dynamics simulation with the Martini 3.0 model to reproduce the experimental salt concentration and pH dependency of different complex coacervates. We showed that coacervates inside vesicles are able to change their shape. In addition, we used these coacervate systems to explore the partitioning of the ubiquitous cytoskeletal protein actin and found that actin spontaneously partitions to all the coacervate peripheries. Therefore, we believe that our study can provide a better understanding of the versatile coacervate platform, where biomolecules partition and gather to fulfill their biological duties.
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Affiliation(s)
- Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University Chengdu 610065 China.,Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Xinyan Wang
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Zhili Wan
- School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
| | - Ying-Lung Steve Tse
- Department of Chemistry, The Chinese University of Hong Kong Sha Tin Hong Kong China
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17
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Baldauf L, van Buren L, Fanalista F, Koenderink GH. Actomyosin-Driven Division of a Synthetic Cell. ACS Synth Biol 2022; 11:3120-3133. [PMID: 36164967 PMCID: PMC9594324 DOI: 10.1021/acssynbio.2c00287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 01/24/2023]
Abstract
One of the major challenges of bottom-up synthetic biology is rebuilding a minimal cell division machinery. From a reconstitution perspective, the animal cell division apparatus is mechanically the simplest and therefore attractive to rebuild. An actin-based ring produces contractile force to constrict the membrane. By contrast, microbes and plant cells have a cell wall, so division requires concerted membrane constriction and cell wall synthesis. Furthermore, reconstitution of the actin division machinery helps in understanding the physical and molecular mechanisms of cytokinesis in animal cells and thus our own cells. In this review, we describe the state-of-the-art research on reconstitution of minimal actin-mediated cytokinetic machineries. Based on the conceptual requirements that we obtained from the physics of the shape changes involved in cell division, we propose two major routes for building a minimal actin apparatus capable of division. Importantly, we acknowledge both the passive and active roles that the confining lipid membrane can play in synthetic cytokinesis. We conclude this review by identifying the most pressing challenges for future reconstitution work, thereby laying out a roadmap for building a synthetic cell equipped with a minimal actin division machinery.
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Affiliation(s)
| | | | - Federico Fanalista
- Department of Bionanoscience,
Kavli Institute of Nanoscience Delft, Delft
University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje Hendrika Koenderink
- Department of Bionanoscience,
Kavli Institute of Nanoscience Delft, Delft
University of Technology, 2629 HZ Delft, The Netherlands
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18
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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19
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Ma Z, Shi S, Ren M, Pang C, Zhan Y, An H, Sun F. Molecular Mechanism of CD44 Homodimerization Modulated by Palmitoylation and Membrane Environments. Biophys J 2022; 121:2671-2683. [PMID: 35733341 DOI: 10.1016/j.bpj.2022.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/21/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
The homodimerization of CD44 plays a key role in an intercellular-to-extracellular signal transduction and tumor progression. Acylated modification and specific membrane environments have been reported to mediate translocation and oligomerization of CD44, however, the underlying molecular mechanism remains elusive. In this study, extensive molecular dynamics simulations are performed to characterize the dimerization of palmitoylated CD44 variants in different bilayer environments. CD44 forms homodimer depending on the cysteines on the juxta-membrane domains, and the dimerization efficiency and packing configurations are defected by their palmitoylated modifications. In the phase-segregated (raft included) membrane, homodimerization of the palmitoylated CD44 is hardly observed, whereas PIP2 addition compensates to realize dimerization. However, the structure of CD44 homodimer formed in the phase-segregated bilayer turns susceptive and PIP2 addition allows for an extensive conformation of the cytoplasmic domain, a proposal prerequisite to access the cytoskeleton linker proteins. The results unravel a delicate competitive relationship between PIP2, lipid raft and palmitoylation in mediating protein homodimerization, which helps to clarify the dynamic dimer conformations and involved cellular signaling of the CD44 likewise proteins.
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Affiliation(s)
- Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Sai Shi
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
| | - Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Chunli Pang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Yong Zhan
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China.
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
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20
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Rems L, Tang X, Zhao F, Pérez-Conesa S, Testa I, Delemotte L. Identification of electroporation sites in the complex lipid organization of the plasma membrane. eLife 2022; 11:e74773. [PMID: 35195069 PMCID: PMC8912918 DOI: 10.7554/elife.74773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study, we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. Additionally, by analysing poration kinetics with Bayesian survival analysis we show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.
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Affiliation(s)
- Lea Rems
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Ljubljana, Faculty of Electrical EngineeringLjubljanaSlovenia
| | - Xinru Tang
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Fangwei Zhao
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Ilaria Testa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
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21
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Jahnke K, Maurer SJ, Weber C, Bücher JE, Schoenit A, D’Este E, Cavalcanti-Adam EA, Göpfrich K. Actomyosin-Assisted Pulling of Lipid Nanotubes from Lipid Vesicles and Cells. NANO LETTERS 2022; 22:1145-1150. [PMID: 35089720 PMCID: PMC8832490 DOI: 10.1021/acs.nanolett.1c04254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Molecular motors are pivotal for intracellular transport as well as cell motility and have great potential to be put to use outside cells. Here, we exploit engineered motor proteins in combination with self-assembly of actin filaments to actively pull lipid nanotubes from giant unilamellar vesicles (GUVs). In particular, actin filaments are bound to the outer GUV membrane and the GUVs are seeded on a heavy meromyosin-coated substrate. Upon addition of ATP, hollow lipid nanotubes with a length of tens of micrometer are pulled from single GUVs due to the motor activity. We employ the same mechanism to pull lipid nanotubes from different types of cells. We find that the length and number of nanotubes critically depends on the cell type, whereby suspension cells form bigger networks than adherent cells. This suggests that molecular machines can be used to exert forces on living cells to probe membrane-to-cortex attachment.
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Affiliation(s)
- Kevin Jahnke
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Stefan J. Maurer
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Cornelia Weber
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | | | - Andreas Schoenit
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Elisa D’Este
- Optical
Microscopy Facility, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Elisabetta Ada Cavalcanti-Adam
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
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22
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Nishizawa M, Walinda E, Morimoto D, Kohn B, Scheler U, Shirakawa M, Sugase K. Effects of Weak Nonspecific Interactions with ATP on Proteins. J Am Chem Soc 2021; 143:11982-11993. [PMID: 34338526 DOI: 10.1021/jacs.0c13118] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Adenosine triphosphate (ATP) is an immensely well-studied metabolite serving multiple key biochemical roles as the major chemical energy currency in living systems, a building block of ribonucleic acids, and a phosphoryl group donor in kinase-mediated signaling. Intriguingly, ATP has been recently proposed to act as a hydrotrope that inhibits aggregation of amyloidogenic proteins; however, the underlying mechanism and the general physicochemical effect that coexistence with ATP exerts on proteins remain unclear. By combining NMR spectroscopy and MD simulations, here we observed weak but unambiguously measurable and concentration-dependent noncovalent interactions between ATP and various proteins. The interactions were most pronounced for an intrinsically disordered protein (α-synuclein) and for residues in flexible regions (e.g., loops or termini) of two representative folded proteins (ubiquitin and the dimeric ubiquitin-binding domain of p62). As shown by solution NMR, a consequence of the ATP-protein interaction was altered hydration of solvent-exposed residues in the protein. The observation that ATP interacted with all three proteins suggests that ATP is a general nonspecific binder of proteins. Several complementary biophysical methods further confirmed that, at physiological concentrations of ∼5-10 mM, ATP starts to form oligomeric states via magnesium-chelating and chelation-independent mechanisms, in agreement with previous studies. Although the observed ATP-protein interaction was relatively weak overall, the high ratio of ATP (monomeric free ATP, mono- and divalent ion-bound ATP, oligomeric and chelated ATP) to proteins in cells suggests that most proteins are likely to encounter transient interactions with ATP (and chemically similar metabolites) that confer metabolite-mediated protein surface protection.
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Affiliation(s)
- Mayu Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Benjamin Kohn
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, 01069 Dresden, Germany
| | - Ulrich Scheler
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, 01069 Dresden, Germany
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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23
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Barvitenko N, Aslam M, Lawen A, Saldanha C, Skverchinskaya E, Uras G, Manca A, Pantaleo A. Two Motors and One Spring: Hypothetic Roles of Non-Muscle Myosin II and Submembrane Actin-Based Cytoskeleton in Cell Volume Sensing. Int J Mol Sci 2021; 22:7967. [PMID: 34360739 PMCID: PMC8347689 DOI: 10.3390/ijms22157967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022] Open
Abstract
Changes in plasma membrane curvature and intracellular ionic strength are two key features of cell volume perturbations. In this hypothesis we present a model of the responsible molecular apparatus which is assembled of two molecular motors [non-muscle myosin II (NMMII) and protrusive actin polymerization], a spring [a complex between the plasma membrane (PM) and the submembrane actin-based cytoskeleton (smACSK) which behaves like a viscoelastic solid] and the associated signaling proteins. We hypothesize that this apparatus senses changes in both the plasma membrane curvature and the ionic strength and in turn activates signaling pathways responsible for regulatory volume increase (RVI) and regulatory volume decrease (RVD). During cell volume changes hydrostatic pressure (HP) changes drive alterations in the cell membrane curvature. HP difference has opposite directions in swelling versus shrinkage, thus allowing distinction between them. By analogy with actomyosin contractility that appears to sense stiffness of the extracellular matrix we propose that NMMII and actin polymerization can actively probe the transmembrane gradient in HP. Furthermore, NMMII and protein-protein interactions in the actin cortex are sensitive to ionic strength. Emerging data on direct binding to and regulating activities of transmembrane mechanosensors by NMMII and actin cortex provide routes for signal transduction from transmembrane mechanosensors to cell volume regulatory mechanisms.
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Affiliation(s)
| | - Muhammad Aslam
- Department of Internal Medicine I, Experimental Cardiology, Justus Liebig University, 35392 Giessen, Germany;
| | - Alfons Lawen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia;
| | - Carlota Saldanha
- Institute of Biochemistry, Institute of Molecular Medicine, Faculty of Medicine University of Lisbon, 1649-028 Lisboa, Portugal;
| | | | - Giuseppe Uras
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London NW3 2PF, UK;
| | - Alessia Manca
- Department of Biomedical Science, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy;
| | - Antonella Pantaleo
- Department of Biomedical Science, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy;
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24
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Eto H, Franquelim HG, Heymann M, Schwille P. Membrane-coated 3D architectures for bottom-up synthetic biology. SOFT MATTER 2021; 17:5456-5466. [PMID: 34106121 DOI: 10.1039/d1sm00112d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
One of the great challenges of bottom-up synthetic biology is to recreate the cellular geometry and surface functionality required for biological reactions. Of particular interest are lipid membrane interfaces where many protein functions take place. However, cellular 3D geometries are often complex, and custom-shaping stable lipid membranes on relevant spatial scales in the micrometer range has been hard to accomplish reproducibly. Here, we use two-photon direct laser writing to 3D print microenvironments with length scales relevant to cellular processes and reactions. We formed lipid bilayers on the surfaces of these printed structures, and we evaluated multiple combinatorial scenarios, where physiologically relevant membrane compositions were generated on several different polymer surfaces. Functional dynamic protein systems were reconstituted in vitro and their self-organization was observed in response to the 3D geometry. This method proves very useful to template biological membranes with an additional spatial dimension, and thus allows a better understanding of protein function in relation to the complex morphology of cells and organelles.
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Affiliation(s)
- Hiromune Eto
- Department for Cellular and Molecular Biophysics, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
| | - Henri G Franquelim
- Department for Cellular and Molecular Biophysics, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
| | - Michael Heymann
- Department for Cellular and Molecular Biophysics, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany. and Department of Intelligent Biointegrative Systems, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Petra Schwille
- Department for Cellular and Molecular Biophysics, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
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25
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Yang Y, Jalali S, Nilsson BL, Dias CL. Binding Mechanisms of Amyloid-like Peptides to Lipid Bilayers and Effects of Divalent Cations. ACS Chem Neurosci 2021; 12:2027-2035. [PMID: 33973758 DOI: 10.1021/acschemneuro.1c00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In several neurodegenerative diseases, cell toxicity can emerge from damage produced by amyloid aggregates to lipid membranes. The details accounting for this damage are poorly understood including how individual amyloid peptides interact with phospholipid membranes before aggregation. Here, we use all-atom molecular dynamics simulations to investigate the molecular mechanisms accounting for amyloid-membrane interactions and the role played by calcium ions in this interaction. Model peptides known to self-assemble into amyloid fibrils and bilayer made from zwitterionic and anionic lipids are used in this study. We find that both electrostatic and hydrophobic interactions contribute to peptide-bilayer binding. In particular, the attraction of peptides to lipid bilayers is dominated by electrostatic interactions between positive residues and negative phosphate moieties of lipid head groups. This attraction is stronger for anionic bilayers than for zwitterionic ones. Hydrophobicity drives the burial of nonpolar residues into the interior of the bilayer producing strong binding in our simulations. Moreover, we observe that the attraction of peptides to the bilayer is significantly reduced in the presence of calcium ions. This is due to the binding of calcium ions to negative phosphate moieties of lipid head groups, which leaves phospholipid bilayers with a net positive charge. Strong binding of the peptide to the membrane occurs less frequently in the presence of calcium ions and involves the formation of a "Ca2+ bridge".
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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26
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Pezeshkian W, Marrink SJ. Simulating realistic membrane shapes. Curr Opin Cell Biol 2021; 71:103-111. [PMID: 33721706 DOI: 10.1016/j.ceb.2021.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. These two central features of biomembranes have been the subject of numerous simulation studies, using a diverse range of computational techniques. Currently, the field is able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Here we highlight recent advances in this topic, identify current bottlenecks, and sketch possible ways ahead.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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27
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Abstract
Giant unilamellar vesicles (GUVs) have gained great popularity as mimicries for cellular membranes. As their sizes are comfortably above the optical resolution limit, and their lipid composition is easily controlled, they are ideal for quantitative light microscopic investigation of dynamic processes in and on membranes. However, reconstitution of functional proteins into the lumen or the GUV membrane itself has proven technically challenging. In recent years, a selection of techniques has been introduced that tremendously improve GUV-assay development and enable the precise investigation of protein-membrane interactions under well-controlled conditions. Moreover, due to these methodological advances, GUVs are considered important candidates as protocells in bottom-up synthetic biology. In this review, we discuss the state of the art of the most important vesicle production and protein encapsulation methods and highlight some key protein systems whose functional reconstitution has advanced the field.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
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28
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Schneider F, Colin-York H, Fritzsche M. Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells. Front Immunol 2021; 11:612542. [PMID: 33505401 PMCID: PMC7829180 DOI: 10.3389/fimmu.2020.612542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.
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Affiliation(s)
- Falk Schneider
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Huw Colin-York
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Marco Fritzsche
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
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29
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Papa R, Penco F, Volpi S, Gattorno M. Actin Remodeling Defects Leading to Autoinflammation and Immune Dysregulation. Front Immunol 2021. [PMID: 33488606 DOI: 10.3389/fimmu.2020.604206)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
A growing number of monogenic immune-mediated diseases have been related to genes involved in pathways of actin cytoskeleton remodeling. Increasing evidences associate cytoskeleton defects to autoinflammatory diseases and primary immunodeficiencies. We reviewed the pathways of actin cytoskeleton remodeling in order to identify inflammatory and immunological manifestations associated to pathological variants. We list more than twenty monogenic diseases, ranging from pure autoinflammatory conditions as familial Mediterranean fever, mevalonate kinase deficiency and PAPA syndrome, to classic and novel primary immunodeficiencies as Wiskott-Aldrich syndrome and DOCK8 deficiency, characterized by the presence of concomitant inflammatory and autoimmune manifestations, such as vasculitis and cytopenia, to severe and recurrent infections. We classify these disorders according to the role of the mutant gene in actin cytoskeleton remodeling, and in particular as disorders of transcription, elongation, branching and activation of actin. This expanding field of rare immune disorders offers a new perspective to all immunologists to better understand the physiological and pathological role of actin cytoskeleton in cells of innate and adaptive immunity.
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Affiliation(s)
- Riccardo Papa
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federica Penco
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Stefano Volpi
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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30
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Papa R, Penco F, Volpi S, Gattorno M. Actin Remodeling Defects Leading to Autoinflammation and Immune Dysregulation. Front Immunol 2021; 11:604206. [PMID: 33488606 PMCID: PMC7817698 DOI: 10.3389/fimmu.2020.604206] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
A growing number of monogenic immune-mediated diseases have been related to genes involved in pathways of actin cytoskeleton remodeling. Increasing evidences associate cytoskeleton defects to autoinflammatory diseases and primary immunodeficiencies. We reviewed the pathways of actin cytoskeleton remodeling in order to identify inflammatory and immunological manifestations associated to pathological variants. We list more than twenty monogenic diseases, ranging from pure autoinflammatory conditions as familial Mediterranean fever, mevalonate kinase deficiency and PAPA syndrome, to classic and novel primary immunodeficiencies as Wiskott-Aldrich syndrome and DOCK8 deficiency, characterized by the presence of concomitant inflammatory and autoimmune manifestations, such as vasculitis and cytopenia, to severe and recurrent infections. We classify these disorders according to the role of the mutant gene in actin cytoskeleton remodeling, and in particular as disorders of transcription, elongation, branching and activation of actin. This expanding field of rare immune disorders offers a new perspective to all immunologists to better understand the physiological and pathological role of actin cytoskeleton in cells of innate and adaptive immunity.
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Affiliation(s)
- Riccardo Papa
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Federica Penco
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Stefano Volpi
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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31
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Sousa FM, Lima LMP, Arnarez C, Pereira MM, Melo MN. Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies. J Chem Inf Model 2021; 61:335-346. [PMID: 33400529 DOI: 10.1021/acs.jcim.0c01077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides are structural units relevant not only in nucleic acids but also as substrates or cofactors in key biochemical reactions. The size- and timescales of such nucleotide-protein interactions fall well within the scope of coarse-grained molecular dynamics, which holds promise of important mechanistic insight. However, the lack of specific parameters has prevented accurate coarse-grained simulations of protein interactions with most nucleotide compounds. In this work, we comprehensively develop coarse-grained parameters for key metabolites/cofactors (FAD, FMN, riboflavin, NAD, NADP, ATP, ADP, AMP, and thiamine pyrophosphate) in different oxidation and protonation states as well as for smaller molecules derived from them (among others, nicotinamide, adenosine, adenine, ribose, thiamine, and lumiflavin), summing up a total of 79 different molecules. In line with the Martini parameterization methodology, parameters were tuned to reproduce octanol-water partition coefficients. Given the lack of existing data, we set out to experimentally determine these partition coefficients, developing two methodological approaches, based on 31P-NMR and fluorescence spectroscopy, specifically tailored to the strong hydrophilicity of most of the parameterized compounds. To distinguish the partition of each relevant protonation species, we further potentiometrically characterized the protonation constants of key molecules. This work successfully builds a comprehensive and relevant set of computational models that will boost the biochemical application of coarse-grained simulations. It does so based on the measurement of partition and acid-base physicochemical data that, in turn, covers important gaps in nucleotide characterization.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Luís M P Lima
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Clément Arnarez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal.,BIOISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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32
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Lamparter L, Galic M. Cellular Membranes, a Versatile Adaptive Composite Material. Front Cell Dev Biol 2020; 8:684. [PMID: 32850810 PMCID: PMC7419611 DOI: 10.3389/fcell.2020.00684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cellular membranes belong to the most vital yet least understood biomaterials of live matter. For instance, its biomechanical requirements substantially vary across species and subcellular sites, raising the question how membranes manage to adjust to such dramatic changes. Central to its adaptability at the cell surface is the interplay between the plasma membrane and the adjacent cell cortex, forming an adaptive composite material that dynamically adjusts its mechanical properties. Using a hypothetical composite material, we identify core challenges, and discuss how cellular membranes solved these tasks. We further muse how pathological changes in material properties affect membrane mechanics and cell function, before closing with open questions and future challenges arising when studying cellular membranes.
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Affiliation(s)
- Lucas Lamparter
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Münster, Münster, Germany.,Cells in Motion Interfaculty Centre, University of Müenster, Münster, Germany
| | - Milos Galic
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Münster, Münster, Germany.,Cells in Motion Interfaculty Centre, University of Müenster, Münster, Germany
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