1
|
Bernard C, Carotenuto AR, Pugno NM, Fraldi M, Deseri L. Modelling lipid rafts formation through chemo-mechanical interplay triggered by receptor-ligand binding. Biomech Model Mechanobiol 2024; 23:485-505. [PMID: 38060155 PMCID: PMC10963483 DOI: 10.1007/s10237-023-01787-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/21/2023] [Indexed: 12/08/2023]
Abstract
Cell membranes, mediator of many biological mechanisms from adhesion and metabolism up to mutation and infection, are highly dynamic and heterogeneous environments exhibiting a strong coupling between biochemical events and structural re-organisation. This involves conformational changes induced, at lower scales, by lipid order transitions and by the micro-mechanical interplay of lipids with transmembrane proteins and molecular diffusion. Particular attention is focused on lipid rafts, ordered lipid microdomains rich of signalling proteins, that co-localise to enhance substance trafficking and activate different intracellular biochemical pathways. In this framework, the theoretical modelling of the dynamic clustering of lipid rafts implies a full multiphysics coupling between the kinetics of phase changes and the mechanical work performed by transmembrane proteins on lipids, involving the bilayer elasticity. This mechanism produces complex interspecific dynamics in which membrane stresses and chemical potentials do compete by determining different morphological arrangements, alteration in diffusive walkways and coalescence phenomena, with a consequent influence on both signalling potential and intracellular processes. Therefore, after identifying the leading chemo-mechanical interactions, the present work investigates from a modelling perspective the spatio-temporal evolution of raft domains to theoretically explain co-localisation and synergy between proteins' activation and raft formation, by coupling diffusive and mechanical phenomena to observe different morphological patterns and clustering of ordered lipids. This could help to gain new insights into the remodelling of cell membranes and could potentially suggest mechanically based strategies to control their selectivity, by orienting intracellular functions and mechanotransduction.
Collapse
Affiliation(s)
- Chiara Bernard
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy
| | - Angelo Rosario Carotenuto
- Department of Structures for Engineering and Architecture, University of Naples "Federico II", Naples, Italy
- Laboratory of Integrated Mechanics and Imaging for Testing and Simulation (LIMITS), University of Naples "Federico II", Naples, Italy
| | - Nicola Maria Pugno
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy
- Laboratory for Bioinspired, Bionic, Nano, Meta Materials and Mechanics, University of Trento, Trento, Italy
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Massimiliano Fraldi
- Department of Structures for Engineering and Architecture, University of Naples "Federico II", Naples, Italy
- Laboratory of Integrated Mechanics and Imaging for Testing and Simulation (LIMITS), University of Naples "Federico II", Naples, Italy
- Département de Physique, LPENS, École Normale Supérieure-PSL, Paris, France
| | - Luca Deseri
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, Italy.
- Department of Mechanical Engineering and Material Sciences, MEMS-SSoE, University of Pittsburgh, Pittsburgh, USA.
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, USA.
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, USA.
| |
Collapse
|
2
|
Abstract
T cell activation is initiated by the recognition of specific antigenic peptides and subsequently accomplished by complex signaling cascades. These aspects have been extensively studied for decades as pivotal factors in the establishment of adaptive immunity. However, how receptors or signaling molecules are organized in the resting state prior to encountering antigens has received less attention. Recent advancements in super-resolution microscopy techniques have revealed topographically controlled pre-formed organization of key molecules involved in antigen recognition and signal transduction on microvillar projections of T cells before activation and substantial effort has been dedicated to characterizing the topological structure of resting T cells over the past decade. This review will summarize our current understanding of how key surface receptors are pre-organized on the T-cell plasma membrane and discuss the potential role of these receptors, which are preassembled prior to ligand binding in the early activation events of T cells.
Collapse
Affiliation(s)
- Yunmin Jung
- Department of Nano-Biomedical Engineering, Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science, Seoul, Republic of Korea
| |
Collapse
|
3
|
Sarkar S, García AE. Presence or Absence of Ras Dimerization Shows Distinct Kinetic Signature in Ras-Raf Interaction. Biophys J 2020; 118:1799-1810. [PMID: 32199071 DOI: 10.1016/j.bpj.2020.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/30/2019] [Accepted: 03/02/2020] [Indexed: 02/07/2023] Open
Abstract
Initiations of cell signaling pathways often occur through the formation of multiprotein complexes that form through protein-protein interactions. Therefore, detecting their presence is central to understanding the function of a cell signaling pathway, aberration of which often leads to fatal diseases, including cancers. However, the multiprotein complexes are often difficult to detect using microscopes due to their small sizes. Therefore, currently, their presence can be only detected through indirect means. In this article, we propose to investigate the presence or absence of protein complexes through some easily measurable kinetic parameters, such as activation rates. As a proof of concept, we investigate the Ras-Raf system, a well-characterized cell signaling system. It has been hypothesized that Ras dimerization is necessary to create activated Raf dimers. Although there are circumstantial evidences supporting the Ras dimerization hypothesis, direct proof of Ras dimerization is still inconclusive. In the absence of conclusive direct experimental proof, this hypothesis can only be examined through indirect evidences of Ras dimerization. In this article, using a multiscale simulation technique, we provide multiple criteria that distinguishes an activation mechanism involving Ras dimerization from another mechanism that does not involve Ras dimerization. The provided criteria will be useful in the investigation of not only Ras-Raf interaction but also other two-protein interactions.
Collapse
Affiliation(s)
- Sumantra Sarkar
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico.
| |
Collapse
|
4
|
Feldman TB, Ivankov OI, Kuklin AI, Murugova TN, Yakovleva MA, Smitienko OA, Kolchugina IB, Round A, Gordeliy VI, Belushkin AV, Ostrovsky MA. Small-angle neutron and X-ray scattering analysis of the supramolecular organization of rhodopsin in photoreceptor membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183000. [DOI: 10.1016/j.bbamem.2019.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 01/16/2023]
|
5
|
Chen M, Peters A, Huang T, Nan X. Ras Dimer Formation as a New Signaling Mechanism and Potential Cancer Therapeutic Target. Mini Rev Med Chem 2016; 16:391-403. [PMID: 26423697 PMCID: PMC5421135 DOI: 10.2174/1389557515666151001152212] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/31/2015] [Accepted: 09/18/2015] [Indexed: 12/12/2022]
Abstract
The K-, N-, and HRas small GTPases are key regulators of cell physiology and are frequently mutated in human cancers. Despite intensive research, previous efforts to target hyperactive Ras based on known mechanisms of Ras signaling have been met with little success. Several studies have provided compelling evidence for the existence and biological relevance of Ras dimers, establishing a new mechanism for regulating Ras activity in cells additionally to GTP-loading and membrane localization. Existing data also start to reveal how Ras proteins dimerize on the membrane. We propose a dimer model to describe Ras-mediated effector activation, which contrasts existing models of Ras signaling as a monomer or as a 5-8 membered multimer. We also discuss potential implications of this model in both basic and translational Ras biology.
Collapse
Affiliation(s)
| | | | | | - Xiaolin Nan
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR.
| |
Collapse
|
6
|
Putative Cell Adhesion Membrane Protein Vstm5 Regulates Neuronal Morphology and Migration in the Central Nervous System. J Neurosci 2016; 36:10181-97. [PMID: 27683913 DOI: 10.1523/jneurosci.0541-16.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/16/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED During brain development, dynamic changes in neuronal membranes perform critical roles in neuronal morphogenesis and migration to create functional neural circuits. Among the proteins that induce membrane dynamics, cell adhesion molecules are important in neuronal membrane plasticity. Here, we report that V-set and transmembrane domain-containing protein 5 (Vstm5), a cell-adhesion-like molecule belonging to the Ig superfamily, was found in mouse brain. Knock-down of Vstm5 in cultured hippocampal neurons markedly reduced the complexity of dendritic structures, as well as the number of dendritic filopodia. Vstm5 also regulates neuronal morphology by promoting dendritic protrusions that later develop into dendritic spines. Using electroporation in utero, we found that Vstm5 overexpression delayed neuronal migration and induced multiple branches in leading processes during corticogenesis. These results indicate that Vstm5 is a new cell-adhesion-like molecule and is critically involved in synaptogenesis and corticogenesis by promoting neuronal membrane dynamics. SIGNIFICANCE STATEMENT Neuronal migration and morphogenesis play critical roles in brain development and function. In this study, we demonstrate for the first time that V-set and transmembrane domain-containing protein 5 (Vstm5), a putative cell adhesion membrane protein, modulates both the position and complexity of central neurons by altering their membrane morphology and dynamics. Vstm5 is also one of the target genes responsible for variations in patient responses to treatments for major depressive disorder. Our results provide the first evidence that Vstm5 is a novel factor involved in the modulation of the neuronal membrane and a critical element in normal neural circuit formation during mammalian brain development.
Collapse
|
7
|
Patrone M, Coroadinha AS, Teixeira AP, Alves PM. Palmitoylation Strengthens Cholesterol-dependent Multimerization and Fusion Activity of Human Cytomegalovirus Glycoprotein B (gB). J Biol Chem 2015; 291:4711-22. [PMID: 26694613 DOI: 10.1074/jbc.m115.682252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Indexed: 11/06/2022] Open
Abstract
Herpesviruses are a large order of animal enveloped viruses displaying a virion fusion mechanism of unusual complexity. Their multipartite machinery has a conserved core made of the gH/gL ancillary complexes and the homo-trimeric fusion protein glycoprotein B (gB). Despite its essential role in starting the viral infection, gB interaction with membrane lipids is still poorly understood. Here, evidence is provided demonstrating that human cytomegalovirus (HCMV) gB depends on the S-palmitoylation of its endodomain for an efficient interaction with cholesterol-rich membrane patches. We found that, unique among herpesviral gB proteins, the HCMV fusion factor has a Cys residue in the C-terminal region that is palmitoylated and mediates methyl-β-cyclodextrin-sensitive self-association of purified gB. A cholesterol-dependent virus-like particle trap assay, based on co-expression of the HIV Gag protein, confirmed that this post-translational modification is functional in the context of cellular membranes. Mutation of the palmitoylated Cys residue to Ala or inhibition of protein palmitoylation decreased HCMV gB export via Gag particles. Moreover, purified gBC777A showed an increased kinetic sensitivity in a cholesterol depletion test, demonstrating that palmitoyl-gB limits outward cholesterol diffusion. Finally, gB palmitoylation was required for full fusogenic activity in human epithelial cells. Altogether, these results uncover the palmitoylation of HCMV gB and its role in gB multimerization and activity.
Collapse
Affiliation(s)
- Marco Patrone
- From the Animal Cell Technology Unit, iBET Instituto de Biologia Experimental e Tecnológica, 2780-901 Oeiras, Portugal, the Biocrystallography Unit, DIBIT Fondazione Centro San Raffaele, 20132 Milano, Italy, and
| | - Ana Sofia Coroadinha
- From the Animal Cell Technology Unit, iBET Instituto de Biologia Experimental e Tecnológica, 2780-901 Oeiras, Portugal, the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2784-505 Oeiras, Portugal
| | - Ana P Teixeira
- From the Animal Cell Technology Unit, iBET Instituto de Biologia Experimental e Tecnológica, 2780-901 Oeiras, Portugal, the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2784-505 Oeiras, Portugal
| | - Paula M Alves
- From the Animal Cell Technology Unit, iBET Instituto de Biologia Experimental e Tecnológica, 2780-901 Oeiras, Portugal, the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2784-505 Oeiras, Portugal
| |
Collapse
|
8
|
Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V. Plasma membrane regulates Ras signaling networks. CELLULAR LOGISTICS 2015; 5:e1136374. [PMID: 27054048 PMCID: PMC4820813 DOI: 10.1080/21592799.2015.1136374] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/31/2022]
Abstract
Ras GTPases activate more than 20 signaling pathways, regulating such essential cellular functions as proliferation, survival, and migration. How Ras proteins control their signaling diversity is still a mystery. Several pieces of evidence suggest that the plasma membrane plays a critical role. Among these are: (1) selective recruitment of Ras and its effectors to particular localities allowing access to Ras regulators and effectors; (2) specific membrane-induced conformational changes promoting Ras functional diversity; and (3) oligomerization of membrane-anchored Ras to recruit and activate Raf. Taken together, the membrane does not only attract and retain Ras but also is a key regulator of Ras signaling. This can already be gleaned from the large variability in the sequences of Ras membrane targeting domains, suggesting that localization, environment and orientation are important factors in optimizing the function of Ras isoforms.
Collapse
Affiliation(s)
- Tanmay Sanjeev Chavan
- Department of Medicinal Chemistry; University of Illinois at Chicago; Chicago, IL USA
| | - Serena Muratcioglu
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Richard Marszalek
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago; Chicago, IL USA
| | - Hyunbum Jang
- Cancer and Inflammation Program; Basic Science Program; Leidos Biomedical Research, Inc.; Frederick National Laboratory for Cancer Research; National Cancer Institute at Frederick; Frederick, MD USA
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program; Basic Science Program; Leidos Biomedical Research, Inc.; Frederick National Laboratory for Cancer Research; National Cancer Institute at Frederick; Frederick, MD USA
- Sackler Institute of Molecular Medicine; Department of Human Genetics and Molecular Medicine; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago; Chicago, IL USA
| |
Collapse
|
9
|
Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. PLoS Comput Biol 2015; 11:e1004407. [PMID: 26367029 PMCID: PMC4569342 DOI: 10.1371/journal.pcbi.1004407] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/15/2015] [Indexed: 01/10/2023] Open
Abstract
Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release.
Collapse
Affiliation(s)
- Alexander Ullrich
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Mathias A. Böhme
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | | | - Harald Depner
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Stephan J. Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
10
|
Schöneberg J, Ullrich A, Noé F. Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC BIOPHYSICS 2014; 7:11. [PMID: 25737778 PMCID: PMC4347613 DOI: 10.1186/s13628-014-0011-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/29/2014] [Indexed: 11/17/2022]
Abstract
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics.
Collapse
Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| | - Alexander Ullrich
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Free University Berlin, Arnimallee 6 14195, Berlin, Germany
| |
Collapse
|
11
|
Szalai B, Hoffmann P, Prokop S, Erdélyi L, Várnai P, Hunyady L. Improved methodical approach for quantitative BRET analysis of G Protein Coupled Receptor dimerization. PLoS One 2014; 9:e109503. [PMID: 25329164 PMCID: PMC4201472 DOI: 10.1371/journal.pone.0109503] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/11/2014] [Indexed: 01/22/2023] Open
Abstract
G Protein Coupled Receptors (GPCR) can form dimers or higher ordered oligomers, the process of which can remarkably influence the physiological and pharmacological function of these receptors. Quantitative Bioluminescence Resonance Energy Transfer (qBRET) measurements are the gold standards to prove the direct physical interaction between the protomers of presumed GPCR dimers. For the correct interpretation of these experiments, the expression of the energy donor Renilla luciferase labeled receptor has to be maintained constant, which is hard to achieve in expression systems. To analyze the effects of non-constant donor expression on qBRET curves, we performed Monte Carlo simulations. Our results show that the decrease of donor expression can lead to saturation qBRET curves even if the interaction between donor and acceptor labeled receptors is non-specific leading to false interpretation of the dimerization state. We suggest here a new approach to the analysis of qBRET data, when the BRET ratio is plotted as a function of the acceptor labeled receptor expression at various donor receptor expression levels. With this method, we were able to distinguish between dimerization and non-specific interaction when the results of classical qBRET experiments were ambiguous. The simulation results were confirmed experimentally using rapamycin inducible heterodimerization system. We used this new method to investigate the dimerization of various GPCRs, and our data have confirmed the homodimerization of V2 vasopressin and CaSR calcium sensing receptors, whereas our data argue against the heterodimerization of these receptors with other studied GPCRs, including type I and II angiotensin, β2 adrenergic and CB1 cannabinoid receptors.
Collapse
Affiliation(s)
- Bence Szalai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
| | - Péter Hoffmann
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Susanne Prokop
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - László Erdélyi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
| | - Péter Várnai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
| | - László Hunyady
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- MTA-SE Laboratory of Molecular Physiology, Budapest, Hungary
- * E-mail:
| |
Collapse
|
12
|
Zhou ZW, Liu C, Li TL, Bruhn C, Krueger A, Min W, Wang ZQ, Carr AM. An essential function for the ATR-activation-domain (AAD) of TopBP1 in mouse development and cellular senescence. PLoS Genet 2013; 9:e1003702. [PMID: 23950734 PMCID: PMC3738440 DOI: 10.1371/journal.pgen.1003702] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/20/2013] [Indexed: 12/03/2022] Open
Abstract
ATR activation is dependent on temporal and spatial interactions with partner proteins. In the budding yeast model, three proteins – Dpb11TopBP1, Ddc1Rad9 and Dna2 - all interact with and activate Mec1ATR. Each contains an ATR activation domain (ADD) that interacts directly with the Mec1ATR:Ddc2ATRIP complex. Any of the Dpb11TopBP1, Ddc1Rad9 or Dna2 ADDs is sufficient to activate Mec1ATRin vitro. All three can also independently activate Mec1ATRin vivo: the checkpoint is lost only when all three AADs are absent. In metazoans, only TopBP1 has been identified as a direct ATR activator. Depletion-replacement approaches suggest the TopBP1-AAD is both sufficient and necessary for ATR activation. The physiological function of the TopBP1 AAD is, however, unknown. We created a knock-in point mutation (W1147R) that ablates mouse TopBP1-AAD function. TopBP1-W1147R is early embryonic lethal. To analyse TopBP1-W1147R cellular function in vivo, we silenced the wild type TopBP1 allele in heterozygous MEFs. AAD inactivation impaired cell proliferation, promoted premature senescence and compromised Chk1 signalling following UV irradiation. We also show enforced TopBP1 dimerization promotes ATR-dependent Chk1 phosphorylation. Our data suggest that, unlike the yeast models, the TopBP1-AAD is the major activator of ATR, sustaining cell proliferation and embryonic development. DNA damage checkpoint signalling is an essential component of the DNA damage response. Many of the key proteins initiating the checkpoint signal have been identified and characterised in yeast. Here we explore the role of the ATR activating domain (AAD) of TopBP1 in embryonic development, cell growth and checkpoint activation using a mouse model. In contrast to yeasts, where the TopBP1 AAD plays a redundant, and thus phenotypically minor, role in ATR activation, our data demonstrate that the mouse TopBP1 AAD is essential for cellular proliferation. Interestingly, this suggests evolution has provided a simpler ATR activation mechanism in metazoans than it has in yeasts.
Collapse
Affiliation(s)
- Zhong-Wei Zhou
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - Cong Liu
- Sussex for Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, Sussex, United Kingdom
| | - Tang-Liang Li
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - Christopher Bruhn
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - Anja Krueger
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - WooKee Min
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - Zhao-Qi Wang
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biology and Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
- * E-mail: (ZQW); (AMC)
| | - Antony M. Carr
- Sussex for Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, Sussex, United Kingdom
- * E-mail: (ZQW); (AMC)
| |
Collapse
|
13
|
Sangiambut S, Channon K, Thomson NM, Sato S, Tsuge T, Doi Y, Sivaniah E. A robust route to enzymatically functional, hierarchically self-assembled peptide frameworks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:2661-2665. [PMID: 23341342 DOI: 10.1002/adma.201204127] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/21/2012] [Indexed: 06/01/2023]
Abstract
The addition of enzyme biofunctionality to self-assembling peptide nanofibers is challenging since such additions can inhibit functionality or self-assembly. We introduce a method for peptide nanofiber enzyme functionalization, demonstrated by the attachment of a polymerization synthase to peptide nanofibers. The enzyme generates a biocompatible, biodegradable biopolyester coat on the fibers with applicablity in medical engineering. This approach provides a template for generation of functional bionanomaterials.
Collapse
Affiliation(s)
- S Sangiambut
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, CB3 0HE, UK
| | | | | | | | | | | | | |
Collapse
|
14
|
Saraiva N, Prole DL, Carrara G, Maluquer de Motes C, Johnson BF, Byrne B, Taylor CW, Smith GL. Human and viral Golgi anti-apoptotic proteins (GAAPs) oligomerize via different mechanisms and monomeric GAAP inhibits apoptosis and modulates calcium. J Biol Chem 2013; 288:13057-67. [PMID: 23508950 PMCID: PMC3642348 DOI: 10.1074/jbc.m112.414367] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Golgi anti-apoptotic proteins (GAAPs) are hydrophobic proteins resident in membranes of the Golgi complex. They protect cells from a range of apoptotic stimuli, reduce the Ca2+ content of intracellular stores, and regulate Ca2+ fluxes. GAAP was discovered in camelpox virus, but it is highly conserved throughout evolution and encoded by all eukaryote genomes examined. GAAPs are part of the transmembrane Bax inhibitor-containing motif (TMBIM) family that also includes other anti-apoptotic and Ca2+-modulating membrane proteins. Most TMBIM members show multiple bands when analyzed by SDS-PAGE, suggesting that they may be oligomeric. However, the molecular mechanisms of oligomerization, the native state of GAAPs in living cells and the functional significance of oligomerization have not been addressed. TMBIM members are thought to have evolved from an ancestral GAAP. Two different GAAPs, human (h) and viral (v)GAAP were therefore selected as models to examine oligomerization of TMBIM family members. We show that both hGAAP and vGAAP in their native states form oligomers and that oligomerization is pH-dependent. Surprisingly, hGAAP and vGAAP do not share the same oligomerization mechanism. Oligomerization of hGAAP is independent of cysteines, but oligomerization of vGAAP depends on cysteines 9 and 60. A mutant vGAAP that is unable to oligomerize revealed that monomeric vGAAP retains both its anti-apoptotic function and its effect on intracellular Ca2+ stores. In conclusion, GAAP can oligomerize in a pH-regulated manner, and monomeric GAAP is functional.
Collapse
Affiliation(s)
- Nuno Saraiva
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Scotti M, Stella L, Shearer EJ, Stover PJ. Modeling cellular compartmentation in one-carbon metabolism. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:343-65. [PMID: 23408533 DOI: 10.1002/wsbm.1209] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Folate-mediated one-carbon metabolism (FOCM) is associated with risk for numerous pathological states including birth defects, cancers, and chronic diseases. Although the enzymes that constitute the biological pathways have been well described and their interdependency through the shared use of folate cofactors appreciated, the biological mechanisms underlying disease etiologies remain elusive. The FOCM network is highly sensitive to nutritional status of several B-vitamins and numerous penetrant gene variants that alter network outputs, but current computational approaches do not fully capture the dynamics and stochastic noise of the system. Combining the stochastic approach with a rule-based representation will help model the intrinsic noise displayed by FOCM, address the limited flexibility of standard simulation methods for coarse-graining the FOCM-associated biochemical processes, and manage the combinatorial complexity emerging from reactions within FOCM that would otherwise be intractable.
Collapse
Affiliation(s)
- Marco Scotti
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | | | | | | |
Collapse
|
16
|
Quaternary Structure Predictions and Structural Communication Features of GPCR Dimers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:105-42. [DOI: 10.1016/b978-0-12-386931-9.00005-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
17
|
Güldenhaupt J, Rudack T, Bachler P, Mann D, Triola G, Waldmann H, Kötting C, Gerwert K. N-Ras forms dimers at POPC membranes. Biophys J 2012; 103:1585-93. [PMID: 23062351 DOI: 10.1016/j.bpj.2012.08.043] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/20/2012] [Accepted: 08/23/2012] [Indexed: 12/18/2022] Open
Abstract
Ras is a central regulator of cellular signaling pathways. It is mutated in 20-30% of human tumors. To perform its function, Ras has to be bound to a membrane by a posttranslationally attached lipid anchor. Surprisingly, we identified here dimerization of membrane anchored Ras by combining attenuated total reflectance Fourier transform infrared spectroscopy, biomolecular simulations, and Förster resonance energy transfer experiments. By analyzing x-ray structural models and molecular-dynamics simulations, we propose a dimerization interface between α-helices 4 and 5 and the loop between β2 and β3. This seems to explain why the residues D47, E49, R135, R161, and R164 of this interface are influencing Ras signaling in cellular physiological experiments, although they are not positioned in the catalytic site. Dimerization could catalyze nanoclustering, which is well accepted for membrane-bound Ras. The interface could provide a new target for a seemingly novel type of small molecule interfering with signal transduction in oncogenic Ras mutants.
Collapse
Affiliation(s)
- Jörn Güldenhaupt
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Bochum, Germany
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Lowalekar SK, Cristofaro V, Radisavljevic ZM, Yalla SV, Sullivan MP. Loss of bladder smooth muscle caveolae in the aging bladder. Neurourol Urodyn 2012; 31:586-92. [PMID: 22374691 DOI: 10.1002/nau.21217] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 08/15/2011] [Indexed: 12/16/2022]
Abstract
AIMS Caveolae are specialized regions of the cell membrane that modulate signal transduction and alterations in these structures affect bladder smooth muscle (BSM) contraction. Since bladder dysfunctions are common in the elderly, we evaluated the effect of aging on the morphology of caveolae and caveolin protein expression in BSM. METHODS Caveolar morphology (number, size, and depth) in BSM was determined from electron microscopy images of young (10 weeks), adult (6-month old), and old (12-month old) rat urinary bladders. Changes in expression levels of caveolin proteins with age were investigated by Western blot and immunofluorescence microscopy. Caveolin-3 gene expression was determined by real-time RT-PCR in young and 19-month-old rat bladders. RESULTS Twelve-month-old animals exhibited 50% fewer BSM caveolae compared to young (P < 0.01). The area of caveolae was significantly decreased at 6 and 12 months. Despite a decrease in the number of BSM caveolae at 12 months, the expression of caveolin-1 and cavin-1 were unaltered with age. In contrast, caveolin-2 and caveolin-3 protein expression and immunoreactivity were reduced in BSM at 6 and 12 months of age. Caveolin-3 gene expression was also downregulated at 19 months compared to young animals. CONCLUSION Biological aging significantly decreases BSM caveolae number and morphology with associated selective alteration in caveolin protein expression. Since caveolae are protected membrane regions that regulate signal transduction, age-related alterations in caveolae and caveolin protein expression could alter BSM contractility resulting in bladder dysfunctions of the elderly.
Collapse
Affiliation(s)
- Samar K Lowalekar
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | |
Collapse
|
19
|
Agnati LF, Guidolin D, Leo G, Guescini M, Pizzi M, Stocchi V, Spano PF, Ghidoni R, Ciruela F, Genedani S, Fuxe K. Possible new targets for GPCR modulation: allosteric interactions, plasma membrane domains, intercellular transfer and epigenetic mechanisms. J Recept Signal Transduct Res 2012; 31:315-31. [PMID: 21929287 DOI: 10.3109/10799893.2011.599393] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
It has been estimated that at least 50% of the drugs available on the market act on G-protein coupled receptors (GPCRs) and most of these are basically or agonists or antagonists of this type of receptors. Herein, we propose new putative targets for drug development based on recent data on GPCR allosterism and on the existence of receptor mosaics (RMs). The main target for drug development is still GPCRs, but the focus is not the orthosteric binding pocket. According to the mosaic model of the plasma membrane, we mainly discuss the possibility of indirect modulatory pharmacological actions on expression/function of GPCRs. In particular, the following two new targets will be analyzed: a) The possibility of pharmacological interventions on the roamer-type of volume transmission (VT), which allow the intercellular transfer of set of signal molecules such as GPCRs, tetraspanins and ribonucleic acids. Thus, there is the possibility of pharmacological interventions on the decoding capabilities of neurons and/or glial cells by means of an action on composition and release of micro-vesicles. b) The possibility of pharmacological interventions on epigenetic mechanisms by taking into account their inter-relationships with GPCRs. As a matter of fact, there are epigenetic changes that are characteristic of periods of developmental plasticity that could provide a target for therapeutic intervention in the event of brain damage. We believe that almost all the biochemical knowledge presently available on GPCRs can be used in the development of these new pharmacological approaches.
Collapse
|
20
|
Brameshuber M, Schütz GJ. Detection and quantification of biomolecular association in living cells using single-molecule microscopy. Methods Enzymol 2012; 505:159-86. [PMID: 22289453 DOI: 10.1016/b978-0-12-388448-0.00017-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During their random motion, biomolecules experience a manifold of interactions that transiently conjoin their paths. It is extremely difficult to measure such binding events directly in the context of a living cell: interactions may be short lived, they may affect only a minority fraction of molecules, or they may not lead to a macroscopically observable effect. We describe here a new single-molecule imaging method that allows for detecting and quantifying associations of mobile molecules. By "thinning out clusters while conserving the stoichiometry of labeling" (TOCCSL), we can virtually dilute the probe directly in the cell, without affecting the fluorescence labeling of single clusters. Essentially, an analysis region is created within the cell by photobleaching; this region is devoid of active probe. Brownian diffusion or other transport processes lead to reentry of active probe into the analysis region. At the onset of the recovery process, single spots can be resolved as well-separated, diffraction-limited signals. Standard single-molecule microscopy then allows for characterizing the spots in terms of their composition and mobility.
Collapse
Affiliation(s)
- Mario Brameshuber
- Biophysics Institute, Johannes Kepler University Linz, Altenbergerstr., Linz, Austria
| | | |
Collapse
|
21
|
Abstract
The specific self-association of proteins to form homodimers and higher order oligomers is an extremely common event in biological systems. In this chapter we review the prevalence of protein oligomerization and discuss the likely origins of this phenomenon. We also outline many of the functional advantages conferred by the dimerization or oligomerization of a wide range of different proteins and in a variety of biological roles, that are likely to have placed a selective pressure on biological systems to evolve and maintain homodimerization/oligomerization interfaces.
Collapse
|
22
|
Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
| | | |
Collapse
|
23
|
Gross LCM, Castell OK, Wallace MI. Dynamic and reversible control of 2D membrane protein concentration in a droplet interface bilayer. NANO LETTERS 2011; 11:3324-3328. [PMID: 21726072 DOI: 10.1021/nl201689v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We form an artificial lipid bilayer between a nanolitre aqueous droplet and a supporting hydrogel immersed in an oil/lipid solution. Manipulation of the axial position of the droplet relative to the hydrogel controls the size of the bilayer formed at the interface; this enables the surface density of integral membrane proteins to be controlled. We are able to modulate the surface density of the β-barrel pore-forming toxin α-hemolysin over a range of 4 orders of magnitude within a time frame of a few seconds. The concentration changes are fully reversible. Membrane protein function and diffusion are unaltered, as measured by single molecule microscopy and single channel electrical recording.
Collapse
Affiliation(s)
- Linda C M Gross
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, U.K
| | | | | |
Collapse
|
24
|
Guidolin D, Ciruela F, Genedani S, Guescini M, Tortorella C, Albertin G, Fuxe K, Agnati LF. Bioinformatics and mathematical modelling in the study of receptor–receptor interactions and receptor oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1267-83. [DOI: 10.1016/j.bbamem.2010.09.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 08/31/2010] [Accepted: 09/26/2010] [Indexed: 10/19/2022]
|
25
|
Comisar WA, Mooney DJ, Linderman JJ. Integrin organization: linking adhesion ligand nanopatterns with altered cell responses. J Theor Biol 2011; 274:120-30. [PMID: 21255586 PMCID: PMC3056075 DOI: 10.1016/j.jtbi.2011.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 11/30/2010] [Accepted: 01/07/2011] [Indexed: 01/23/2023]
Abstract
Integrin receptors bind to adhesion ligand (e.g. arginine-glycine-aspartic acid or RGD containing peptides) on extracellular matrix and organize into high-density complexes which mediate many cell behaviors. Biomaterials with RGD nanopatterned into multivalent "islands" (∼30-70 nm diameter) have been shown to alter cell responses, although the length scale of pattern features is orders of magnitude smaller than adhesion complexes. In this work, we employ together for the first time an extensive data set on osteoblast responses as a function of ligand nanopatterns, a computational model of integrin binding to ligand nanopatterns, and new measures of integrin organization on the cell surface. We quantify, at multiple length scales, integrin organization generated in silico as a function of RGD nanopattern parameters. We develop a correlative model relating these measures of in silico integrin organization and in vitro MC3T3 preosteoblast cell responses as functions of the same RGD nanopatterns: cell spreading correlates with the number of bound integrins, focal adhesion kinase (FAK) phosphorylation correlates with small, homogeneously distributed clusters of integrins, and osteogenic differentiation correlates with large, heterogeneously distributed integrin clusters. These findings highlight the significance of engineering biomaterials at the nanolevel and suggest new approaches to understanding the mechanisms linking integrin organization to cell responses.
Collapse
Affiliation(s)
- W. A. Comisar
- Department of Chemical Engineering, University of Michigan, 2300 Hayward St., 3074 HH Dow Bldg, Ann Arbor, MI 48109, USA
| | - D. J. Mooney
- Division of Engineering and Applied Sciences, Harvard University, 40 Oxford St., Rm 415, Cambridge, MA 02138, USA
| | - J. J. Linderman
- Department of Chemical Engineering, University of Michigan, 2300 Hayward St., 3074 HH Dow Bldg, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel Blvd., 1107 CA Gerstacker Bldg, Ann Arbor, MI 48109, USA
| |
Collapse
|
26
|
Costa MN, Radhakrishnan K, Edwards JS. Monte Carlo simulations of plasma membrane corral-induced EGFR clustering. J Biotechnol 2010; 151:261-70. [PMID: 21167222 DOI: 10.1016/j.jbiotec.2010.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 11/30/2010] [Accepted: 12/04/2010] [Indexed: 11/26/2022]
Abstract
Experimental evidence suggests that the cell membrane is a highly organized structure that is compartmentalized by the underlying membrane cytoskeleton (MSK). The interaction between the cell membrane and the cytoskeleton led to the "picket-fence" model, which was proposed to explain certain aspects of membrane compartmentalization. This model assumes that the MSK hinders and confines the motion of receptors and lipids to compartments in the membrane. However, the impact of the MSK on receptor clustering, aggregation, and downstream signaling remains unclear. For example, some evidence suggests that the MSK enhances dimerization, while other evidence suggests decreased dimerization and signaling. Herein, we use computational Monte Carlo simulations to examine the effects of MSK density and receptor concentration on receptor dimerization and clustering. Preliminary results suggest that the MSK may have the potential to induce receptor clustering, which is a function of both picket-fence density and receptor concentration.
Collapse
Affiliation(s)
- Michelle N Costa
- Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131, United States
| | | | | |
Collapse
|
27
|
Fatmi MQ, Chang CEA. The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase. PLoS Comput Biol 2010; 6:e1000994. [PMID: 21085641 PMCID: PMC2978696 DOI: 10.1371/journal.pcbi.1000994] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 10/08/2010] [Indexed: 11/25/2022] Open
Abstract
The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS). TRPS uses a set of α/β–dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand–bound conformations. Our simulations also revealed that the α/β–dimeric unit stabilizes the substrate–protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function. Conformational changes of enzymes are often related to regulating and creating an optimal environment for efficient chemistry. An increasing number of evidences also indicate that oligomerization/co-localization of proteins contributes to the efficiency of metabolic pathways. Although static structures have been available for many multi-enzyme complexes, their efficiency is also governed by the synergistic regulation between the multi-units. Our study applies molecular dynamics and Brownian dynamics simulations to the model system, the tryptophan synthase complex. The multi-enzyme complex is a bienzyme nanomachine and its catalytic activity is intimately related to the allosteric signaling and the metabolite transfer between its α– and β–subunits connected by a 25-Å long channel. Our studies suggest that the binding partner is crucial for the ligand binding processes. Although the isolated monomers are stable in the ligand–free state and can form stable interaction if the substrate is in the final bound conformation, it has higher energy barrier when ligand binds to the active site. We also show that the channel does not always exist, but it may be blocked before the enzyme reaches its final bound conformation. The results highlight the importance of forming protein complexes and the cooperative changes during different states.
Collapse
Affiliation(s)
- M. Qaiser Fatmi
- Department of Chemistry, University of California, Riverside, Riverside, California, United States of America
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, California, United States of America
- * E-mail:
| |
Collapse
|
28
|
Radhakrishnan K, Halász A, Vlachos D, Edwards JS. Quantitative understanding of cell signaling: the importance of membrane organization. Curr Opin Biotechnol 2010; 21:677-82. [PMID: 20829029 DOI: 10.1016/j.copbio.2010.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 12/13/2022]
Abstract
Systems biology modeling of signal transduction pathways traditionally employs ordinary differential equations, deterministic models based on the assumptions of spatial homogeneity. However, this can be a poor approximation for certain aspects of signal transduction, especially its initial steps: the cell membrane exhibits significant spatial organization, with diffusion rates approximately two orders of magnitude slower than those in the cytosol. Thus, to unravel the complexities of signaling pathways, quantitative models must consider spatial organization as an important feature of cell signaling. Furthermore, spatial separation limits the number of molecules that can physically interact, requiring stochastic simulation methods that account for individual molecules. Herein, we discuss the need for mathematical models and experiments that appreciate the importance of spatial organization in the membrane.
Collapse
Affiliation(s)
- Krishnan Radhakrishnan
- Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | | | | | | |
Collapse
|
29
|
Kuhn C, Bufe B, Batram C, Meyerhof W. Oligomerization of TAS2R Bitter Taste Receptors. Chem Senses 2010; 35:395-406. [DOI: 10.1093/chemse/bjq027] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Bonchev D, Thomas S, Apte A, Kier LB. Cellular automata modelling of biomolecular networks dynamics. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:77-102. [PMID: 20373215 DOI: 10.1080/10629360903568580] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk.
Collapse
Affiliation(s)
- D Bonchev
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Center for the Study of Biological Complexity, Richmond, Virginia, USA.
| | | | | | | |
Collapse
|
31
|
Lipid raft-mediated regulation of G-protein coupled receptor signaling by ligands which influence receptor dimerization: a computational study. PLoS One 2009; 4:e6604. [PMID: 19668374 PMCID: PMC2719103 DOI: 10.1371/journal.pone.0006604] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 07/22/2009] [Indexed: 11/19/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are the largest family of cell surface receptors; they activate heterotrimeric G-proteins in response to ligand stimulation. Although many GPCRs have been shown to form homo- and/or heterodimers on the cell membrane, the purpose of this dimerization is not known. Recent research has shown that receptor dimerization may have a role in organization of receptors on the cell surface. In addition, microdomains on the cell membrane termed lipid rafts have been shown to play a role in GPCR localization. Using a combination of stochastic (Monte Carlo) and deterministic modeling, we propose a novel mechanism for lipid raft partitioning of GPCRs based on reversible dimerization of receptors and then demonstrate that such localization can affect GPCR signaling. Modeling results are consistent with a variety of experimental data indicating that lipid rafts have a role in amplification or attenuation of G-protein signaling. Thus our work suggests a new mechanism by which dimerization-inducing or inhibiting characteristics of ligands can influence GPCR signaling by controlling receptor organization on the cell membrane.
Collapse
|
32
|
Abstract
In cell membranes, membrane proteins occupy approximately 30% of the total surface area. Crowding effects similar to those in the solution phase are thus to be expected. In addition, there are crowding effects unique to proteins bound to the two-dimensional membranes, such as those exerted on the equilibration of a protein between two membrane orientations and on the redistribution of proteins between different locations in a cell membrane. This article aims to present a theoretical framework for understanding the various crowding effects within membranes. For illustration, the theory is used to analyze previously published experimental and simulation data. It is hoped that the article will encourage quantitative analyses in future experiments and spur systematic investigation of membrane crowding effects.
Collapse
Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
| |
Collapse
|
33
|
Costa MN, Radhakrishnan K, Wilson BS, Vlachos DG, Edwards JS. Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction. PLoS One 2009; 4:e6316. [PMID: 19626123 PMCID: PMC2710010 DOI: 10.1371/journal.pone.0006316] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 06/17/2009] [Indexed: 01/24/2023] Open
Abstract
Background The ErbB family of receptors activates intracellular signaling pathways that control cellular proliferation, growth, differentiation and apoptosis. Given these central roles, it is not surprising that overexpression of the ErbB receptors is often associated with carcinogenesis. Therefore, extensive laboratory studies have been devoted to understanding the signaling events associated with ErbB activation. Methodology/Principal Findings Systems biology has contributed significantly to our current understanding of ErbB signaling networks. However, although computational models have grown in complexity over the years, little work has been done to consider the spatial-temporal dynamics of receptor interactions and to evaluate how spatial organization of membrane receptors influences signaling transduction. Herein, we explore the impact of spatial organization of the epidermal growth factor receptor (ErbB1/EGFR) on the initiation of downstream signaling. We describe the development of an algorithm that couples a spatial stochastic model of membrane receptors with a nonspatial stochastic model of the reactions and interactions in the cytosol. This novel algorithm provides a computationally efficient method to evaluate the effects of spatial heterogeneity on the coupling of receptors to cytosolic signaling partners. Conclusions/Significance Mathematical models of signal transduction rarely consider the contributions of spatial organization due to high computational costs. A hybrid stochastic approach simplifies analyses of the spatio-temporal aspects of cell signaling and, as an example, demonstrates that receptor clustering contributes significantly to the efficiency of signal propagation from ligand-engaged growth factor receptors.
Collapse
Affiliation(s)
- Michelle N. Costa
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Krishnan Radhakrishnan
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Dionisios G. Vlachos
- Department of Chemical Engineering, University of Delaware, Newark, Delaware, United States of America
| | - Jeremy S. Edwards
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
- Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- * E-mail:
| |
Collapse
|
34
|
Kobayashi H, Azuma R, Yasunaga T. Expression of excess receptors and negative feedback control of signal pathways are required for rapid activation and prompt cessation of signal transduction. Cell Commun Signal 2009; 7:3. [PMID: 19254388 PMCID: PMC2666736 DOI: 10.1186/1478-811x-7-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/03/2009] [Indexed: 01/22/2023] Open
Abstract
Background Cellular signal transduction is initiated by the binding of extracellular ligands to membrane receptors. Receptors are often expressed in excess, and cells are activated when a small number of receptors bind ligands. Intracellular signal proteins are activated at a high level soon after ligand binding, and the activation level decreases in a negative feedback manner without ligand clearance. Why are excess receptors required? What is the physiological significance of the negative feedback regulation? Results To answer these questions, we developed a Monte Carlo simulation program to kinetically analyze signal pathways using the model in which ligands are bound to receptors and then membrane complexes with other membrane proteins are formed. Our simulation results showed that excess receptors are not required for cell activation when the dissociation constant (Kd) of the ligand-receptor complex is 10-10 M or less. However, such low Kd values cause delayed signal shutdown after ligand clearance from the extracellular space. In contrast, when the Kd was 10-8 M and the ligand level was less than 1 μM, excess receptors were required for prompt signal propagation and rapid signal cessation after ligand clearance. An initial increase in active cytosolic signal proteins to a high level is required for rapid activation of cellular signal pathways, and a low level of active signal proteins is essential for the rapid shutdown of signal pathways after ligand clearance. Conclusion The present kinetic analysis revealed that excess receptors and negative feedback regulation promote activation and cessation of signal transduction with a low amount of extracellular ligand.
Collapse
Affiliation(s)
- Hiroshi Kobayashi
- Department of Biochemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan.
| | | | | |
Collapse
|
35
|
Collins SD, Chatterjee A, Vlachos DG. Coarse-grained kinetic Monte Carlo models: Complex lattices, multicomponent systems, and homogenization at the stochastic level. J Chem Phys 2009; 129:184101. [PMID: 19045380 DOI: 10.1063/1.3005225] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
On-lattice kinetic Monte Carlo (KMC) simulations have extensively been applied to numerous systems. However, their applicability is severely limited to relatively short time and length scales. Recently, the coarse-grained MC (CGMC) method was introduced to greatly expand the reach of the lattice KMC technique. Herein, we extend the previous spatial CGMC methods to multicomponent species and/or site types. The underlying theory is derived and numerical examples are presented to demonstrate the method. Furthermore, we introduce the concept of homogenization at the stochastic level over all site types of a spatially coarse-grained cell. Homogenization provides a novel coarsening of the number of processes, an important aspect for complex problems plagued by the existence of numerous microscopic processes (combinatorial complexity). As expected, the homogenized CGMC method outperforms the traditional KMC method on computational cost while retaining good accuracy.
Collapse
Affiliation(s)
- Stuart D Collins
- Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
| | | | | |
Collapse
|
36
|
|
37
|
Vlachos DG. Temporal coarse-graining of microscopic-lattice kinetic Monte Carlo simulations via tau leaping. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:046713. [PMID: 18999567 DOI: 10.1103/physreve.78.046713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Indexed: 05/27/2023]
Abstract
A coarse-time-step method is presented that enables the execution of multiple events at each time increment of microscopic-lattice kinetic Monte Carlo simulations. The method employs the n-fold method to create groups of reactions in which the tau-leap algorithm of Gillespie, originally proposed for well-mixed systems, is applied. Creation of groups of reactions is an essential step to avoid violation of the leap condition that arises when the tau-leap algorithm is applied to a single site. The method is general, very easy to implement, and can result in substantial computational savings when global updating is employed. An illustrative example from crystal growth of a simple cubic lattice with the solid-on-solid approximation is presented.
Collapse
Affiliation(s)
- D G Vlachos
- Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA.
| |
Collapse
|
38
|
|
39
|
Batada NN, Shepp LA, Siegmund DO, Levitt M. Spatial regulation and the rate of signal transduction activation. PLoS Comput Biol 2006; 2:e44. [PMID: 16699596 PMCID: PMC1458967 DOI: 10.1371/journal.pcbi.0020044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 03/21/2006] [Indexed: 11/18/2022] Open
Abstract
Of the many important signaling events that take place on the surface of a mammalian cell, activation of signal transduction pathways via interactions of cell surface receptors is one of the most important. Evidence suggests that cell surface proteins are not as freely diffusible as implied by the classic fluid mosaic model and that their confinement to membrane domains is regulated. It is unknown whether these dynamic localization mechanisms function to enhance signal transduction activation rate or to minimize cross talk among pathways that share common intermediates. To determine which of these two possibilities is more likely, we derive an explicit equation for the rate at which cell surface membrane proteins interact based on a Brownian motion model in the presence of endocytosis and exocytosis. We find that in the absence of any diffusion constraints, cell surface protein interaction rate is extremely high relative to cytoplasmic protein interaction rate even in a large mammalian cell with a receptor abundance of a mere two hundred molecules. Since a larger number of downstream signaling events needs to take place, each occurring at a much slower rate than the initial activation via association of cell surface proteins, we conclude that the role of co-localization is most likely that of cross-talk reduction rather than coupling efficiency enhancement.
Collapse
Affiliation(s)
- Nizar N Batada
- Program in Biophysics, Stanford University, Stanford, California, USA.
| | | | | | | |
Collapse
|
40
|
Fricke GM, Thomas JL. Receptor aggregation by intermembrane interactions: a Monte Carlo study. Biophys Chem 2005; 119:205-11. [PMID: 16226368 DOI: 10.1016/j.bpc.2005.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 09/07/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
The lateral organization of receptors on cell surfaces is critically important to their function; many receptors transmit transmembrane signals when redistributed into clusters, while the response of others is potentiated by their aggregation. Cell-cell contact can play a crucial role in receptor aggregation, even when the bonds between receptors on one cell and ligands on the other are monovalent. Monte Carlo simulations on a two-membrane model were carried out to determine whether weak enthalpic interactions among receptors in one membrane, and among ligands in another, can work synergistically to give large-scale clustering when the two membranes are brought into contact. The simulations give support to such a clustering mechanism. In addition, because clustering is a cooperative process akin to a phase separation, individual receptors and ligands may undergo repeated binding and unbinding while in a clustered "phase," and a single ligand could interact with multiple different receptor partners. The results suggest a resolution of the dichotomy between serial triggering and aggregation models of T cell activation.
Collapse
Affiliation(s)
- G Matthew Fricke
- Department of Computer Science, University of New Mexico, Albuquerque, NM, USA
| | | |
Collapse
|
41
|
Fanelli F, De Benedetti PG. Computational Modeling Approaches to Structure−Function Analysis of G Protein-Coupled Receptors. Chem Rev 2005; 105:3297-351. [PMID: 16159154 DOI: 10.1021/cr000095n] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute and Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41100 Modena, Italy.
| | | |
Collapse
|
42
|
Monine MI, Haugh JM. Reactions on cell membranes: comparison of continuum theory and Brownian dynamics simulations. J Chem Phys 2005; 123:074908. [PMID: 16229621 PMCID: PMC1752218 DOI: 10.1063/1.2000236] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Biochemical transduction of signals received by living cells typically involves molecular interactions and enzyme-mediated reactions at the cell membrane, a problem that is analogous to reacting species on a catalyst surface or interface. We have developed an efficient Brownian dynamics algorithm that is especially suited for such systems and have compared the simulation results with various continuum theories through prediction of effective enzymatic rate constant values. We specifically consider reaction versus diffusion limitation, the effect of increasing enzyme density, and the spontaneous membrane association/dissociation of enzyme molecules. In all cases, we find the theory and simulations to be in quantitative agreement. This algorithm may be readily adapted for the stochastic simulation of more complex cell signaling systems.
Collapse
Affiliation(s)
- Michael I Monine
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, 911 Partners Way, Raleigh, North Carolina 27695-7905, USA
| | | |
Collapse
|
43
|
Abstract
A wide range of approaches has been applied to examine the quaternary structure of G protein-coupled receptors, the basis of such protein-protein interactions and how such interactions might modulate the pharmacology and function of these receptors. These include co-immunoprecipitation, various adaptations of resonance energy transfer techniques, functional complementation studies and the analysis of ligand-binding data. Each of the available techniques has limitations that restrict interpretation of the data. However, taken together, they provide a coherent body of evidence indicating that many, if not all, G protein-coupled receptors exist and function as dimer/oligomers. Herein we assess the widely applied techniques and discuss the relative benefits and limitations of these approaches.
Collapse
Affiliation(s)
- Graeme Milligan
- Molecular Pharmacology Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, UK
| | | |
Collapse
|
44
|
Brinkerhoff CJ, Linderman JJ. Integrin dimerization and ligand organization: key components in integrin clustering for cell adhesion. TISSUE ENGINEERING 2005; 11:865-76. [PMID: 15998226 DOI: 10.1089/ten.2005.11.865] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cell adhesion requires both integrin occupancy and integrin clustering. In this work, we investigate a mechanism based on organizing ligand into islands and integrin dimerization for the initiation of integrin clustering. To study integrin clustering and integrin occupancy we develop a two-dimensional Monte Carlo lattice description of the cell-substrate interface to simulate the diffusion and reaction of integrins. We demonstrate that integrin dimerization can drive integrins into clusters of sizes greater than two. Ligand organization or integrin dimerization alone is unable to increase the number of bound integrins, but when both are present they cooperate to increase both binding and clustering of integrins. In addition, when integrin dimerization and ligand organization are both present large integrin clusters, which may act as nucleation sites for the formation of adhesion complexes, are observed. These results describe a potential mechanism for the clustering of integrin receptors and avidity modulation in cellular adhesion and have implications for the designs of surfaces to control cell responses to external ligands and to manipulate cell adhesion for tissue-engineering applications.
Collapse
|
45
|
Ciuculescu ED, Mekmouche Y, Faller P. Metal-Binding Properties of the Peptide APP170-188: A Model of the ZnII-Binding Site of Amyloid Precursor Protein (APP). Chemistry 2005; 11:903-9. [PMID: 15593132 DOI: 10.1002/chem.200400786] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Amyloid precursor protein (APP) plays a key role in Alzheimer's disease (AD), although the function of this membrane protein is still unclear. Metal ions are implicated in AD and they also interact with APP. APP possesses a strong ZnII binding site, which is evolutionary conserved. In this paper a synthetic peptide, APP170-188, with a sequence corresponding to the conserved ZnII-binding domain of APP, was synthesised and its metal-binding properties analysed. Titration experiments pointed to the binding of a stoichiometric amount of divalent ions. Further studies indicated that the binding of divalent metals like ZnII, CdII and CoII induces the dimerisation of the peptide. This dimer contains a dinuclear cluster in which the two divalent metals are bridged by two thiolate ligands from cysteine residues. The other two ligands of the tetrahedral coordination sites of each metal ion are terminal thiolate ligands. This structure was supported by the following arguments. The complex formed with CoII presents the characteristic features for tetrahedral tetrathiolate coordination in its UV-visible spectrum. The sequence of APP170-188 contains only three cysteine residues, which is incompatible with a monomeric CoII-APP170-188 complex. EPR measurements of the complex with one equivalent of CoII show almost no signal at 4 K, which is compatible with an antiferromagnetic spin-coupling of the metal ions in a cluster structure. Size-exclusion chromatography indicated that the elution time for the complexes with ZnII and CdII corresponds to the expected molecular weight of a dimer. The circular dichroism (CD) spectrum of the complex with one equivalent of CdII shows a band at 265 nm+, and an ellipticity similar to those observed for similar CdII-thiolate clusters. Possible biological implications of the ZnII binding site and the metal-induced dimerisation are discussed.
Collapse
Affiliation(s)
- Eliza-Diana Ciuculescu
- Laboratoire de Chimie de Coordination, CNRS UPR 8241 (associated with University Toulouse III), 205 route de Narbonne, 31077 Toulouse Cedex, France
| | | | | |
Collapse
|
46
|
Vlachos DG. A Review of Multiscale Analysis: Examples from Systems Biology, Materials Engineering, and Other Fluid–Surface Interacting Systems. ADVANCES IN CHEMICAL ENGINEERING - MULTISCALE ANALYSIS 2005. [DOI: 10.1016/s0065-2377(05)30001-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
47
|
Abstract
The self-association of proteins to form dimers and higher-order oligomers is a very common phenomenon. Recent structural and biophysical studies show that protein dimerization or oligomerization is a key factor in the regulation of proteins such as enzymes, ion channels, receptors and transcription factors. In addition, self-association can help to minimize genome size, while maintaining the advantages of modular complex formation. Oligomerization, however, can also have deleterious consequences when nonnative oligomers associated with pathogenic states are generated. Specific protein dimerization is integral to biological function, structure and control, and must be under substantial selection pressure to be maintained with such frequency throughout biology.
Collapse
Affiliation(s)
- Neelan J Marianayagam
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | | |
Collapse
|
48
|
Galle J, Loeffler M, Drasdo D. Modeling the effect of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro. Biophys J 2004; 88:62-75. [PMID: 15475585 PMCID: PMC1305039 DOI: 10.1529/biophysj.104.041459] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We present a three-dimensional individual cell-based, biophysical model to study the effect of normal and malfunctioning growth regulation and control on the spatial-temporal organization of growing cell populations in vitro. The model includes explicit representations of typical epithelial cell growth regulation and control mechanisms, namely 1), a cell-cell contact-mediated form of growth inhibition; 2), a cell-substrate contact-dependent cell-cycle arrest; and 3), a cell-substrate contact-dependent programmed cell death (anoikis). The model cells are characterized by experimentally accessible biomechanical and cell-biological parameters. First, we study by variation of these cell-specific parameters which of them affect the macroscopic morphology and growth kinetics of a cell population within the initial expanding phase. Second, we apply selective knockouts of growth regulation and control mechanisms to investigate how the different mechanisms collectively act together. Thereby our simulation studies cover the growth behavior of epithelial cell populations ranging from undifferentiated stem cell populations via transformed variants up to tumor cell lines in vitro. We find that the cell-specific parameters, and in particular the strength of the cell-substrate anchorage, have a significant impact on the population morphology. Furthermore, they control the efficacy of the growth regulation and control mechanisms, and consequently tune the transition from controlled to uncontrolled growth that is induced by the failures of these mechanisms. Interestingly, however, we find the qualitative and quantitative growth kinetics to be remarkably robust against variations of cell-specific parameters. We compare our simulation results with experimental findings on a number of epithelial and tumor cell populations and suggest in vitro experiments to test our model predictions.
Collapse
Affiliation(s)
- Jörg Galle
- Interdisciplinary Centre for Bioinformatics, Leipzig, Germany; Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany; and Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Markus Loeffler
- Interdisciplinary Centre for Bioinformatics, Leipzig, Germany; Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany; and Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Dirk Drasdo
- Interdisciplinary Centre for Bioinformatics, Leipzig, Germany; Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany; and Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| |
Collapse
|
49
|
Brinkerhoff CJ, Woolf PJ, Linderman JJ. Monte Carlo simulations of receptor dynamics: insights into cell signaling. J Mol Histol 2004; 35:667-77. [PMID: 15614622 DOI: 10.1007/s10735-004-2663-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Revised: 03/20/2004] [Indexed: 10/26/2022]
Abstract
Many receptor-level processes involve the diffusion and reaction of receptors with other membrane-localized molecules. Monte Carlo simulation is a powerful technique that allows us to track the motions and discrete reactions of individual receptors, thus simulating receptor dynamics and the early events of signal transduction. In this paper, we discuss simulations of two receptor processes, receptor dimerization and G-protein activation. Our first set of simulations demonstrates how receptor dimerization can create clusters of receptors via partner switching and the relevance of this clustering for receptor cross-talk and integrin signaling. Our second set of simulations investigates the activation and desensitization of G-protein coupled receptors when either a single agonist or both an agonist and an antagonist are present. For G-protein coupled receptor systems in the presence of an agonist alone, the dissociation rate constant of agonist is predicted to affect the ratio of G-protein activation to receptor phosphorylation. Similarly, this ratio is affected by the antagonist dissociation rate constant when both agonist and antagonist are present. The relationship of simulation predictions to experimental findings and potential applications of our findings are also discussed.
Collapse
|
50
|
Woolf PJ, Linderman JJ. An algebra of dimerization and its implications for G-protein coupled receptor signaling. J Theor Biol 2004; 229:157-68. [PMID: 15207471 DOI: 10.1016/j.jtbi.2004.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Revised: 02/23/2004] [Accepted: 03/12/2004] [Indexed: 10/26/2022]
Abstract
Many species of receptors form dimers, but how can we use this information to make predictions about signal transduction? This problem is particularly difficult when receptors dimerize with many different species, leading to a combinatoric increase in the possible number of dimer pairs. As an example system, we focus on receptors in the G-protein coupled receptor (GPCR) family. GPCRs have been shown to reversibly form dimers, but this dimerization does not directly affect signal transduction. Here we present a new theoretical framework called a dimerization algebra. This algebra provides a systematic and rational way to represent, manipulate, and in some cases simplify large and often complicated networks of dimerization interactions. To compliment this algebra, Monte Carlo simulations are used to predict dimerization's effect on receptor organization on the membrane, signal transduction, and internalization. These simulation results are directly comparable to various experimental measures such as fluorescence resonance energy transfer (FRET), and as such provide a link between the dimerization algebra and experimental data. As an example, we show how the algebra and computational results can be used to predict the effects of dimerization on the dopamine D2 and somatastatin SSTR1 receptors. When these predictions were compared to experimental findings from the literature, good agreement was found, demonstrating the utility of our approach. Applications of this work to the development of a novel class of dimerization-modulating drugs are also discussed.
Collapse
Affiliation(s)
- Peter J Woolf
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | | |
Collapse
|