1
|
Wilfling F, Kaksonen M, Stachowiak J. Protein condensates as flexible platforms for membrane traffic. Curr Opin Cell Biol 2023; 85:102258. [PMID: 37832166 PMCID: PMC11165926 DOI: 10.1016/j.ceb.2023.102258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
With an essential role in nearly every physiological process and disease state, trafficking vesicles are fundamental to cell biology. Canonical understanding of membrane traffic has been driven by key achievements in structural biology. Nonetheless, discoveries over the past few years progressively point to the critical role of intrinsically disordered domains and proteins, which lack a well-defined secondary structure. From the initiation of endocytosis and the sequestration of synaptic vesicles to the stabilization of endoplasmic reticulum exit sites and the extension of the autophagic cup, flexible protein condensates, rich in intrinsic disorder, are increasingly implicated. While important debates about the physical nature and mechanistic interpretation of these findings remain, the significance of transient, multivalent protein assemblies in membrane traffic is increasingly clear.
Collapse
Affiliation(s)
- Florian Wilfling
- Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, Frankfurt a. M., Germany.
| | - Marko Kaksonen
- University of Geneva, Department of Biochemistry, Geneva, Switzerland.
| | - Jeanne Stachowiak
- University of Texas at Austin, Department of Biomedical Engineering, USA; University of Texas at Austin, Department of Chemical Engineering, USA.
| |
Collapse
|
2
|
Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions. J Membr Biol 2022; 255:237-259. [PMID: 35451616 PMCID: PMC9028910 DOI: 10.1007/s00232-022-00237-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022]
Abstract
Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein’s ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure–function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.
Collapse
|
3
|
Kozak M, Kaksonen M. Condensation of Ede1 promotes the initiation of endocytosis. eLife 2022; 11:72865. [PMID: 35412456 PMCID: PMC9064294 DOI: 10.7554/elife.72865] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 04/01/2022] [Indexed: 11/27/2022] Open
Abstract
Clathrin-mediated endocytosis is initiated by a network of weakly interacting proteins through a poorly understood mechanism. Ede1, the yeast homolog of mammalian Eps15, is an early-arriving endocytic protein and a key initiation factor. In the absence of Ede1, most other early endocytic proteins lose their punctate localization and endocytic uptake is decreased. We show that in yeast cells, cytosolic concentration of Ede1 is buffered at a critical level. Excess amounts of Ede1 form large condensates which recruit other endocytic proteins and exhibit properties of phase-separated liquid droplets. We demonstrate that the central region of Ede1, containing a coiled-coil and a prion-like region, is essential for both the condensate formation and the function of Ede1 in endocytosis. The functionality of Ede1 mutants lacking the central region can be partially rescued by an insertion of heterologous prion-like domains. Conversely, fusion of a heterologous lipid-binding domain with the central region of Ede1 can promote clustering into stable plasma membrane domains. We propose that the ability of Ede1 to form condensed networks supports the clustering of early endocytic proteins and promotes the initiation of endocytosis.
Collapse
Affiliation(s)
- Mateusz Kozak
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| |
Collapse
|
4
|
Shafat Z, Ahmed A, Parvez MK, Islam A, Parveen S. Intrinsically disordered regions in the rodent hepevirus proteome. Bioinformation 2022; 18:111-118. [PMID: 36420436 PMCID: PMC9649497 DOI: 10.6026/97320630018111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/03/2022] [Accepted: 01/03/2022] [Indexed: 09/19/2023] Open
Abstract
Hepatitis E virus (HEV) is the causative agent of Hepatitis E infections across the world. Intrinsically disordered protein regions (IDPRs) or intrinsically disordered proteins (IDPs) are regions or proteins that are characterized by lack of definite structure. These IDPRs or IDPs play significant roles in a wide range of biological processes, such as cell cycle regulation, control of signaling pathways, etc. IDPR/IDP in proteins is associated with the virus's pathogenicity and infectivity. The prevalence of IDPR/IDP in rat HEV proteome remains undetermined. Hence, we examined the unstructured/disordered regions of the open reading frame (ORF) encoded proteins of rat HEV by analyzing the prevalence of intrinsic disorder. The intrinsic disorder propensity analysis showed that the different ORF proteins consisted of varying fraction of intrinsic disorder. The protein ORF3 was identified with maximum propensity for intrinsic disorder while the ORF6 protein had the least fraction of intrinsic disorder. The analysis revealed ORF6 as a structured protein (ORDP); ORF1 and ORF4 as moderately disordered proteins (IDPRs); and ORF3 and ORF5 as highly disordered proteins (IDPs). The protein ORF2 was found to be moderately as well as highly disordered using different predictors, thus, was categorized into both IDPR and IDP. Such disordered regions have important roles in pathogenesis and replication of viruses.
Collapse
Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
5
|
Hydrogen Peroxide and Amyotrophic Lateral Sclerosis: From Biochemistry to Pathophysiology. Antioxidants (Basel) 2021; 11:antiox11010052. [PMID: 35052556 PMCID: PMC8773294 DOI: 10.3390/antiox11010052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/18/2021] [Accepted: 12/24/2021] [Indexed: 11/19/2022] Open
Abstract
Free radicals are unstable chemical reactive species produced during Redox dyshomeostasis (RDH) inside living cells and are implicated in the pathogenesis of various neurodegenerative diseases. One of the most complicated and life-threatening motor neurodegenerative diseases (MND) is amyotrophic lateral sclerosis (ALS) because of the poor understanding of its pathophysiology and absence of an effective treatment for its cure. During the last 25 years, researchers around the globe have focused their interest on copper/zinc superoxide dismutase (Cu/Zn SOD, SOD1) protein after the landmark discovery of mutant SOD1 (mSOD1) gene as a risk factor for ALS. Substantial evidence suggests that toxic gain of function due to redox disturbance caused by reactive oxygen species (ROS) changes the biophysical properties of native SOD1 protein thus, instigating its fibrillization and misfolding. These abnormal misfolding aggregates or inclusions of SOD1 play a role in the pathogenesis of both forms of ALS, i.e., Sporadic ALS (sALS) and familial ALS (fALS). However, what leads to a decrease in the stability and misfolding of SOD1 is still in question and our scientific knowledge is scarce. A large number of studies have been conducted in this area to explore the biochemical mechanistic pathway of SOD1 aggregation. Several studies, over the past two decades, have shown that the SOD1-catalyzed biochemical reaction product hydrogen peroxide (H2O2) at a pathological concentration act as a substrate to trigger the misfolding trajectories and toxicity of SOD1 in the pathogenesis of ALS. These toxic aggregates of SOD1 also cause aberrant localization of TAR-DNA binding protein 43 (TDP-43), which is characteristic of neuronal cytoplasmic inclusions (NCI) found in ALS. Here in this review, we present the evidence implicating the pivotal role of H2O2 in modulating the toxicity of SOD1 in the pathophysiology of the incurable and highly complex disease ALS. Also, highlighting the role of H2O2 in ALS, we believe will encourage scientists to target pathological concentrations of H2O2 thereby halting the misfolding of SOD1.
Collapse
|
6
|
Villagomez FR, Diaz-Valencia JD, Ovalle-García E, Antillón A, Ortega-Blake I, Romero-Ramírez H, Cerna-Cortes JF, Rosales-Reyes R, Santos-Argumedo L, Patiño-López G. TBC1D10C is a cytoskeletal functional linker that modulates cell spreading and phagocytosis in macrophages. Sci Rep 2021; 11:20946. [PMID: 34686741 PMCID: PMC8536695 DOI: 10.1038/s41598-021-00450-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/11/2021] [Indexed: 12/14/2022] Open
Abstract
Cell spreading and phagocytosis are notably regulated by small GTPases and GAP proteins. TBC1D10C is a dual inhibitory protein with GAP activity. In immune cells, TBC1D10C is one of the elements regulating lymphocyte activation. However, its specific role in macrophages remains unknown. Here, we show that TBC1D10C engages in functions dependent on the cytoskeleton and plasma membrane reorganization. Using ex vivo and in vitro assays, we found that elimination and overexpression of TBC1D10C modified the cytoskeletal architecture of macrophages by decreasing and increasing the spreading ability of these cells, respectively. In addition, TBC1D10C overexpression contributed to higher phagocytic activity against Burkholderia cenocepacia and to increased cell membrane tension. Furthermore, by performing in vitro and in silico analyses, we identified 27 TBC1D10C-interacting proteins, some of which were functionally classified as protein complexes involved in cytoskeletal dynamics. Interestingly, we identified one unreported TBC1D10C-intrinsically disordered region (IDR) with biological potential at the cytoskeleton level. Our results demonstrate that TBC1D10C shapes macrophage activity by inducing reorganization of the cytoskeleton-plasma membrane in cell spreading and phagocytosis. We anticipate our results will be the basis for further studies focused on TBC1D10C. For example, the specific molecular mechanism in Burkholderia cenocepacia phagocytosis and functional analysis of TBC1D10C-IDR are needed to further understand its role in health and disease.
Collapse
Affiliation(s)
- Fabian R Villagomez
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico.,Laboratorio de Microbiología Molecular, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Juan D Diaz-Valencia
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico
| | - Erasmo Ovalle-García
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Armando Antillón
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Iván Ortega-Blake
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Héctor Romero-Ramírez
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad De México, Mexico
| | - Jorge F Cerna-Cortes
- Laboratorio de Microbiología Molecular, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Roberto Rosales-Reyes
- Laboratorio de Infectología, Microbiología e Inmunología Clínica, Unidad de Investigación en Medicina Experimental de la Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Leopoldo Santos-Argumedo
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad De México, Mexico
| | - Genaro Patiño-López
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico.
| |
Collapse
|
7
|
Shafat Z, Ahmed A, Parvez MK, Parveen S. Sequence to structure analysis of the ORF4 protein from Hepatitis E virus. Bioinformation 2021; 17:818-828. [PMID: 35539889 PMCID: PMC9049080 DOI: 10.6026/97320630017818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis E virus (HEV) is the main cause of acute hepatitis worldwide. HEV accounts for up to 30% mortality rate in pregnant women, with highest incidences reported for genotype 1 (G1) HEV. The contributing factors in adverse cases during pregnancy in women due to HEV infection is still debated. The mechanism underlying the pathogenesis of viral infection is attributed to different genomic component of HEV, i.e., open reading frames (ORFs): ORF1, ORF2, ORF3 and ORF4. Recently, ORF4 has been discovered in enhancing the replication of GI isolates of HEV through regulation of an IRES-like RNA element. However, its characterization through computational methodologies remains unexplored. In this novel study, we provide comprehensive overview of ORF4 protein's genetic and molecular characteristics through analyzing its sequence and different structural levels. A total of three different datasets (Human, Rat and Ferret) of ORF4 genomes were built and comparatively analyzed. Several non-synonymous mutations in conjunction with higher entropy values were observed in rat and ferret datasets, however, limited variation was observed in human ORF4 genomes. Higher transition to tranversion ratio was observed in the ORF4 genomes. Studies have reported the association of intrinsic disordered proteins (IDP) with drug discovery due to its role in several signaling and regulatory processes through protein-protein interactions (PPIs). As PPIs are potent drug target sources, thus the ORF4 protein was explored by analyzing its polypeptide structure in order to shed light on its intrinsic disorder. Pressures that lead towards preponderance of disordered-promoting amino acid residues shaped the evolution of ORF4. The intrinsic disorder propensity analysis revealed ORF4 protein (Human) as a highly disordered protein (IDP). Predominance of coils and lack of secondary structure further substantiated our findings suggesting its involvement in binding to ligand molecules. Thus, ORF4 contributes to cellular signaling processes through protein-protein interactions, as IDPs are targets for regulation to accelerate the process of drug designing strategies against HEV infections.
Collapse
Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
8
|
Jagannathan NS, Hogue CWV, Tucker-Kellogg L. Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2. PLoS Comput Biol 2021; 17:e1008474. [PMID: 33406091 PMCID: PMC7787433 DOI: 10.1371/journal.pcbi.1008474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/27/2020] [Indexed: 11/22/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are prevalent in the eukaryotic proteome. Common functional roles of IDRs include forming flexible linkers or undergoing allosteric folding-upon-binding. Recent studies have suggested an additional functional role for IDRs: generating steric pressure on the plasma membrane during endocytosis, via molecular crowding. However, in order to accomplish useful functions, such crowding needs to be regulated in space (e.g., endocytic hotspots) and time (e.g., during vesicle formation). In this work, we explore binding-induced regulation of IDR steric volume. We simulate the IDRs of two proteins from Clathrin-mediated endocytosis (CME) to see if their conformational spaces are regulated via binding-induced expansion. Using Monte-Carlo computational modeling of excluded volumes, we generate large conformational ensembles (3 million) for the IDRs of Epsin and Eps15 and dock the conformers to the alpha subunit of Adaptor Protein 2 (AP2α), their CME binding partner. Our results show that as more molecules of AP2α are bound, the Epsin-derived ensemble shows a significant increase in global dimensions, measured as the radius of Gyration (RG) and the end-to-end distance (EED). Unlike Epsin, Eps15-derived conformers that permit AP2α binding at one motif were found to be more likely to accommodate binding of AP2α at other motifs, suggesting a tendency toward co-accessibility of binding motifs. Co-accessibility was not observed for any pair of binding motifs in Epsin. Thus, we speculate that the disordered regions of Epsin and Eps15 perform different roles during CME, with accessibility in Eps15 allowing it to act as a recruiter of AP2α molecules, while binding-induced expansion of the Epsin disordered region could impose steric pressure and remodel the plasma membrane during vesicle formation. Protein functions were originally believed to arise from ordered protein structures. This dogma was later challenged by the identification of intrinsically disordered proteins that lack specific structure. The functional roles of such proteins usually fell in two categories–exploiting the disorder for flexibility (like floppy connector), or imposing order upon binding to an external partner. In this study we explore the possibility of an alternative mechanism that harnesses disorder for function through regulated molecular crowding. Specifically, we use modeling to study two proteins involved in reshaping the cell membrane, Epsin and Eps15. We ask if they undergo binding-induced expansion, where binding of an external partner AP2 causes not a transition toward order, but rather an energetically favorable increase in propensity to occupy larger volumes. Our results show that Epsin tends to occupy a larger volume when bound to AP2, consistent with increased molecular crowding, which could help reshape the cell membrane. Such regulation of disorder via binding (without folding) opens hitherto unexplored avenues that cells might employ to harness disorder.
Collapse
Affiliation(s)
- N. Suhas Jagannathan
- Cancer & Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
- Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore
| | - Christopher W. V. Hogue
- Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Lisa Tucker-Kellogg
- Cancer & Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore
- Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore
- * E-mail:
| |
Collapse
|
9
|
Day KJ, Stachowiak JC. Biophysical forces in membrane bending and traffic. Curr Opin Cell Biol 2020; 65:72-77. [PMID: 32229366 PMCID: PMC7529674 DOI: 10.1016/j.ceb.2020.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 11/20/2022]
Abstract
Intracellular trafficking requires extensive changes in membrane morphology. Cells use several distinct molecular factors and physical cues to remodel membranes. Here, we highlight recent advances in identifying the biophysical mechanisms of membrane curvature generation. In particular, we focus on the cooperation of molecular and physical drivers of membrane bending during three stages of vesiculation: budding, cargo selection, and scission. Taken together, the studies reviewed here emphasize that, rather than a single dominant mechanism, several mechanisms typically work in parallel during each step of membrane remodeling. Important challenges for the future of this field are to understand how multiple mechanisms work together synergistically and how a series of stochastic events can be combined to achieve a deterministic result-assembly of the trafficking vesicle.
Collapse
Affiliation(s)
- Kasey J Day
- Department of Biomedical Engineering, 107 W. Dean Keeton St., C0800, Austin, TX, 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, 107 W. Dean Keeton St., C0800, Austin, TX, 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Norman Hackerman Building, 100 East 24th St., NHB 4500, Austin, TX, 78712, USA.
| |
Collapse
|
10
|
Antoszewski A, Feng CJ, Vani BP, Thiede EH, Hong L, Weare J, Tokmakoff A, Dinner AR. Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding. J Phys Chem B 2020; 124:5571-5587. [PMID: 32515958 PMCID: PMC7774804 DOI: 10.1021/acs.jpcb.0c03521] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The protein hormone insulin exists in various oligomeric forms, and a key step in binding its cellular receptor is dissociation of the dimer. This dissociation process and its corresponding association process have come to serve as paradigms of coupled (un)folding and (un)binding more generally. Despite its fundamental and practical importance, the mechanism of insulin dimer dissociation remains poorly understood. Here, we use molecular dynamics simulations, leveraging recent developments in umbrella sampling, to characterize the energetic and structural features of dissociation in unprecedented detail. We find that the dissociation is inherently multipathway with limiting behaviors corresponding to conformational selection and induced fit, the two prototypical mechanisms of coupled folding and binding. Along one limiting path, the dissociation leads to detachment of the C-terminal segment of the insulin B chain from the protein core, a feature believed to be essential for receptor binding. We simulate IR spectroscopy experiments to aid in interpreting current experiments and identify sites where isotopic labeling can be most effective for distinguishing the contributions of the limiting mechanisms.
Collapse
Affiliation(s)
- Adam Antoszewski
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chi-Jui Feng
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bodhi P Vani
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Erik H Thiede
- Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Statistics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lu Hong
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jonathan Weare
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
11
|
Zeno WF, Snead WT, Thatte AS, Stachowiak JC. Structured and intrinsically disordered domains within Amphiphysin1 work together to sense and drive membrane curvature. SOFT MATTER 2019; 15:8706-8717. [PMID: 31621751 PMCID: PMC6934260 DOI: 10.1039/c9sm01495k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cellular membranes undergo remodeling during many cellular processes including endocytosis, cytoskeletal protrusion, and organelle biogenesis. During these events, specialized proteins sense and amplify fluctuations in membrane curvature to create stably curved architectures. Amphiphysin1 is a multi-domain protein containing an N-terminal crescent-shaped BAR (Bin/Amphiphysin/Rvs) domain and a C-terminal domain that is largely disordered. When studied in isolation, the BAR domain of Amphiphysin1 senses membrane curvature and generates membrane tubules. However, the disordered domain has been largely overlooked in these studies. Interestingly, our recent work has demonstrated that the disordered domain is capable of substantially amplifying the membrane remodeling ability of the BAR domain. However, the physical mechanisms responsible for these effects are presently unclear. Here we elucidated the functional role of the disordered domain by gradually truncating it, creating a family of mutant proteins, each of which contained the BAR domain and a fraction of the disordered domain. Using quantitative fluorescence and electron microscopy, our results indicate that the disordered domain contributes to membrane remodeling by making it more difficult for the protein to bind to and assemble on flat membrane surfaces. Specifically, we found that the disordered domain began to significantly impact membrane remodeling when its projected area exceeded that of the BAR domain. Once this threshold was crossed, steric interactions with the membrane surface and with neighboring disordered domains gave rise to increased curvature sensing and membrane vesiculation, respectively. These findings provide insight into the synergy between structured and disordered domains, each of which play important biophysical roles in membrane remodeling.
Collapse
Affiliation(s)
- Wade F Zeno
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Wilton T Snead
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Ajay S Thatte
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA. and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
12
|
Zeno WF, Thatte AS, Wang L, Snead WT, Lafer EM, Stachowiak JC. Molecular Mechanisms of Membrane Curvature Sensing by a Disordered Protein. J Am Chem Soc 2019; 141:10361-10371. [PMID: 31180661 DOI: 10.1021/jacs.9b03927] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ability of proteins to sense membrane curvature is essential for the initiation and assembly of curved membrane structures. Established mechanisms of curvature sensing rely on proteins with specific structural features. In contrast, it has recently been discovered that intrinsically disordered proteins, which lack a defined three-dimensional fold, can also be potent sensors of membrane curvature. How can an unstructured protein sense the structure of the membrane surface? Many disordered proteins that associate with membranes have two key physical features: a high degree of conformational entropy and a high net negative charge. Binding of such proteins to membrane surfaces results simultaneously in a decrease in conformational entropy and an increase in electrostatic repulsion by anionic lipids. Here we show that each of these effects gives rise to a distinct mechanism of curvature sensing. Specifically, as the curvature of the membrane increases, the steric hindrance between the disordered protein and membrane is reduced, leading to an increase in chain entropy. At the same time, increasing membrane curvature increases the average separation between anionic amino acids and lipids, creating an electrostatic preference for curved membranes. Using quantitative imaging of membrane vesicles, our results demonstrate that long disordered amino acid chains with low net charge sense curvature predominately through the entropic mechanism. In contrast, shorter, more highly charged amino acid chains rely largely on the electrostatic mechanism. These findings provide a roadmap for predicting and testing the curvature sensitivity of the large and diverse set of disordered proteins that function at cellular membranes.
Collapse
Affiliation(s)
- Wade F Zeno
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Ajay S Thatte
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Liping Wang
- Department of Biochemistry and Structural Biology , The University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Wilton T Snead
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology , The University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institute for Cellular and Molecular Biology , The University of Texas at Austin , Austin , Texas 78712 , United States
| |
Collapse
|
13
|
At the Heart of Bacterial Cytokinesis: The Z Ring. Trends Microbiol 2019; 27:781-791. [PMID: 31171437 DOI: 10.1016/j.tim.2019.04.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/22/2019] [Accepted: 04/29/2019] [Indexed: 11/20/2022]
Abstract
Bacterial cell division is mediated by the divisome which is organized by the Z ring, a cytoskeletal element formed by the polymerization of the tubulin homologue FtsZ. Despite billions of years of bacterial evolution, the Z ring is nearly universal among bacteria that have a cell wall and divide by binary fission. Recent studies have revealed the mechanism of cooperative assembly of FtsZ and that the Z ring consists of patches of FtsZ filaments tethered to the membrane that treadmill to distribute the septal biosynthetic machinery. Here, we summarize these advances and discuss questions raised by these new findings.
Collapse
|
14
|
Mohammad IL, Mateos B, Pons M. The disordered boundary of the cell: emerging properties of membrane-bound intrinsically disordered proteins. Biomol Concepts 2019; 10:25-36. [DOI: 10.1515/bmc-2019-0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/28/2019] [Indexed: 12/12/2022] Open
Abstract
AbstractWe define the disordered boundary of the cell (DBC) as the system formed by membrane tethered intrinsically disordered protein regions, dynamically coupled to the underlying membrane.The emerging properties of the DBC makes it a global system of study, which cannot be understood from the individual properties of their components. Similarly, the properties of lipid bilayers cannot be understood from just the sum of the properties of individual lipid molecules.The highly anisotropic confined environment, restricting the position and orientation of interacting sites, is affecting the properties of individual disordered proteins. In fact, the collective effect caused by high concentrations of disordered proteins extend beyond the sum of individual effects.Examples of emerging properties of the DBC include enhanced protein-protein interactions, protein-driven phase separations, Z-compartmentalization, and protein modulated electrostatics.
Collapse
Affiliation(s)
- Irrem-Laareb Mohammad
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, 08028Barcelona, Spain
| | - Borja Mateos
- Max F. Perutz Laboratories, Department of Computational and Structural Biology, University of Vienna, Campus Vienna Biocenter 5, 1030Vienna, Austria
| | - Miquel Pons
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, 08028Barcelona, Spain
| |
Collapse
|
15
|
Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing. Nat Commun 2018; 9:4152. [PMID: 30297718 PMCID: PMC6175956 DOI: 10.1038/s41467-018-06532-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/06/2018] [Indexed: 12/12/2022] Open
Abstract
The ability of proteins to sense membrane curvature is essential to cellular function. All known sensing mechanisms rely on protein domains with specific structural features such as wedge-like amphipathic helices and crescent-shaped BAR domains. Yet many proteins that contain these domains also contain large intrinsically disordered regions. Here we report that disordered domains are themselves potent sensors of membrane curvature. Comparison of Monte Carlo simulations with in vitro and live-cell measurements demonstrates that the polymer-like behavior of disordered domains found in endocytic proteins drives them to partition preferentially to convex membrane surfaces, which place fewer geometric constraints on their conformational entropy. Further, proteins containing both structured curvature sensors and disordered regions are more than twice as curvature sensitive as their respective structured domains alone. These findings demonstrate an entropic mechanism of curvature sensing that is independent of protein structure and illustrate how structured and disordered domains can synergistically enhance curvature sensitivity. Many proteins which sense membrane curvature contain intrinsically disordered domains. Here the authors use Monte Carlo simulations combined with experimental approaches and report that disordered domains are potent sensors of membrane curvature.
Collapse
|
16
|
Abstract
Alzheimer's disease is characterized in part by the intracellular misfolding and aggregation of tau protein. The aggregates, which range in size from small oligomers to large filaments, are markers for disease diagnosis and staging, potential vectors for disease propagation, and candidate sources of neurotoxicity. Here we present protocols for synthesizing large tau aggregates characterized by filamentous morphology and cross-β-sheet structure from monomeric full-length tau precursors in vitro. We also describe their detection and quantification through thioflavin dye binding, filter trap, and transmission electron microscopy methods. These methods cover applications requiring high-throughput capability as well as those requiring high-resolution analysis of aggregation mechanism.
Collapse
|
17
|
Busch DJ, Houser JR, Hayden CC, Sherman MB, Lafer EM, Stachowiak JC. Intrinsically disordered proteins drive membrane curvature. Nat Commun 2015. [PMID: 26204806 PMCID: PMC4515776 DOI: 10.1038/ncomms8875] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Assembly of highly curved membrane structures is essential to cellular physiology. The prevailing view has been that proteins with curvature-promoting structural motifs, such as wedge-like amphipathic helices and crescent-shaped BAR domains, are required for bending membranes. Here we report that intrinsically disordered domains of the endocytic adaptor proteins, Epsin1 and AP180 are highly potent drivers of membrane curvature. This result is unexpected since intrinsically disordered domains lack a well-defined three-dimensional structure. However, in vitro measurements of membrane curvature and protein diffusivity demonstrate that the large hydrodynamic radii of these domains generate steric pressure that drives membrane bending. When disordered adaptor domains are expressed as transmembrane cargo in mammalian cells, they are excluded from clathrin-coated pits. We propose that a balance of steric pressure on the two surfaces of the membrane drives this exclusion. These results provide quantitative evidence for the influence of steric pressure on the content and assembly of curved cellular membrane structures. Proteins that bend membranes often contain curvature-promoting structural motifs such as wedges or crescent-shaped domains. Busch et al. report that intrinsically disordered domains can also drive membrane curvature and provide evidence that steric pressure driven by protein crowding mediates this effect.
Collapse
Affiliation(s)
- David J Busch
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton, Austin, Texas 78712, USA
| | - Justin R Houser
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton, Austin, Texas 78712, USA
| | - Carl C Hayden
- 1] Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton, Austin, Texas 78712, USA [2] Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 1.224 Medical Research Building, Galveston, Texas 77555, USA
| | - Eileen M Lafer
- Department of Biochemistry and Center for Biomedical Neuroscience, The University of Texas Health Science Center at San Antonio, UTHSCSA Biochemistry 415B, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | - Jeanne C Stachowiak
- 1] Department of Biomedical Engineering, The University of Texas at Austin, 107 W Dean Keeton, Austin, Texas 78712, USA [2] Institute for Cellular and Molecular Biology, The University of Texas at Austin, 107 W Dean, Keeton,Texas 78712, USA
| |
Collapse
|
18
|
Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Int J Mol Sci 2015; 16:15743-60. [PMID: 26184172 PMCID: PMC4519922 DOI: 10.3390/ijms160715743] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/17/2015] [Accepted: 07/01/2015] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an "indirect/reflected" detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR). This approach employs a "chimeric membrane protein"-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding)-fold domain (named NfeDC domain), connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.
Collapse
Affiliation(s)
- Natsuko Goda
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kana Shimizu
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo 135-0046, Japan.
| | - Yohta Kuwahara
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
| | - Takeshi Tenno
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hidekazu Hiroaki
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| |
Collapse
|
19
|
Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML. Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts. PLoS Comput Biol 2015; 11:e1004130. [PMID: 25884760 PMCID: PMC4401789 DOI: 10.1371/journal.pcbi.1004130] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/14/2015] [Indexed: 12/16/2022] Open
Abstract
Protein phosphorylation plays a central role in creating a highly dynamic network of interacting proteins that reads and responds to signals from growth factors in the cellular microenvironment. Cells of the neural crest employ multiple signaling mechanisms to control migration and differentiation during development. It is known that defects in these mechanisms cause neuroblastoma, but how multiple signaling pathways interact to govern cell behavior is unknown. In a phosphoproteomic study of neuroblastoma cell lines and cell fractions, including endosomes and detergent-resistant membranes, 1622 phosphorylated proteins were detected, including more than half of the receptor tyrosine kinases in the human genome. Data were analyzed using a combination of graph theory and pattern recognition techniques that resolve data structure into networks that incorporate statistical relationships and protein-protein interaction data. Clusters of proteins in these networks are indicative of functional signaling pathways. The analysis indicates that receptor tyrosine kinases are functionally compartmentalized into distinct collaborative groups distinguished by activation and intracellular localization of SRC-family kinases, especially FYN and LYN. Changes in intracellular localization of activated FYN and LYN were observed in response to stimulation of the receptor tyrosine kinases, ALK and KIT. The results suggest a mechanism to distinguish signaling responses to activation of different receptors, or combinations of receptors, that govern the behavior of the neural crest, which gives rise to neuroblastoma. Neuroblastoma is a childhood cancer for which therapeutic progress has been slow. We analyzed a large number phosphorylated proteins in neuroblastoma cells to discern patterns that indicate functional signal transduction pathways. To analyze the data, we developed novel techniques that resolve data structure and visualize that structure as networks that represent both protein interactions and statistical relationships. We also fractionated neuroblastoma cells to examine the location of signaling proteins in different membrane fractions and organelles. The analysis revealed that signaling pathways are functionally and physically compartmentalized into distinct collaborative groups distinguished by phosphorylation patterns and intracellular localization. We found that two related proteins (FYN and LYN) act like central hubs in the tyrosine kinase signaling network that change intracellular localization and activity in response to activation of different receptors.
Collapse
Affiliation(s)
- Juan Palacios-Moreno
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America
| | - Lauren Foltz
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America
| | - Ailan Guo
- Cell Signaling Technology, Inc., Danvers, Massachusetts, United States of America
| | - Matthew P. Stokes
- Cell Signaling Technology, Inc., Danvers, Massachusetts, United States of America
| | - Emily D. Kuehn
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lynn George
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
| | - Michael Comb
- Cell Signaling Technology, Inc., Danvers, Massachusetts, United States of America
| | - Mark L. Grimes
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America
- * E-mail:
| |
Collapse
|
20
|
Pierce BD, Toptygin D, Wendland B. Pan1 is an intrinsically disordered protein with homotypic interactions. Proteins 2013; 81:1944-63. [PMID: 23801378 DOI: 10.1002/prot.24342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/03/2013] [Accepted: 05/19/2013] [Indexed: 01/08/2023]
Abstract
The yeast scaffold protein Pan1 contains two EH domains at its N-terminus, a predicted coiled-coil central region, and a C-terminal proline-rich domain. Pan1 is also predicted to contain regions of intrinsic disorder, characteristic of proteins that have many binding partners. In vitro biochemical data suggest that Pan1 exists as a dimer, and we have identified amino acids 705 to 848 as critical for this homotypic interaction. Tryptophan fluorescence was used to further characterize Pan1 conformational states. Pan1 contains four endogenous tryptophans, each in a distinct region of the protein: Trp(312) and Trp(642) are each in an EH domain, Trp(957) is in the central region, and Trp(1280) is a critical residue in the Arp2/3 activation domain. To examine the local environment of each of these tryptophans, three of the four tryptophans were mutagenized to phenylalanine to create four proteins, each with only one tryptophan residue. When quenched with acrylamide, these single tryptophan mutants appeared to undergo collisional quenching exclusively and were moderately accessible to the acrylamide molecule. Quenching with iodide or cesium, however, revealed different Stern-Volmer constants due to unique electrostatic environments of the tryptophan residues. Time-resolved fluorescence anisotropy data confirmed structural and disorder predictions of Pan1. Further experimentation to fully develop a model of Pan1 conformational dynamics will assist in a deeper understanding of the mechanisms of endocytosis.
Collapse
Affiliation(s)
- B D Pierce
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, 21218
| | | | | |
Collapse
|
21
|
Wang J, Ptacek JB, Kirkegaard K, Bullitt E. Double-membraned liposomes sculpted by poliovirus 3AB protein. J Biol Chem 2013; 288:27287-27298. [PMID: 23908350 DOI: 10.1074/jbc.m113.498899] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Infection with many positive-strand RNA viruses dramatically remodels cellular membranes, resulting in the accumulation of double-membraned vesicles that resemble cellular autophagosomes. In this study, a single protein encoded by poliovirus, 3AB, is shown to be sufficient to induce the formation of double-membraned liposomes via the invagination of single-membraned liposomes. Poliovirus 3AB is a 109-amino acid protein with a natively unstructured N-terminal domain. HeLa cells transduced with 3AB protein displayed intracellular membrane disruption; specifically, the formation of cytoplasmic invaginations. The ability of a single viral protein to produce structures of similar topology to cellular autophagosomes should facilitate the understanding of both cellular and viral mechanisms for membrane remodeling.
Collapse
Affiliation(s)
- Jing Wang
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Jennifer B Ptacek
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94301
| | - Karla Kirkegaard
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94301.
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118.
| |
Collapse
|
22
|
Structural disorder provides increased adaptability for vesicle trafficking pathways. PLoS Comput Biol 2013; 9:e1003144. [PMID: 23874186 PMCID: PMC3715437 DOI: 10.1371/journal.pcbi.1003144] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 06/02/2013] [Indexed: 01/07/2023] Open
Abstract
Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (∼23%) than the other two, COPI (∼9%) and COPII (∼8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes. Vesicle trafficking systems are fundamental among cellular transport mechanisms; various cargo molecules are transported via different coated vesicles to their specific destinations in every eukaryotic cell. Clathrin-coated vesicles mediate endocytosis and the late secretory route, while the COat Protein I and II (COPI and COPII) vesicle trafficking routes are responsible for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar basic principles, regulatory mechanisms and structural features of the three systems, their molecular machinery, functions, and evolutionary characteristics vastly differ. We investigated and compared these three routes and their basic functional protein groups from the structural disorder point of view, since disordered protein regions could provide a broad variety of functional and evolutionary advantages for them. We found that structurally disordered protein segments are most abundant in the clathrin system, which might explain the observed inherent plasticity, increased adaptability and exceptional robustness of this route. We support our hypothesis by two analyses on protein multi-functionality and tissue specificity, both being indicative of evolutionary adaptability. Clathrin pathway proteins stand out in both measures, with their disordered regions being largely responsible for their outstanding capabilities.
Collapse
|
23
|
Guharoy M, Szabo B, Martos SC, Kosol S, Tompa P. Intrinsic Structural Disorder in Cytoskeletal Proteins. Cytoskeleton (Hoboken) 2013; 70:550-71. [DOI: 10.1002/cm.21118] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Mainak Guharoy
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels Belgium
| | - Beata Szabo
- Institute of Enzymology; Research Centre for Natural Sciences, Hungarian Academy of Sciences; Budapest Hungary
| | | | - Simone Kosol
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels Belgium
- Institute of Enzymology; Research Centre for Natural Sciences, Hungarian Academy of Sciences; Budapest Hungary
| |
Collapse
|
24
|
Kalmar L, Acs V, Silhavy D, Tompa P. Long-range interactions in nonsense-mediated mRNA decay are mediated by intrinsically disordered protein regions. J Mol Biol 2012; 424:125-31. [PMID: 22971338 DOI: 10.1016/j.jmb.2012.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 08/09/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
In nonsense-mediated mRNA decay (NMD), large protein complexes cooperate to trigger degradation of mRNA with a premature termination codon. Due to the extreme variation in the size and topology of its mRNA substrate, the structural underpinning of the fidelity of NMD is little understood. Based on bioinformatic predictions, we suggest that fly-casting mechanisms enabled by long disordered regions in NMD complexes are exploited for the underlying effective long-range communication.
Collapse
Affiliation(s)
- Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Karolina út 29, H-1113 Budapest, Hungary
| | | | | | | |
Collapse
|
25
|
Abstract
Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in eukaryotes than in prokaryotes. To refine this view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish eukaryotes from prokaryotes. Unexpectedly, the highest levels--and highest variability--of predicted disorder is found in protists, i.e. single-celled eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established.
Collapse
Affiliation(s)
- Rita Pancsa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
| |
Collapse
|
26
|
Novel strategies for drug discovery based on Intrinsically Disordered Proteins (IDPs). Int J Mol Sci 2011; 12:3205-19. [PMID: 21686180 PMCID: PMC3116186 DOI: 10.3390/ijms12053205] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/28/2011] [Accepted: 05/09/2011] [Indexed: 11/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. Numerous IDPs have close relationships with human diseases such as tumor, Parkinson disease, Alzheimer disease, diabetes, and so on. These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. Most of them in the disease datasets have more interactants and hence the size of the disease-associated IDPs interaction network is simultaneously increased. For example, the tumor suppressor protein p53 is an intrinsically disordered protein and also a hub protein in the p53 interaction network; α-synuclein, an intrinsically disordered protein involved in Parkinson diseases, is also a hub of the protein network. The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. Therefore, novel strategies for drug discovery based on IDPs are in the ascendant. It is dependent on the features of IDPs to develop the novel strategies. It is found out that IDPs have unique structural features such as high flexibility and random coil-like conformations which enable them to participate in both the “one to many” and “many to one” interaction. Accordingly, in order to promote novel strategies for drug discovery, it is essential that more and more features of IDPs are revealed by experimental and computing methods.
Collapse
|
27
|
Brender JR, Nanga RPR, Popovych N, Soong R, Macdonald PM, Ramamoorthy A. The amyloidogenic SEVI precursor, PAP248-286, is highly unfolded in solution despite an underlying helical tendency. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1808:1161-9. [PMID: 21262195 PMCID: PMC3062746 DOI: 10.1016/j.bbamem.2011.01.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 01/12/2011] [Accepted: 01/18/2011] [Indexed: 11/18/2022]
Abstract
Amyloid fibers in human semen known as SEVI (semen-derived enhancer of viral infection) dramatically increase the infectivity of HIV and other enveloped viruses, which appears to be linked to the promotion of bridging interactions and the neutralization of electrostatic repulsion between the host and the viral cell membranes. The SEVI precursor PAP(248-286) is mostly disordered when bound to detergent micelles, in contrast to the highly α-helical structures found for most amyloid proteins. To determine the origin of this difference, the structures of PAP(248-286) were solved in aqueous solution and with 30% and 50% trifluoroethanol. In solution, pulsed field gradient (PFG)-NMR and (1)H-(1)H NOESY experiments indicate that PAP(248-286) is unfolded to an unusual degree for an amyloidogenic peptide but adopts significantly helical structures in TFE solutions. The clear differences between the structures of PAP(248-286) in TFE and SDS indicate electrostatic interactions play a large role in the folding of the peptide, consistent with the slight degree of penetration of PAP(248-286) into the hydrophobic core of the micelle. This is another noticeable difference between PAP(248-286) and other amyloid peptides, which generally show penetration into at least the headgroup region of the bilayer, and may explain some of the unusual properties of SEVI.
Collapse
Affiliation(s)
- Jeffrey R. Brender
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ravi Prakash Reddy Nanga
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nataliya Popovych
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ronald Soong
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Peter M. Macdonald
- Department of Chemical & Physical Sciences, University of Toronto at Mississauga, Mississauga, Canada
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
28
|
Boulais J, Trost M, Landry CR, Dieckmann R, Levy ED, Soldati T, Michnick SW, Thibault P, Desjardins M. Molecular characterization of the evolution of phagosomes. Mol Syst Biol 2011; 6:423. [PMID: 20959821 PMCID: PMC2990642 DOI: 10.1038/msb.2010.80] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 09/15/2010] [Indexed: 11/23/2022] Open
Abstract
First large-scale comparative proteomics/phosphoproteomics study characterizing some of the key steps that contributed to the remodeling of phagosomes that occurred during evolution. Comparison of profiling analyses of isolated phagosomes from three distant organisms (Dictyostelium, Drosophila, and mouse) revealed a protein core that defines a potential ‘ancient' phagosome and a set of 50 proteins that emerged while adaptive immunity was already well established. Gene duplication events of mouse phagosome paralogs occurred mostly in Bilateria and Euteleostomi, coinciding with the emergence of innate and adaptive immunity, and thus, provided the functional innovations needed for the establishment of these two crucial evolutionary steps of the immune system. Phosphoproteomics of isolated phagosomes from the same three distant species indicate that the phagosome phosphoproteome has been extensively modified during evolution. Still, some phosphosites have been maintained for >1.2 billion years, and thus, highlight their particular significance in the regulation of key phagosomal functions.
Phagocytosis is the process by which multiple cell types internalize large particulate material from the external milieu. The functional properties of phagosomes are acquired through a complex maturation process, referred to as phagolysosome biogenesis. This pathway involves a series of rapid interactions with organelles of the endocytic apparatus, enabling the gradual transformation of newly formed phagosomes into phagolysosomes in which proteolytic degradation occurs. The degradative environment encountered in the phagosome lumen has enabled the use of phagocytosis as a predation mechanism for feeding (phagotrophy) in amoeba, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in jawed vertebrates (fish), initiate a sustained immune response. High-throughput proteomics profiling of isolated phagosomes has been tremendously helpful for the molecular comprehension of this organelle. This approach is achieved by feeding low buoyancy latex beads to phagocytic cells, enabling the subsequent isolation of latex bead-containing phagosomes, away from all the other cell organelles, by a single-isopicnic centrifugation in sucrose gradient. In order to characterize some of the key steps that contributed to the remodeling of phagosomes during evolution, we isolated this organelle from three distant organisms: the amoeba Dictyostelium discoideum, the fruit fly Drosophila melanogaster, and mouse (Mus musculus) that use phagocytosis for different purposes, and performed detailed proteomics and phosphoproteomics analyses with unparallel protein coverage for this organelle (two- to four-fold enhancements in identified proteins). In order to establish the origin of the mouse phagosome proteome, we performed comparative analyses among 39 taxa including plants/algea, unicellular organisms, fungi, and more complex animal multicellular organisms. These genomic comparisons indicated that a large proportion of the mouse phagosome proteome is of ancient origin (73.1% of the proteome is conserved in eukaryotic organisms) (Figure 2A). This stresses the fact that phagocytosis is a very ancient process, as shown by its possible involvement in the emergence of eukaryotic cells (eukaryogenesis). Indeed, we identified close to 300 phagosome mouse proteins also present on Drosophila and Dictyostelium phagosomes, defining a potential ‘ancient' core of proteins from which the immune functions of phagosomes likely evolved. Around 16.7% of the mouse phagosome proteins appeared in organisms that use phagocytosis for innate immunity (Bilateria to Chordata), whereas 10.2% appeared in Euteleostomi or Tetrapoda where phagosomes have an important function in linking the killing of microorganisms with the development of a specific sustained immune response following antigen recognition. The phagosome is made of molecules taken from a variety of sources within the cell, including the cytoplasm, the cytoskeleton and membrane organelles. Despite the evolution and diversification of these various cellular systems, the mammalian phagosome proteome is made preferentially of ancient proteins (Figure 2B). Comparison of functional annotation during evolution highlighted the emergence of specific phagosomal functions at various steps during evolution (Figure 2C). Some of these proteins and their point of origin during evolution are highlighted in Figure 2D. Strikingly, we identified in Tetrapods a set of 50 proteins that arose while adaptive immunity was already well established in teleosts (fish), indicating that the phagocytic system is still evolving. Our study highlights the fact that the functional properties of phagosomes emerged by the remodeling of ancient molecules, the addition of novel components, and the duplication of existing proteins (paralogs) leading to the formation of molecular machines of mixed origin. Gene duplication is a process that contributed continuously to the complexification of the mouse proteome during evolution. In sharp contrast, paralog analysis indicated that the phagosome proteome was mainly reorganized through two periods of gene duplication, in Bilateria and Euteleostomi, coinciding with the emergence of adaptive immunity (in jawed fish), and innate immunity (at the split between Metazoa and Bilateria). These results strongly suggest that selective constraints may have favored the maintenance of phagosome paralogs to ensure the establishment of novel functions associated with this organelle at these two crucial evolutionary steps of the immune system. The emergence of genes associated to the MHC locus in mammals that appeared originally in the genome of jawed fishes, contributed to the development of complex molecular mechanisms linking innate (our immune system that defends the host from infection in a non-specific manner) and adaptive immunity (the part of the immune system triggered specifically after antigen recognition). Several of the genes of this locus encode proteins known to have important functions in antigen presentation, such as subunits of the immunoproteasome (LMP2 and LMP7), MHC class I and class II molecules, as well as tapasin and the transporter associated with antigen processing (TAP1 and TAP2), involved in the transport and loading of peptides on MHC class I molecules (Figure 6). In addition to their ability to present peptides on MHC class II molecules, phagosomes of vertebrates have been shown to be competent for the presentation of exogenous peptides on MHC class I molecules, a process referred to as cross-presentation. From a functional point of view, the involvement of phagosomes in antigen cross-presentation is the outcome of the successful integration of a wide range of multimolecular components that emerged throughout evolution (Figure 6). The trimming of exogenous proteins into small peptides that can be loaded on MHC class I molecules is inherited from the phagotrophic properties of unicellular organisms, where internalized bacteria are degraded into basic molecules and used as a source of nutrients. Ancient processes have therefore been co-opted (the use of an existing biological structure or feature for a new function) for new functionalities. A summarizing model of the various steps that enabled phagosome antigen presentation is presented in Figure 6. This model highlights the fact that although antigen presentation is unique to evolutionary recent phagosomes (starting in jawed fishes about 450 million years ago), it uses and integrates molecular machines composed of proteins that emerged throughout evolution. In summary, we present here the first large-scale comparative proteomics/phosphoproteomics study characterizing some of the key evolutionary steps that contributed to the remodeling of phagosomes during evolution. Functional properties of this organelle emerged by the remodeling of ancient molecules, the addition of novel components, the extensive adaption of protein phosphorylation sites and the duplication of existing proteins leading to the formation of molecular machines of mixed origin. Amoeba use phagocytosis to internalize bacteria as a source of nutrients, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in vertebrates, initiate a sustained immune response. By using a large-scale approach to identify and compare the proteome and phosphoproteome of phagosomes isolated from distant organisms, and by comparative analysis over 39 taxa, we identified an ‘ancient' core of phagosomal proteins around which the immune functions of this organelle have likely organized. Our data indicate that a larger proportion of the phagosome proteome, compared with the whole cell proteome, has been acquired through gene duplication at a period coinciding with the emergence of innate and adaptive immunity. Our study also characterizes in detail the acquisition of novel proteins and the significant remodeling of the phagosome phosphoproteome that contributed to modify the core constituents of this organelle in evolution. Our work thus provides the first thorough analysis of the changes that enabled the transformation of the phagosome from a phagotrophic compartment into an organelle fully competent for antigen presentation.
Collapse
Affiliation(s)
- Jonathan Boulais
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, Québec, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Zhuo Y, Ilangovan U, Schirf V, Demeler B, Sousa R, Hinck AP, Lafer EM. Dynamic interactions between clathrin and locally structured elements in a disordered protein mediate clathrin lattice assembly. J Mol Biol 2010; 404:274-90. [PMID: 20875424 PMCID: PMC2981644 DOI: 10.1016/j.jmb.2010.09.044] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 09/17/2010] [Accepted: 09/17/2010] [Indexed: 11/22/2022]
Abstract
Assembly of clathrin lattices is mediated by assembly/adaptor proteins that contain domains that bind lipids or membrane-bound cargo proteins and clathrin binding domains (CBDs) that recruit clathrin. Here, we characterize the interaction between clathrin and a large fragment of the CBD of the clathrin assembly protein AP180. Mutational, NMR chemical shift, and analytical ultracentrifugation analyses allowed us to precisely define two clathrin binding sites within this fragment, each of which is found to bind weakly to the N-terminal domain of the clathrin heavy chain (TD). The locations of the two clathrin binding sites are consistent with predictions from sequence alignments of previously identified clathrin binding elements and, by extension, indicate that the complete AP180 CBD contains ∼12 degenerate repeats, each containing a single clathrin binding site. Sequence and circular dichroism analyses have indicated that the AP180 CBD is predominantly unstructured and our NMR analyses confirm that this is largely the case for the AP180 fragment characterized here. Unexpectedly, unlike the many proteins that undergo binding-coupled folding upon interaction with their binding partners, the AP180 fragment is similarly unstructured in its bound and free states. Instead, we find that this fragment exhibits localized β-turn-like structures at the two clathrin binding sites both when free and when bound to clathrin. These observations are incorporated into a model in which weak binding by multiple, pre-structured clathrin binding elements regularly dispersed throughout a largely unstructured CBD allows efficient recruitment of clathrin to endocytic sites and dynamic assembly of the clathrin lattice.
Collapse
Affiliation(s)
- Yue Zhuo
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Udayar Ilangovan
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Virgil Schirf
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Andrew P. Hinck
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Eileen M. Lafer
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
- Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| |
Collapse
|
30
|
Nanga RP, Brender JR, Vivekanandan S, Popovych N, Ramamoorthy A. NMR structure in a membrane environment reveals putative amyloidogenic regions of the SEVI precursor peptide PAP(248-286). J Am Chem Soc 2009; 131:17972-9. [PMID: 19995078 PMCID: PMC2792124 DOI: 10.1021/ja908170s] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Semen is the main vector for HIV transmission worldwide. Recently, a peptide fragment (PAP(248-286)) has been isolated from seminal fluid that dramatically enhances HIV infectivity by up to 4-5 orders of magnitude. PAP(248-286) appears to enhance HIV infection by forming amyloid fibers known as SEVI, which are believed to enhance the attachment of the virus by bridging interactions between virion and host-cell membranes. We have solved the atomic-level resolution structure of the SEVI precursor PAP(248-286) using NMR spectroscopy in SDS micelles, which serve as a model membrane system. PAP(248-286), which does not disrupt membranes like most amyloid proteins, binds superficially to the surface of the micelle, in contrast to other membrane-disruptive amyloid peptides that generally penetrate into the core of the membrane. The structure of PAP(248-286) is unlike most amyloid peptides in that PAP(248-286) is mostly disordered when bound to the surface of the micelle, as opposed to the alpha-helical structures typically found of most amyloid proteins. The highly disordered nature of the SEVI peptide may explain the unique ability of SEVI amyloid fibers to enhance HIV infection as partially disordered amyloid fibers will have a greater capture radius for the virus than compact amyloid fibers. Two regions of nascent structure (an alpha-helix from V262-H270 and a dynamic alpha/3(10) helix from S279-L283) match the prediction of highly amyloidogenic sequences and may serve as nuclei for aggregation and amyloid fibril formation. The structure presented here can be used for the rational design of mutagenesis studies on SEVI amyloid formation and viral infection enhancement.
Collapse
Affiliation(s)
- Ravi P. Nanga
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Jeffrey R. Brender
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Subramanian Vivekanandan
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nataliya Popovych
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
31
|
MACC1 - more than metastasis? Facts and predictions about a novel gene. J Mol Med (Berl) 2009; 88:11-8. [PMID: 19787327 DOI: 10.1007/s00109-009-0537-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 08/30/2009] [Accepted: 09/04/2009] [Indexed: 01/05/2023]
Abstract
We recently identified the metastasis-associated in colon cancer 1 (MACC1) gene by a genome-wide search for differentially expressed genes in human colon cancer tissues, metastases, and normal tissues. Based on MACC1 expression in primary colon cancers, which did not present with metastases, our negative and positive prediction for metachronous metastasis was correct in 80% and 74% of cases, respectively. The 5-year-survival was 80% for MACC1 low expressors, but 15% for individuals who showed high MACC1 expression in their primary tumors. MACC1 induces migration, invasion and proliferation in cell culture, and liver and lung metastases in xenograft models. Here, we describe features of MACC1 beyond its utility as an indicator of metastasis. We elucidate its genomic localization and organization, its predicted splice variants, and single nucleotide polymorphisms. We discuss the MACC1 protein domain structure, posttranslational modifications, its conservation through evolution, and some family ties to SH3BP4. Furthermore, we summarize the predicted expressions of MACC1 in normal and malignant human tissues. We also evaluate the MACC1 levels in the context of one of its transcriptional targets, the receptor tyrosine kinase Met that activates the hepatocyte growth factor/Met signaling pathway, leading to enhanced cell motility, invasion, and metastasis.
Collapse
|
32
|
Gibson TJ. Cell regulation: determined to signal discrete cooperation. Trends Biochem Sci 2009; 34:471-82. [PMID: 19744855 DOI: 10.1016/j.tibs.2009.06.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 06/02/2009] [Accepted: 06/04/2009] [Indexed: 11/25/2022]
Abstract
Do kinases cascade? How well is cell regulation understood? What are the best ways to model regulatory systems? Attempts to answer such questions can have bearings on the way in which research is conducted. Fortunately there are recurring themes in regulatory processes from many different cellular contexts, which might provide useful guidance. Three principles seem to be almost universal: regulatory interactions are cooperative; regulatory decisions are made by large dynamic protein complexes; and regulation is intricately networked. A fourth principle, although not universal, is remarkably common: regulatory proteins are actively placed where they are needed. Here, I argue that the true nature of cell signalling and our perceptions of it are in a state of discord. This raises the question: Are our misconceptions detrimental to progress in biomedical science?
Collapse
Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| |
Collapse
|
33
|
Tompa P. Structural disorder in amyloid fibrils: its implication in dynamic interactions of proteins. FEBS J 2009; 276:5406-15. [PMID: 19712107 DOI: 10.1111/j.1742-4658.2009.07250.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are occasionally converted from their normal soluble state to highly ordered fibrillar aggregates (amyloids), which give rise to pathological conditions that range from neurodegenerative disorders to systemic amyloidoses. Recent methodological advances in solid-state NMR and EPR spectroscopy have enabled determination of the 3D structure of several amyloids at residue-level resolution. The general picture that emerges is that amyloids constitute parallel beta sheets, in which individual polypeptide chains run roughly perpendicular to the major axis of the fibril and are stacked in-register. Thus, the unifying theme of amyloid formation is the structural transition from an initial globular or intrinsically disordered state to a highly ordered regular form. In this minireview, we show that this description is somewhat oversimplified, because part of the polypeptide chain in the amyloid remains intrinsically disordered and does not become part of the ordered core. As demonstrated through examples such as the amyloids of alpha-synuclein and Abeta peptide and the yeast prions HET-s and Ure2p, these disordered segments are depleted in amino acids NQFYV and are enriched in DEKP. They are also significantly more charged and have a higher predicted disordered value than segments in the cross-beta core. We suggest that structural disorder in amyloid is a special case of 'fuzziness', i.e. disorder in the bound state that may serve different functions, such as the accommodation of destabilizing residues and the mediation of secondary interactions between protofibrils.
Collapse
Affiliation(s)
- P Tompa
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
| |
Collapse
|
34
|
Rajagopal C, Stone KL, Francone VP, Mains RE, Eipper BA. Secretory granule to the nucleus: role of a multiply phosphorylated intrinsically unstructured domain. J Biol Chem 2009; 284:25723-34. [PMID: 19635792 DOI: 10.1074/jbc.m109.035782] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intrinsically unstructured domains occur in one-third of all proteins and are characterized by conformational flexibility, protease sensitivity, and the occurrence of multiple phosphorylation. They provide large interfaces for diverse protein-protein interactions. Peptidylglycine alpha-amidating monooxygenase (PAM), an enzyme essential for neuropeptide biosynthesis, is a secretory granule membrane protein. As one of the few proteins spanning the granule membrane, PAM is a candidate to relay information about the status of the granule pool and conditions in the granule lumen. Here, we show that the PAM cytosolic domain is unstructured. Mass spectroscopy and two-dimensional gel electrophoresis demonstrated phosphorylation at 10-12 sites in the cytosolic domain. Stimulation of exocytosis resulted in coupled phosphorylation and dephosphorylation of specific sites and in the endoproteolytic release of a soluble, proteasome-sensitive cytosolic domain fragment. Analysis of granule-rich tissues, such as pituitary and heart, showed that a similar fragment was generated endogenously and translocated to the nucleus. This multiply phosphorylated unstructured domain may act as a signaling molecule that relays information from secretory granules to both cytosol and nucleus.
Collapse
Affiliation(s)
- Chitra Rajagopal
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | | | | | | | | |
Collapse
|
35
|
Shiozawa K, Konarev PV, Neufeld C, Wilmanns M, Svergun DI. Solution structure of human Pex5.Pex14.PTS1 protein complexes obtained by small angle X-ray scattering. J Biol Chem 2009; 284:25334-42. [PMID: 19584060 DOI: 10.1074/jbc.m109.002311] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Pex5p receptor recognizes newly synthesized peroxisomal matrix proteins which have a C-terminal peroxisomal targeting signal to the peroxisome. After docking to protein complexes on the membrane, these proteins are translocated across the membrane. The docking mechanism remains unclear, as no structural data on the multicomponent docking complex are available. As the interaction of the cargo-loaded Pex5p receptor and the peroxisomal membrane protein Pex14p is the essential primary docking step, we have investigated the solution structure of these complexes by small angle x-ray scattering and static light scattering. Titration studies yielded a 1:6 stoichiometry for the Pex5p.Pex14p complex, and low resolution structural models were reconstructed from the x-ray scattering data. The free full-length human Pex5p is monomeric in solution, with an elongated, partially unfolded N-terminal domain. The model of the complex reveals that the N terminus of Pex5p remains extended in the presence of cargo and Pex14p, the latter proteins being significantly intermingled with the Pex5p moiety. These results suggest that the extended structure of Pex5p may play a role in interactions with other substrates such as lipids and membrane proteins during the formation of functional multiprotein complexes.
Collapse
Affiliation(s)
- Kumiko Shiozawa
- European Molecular Biology Laboratory-Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | | | | | | | | |
Collapse
|
36
|
Affiliation(s)
- G Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | | | | |
Collapse
|
37
|
Miwa HE, Gerken TA, Huynh TD, Duesler LR, Cotter M, Hering TM. Conserved sequence in the aggrecan interglobular domain modulates cleavage by ADAMTS-4 and ADAMTS-5. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1790:161-72. [PMID: 19101611 PMCID: PMC2656578 DOI: 10.1016/j.bbagen.2008.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 11/03/2008] [Accepted: 11/19/2008] [Indexed: 11/29/2022]
Abstract
BACKGROUND Cleavage of aggrecan by ADAMTS proteinases at specific sites within highly conserved regions may be important to normal physiological enzyme functions, as well as pathological degradation. METHODS To examine ADAMTS selectivity, we assayed ADAMTS-4 and -5 cleavage of recombinant bovine aggrecan mutated at amino acids N-terminal or C-terminal to the interglobular domain cleavage site. RESULTS Mutations of conserved amino acids from P18 to P12 to increase hydrophilicity resulted in ADAMTS-4 cleavage inhibition. Mutation of Thr, but not Asn within the conserved N-glycosylation motif Asn-Ile-Thr from P6 to P4 enhanced cleavage. Mutation of conserved Thr residues from P22 to P17 to increase hydrophobicity enhanced ADAMTS-4 cleavage. A P4' Ser377Gln mutant inhibited cleavage by ADAMTS-4 and -5, while a neutral Ser377Ala mutant and species mimicking mutants Ser377Thr, Ser377Asn, and Arg375Leu were cleaved normally by ADAMTS-4. The Ser377Thr mutant, however, was resistant to cleavage by ADAMTS-5. CONCLUSION We have identified multiple conserved amino acids within regions N- and C-terminal to the site of scission that may influence enzyme-substrate recognition, and may interact with exosites on ADAMTS-4 and ADAMTS-5. GENERAL SIGNIFICANCE Inhibition of the binding of ADAMTS-4 and ADAMTS-5 exosites to aggrecan should be explored as a therapeutic intervention for osteoarthritis.
Collapse
Affiliation(s)
- Hazuki E Miwa
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
| | - Thomas A Gerken
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
- Department of Pediatrics†, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
| | - Tru D Huynh
- Department of Orthopaedics, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
| | - Lori R Duesler
- Department of Orthopaedics, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
| | - Meghan Cotter
- Department of Anatomy¶, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
| | - Thomas M. Hering
- Department of Orthopaedics, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106
| |
Collapse
|
38
|
Timsit Y, Acosta Z, Allemand F, Chiaruttini C, Springer M. The role of disordered ribosomal protein extensions in the early steps of eubacterial 50 S ribosomal subunit assembly. Int J Mol Sci 2009; 10:817-834. [PMID: 19399222 PMCID: PMC2672003 DOI: 10.3390/ijms10030817] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 02/23/2009] [Accepted: 02/24/2009] [Indexed: 12/23/2022] Open
Abstract
Although during the past decade research has shown the functional importance of disorder in proteins, many of the structural and dynamics properties of intrinsically unstructured proteins (IUPs) remain to be elucidated. This review is focused on the role of the extensions of the ribosomal proteins in the early steps of the assembly of the eubacterial 50 S subunit. The recent crystallographic structures of the ribosomal particles have revealed the picture of a complex assembly pathway that condenses the rRNA and the ribosomal proteins into active ribosomes. However, little is know about the molecular mechanisms of this process. It is thought that the long basic r-protein extensions that penetrate deeply into the subunit cores play a key role through disorder-order transitions and/or co-folding mechanisms. A current view is that such structural transitions may facilitate the proper rRNA folding. In this paper, the structures of the proteins L3, L4, L13, L20, L22 and L24 that have been experimentally found to be essential for the first steps of ribosome assembly have been compared. On the basis of their structural and dynamics properties, three categories of extensions have been identified. Each of them seems to play a distinct function. Among them, only the coil-helix transition that occurs in a phylogenetically conserved cluster of basic residues of the L20 extension appears to be strictly required for the large subunit assembly in eubacteria. The role of alpha helix-coil transitions in 23 S RNA folding is discussed in the light of the calcium binding protein calmodulin that shares many structural and dynamics properties with L20.
Collapse
Affiliation(s)
- Youri Timsit
- Laboratoire de Cristallographie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
- Author to whom correspondence should be addressed; E-mail:
; Tel. +01-58-41-51-66
| | - Zahir Acosta
- Laboratoire de Cristallographie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
| | - Frédéric Allemand
- Laboratoire de Biochimie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
(F.A.);
(C.C.);
(M.S.)
| | - Claude Chiaruttini
- Laboratoire de Biochimie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
(F.A.);
(C.C.);
(M.S.)
| | - Mathias Springer
- Laboratoire de Biochimie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
(F.A.);
(C.C.);
(M.S.)
| |
Collapse
|
39
|
The Desmoglein-Specific Cytoplasmic Region Is Intrinsically Disordered in Solution and Interacts with Multiple Desmosomal Protein Partners. J Mol Biol 2009; 386:531-43. [DOI: 10.1016/j.jmb.2008.12.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 11/23/2022]
|
40
|
Lanza DCF, Silva JC, Assmann EM, Quaresma AJC, Bressan GC, Torriani IL, Kobarg J. Human FEZ1 has characteristics of a natively unfolded protein and dimerizes in solution. Proteins 2009; 74:104-21. [PMID: 18615714 DOI: 10.1002/prot.22135] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The fasciculation and elongation protein Zeta 1 (FEZ1) is the mammalian orthologue of the Caenorhabditis elegans protein UNC-76, which is necessary for axon growth. Human FEZ1 interacts with Protein Kinase C (PKC) and several regulatory proteins involved in functions ranging from microtubule associated transport to transcriptional regulation. Theoretical prediction, circular dichroism, fluorescence spectroscopy, and limited proteolysis of recombinant FEZ1 suggest that it contains disordered regions, especially in its N-terminal region, and that it may belong to the group of natively unfolded proteins. Small angle X-ray scattering experiments indicated a mainly disordered conformation, proved that FEZ1 is a dimer of elongated shape and provided overall dimensional parameters for the protein. In vitro pull down experiments confirmed these results and demonstrated that dimerization involves the N-terminus. Ab-initio 3D low resolution models of the full-length conformation of the dimeric constructs 6xHis-FEZ1(1-392) and 6xHis-FEZ1(1-227) were obtained. Furthermore, we performed in vitro phosphorylation assays of FEZ1 with PKC. The phosphorylation occurred mainly in its C-terminal region, and does not cause any significant conformational changes, but nonetheless inhibited its interaction with the FEZ1 interacting domain of the protein CLASP2 in vitro. The C terminus of FEZ1 has been reported to bind to several interacting proteins. This suggests that FEZ1 binding and transport function of interacting proteins may be subject to regulation by phosphorylation.
Collapse
|
41
|
Paiardini A, Caputo V. Insights into the interaction of sortilin with proneurotrophins: a computational approach. Neuropeptides 2008; 42:205-14. [PMID: 18191449 DOI: 10.1016/j.npep.2007.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 10/29/2007] [Accepted: 11/22/2007] [Indexed: 12/22/2022]
Abstract
Sortilin is a member of the recently discovered family of type-1 transmembrane Vps10p-domain receptors, which are expressed in several tissues, including brain and spinal chord. It has been recently demonstrated that the interaction between sortilin and the N-terminal portion of the precursor forms of the nerve growth factor (pro-NGF) and the brain-derived neurotrophic factor (pro-BDNF) represents a key event in the process that controls neurotrophins-mediated cell survival and death in developing neuronal tissue and post-traumatic neuronal apoptosis. Moreover, it is known that the cleavage of the N-terminal propeptide of sortilin is required for full functional activity of the receptor. The propeptide, indeed, hinders ligands from accessing the binding site of sortilin. However, to date, the molecular mechanism underlying the interaction between sortilin and pro-NGF/pro-BDNF remains unknown. By means of computational approaches, we suggest that the N-terminal Vps10p domain of sortilin, which is responsible for the interaction with the neurotrophins, adopts a beta-propeller fold, and that the N-terminal regions of sortilin, pro-NGF and pro-BDNF are mainly intrinsically disordered regions (IDRs). The following mechanism is therefore proposed: the Vps10p-domain of sortilin is a beta-propeller able to bind its own IDR and the IDRs of neurotrophins. The excision of its N-terminal disordered peptide allows the interaction with the intrinsically disordered N-terminus of pro-BDNF and pro-NGF, possibly through a disorder-to-order transition behaviour.
Collapse
Affiliation(s)
- Alessandro Paiardini
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università di Roma La Sapienza, Piazzale Aldo Moro 5, Via degli Apuli 9, 00185 Rome, Italy.
| | | |
Collapse
|
42
|
Hegyi H, Tompa P. Intrinsically disordered proteins display no preference for chaperone binding in vivo. PLoS Comput Biol 2008; 4:e1000017. [PMID: 18369417 PMCID: PMC2265518 DOI: 10.1371/journal.pcbi.1000017] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 01/31/2008] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered/unstructured proteins (IDPs) are extremely sensitive to proteolysis in vitro, but show no enhanced degradation rates in vivo. Their existence and functioning may be explained if IDPs are preferentially associated with chaperones in the cell, which may offer protection against degradation by proteases. To test this inference, we took pairwise interaction data from high-throughput interaction studies and analyzed to see if predicted disorder correlates with the tendency of chaperone binding by proteins. Our major finding is that disorder predicted by the IUPred algorithm actually shows negative correlation with chaperone binding in E. coli, S. cerevisiae, and metazoa species. Since predicted disorder positively correlates with the tendency of partner binding in the interactome, the difference between the disorder of chaperone-binding and non-binding proteins is even more pronounced if normalized to their overall tendency to be involved in pairwise protein–protein interactions. We argue that chaperone binding is primarily required for folding of globular proteins, as reflected in an increased preference for chaperones of proteins in which at least one Pfam domain exists. In terms of the functional consequences of chaperone binding of mostly disordered proteins, we suggest that its primary reason is not the assistance of folding, but promotion of assembly with partners. In support of this conclusion, we show that IDPs that bind chaperones also tend to bind other proteins. Intrinsically disordered/unstructured proteins (IDPs) defy the classical structure–function paradigm because they exist and function without a well-defined 3-D structure. These proteins are extremely sensitive to degradation in the test tube, but show no enhanced degradation rates in the cell. To resolve this apparent contradiction, we tested whether IDPs are protected by interaction with accessory proteins, chaperones, often implicated in guarding other proteins in the cell. Our major finding is that disorder predicted by the IUPred algorithm actually shows negative correlation with chaperone binding in various species. To explain this finding, we argue that IDPs are protected in the cell from proteases by their special amino acid composition, and also by the tight regulation of intracellular proteases. Thus, the primary reason for their chaperone binding is not protection from degradation, but promotion of assembly with partners.
Collapse
Affiliation(s)
- Hedi Hegyi
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
| | | |
Collapse
|
43
|
Kawasaki T, Kobayashi T, Ueyama T, Shirai Y, Saito N. Regulation of clathrin-dependent endocytosis by diacylglycerol kinase delta: importance of kinase activity and binding to AP2alpha. Biochem J 2008; 409:471-9. [PMID: 17880279 DOI: 10.1042/bj20070755] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DGKdelta (diacylglycerol kinase delta), which phosphorylates DAG (diacylglycerol) and converts it into PA (phosphatidic acid), has an important role in signal transduction. In the present study, we have demonstrated the molecular mechanism of DGKdelta-mediated regulation of clathrin-dependent endocytosis that controls the internalization, recycling and degradation of receptors. Involvement of DGKdelta in the regulation of clathrin-dependent endocytosis was previously proposed following genome-wide RNAi (RNA interference) screening. Clathrin-coated pits are mainly formed by clathrin and AP-2 (adaptor protein 2) complex. These proteins assemble a polyhedral lattice at the membrane and gather several endocytic accessory proteins. As the intracellular localization of DGKdelta2 overlapped with clathrin-coated pits, we predicted the possible regulation of clathrin-dependent endocytosis by DGKdelta2 and its interaction with some endocytosis-regulatory proteins. DGKdelta2 contained the DXF-type binding motifs, and DGKdelta2 bound to AP2alpha, a subunit of the AP-2 complex. DGKdelta2 interacted with the platform subdomain in the AP2alpha ear domain via F369DTFRIL and D746PF sequences in the catalytic domain of DGKdelta2. For further insight into the role for DGKdelta2 in clathrin-dependent endocytosis, we measured the transferrin and EGF (epidermal growth factor) uptake-expressing wild-type or mutant DGKdelta2 under knockdown of endogenous DGKdelta. Mutants lacking binding ability to AP2alpha as well as kinase-negative mutants could not compensate for the uptake of transferrin inhibited by siRNA (small interfering RNA) treatment, whereas overexpression of wild-type DGKdelta2 completely recovered the transferrin uptake. These results demonstrate that binding between DGKdelta2 and AP2alpha is involved in the transferrin internalization and that DGK activity is also necessary for the regulation of the endocytic process.
Collapse
Affiliation(s)
- Takumi Kawasaki
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Kobe 657-8501, Japan
| | | | | | | | | |
Collapse
|
44
|
Morillas M, Eberl H, Allain FT, Glockshuber R, Kuennemann E. Novel Enzymatic Activity Derived from the Semliki Forest Virus Capsid Protein. J Mol Biol 2008; 376:721-35. [DOI: 10.1016/j.jmb.2007.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 11/13/2007] [Accepted: 11/16/2007] [Indexed: 10/22/2022]
|
45
|
DeRegis CJ, Rahl PB, Hoffman GR, Cerione RA, Collins RN. Mutational analysis of betaCOP (Sec26p) identifies an appendage domain critical for function. BMC Cell Biol 2008; 9:3. [PMID: 18211691 PMCID: PMC2262067 DOI: 10.1186/1471-2121-9-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Accepted: 01/22/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The appendage domain of the gammaCOP subunit of the COPI vesicle coat bears a striking structural resemblance to adaptin-family appendages despite limited primary sequence homology. Both the gammaCOP appendage domain and an equivalent region on betaCOP contain the FxxxW motif; the conservation of this motif suggested the existence of a functional appendage domain in betaCOP. RESULTS Sequence comparisons in combination with structural prediction tools show that the fold of the COOH-terminus of Sec26p is strongly predicted to closely mimic that of adaptin-family appendages. Deletion of the appendage domain of Sec26p results in inviability in yeast, over-expression of the deletion construct is dominant negative and mutagenesis of this region identifies residues critical for function. The ArfGAP Glo3p was identified via suppression screening as a potential downstream modulator of Sec26p in a manner that is independent of the GAP activity of Glo3p but requires the presence of the COOH-terminal ISS motifs. CONCLUSION Together, these results indicate an essential function for the predicted betaCOP appendage and suggest that both COPI appendages perform a biologically active regulatory role with a structure related to adaptin-family appendage domains.
Collapse
Affiliation(s)
- Carol J DeRegis
- Graduate Program in Comparative Biomedical Sciences, Cornell University, Ithaca NY 14853, USA
| | - Peter B Rahl
- Graduate Program in Pharmacology, Cornell University, Ithaca, NY 14853, USA
| | - Gregory R Hoffman
- Graduate Program in Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Richard A Cerione
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ruth N Collins
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Medicine, Cornell University, C4-109 Veterinary Medical Center, Ithaca, NY 14853, USA
| |
Collapse
|
46
|
Li M, Song J. The N- and C-termini of the human Nogo molecules are intrinsically unstructured: bioinformatics, CD, NMR characterization, and functional implications. Proteins 2007; 68:100-8. [PMID: 17397058 DOI: 10.1002/prot.21385] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RTN4 or Nogo proteins are composed of three alternative splice forms, namely 1192-residue Nogo-A, 373-residue Nogo-B, and 199-residue Nogo-C. Nogo proteins have received intense attentions because they have been implicated in a variety of critical cellular processes including CNS neuronal regeneration, vascular remodeling, apoptosis, interaction with beta-amyloid protein converting enzyme, and generation/maintenance of the tubular network of the endoplasmic reticulum (ER). Despite their significantly-different N-terminal lengths, they share a conserved C-terminal reticulon-homology domain consisting of two transmembrane fragments, a 66-residue extracellular loop Nogo-66 and a 38-residue C-tail carrying ER retention motif. Nogo-A owns the largest N-terminus with 1016 residues while the Nogo-B has an N-terminus almost identical to the first 200 residues of Nogo-A. So far, except for our previous determination of the Nogo-66 solution structure, no structural characterization of the other Nogo regions has been reported. In the present study, we initiated a systematically investigation of structural properties of Nogo molecules by a combined use of bioinformatics, CD, and NMR spectroscopy. The results led to two striking findings: (1) in agreement with bioinformatics prediction, the N- and C-termini of Nogo-B were experimentally demonstrated to be intrinsically unstructured by CD, two-dimensional 1H 15N NMR HSQC, hydrogen exchange, and 15N heteronuclear NOE characterization. (2) Further studies showed that the 1016-residue N-terminus of Nogo-A was again highly disordered. Therefore, it appears that being intrinsically-unstructured allows Nogo molecules to serve as double-faceted functional players, with one set of functions involved in cellular signaling processes essential for CNS neuronal regeneration, vascular remodeling, apoptosis and so forth and with another in generating/maintaining membrane-related structures. We propose that this mechanism may represent a general strategy to place the formation/maintenance of membrane-related structures under the direct regulation of the cellular signaling.
Collapse
Affiliation(s)
- Minfen Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260
| | | |
Collapse
|
47
|
Structural disorder promotes assembly of protein complexes. BMC STRUCTURAL BIOLOGY 2007; 7:65. [PMID: 17922903 PMCID: PMC2194777 DOI: 10.1186/1472-6807-7-65] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 10/08/2007] [Indexed: 11/21/2022]
Abstract
Background The idea that the assembly of protein complexes is linked with protein disorder has been inferred from a few large complexes, such as the viral capsid or bacterial flagellar system, only. The relationship, which suggests that larger complexes have more disorder, has never been systematically tested. The recent high-throughput analyses of protein-protein interactions and protein complexes in the cell generated data that enable to address this issue by bioinformatic means. Results In this work we predicted structural disorder for both E. coli and S. cerevisiae, and correlated it with the size of complexes. Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes. The distribution of disorder has a median value of 10% in yeast for complexes of 2–4 components (6% in E. coli), but 18% for complexes in the size range of 11–100 proteins (12% in E. coli). The level of disorder as assessed for regions longer than 30 consecutive disordered residues shows an even stronger division between small and large complexes (median values about 4% for complexes of 2–4 components, but 12% for complexes of 11–100 components in yeast). The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2–4 components, and 9.6% for complexes of 11–100 components in yeast). Further analysis shows that this correlation is not directly linked with the increased disorder in hub proteins, but reflects a genuine systemic property of the proteins that make up the complexes. Conclusion Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.
Collapse
|
48
|
Woods WS, Boettcher JM, Zhou DH, Kloepper KD, Hartman KL, Ladror DT, Qi Z, Rienstra CM, George JM. Conformation-specific binding of alpha-synuclein to novel protein partners detected by phage display and NMR spectroscopy. J Biol Chem 2007; 282:34555-67. [PMID: 17893145 DOI: 10.1074/jbc.m705283200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alpha-synuclein (AS) is an intrinsically unstructured protein in aqueous solution but is capable of forming beta-sheet-rich fibrils that accumulate as intracytoplasmic inclusions in Parkinson disease and certain other neurological disorders. However, AS binding to phospholipid membranes leads to a distinct change in protein conformation, stabilizing an extended amphipathic alpha-helical domain reminiscent of the exchangeable apolipoproteins. To better understand the significance of this conformational change, we devised a novel bacteriophage display screen to identify protein binding partners of helical AS and have identified 20 proteins with roles in diverse cellular processes related to membrane trafficking, ion channel modulation, redox metabolism, and gene regulation. To verify that the screen identifies proteins with specificity for helical AS, we further characterized one of these candidates, endosulfine alpha (ENSA), a small cAMP-regulated phosphoprotein implicated in the regulation of insulin secretion but also expressed abundantly in the brain. We used solution NMR to probe the interaction between ENSA and AS on the surface of SDS micelles. Chemical shift perturbation mapping experiments indicate that ENSA interacts specifically with residues in the N-terminal helical domain of AS in the presence of SDS but not in aqueous buffer lacking SDS. The ENSA-related protein ARPP-19 (cAMP-regulated phosphoprotein 19) also displays specific interactions with helical AS. These results confirm that the helical N terminus of AS can mediate specific interactions with other proteins and suggest that membrane binding may regulate the physiological activity of AS in vivo.
Collapse
Affiliation(s)
- Wendy S Woods
- Department of Molecular and Integrative Physiology, University of Illinois, 407 S. Goodwin Avenue, Urbana, IL 61801, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Leliveld SR, Korth C. The use of conformation-specific ligands and assays to dissect the molecular mechanisms of neurodegenerative diseases. J Neurosci Res 2007; 85:2285-97. [PMID: 17497676 DOI: 10.1002/jnr.21353] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The use of conformation-specific ligands has been closely linked to progress in the molecular characterization of neurodegenerative diseases. Deposition of misfolded or misprocessed proteins is now recognized as a hallmark of all neurodegenerative diseases. Initially, dyes like Congo red and thioflavin T were used as crudely conformation-specific ligands for staining the beta-sheeted protein components of amyloid deposits in neurodegenerative diseases such as Alzheimer disease (AD) and prion disease, the two diseases in which protein conformations were distinguished early on. This conformational characterization of extracellular protein deposits with dyes ultimately led to the identification of key players in the disease processes. The recent discovery of intermediate conformational species, i.e., soluble oligomers for AD and PK-sensitive PrP(Sc) for prion disease, whose conformation and assembly are thought to be distinct from both the physiological and the fibrillar conformational states, replaced the former notion that the microscopic protein deposits themselves caused disease. This insight and the generation of conformation-specific monoclonal antibodies to these conformers further advanced diagnosis and the understanding of molecular mechanisms of AD and are likely to do so in other neurodegenerative diseases. Here we review how conformer distinction performed by a variety of different techniques, including biophysical, biochemical, and antibody-based methods, led to the current molecular concepts of AD and the prion diseases. We provide an outlook on the application of these techniques in advancing the understanding of molecular mechanisms of other neurodegenerative diseases or degenerative brain conditions.
Collapse
Affiliation(s)
- S Rutger Leliveld
- Institute for Neuroscience and Biophysics (INB-2) at the Research Centre Jülich, Jülich, Germany
| | | |
Collapse
|
50
|
Rakhit R, Chakrabartty A. Structure, folding, and misfolding of Cu,Zn superoxide dismutase in amyotrophic lateral sclerosis. Biochim Biophys Acta Mol Basis Dis 2006; 1762:1025-37. [PMID: 16814528 DOI: 10.1016/j.bbadis.2006.05.004] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/15/2006] [Accepted: 05/16/2006] [Indexed: 11/16/2022]
Abstract
Fourteen years after the discovery that mutations in Cu, Zn superoxide dismutase (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS), the mechanism by which mutant SOD1 exerts toxicity remains unknown. The two principle hypotheses are (a) oxidative damage stemming from aberrant SOD1 redox chemistry, and (b) misfolding of the mutant protein. Here we review the structure and function of wild-type SOD1, as well as the changes to the structure and function in mutant SOD1. The relative merits of the two hypotheses are compared and a common unifying principle is outlined. Lastly, the potential for therapies targeting SOD1 misfolding is discussed.
Collapse
Affiliation(s)
- Rishi Rakhit
- Department of Biochemistry, University of Toronto, University Health Network, Toronto Medical Discovery Tower, Medical and Related Sciences (MaRS), 101 College Street, Toronto, ON, Canada, M5G 1L7
| | | |
Collapse
|