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Debler EW, Hsia KC, Nagy V, Seo HS, Hoelz A. Characterization of the membrane-coating Nup84 complex. Nucleus 2010. [DOI: 10.4161/nucl.11120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Debler EW, Hsia KC, Nagy V, Seo HS, Hoelz A. Characterization of the membrane-coating Nup84 complex: paradigm for the nuclear pore complex structure. Nucleus 2010; 1:150-7. [PMID: 21326946 DOI: 10.4161/nucl.1.2.11120] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Accepted: 01/03/2010] [Indexed: 11/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) function as selective gates for nucleocytoplasmic transport. Although the NPC was discovered more than half a century ago, our knowledge of NPC components in atomic detail has exploded only over the past few years. Recent structural, biochemical, and in vivo studies of NPC components, in particular the membrane-coating heptameric Nup84 complex, have shed light onto the NPC architecture as well as onto its dynamic nature. Striking similarities were revealed between the components of the NPC and of coat protein complexes in the endocytic and secretory pathways, supporting their common evolutionary origin in a progenitor protocoatomer. Here, we summarize these findings and discuss emerging concepts that underlie the molecular architecture and the dynamics of the NPC. We conclude that the uncovered principles are not limited to the NPC, but are likely to extend to other macromolecular assemblies.
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Affiliation(s)
- Erik W Debler
- Laboratory of Cell Biology, The Rockefeller University, New York, NY, USA
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Menon AL, Poole FL, Cvetkovic A, Trauger SA, Kalisiak E, Scott JW, Shanmukh S, Praissman J, Jenney FE, Wikoff WR, Apon JV, Siuzdak G, Adams MWW. Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome. Mol Cell Proteomics 2008; 8:735-51. [PMID: 19043064 DOI: 10.1074/mcp.m800246-mcp200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Virtually all cellular processes are carried out by dynamic molecular assemblies or multiprotein complexes, the compositions of which are largely undefined. They cannot be predicted solely from bioinformatics analyses nor are there well defined techniques currently available to unequivocally identify protein complexes (PCs). To address this issue, we attempted to directly determine the identity of PCs from native microbial biomass using Pyrococcus furiosus, a hyperthermophilic archaeon that grows optimally at 100 degrees C, as the model organism. Novel PCs were identified by large scale fractionation of the native proteome using non-denaturing, sequential column chromatography under anaerobic, reducing conditions. A total of 967 distinct P. furiosus proteins were identified by mass spectrometry (nano LC-ESI-MS/MS), representing approximately 80% of the cytoplasmic proteins. Based on the co-fractionation of proteins that are encoded by adjacent genes on the chromosome, 106 potential heteromeric PCs containing 243 proteins were identified, only 20 of which were known or expected. In addition to those of unknown function, novel and uncharacterized PCs were identified that are proposed to be involved in the metabolism of amino acids (10), carbohydrates (four), lipids (two), vitamins and metals (three), and DNA and RNA (nine). A further 30 potential PCs were classified as tentative, and the remaining potential PCs (13) were classified as weakly interacting. Some major advantages of native biomass fractionation for PC identification are that it provides a road map for the (partial) purification of native forms of novel and uncharacterized PCs, and the results can be utilized for the recombinant production of low abundance PCs to provide enough material for detailed structural and biochemical analyses.
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Affiliation(s)
- Angeli Lal Menon
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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Alemán C, Zanuy D, Jiménez AI, Cativiela C, Haspel N, Zheng J, Casanovas J, Wolfson H, Nussinov R. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids. Phys Biol 2006; 3:S54-62. [PMID: 16582465 DOI: 10.1088/1478-3975/3/1/s06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Physically building complex multi-molecular structures from naturally occurring biological macromolecules has aroused a great deal of interest. Here we focus on nanostructures composed of re-engineered, natural 'foldamer' building blocks. Our aim is to provide some of the underlying concepts and schemes for crafting structures utilizing such conformationally relatively stable molecular components. We describe how, via chemical biology strategies, it is further possible to chemically manipulate the foldamer building blocks toward specific shape-driven structures, which in turn could be used toward potential-designed functions. We outline the criteria in choosing candidate foldamers from the vast biological repertoire, and how to enhance their stability through selected targeted replacements by non-proteinogenic conformationally constrained amino acids. These approaches combine bioinformatics, high performance computations and mathematics with synthetic organic chemistry. The resulting artificially engineered self-organizing molecular scale structures take advantage of nature's nanobiology toolkit and at the same time improve on it, since their new targeted function differs from that optimized by evolution. The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, ETS d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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Mohd Jaafar F, Attoui H, Bahar MW, Siebold C, Sutton G, Mertens PPC, De Micco P, Stuart DI, Grimes JM, De Lamballerie X. The Structure and Function of the Outer Coat Protein VP9 of Banna Virus. Structure 2005; 13:17-28. [PMID: 15642258 DOI: 10.1016/j.str.2004.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 10/21/2004] [Accepted: 10/21/2004] [Indexed: 11/22/2022]
Abstract
Banna virus (BAV: genus Seadornavirus, family Reoviridae) has a double-shelled morphology similar to rotavirus and bluetongue virus. The structure of BAV outer-capsid protein VP9 was determined by X-ray crystallography at 2.6 A resolution, revealing a trimeric molecule, held together by an N-terminal helical bundle, reminiscent of coiled-coil structures found in fusion-active proteins such as HIV gp41. The major domain of VP9 contains stacked beta sheets with marked structural similarities to the receptor binding protein VP8 of rotavirus. Anti-VP9 antibodies neutralize viral infectivity, and, remarkably, pretreatment of cells with trimeric VP9 increased viral infectivity, indicating that VP9 is involved in virus attachment to cell surface and subsequent internalization. Sequence similarities were also detected between BAV VP10 and VP5 portion of rotavirus VP4, suggesting that the receptor binding and internalization apparatus, which is a single gene product activated by proteoloysis in rotavirus, is the product of two separate genome segments in BAV.
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Affiliation(s)
- Fauziah Mohd Jaafar
- Unité des Virus Emergents EA3292, EFS Alpes-Méditerranée and Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13005 Marseille, France
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Denisov IG, Grinkova YV, Lazarides AA, Sligar SG. Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size. J Am Chem Soc 2004; 126:3477-87. [PMID: 15025475 DOI: 10.1021/ja0393574] [Citation(s) in RCA: 811] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using a recently described self-assembly process (Bayburt, T. H.; Grinkova, Y. V.; Sligar, S. G. Nano Letters 2002, 2, 853-856), we prepared soluble monodisperse discoidal lipid/protein particles with controlled size and composition, termed Nanodiscs, in which the fragment of dipalmitoylphosphatidylcholine (DPPC) bilayer is surrounded by a helical protein belt. We have customized the size of these particles by changing the length of the amphipathic helical part of this belt, termed membrane scaffold protein (MSP). Herein we describe the design of extended and truncated MSPs, the optimization of self-assembly for each of these proteins, and the structure and composition of the resulting Nanodiscs. We show that the length of the protein helix surrounding the lipid part of a Nanodisc determines the particle diameter, as measured by HPLC and small-angle X-ray scattering (SAXS). Using different scaffold proteins, we obtained Nanodiscs with the average size from 9.5 to 12.8 nm with a very narrow size distribution (+/-3%). Functionalization of the N-terminus of the scaffold protein does not perturb their ability to form homogeneous discoidal structures. Detailed analysis of the solution scattering confirms the presence of a lipid bilayer of 5.5 nm thickness in Nanodiscs of different sizes. The results of this study provide an important structural characterization of self-assembled phospholipid bilayers and establish a framework for the design of soluble amphiphilic nanoparticles of controlled size.
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Affiliation(s)
- I G Denisov
- Departments of Biochemistry and Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA
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Kainov DE, Butcher SJ, Bamford DH, Tuma R. Conserved intermediates on the assembly pathway of double-stranded RNA bacteriophages. J Mol Biol 2003; 328:791-804. [PMID: 12729755 DOI: 10.1016/s0022-2836(03)00322-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Double-stranded RNA (dsRNA) viruses are complex RNA processing machines that sequentially perform packaging, replication and transcription of their genomes. In order to characterize the assembly intermediates of such a machine we have developed an efficient in vitro assembly system for the procapsid of bacteriophage phi8. The major structural protein P1 is a stable and soluble tetramer. Three tetramers associate with a P2 monomer (RNA-dependent RNA polymerase) to form the nucleation complex. This complex is further stabilized by a P4 hexamer (packaging motor). Further assembly proceeds via rapid addition of individual building blocks. The incorporation of the packaging and replication machinery is under kinetic control. The in vitro assembled procapsids perform packaging, replication and transcription of viral RNA. Comparison with another dsRNA phage, phi6, indicates conservation of key assembly intermediates in the absence of sequence homology and suggests that a general assembly mechanism for the dsRNA virus lineage may exist.
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Affiliation(s)
- Denis E Kainov
- Department of Biosciences, Institute of Biotechnology, University of Helsinki, Finland
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Affiliation(s)
- Michael S Chapman
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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Van Regenmortel MHV. Reductionism and the search for structure-function relationships in antibody molecules. J Mol Recognit 2002; 15:240-7. [PMID: 12447900 DOI: 10.1002/jmr.584] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
One of the claims of reductionism is that it can explain all the features of living systems by an analysis of their physico-chemical constituents. Such a claim disregards the existence in biological systems of emergent properties that do not exist in their isolated components but which allow autonomous organisms to be directively organized in a self-regulated and integrated manner. It is not possible to describe biological systems adequately without using functional language that is meaningless in the physical sciences. The description of biological functions is also an essential part of immunology and functional explanations are more useful than causal explanations also in this discipline. Since causality is not a relation between a material object and an event, the structure of an antibody cannot be the cause of its binding activity. When structure-function relationships are analysed, the search should be for correlations rather than for causal relations. Methods used to find correlations between the atomic structure of antibody binding sites and their binding activity are mostly based on mutagenesis studies. Since the effect of any mutation depends on the molecular context, it is usually very difficult to predict the effects of multiple mutations on antibody function. Our knowledge of the molecular basis of antigen-antibody recognition has led to the expectation that it may be possible to develop new vaccines using molecular design principles. Such unwarranted hopes arise because of a confusion between antigenicity and immunogenicity. Although knowledge of antibody structure is of little use in vaccine design, it may help to develop therapeutic inhibitors and antibodies effective in the passive immunotherapy of viral infection.
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Abstract
Viruses vastly outnumber their host cells and must present a huge selective pressure. It is also becoming evident that only a small percent of the eukaryotic genome codes for molecules involved in cellular structures and functions, and that much of the remainder may have a viral origin. Viruses clearly play a central role in the biosphere, but how is this viral world organized? Classification was originally based on virus morphology and the particular host infected, but now there is an increasing trend to rely on sequence information. The type of genome (e.g., RNA or DNA, single- or double-stranded) provides fundamental classification criteria, while sequence comparisons can provide fine mapping for closely related viruses. However, it is currently very difficult to identify long-range evolutionary relationships. We present here a different approach, based on the idea that each virus has an innate "self." When the structures and functions characteristic of this "self" are identified, then they uncover relationships beyond those accessible from sequence information alone. The new approach is illustrated by sketching some possible viral lineages. We propose that urviruses were present before the division of cellular life into its current domains, and that the viral world has lineages that can be traced back to the root of the universal tree of life.
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Affiliation(s)
- Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, PO Box 56 (Viikinkaari 5), Helsinki FIN-00014, Finland.
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Ward TH, Polishchuk RS, Caplan S, Hirschberg K, Lippincott-Schwartz J. Maintenance of Golgi structure and function depends on the integrity of ER export. J Cell Biol 2001; 155:557-70. [PMID: 11706049 PMCID: PMC2198855 DOI: 10.1083/jcb.200107045] [Citation(s) in RCA: 342] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The Golgi apparatus comprises an enormous array of components that generate its unique architecture and function within cells. Here, we use quantitative fluorescence imaging techniques and ultrastructural analysis to address whether the Golgi apparatus is a steady-state or a stable organelle. We found that all classes of Golgi components are dynamically associated with this organelle, contrary to the prediction of the stable organelle model. Enzymes and recycling components are continuously exiting and reentering the Golgi apparatus by membrane trafficking pathways to and from the ER, whereas Golgi matrix proteins and coatomer undergo constant, rapid exchange between membrane and cytoplasm. When ER to Golgi transport is inhibited without disrupting COPII-dependent ER export machinery (by brefeldin A treatment or expression of Arf1[T31N]), the Golgi structure disassembles, leaving no residual Golgi membranes. Rather, all Golgi components redistribute into the ER, the cytoplasm, or to ER exit sites still active for recruitment of selective membrane-bound and peripherally associated cargos. A similar phenomenon is induced by the constitutively active Sar1[H79G] mutant, which has the additional effect of causing COPII-associated membranes to cluster to a juxtanuclear region. In cells expressing Sar1[T39N], a constitutively inactive form of Sar1 that completely disrupts ER exit sites, Golgi glycosylation enzymes, matrix, and itinerant proteins all redistribute to the ER. These results argue against the hypothesis that the Golgi apparatus contains stable components that can serve as a template for its biogenesis. Instead, they suggest that the Golgi complex is a dynamic, steady-state system, whose membranes can be nucleated and are maintained by the activities of the Sar1-COPII and Arf1-coatomer systems.
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Affiliation(s)
- T H Ward
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National institutes of Health, Bethesda, MD 20892, USA
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Abstract
The completion of the Arabidopsis thaliana (mustard weed) genome sequence constitutes a major breakthrough in plant biology. It will revolutionize how we answer questions about the biology and evolution of plants as well as how we confront and resolve world-wide agricultural problems.
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Affiliation(s)
- A Theologis
- Plant Gene Expression Center, Buchanan Street, Albany, CA 94710, USA.
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