The Experts below are selected from a list of 303 Experts worldwide ranked by ideXlab platform
Juan S Bonifacino - One of the best experts on this subject based on the ideXlab platform.
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Coat Proteins shaping membrane transport
Nature Reviews Molecular Cell Biology, 2003Co-Authors: Juan S Bonifacino, Jennifer LippincottschwartzAbstract:Coat Proteins allow the selective transfer of macromolecules from one membrane-enclosed compartment to another by concentrating macromolecules into specialized membrane patches and then deforming these patches into small Coated vesicles. Recent findings indicate that Coat Proteins might also participate in the differentiation of membrane domains within organelles and large transport carriers, as well as in the association of the carriers with the cytosketelon and with acceptor organelles.
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transport
Nature reviews. Molecular cell biology, 2003Co-Authors: Juan S Bonifacino, Jennifer Lippincott-schwartzAbstract:Coat Proteins allow the selective transfer of macromolecules from one membrane-enclosed compartment to another by concentrating macromolecules into specialized membrane patches and then deforming these patches into small Coated vesicles. Recent findings indicate that Coat Proteins might also participate in the differentiation of membrane domains within organelles and large transport carriers, as well as in the association of the carriers with the cytosketelon and with acceptor organelles.
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linking cargo to vesicle formation receptor tail interactions with Coat Proteins
Current Opinion in Cell Biology, 1997Co-Authors: Tomas Kirchhausen, Juan S Bonifacino, Howard RiezmanAbstract:How soluble cargo molecules concentrate into budding vesicles is the subject of intensive current research. Clathrin-based vesiculation from the plasma membrane and the trans-Golgi network constitutes the best described system that supports this sorting process. Soluble ligands bind to specific transmembrane receptors which have been shown to interact directly with clathrin adaptor complexes, components of clathrin Coats. At the same time, these clathrin adaptors facilitate clathrin Coat assembly and probably regulate the recruitment of the rest of the Coat components. Recent studies have looked at both the interaction of receptor tails with adaptors and the assembly of the clathrin Coat. Progress has also been made in elucidating how soluble cargo molecules may be concentrated for exit from the endoplasmic reticulum.
Paul Van Der Schoot - One of the best experts on this subject based on the ideXlab platform.
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role of charge regulation and size polydispersity in nanoparticle encapsulation by viral Coat Proteins
Journal of Physical Chemistry B, 2015Co-Authors: Remy Kusters, Hsiangku Lin, Roya Zandi, Irina B Tsvetkova, Bogdan Dragnea, Paul Van Der SchootAbstract:Nanoparticles can be encapsulated by virus Coat Proteins if their surfaces are functionalized to acquire a sufficiently large negative charge. A minimal surface charge is required to overcome (i) repulsive interactions between the positively charged RNA-binding domains on the Proteins and (ii) the loss of mixing and translational entropy of RNA and capsid Coat Proteins. Here, we present a model describing the encapsulation of spherical particles bearing weakly acidic surface groups and investigate how charge regulation and size polydispersity impact upon the encapsulation efficiency of gold nanoparticles by model Coat Proteins. We show that the surface charge density of these particles cannot be assumed fixed, but that it adjusts itself to minimize electrostatic repulsion between the charges on them and maximize the attractive interaction with the RNA binding domains on the Proteins. Charge regulation in combination with the natural variation of particle radii has a large effect on the encapsulation efficiency: it makes it much more gradual despite its inherently cooperative nature. Our calculations rationalize recent experimental observations on the coassembly of gold nanoparticles by brome mosaic virus Coat Proteins.
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impact of charge variation on the encapsulation of nanoparticles by virus Coat Proteins
Physical Biology, 2012Co-Authors: Hsiangku Lin, Paul Van Der Schoot, Roya ZandiAbstract:Electrostatic interaction is the driving force for the encapsulation by virus Coat Proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al (2010 ACS Nano 4 3853–60) found the encapsulation efficiency to sensitively depend on the interplay between the surface charge density of negatively charged gold nanoparticles and the number of positive charges on the RNA binding domains of the Proteins. Surprisingly, these experiments reveal that despite the highly cooperative nature of the co-assembly at low pH, the efficiency of encapsulation is a gradual function of their surface charge density. We present a simple all-or-nothing mass action law combined with an electrostatic interaction model to explain the experiments. We find quantitative agreement with experimental observations, supporting the existence of a natural statistical charge distribution between nanoparticles.
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multishell structures of virus Coat Proteins
Journal of Physical Chemistry B, 2010Co-Authors: Peter Prinsen, Paul Van Der Schoot, William M Gelbart, Charles M KnoblerAbstract:Under conditions of low ionic strength and a pH ranging between about 3.7 and 5.0, solutions of purified Coat Proteins of cowpea chlorotic mottle virus (CCMV) form spherical multishell structures in the absence of viral RNA. The outer surfaces of the shells in these structures are negatively charged, whereas the inner surfaces are positively charged due to a disordered cationic N-terminal domain of the capsid protein, the arginine-rich RNA-binding motif that protrudes into the interior. We show that the main forces stabilizing these multishells are counterion release combined with a lower charge density in the RNA-binding motif region of the outer shells due to their larger radii of curvature, arguing that these compensate for the outer shells not being able to adopt the smaller, optimal, radius of curvature of the inner shell. This explains why the structures are only stable at low ionic strengths at pHs for which the outer surface is negatively charged and why the larger outer shells are not observed separately in solution. We show how to calculate the free energy of shells of nonoptimal radius of curvature from the elastic properties of the native shell. The spacing between shells is determined mainly by the entropic elasticity of the RNA-binding motifs. Although we focus on CCMV multishells, we also predict the solution conditions under which multishells formed by CCMV Coat protein mutants with a lower RNA-binding motif charge are stable, and we examine other viruses as well. We conclude that at a given surface charge density, the boundaries separating regions of stable multishells with different numbers of shells shift to lower ionic strengths upon either increasing the length of the RNA-binding motif, increasing the stiffness of the shells, or decreasing the charge per RNA-binding motif.
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counterion release stabilizes multi shell structures of virus Coat Proteins
Biophysical Journal, 2009Co-Authors: Peter Prinsen, Paul Van Der Schoot, William M Gelbart, Charles M KnoblerAbstract:Under conditions of low ionic strength and a pH between about 3.5 and 5.0, solutions of purified Coat Proteins of cowpea chlorotic mottle virus (CCMV) form spherical multi-shell structures in the absence of viral RNA. The native protein shell, which has an outer diameter of about 28 nm and is built up from 180 Coat Proteins, forms the inner shell and is surrounded by one or two larger concentric shells. We show that counterion release is the main force stabilizing these multi-shell structures, arguing that this compensates for the outer shells not being able to adopt their smaller optimal radius of curvature. This explains why the structures are only stable at low enough ionic strengths and why we never see the larger outer shells separately in solution. The inner surfaces of the shells are positively charged over a large range of pH values, with most of the positive charge residing on the last 10 nm of the N-terminus side of the protein, which sticks out into the interior. Our calculations show that the multi-shell structures are only stable when the outer surface of the shells is negatively charged, which is above a pH of about 3.5. The fact that we do not see multi-shells at high pH (>5.0) is explained by looking at the stability of the pentamers and hexamers of protein dimers, the building blocks of the shells. Although we focus on CCMV multi-shells, structures of this kind should arise generally in any situation where an attraction between concentric spherical (or cylindrical) shells competes with a preferred spontaneous curvature.
David S. Peabody - One of the best experts on this subject based on the ideXlab platform.
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RNA recognition site of PP7 Coat protein
Nucleic acids research, 2002Co-Authors: Francis Lim, David S. PeabodyAbstract:The Coat Proteins of different single-strand RNA phages use a common protein tertiary structural framework to recognize different RNA hairpins and thus offer a natural model for understanding the molecular basis of RNA-binding specificity. Here we describe the RNA structural requirements for binding to the Coat protein of bacteriophage PP7, an RNA phage of Pseudomonas. Its recognition specificity differs substantially from those of the Coat Proteins of its previously characterized relatives such as the coliphages MS2 and Qbeta. Using designed variants of the wild-type RNA, and selection of binding-competent sequences from random RNA sequence libraries (i.e. SELEX) we find that tight binding to PP7 Coat protein is favored by the existence of an 8 bp hairpin with a bulged purine on its 5' side separated by 4 bp from a 6 nt loop having the sequence Pu-U-A-G/U-G-Pu. However, another structural class possessing only some of these features is capable of binding almost as tightly.
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The RNA-binding site of bacteriophage Qbeta Coat protein.
The Journal of biological chemistry, 1996Co-Authors: Francis Lim, Marc Spingola, David S. PeabodyAbstract:Abstract The Coat Proteins of the RNA bacteriophages Qβ and MS2 are specific RNA binding Proteins. Although they possess common tertiary structures, they bind different RNA stem loops and thus provide useful models of specific protein-RNA recognition. Although the RNA-binding site of MS2 Coat protein has been extensively characterized previously, little is known about Qβ. Here we describe the isolation of mutants that define the RNA-binding site of Qβ Coat protein, showing that, as with MS2, it resides on the surface of a large β-sheet. Mutations are also described that convert Qβ Coat protein to the RNA binding specificity of MS2. The results of these and other studies indicate that, although they bind different RNAs, the binding sites of the two Coat Proteins are sufficiently similar that each is easily converted by mutation to the RNA binding specificity of the other.
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Crystal structure of the Coat protein from the GA bacteriophage: model of the unassembled dimer.
Protein science : a publication of the Protein Society, 1996Co-Authors: Carol A. White, Richard S. Mitchell, John Wickersham, Ramadurgam Kodandapani, David S. Peabody, Kathryn R. ElyAbstract:There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral Coat Proteins. Coat Proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the Coat protein from a Group II phage GA is reported and compared to the Group I MS2 Coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the Coat protein is similar to the Group I MS2 Coat protein in the intact virus (Golmohammadi R, Valegard K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 Coat Proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the Proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 Coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these Coat Proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.
Thomas E. Kreis - One of the best experts on this subject based on the ideXlab platform.
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Coat Proteins regulating membrane traffic.
International review of cytology, 2000Co-Authors: Suzie J. Scales, Marie Gomez, Thomas E. KreisAbstract:This review focuses on the roles of Coat Proteins in regulating the membrane traffic of eukaryotic cells. Coat Proteins are recruited to the donor organelle membrane from a cytosolic pool by specific small GTP-binding Proteins and are required for the budding of Coated vesicles. This review first describes the four types of Coat complexes that have been characterized so far: clathrin and its adaptors, the adaptor-related AP-3 complex, COPI, and COPII. It then discusses the ascribed functions of Coat Proteins in vesicular transport, including the physical deformation of the membrane into a bud, the selection of cargo, and the targeting of the budded vesicle. It also mentions how the Coat Proteins may function in an alternative model for transport, namely via tubular connections, and how traffic is regulated. Finally, this review outlines the evidence that related Coat Proteins may regulate other steps of membrane traffic.
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Cytoplasmic Coat Proteins involved in endosome function
Cell, 1995Co-Authors: J. Andrew Whitney, David Sheff, Marie Gomez, Thomas E. Kreis, Ira MellmanAbstract:Abstract Endosomes are intermediates for a complex series of sorting and transport events that occur during receptor-mediated endocytosis. These involve the recognition of targeting determinants on the cytoplasmic domains of many membrane Proteins as well as the formation of specific transport vesicles. Accordingly, endosome function is likely to be governed by the regulated assembly of cytoplasmic Coat complexes. We have found that, in vitro, endosomes recruit a characteristic set of cytoplasmic Proteins in a GTPγS-stimulated and brefeldin A-sensitive fashion. Among these are members of the COP-1 and ARF families of Coat Proteins. In addition, endosomes were also found to assemble distinct, clathrin-like Coats. Since micro-injection of antibodies to β-COP inhibits the entry of enveloped viruses via the endocytic pathway, it is apparent that the recruitment of COP-I or COP-I-related Proteins plays an important role in the function of endosomes in intact cells.
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Coat Proteins in intracellular membrane transport
Current opinion in cell biology, 1994Co-Authors: Thomas E. Kreis, Rainer PepperkokAbstract:Transport of newly synthesized material from the endoplasmic reticulum (ER) towards the Golgi complex, through the Golgi cisternae, and out of the trans-Golgi network (TGN) is thought to be mediated by vesicular carriers. Different types of vesicle are involved in this biosynthetic membrane traffic. All are Coated with protein complexes on their cytoplasmic surface. COP-Coated vesicles have recently been implicated in transport of cargo from the ER to the TGN, and clathrin-Coated vesicles from the TGN to endosomes, but the carriers moving material to the cell surface are still unknown. Sequence homologies between subunits of the COP- and the clathrin-adaptor complexes suggest that Coat Proteins may belong to a family of Proteins with related functions. The precise role of the Coat Proteins is not fully understood, although they have been implicated in clustering of cargo into buds and in budding of vesicles. In addition, Coat Proteins may play an essential role in targeting of transport intermediates and may serve to regulate membrane fusion.
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recruitment of Coat Proteins onto golgi membranes in intact and permeabilized cells effects of brefeldin a and g protein activators
Cell, 1992Co-Authors: Margaret S. Robinson, Thomas E. KreisAbstract:Abstract Brefeldin A (BFA) causes a rapid redistribution of Coat Proteins (e.g., γ-adaptin) associated with the clathrin-Coated vesicles that bud from the trans-Golgi network (TGN), while the clathrin-Coated vesicles that bud from the plasma membrane are unaffected. γ-Adaptin redistributes with the same kinetics as β-COP, a Coat protein associated with the non-clathrin-Coated vesicles that bud from the Golgi complex. Upon removal of BFA, however, γ-adaptin recovers its perinuclear distribution more rapidly. Redistribution of both Proteins can be prevented by pretreating cells with AIF 4 − . Recruitment of adaptors from the cytosol onto the TGN membrane has been reconstituted in a permeabilized cell system and is increased by addition of GTPγS and blocked by addition of BFA. These results suggest a role for G Proteins in the control of the clathrin-Coated vesicle cycle at the TGN and further extend the similarities between clathrin-Coated vesicles and non-clathrin-Coated vesicles.
Charles M Knobler - One of the best experts on this subject based on the ideXlab platform.
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multishell structures of virus Coat Proteins
Journal of Physical Chemistry B, 2010Co-Authors: Peter Prinsen, Paul Van Der Schoot, William M Gelbart, Charles M KnoblerAbstract:Under conditions of low ionic strength and a pH ranging between about 3.7 and 5.0, solutions of purified Coat Proteins of cowpea chlorotic mottle virus (CCMV) form spherical multishell structures in the absence of viral RNA. The outer surfaces of the shells in these structures are negatively charged, whereas the inner surfaces are positively charged due to a disordered cationic N-terminal domain of the capsid protein, the arginine-rich RNA-binding motif that protrudes into the interior. We show that the main forces stabilizing these multishells are counterion release combined with a lower charge density in the RNA-binding motif region of the outer shells due to their larger radii of curvature, arguing that these compensate for the outer shells not being able to adopt the smaller, optimal, radius of curvature of the inner shell. This explains why the structures are only stable at low ionic strengths at pHs for which the outer surface is negatively charged and why the larger outer shells are not observed separately in solution. We show how to calculate the free energy of shells of nonoptimal radius of curvature from the elastic properties of the native shell. The spacing between shells is determined mainly by the entropic elasticity of the RNA-binding motifs. Although we focus on CCMV multishells, we also predict the solution conditions under which multishells formed by CCMV Coat protein mutants with a lower RNA-binding motif charge are stable, and we examine other viruses as well. We conclude that at a given surface charge density, the boundaries separating regions of stable multishells with different numbers of shells shift to lower ionic strengths upon either increasing the length of the RNA-binding motif, increasing the stiffness of the shells, or decreasing the charge per RNA-binding motif.
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counterion release stabilizes multi shell structures of virus Coat Proteins
Biophysical Journal, 2009Co-Authors: Peter Prinsen, Paul Van Der Schoot, William M Gelbart, Charles M KnoblerAbstract:Under conditions of low ionic strength and a pH between about 3.5 and 5.0, solutions of purified Coat Proteins of cowpea chlorotic mottle virus (CCMV) form spherical multi-shell structures in the absence of viral RNA. The native protein shell, which has an outer diameter of about 28 nm and is built up from 180 Coat Proteins, forms the inner shell and is surrounded by one or two larger concentric shells. We show that counterion release is the main force stabilizing these multi-shell structures, arguing that this compensates for the outer shells not being able to adopt their smaller optimal radius of curvature. This explains why the structures are only stable at low enough ionic strengths and why we never see the larger outer shells separately in solution. The inner surfaces of the shells are positively charged over a large range of pH values, with most of the positive charge residing on the last 10 nm of the N-terminus side of the protein, which sticks out into the interior. Our calculations show that the multi-shell structures are only stable when the outer surface of the shells is negatively charged, which is above a pH of about 3.5. The fact that we do not see multi-shells at high pH (>5.0) is explained by looking at the stability of the pentamers and hexamers of protein dimers, the building blocks of the shells. Although we focus on CCMV multi-shells, structures of this kind should arise generally in any situation where an attraction between concentric spherical (or cylindrical) shells competes with a preferred spontaneous curvature.