101
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Kraatz S, Guichard P, Obbineni JM, Olieric N, Hatzopoulos GN, Hilbert M, Sen I, Missimer J, Gönczy P, Steinmetz MO. The Human Centriolar Protein CEP135 Contains a Two-Stranded Coiled-Coil Domain Critical for Microtubule Binding. Structure 2016; 24:1358-1371. [PMID: 27477386 DOI: 10.1016/j.str.2016.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 11/24/2022]
Abstract
Centrioles are microtubule-based structures that play important roles notably in cell division and cilium biogenesis. CEP135/Bld10p family members are evolutionarily conserved microtubule-binding proteins important for centriole formation. Here, we analyzed in detail the microtubule-binding activity of human CEP135 (HsCEP135). X-ray crystallography and small-angle X-ray scattering in combination with molecular modeling revealed that the 158 N-terminal residues of HsCEP135 (HsCEP135-N) form a parallel two-stranded coiled-coil structure. Biochemical, cryo-electron, and fluorescence microscopy analyses revealed that in vitro HsCEP135-N interacts with tubulin, protofilaments, and microtubules and induces the formation of microtubule bundles. We further identified a 13 amino acid segment spanning residues 96-108, which represents a major microtubule-binding site in HsCEP135-N. Within this segment, we identified a cluster of three lysine residues that contribute to the microtubule bundling activity of HsCEP135-N. Our results provide the first structural information on CEP135/Bld10p proteins and offer insights into their microtubule-binding mechanism.
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Affiliation(s)
- Sebastian Kraatz
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Paul Guichard
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Jagan M Obbineni
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Georgios N Hatzopoulos
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Manuel Hilbert
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Indrani Sen
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - John Missimer
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland.
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102
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Lou C, Martos-Maldonado MC, Madsen CS, Thomsen RP, Midtgaard SR, Christensen NJ, Kjems J, Thulstrup PW, Wengel J, Jensen KJ. Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic. Nat Commun 2016; 7:12294. [PMID: 27464951 PMCID: PMC4974474 DOI: 10.1038/ncomms12294] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 06/15/2016] [Indexed: 01/22/2023] Open
Abstract
Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide–oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design. Peptide and oligonucleotide systems are known to self-assemble both in nature and artificial systems. Here, the authors combine both forms of self-assembly through the synthesis of peptideoligonucleotide conjugates and show formation of a three-helix structure that dimerises at higher concentrations.
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Affiliation(s)
- Chenguang Lou
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Manuel C Martos-Maldonado
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Charlotte S Madsen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Rasmus P Thomsen
- Biomolecular Nanoscale Engineering Center and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen Ø 2100, Denmark
| | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Jørgen Kjems
- Biomolecular Nanoscale Engineering Center and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø 2100, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Knud J Jensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
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103
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The C-terminal region of the transcriptional regulator THAP11 forms a parallel coiled-coil domain involved in protein dimerization. J Struct Biol 2016; 194:337-46. [DOI: 10.1016/j.jsb.2016.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 11/15/2022]
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104
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Spencer RK, Hochbaum AI. X-ray Crystallographic Structure and Solution Behavior of an Antiparallel Coiled-Coil Hexamer Formed by de Novo Peptides. Biochemistry 2016; 55:3214-23. [DOI: 10.1021/acs.biochem.6b00201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
| | - Allon I. Hochbaum
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
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105
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Li C, Ching Han Chang C, Nagel J, Porebski BT, Hayashida M, Akutsu T, Song J, Buckle AM. Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Brief Bioinform 2016; 17:270-82. [PMID: 26177815 PMCID: PMC6078162 DOI: 10.1093/bib/bbv047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Indexed: 12/19/2022] Open
Abstract
Coiled-coils refer to a bundle of helices coiled together like strands of a rope. It has been estimated that nearly 3% of protein-encoding regions of genes harbour coiled-coil domains (CCDs). Experimental studies have confirmed that CCDs play a fundamental role in subcellular infrastructure and controlling trafficking of eukaryotic cells. Given the importance of coiled-coils, multiple bioinformatics tools have been developed to facilitate the systematic and high-throughput prediction of CCDs in proteins. In this article, we review and compare 12 sequence-based bioinformatics approaches and tools for coiled-coil prediction. These approaches can be categorized into two classes: coiled-coil detection and coiled-coil oligomeric state prediction. We evaluated and compared these methods in terms of their input/output, algorithm, prediction performance, validation methods and software utility. All the independent testing data sets are available at http://lightning.med.monash.edu/coiledcoil/. In addition, we conducted a case study of nine human polyglutamine (PolyQ) disease-related proteins and predicted CCDs and oligomeric states using various predictors. Prediction results for CCDs were highly variable among different predictors. Only two peptides from two proteins were confirmed to be CCDs by majority voting. Both domains were predicted to form dimeric coiled-coils using oligomeric state prediction. We anticipate that this comprehensive analysis will be an insightful resource for structural biologists with limited prior experience in bioinformatics tools, and for bioinformaticians who are interested in designing novel approaches for coiled-coil and its oligomeric state prediction.
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106
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Fraga KJ, Joo H, Tsai J. An amino acid code to define a protein's tertiary packing surface. Proteins 2015; 84:201-16. [PMID: 26575337 DOI: 10.1002/prot.24966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/24/2015] [Accepted: 11/09/2015] [Indexed: 01/28/2023]
Abstract
One difficult aspect of the protein-folding problem is characterizing the nonspecific interactions that define packing in protein tertiary structure. To better understand tertiary structure, this work extends the knob-socket model by classifying the interactions of a single knob residue packed into a set of contiguous sockets, or a pocket made up of 4 or more residues. The knob-socket construct allows for a symbolic two-dimensional mapping of pockets. The two-dimensional mapping of pockets provides a simple method to investigate the variety of pocket shapes to understand the geometry of protein tertiary surfaces. The diversity of pocket geometries can be organized into groups of pockets that share a common core, which suggests that some interactions in pockets are ancillary to packing. Further analysis of pocket geometries displays a preferred configuration that is right-handed in α-helices and left-handed in β-sheets. The amino acid composition of pockets illustrates the importance of nonpolar amino acids in packing as well as position specificity. As expected, all pocket shapes prefer to pack with hydrophobic knobs; however, knobs are not selective for the pockets they pack. Investigating side-chain rotamer preferences for certain pocket shapes uncovers no strong correlations. These findings allow a simple vocabulary based on knobs and sockets to describe protein tertiary packing that supports improved analysis, design, and prediction of protein structure.
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Affiliation(s)
- Keith J Fraga
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
| | - Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
| | - Jerry Tsai
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
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107
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Dobson L, Nyitray L, Gáspári Z. A conserved charged single α-helix with a putative steric role in paraspeckle formation. RNA (NEW YORK, N.Y.) 2015; 21:2023-2029. [PMID: 26428695 PMCID: PMC4647456 DOI: 10.1261/rna.053058.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Paraspeckles are subnuclear particles involved in the regulation of mRNA expression. They are formed by the association of DBHS family proteins and the NEAT1 long noncoding RNA. Here, we show that a recently identified structural motif, the charged single α-helix, is largely conserved in the DBHS family. Based on the available structural data and a previously suggested multimerization scheme of DBHS proteins, we built a structural model of a (PSPC1/NONO)(n) multimer that might have relevance in paraspeckle formation. Our model contains an extended coiled-coil region that is followed by and partially overlaps with the predicted charged single α-helix. We suggest that the charged single α-helix can act as an elastic ruler governing the exact positioning of the dimeric core structures relative to each other during paraspeckle assembly along the NEAT1 noncoding RNA.
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Affiliation(s)
- László Dobson
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, H-1083 Budapest, Hungary
| | - László Nyitray
- Eötvös Loránd University, Department of Biochemistry, H-1117 Budapest, Hungary
| | - Zoltán Gáspári
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, H-1083 Budapest, Hungary
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108
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Structural Change in the Dynein Stalk Region Associated with Two Different Affinities for the Microtubule. J Mol Biol 2015; 428:1886-96. [PMID: 26585405 DOI: 10.1016/j.jmb.2015.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/08/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022]
Abstract
Dynein is a large microtubule-based motor complex that requires tight coupling of intra-molecular ATP hydrolysis with the generation of mechanical force and track-binding activity. However, the microtubule-binding domain is structurally separated by about 15nm from the nucleotide-binding sites by a coiled-coil stalk. Thus, long-range two-way communication is necessary for coordination between the catalytic cycle of ATP hydrolysis and dynein's track-binding affinities. To investigate the structural changes that occur in the dynein stalk region to produce two different microtubule affinities, here we improve the resolution limit of the previously reported structure of the entire stalk region and we investigate structural changes in the dynein stalk and strut/buttress regions by comparing currently available X-ray structures. In the light of recent crystal structures, the basis of the transition from the low-affinity to the high-affinity coiled-coil registry is discussed. A concerted movement model previously reported by Carter and Vale is modified more specifically, and we proposed it as the open zipper model.
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109
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Caillat C, Fish A, Pefani DE, Taraviras S, Lygerou Z, Perrakis A. The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2278-86. [PMID: 26527144 PMCID: PMC4631479 DOI: 10.1107/s1399004715016892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/09/2015] [Indexed: 12/14/2022]
Abstract
GemC1, together with Idas and Geminin, an important regulator of DNA-replication licensing and differentiation decisions, constitute a superfamily sharing a homologous central coiled-coil domain. To better understand this family of proteins, the crystal structure of a GemC1 coiled-coil domain variant engineered for better solubility was determined to 2.2 Å resolution. GemC1 shows a less typical coiled coil compared with the Geminin homodimer and the Geminin-Idas heterodimer structures. It is also shown that both in vitro and in cells GemC1 interacts with Geminin through its coiled-coil domain, forming a heterodimer that is more stable that the GemC1 homodimer. Comparative analysis of the thermal stability of all of the possible superfamily complexes, using circular dichroism to follow the unfolding of the entire helix of the coiled coil, or intrinsic tryptophan fluorescence of a unique conserved N-terminal tryptophan, shows that the unfolding of the coiled coil is likely to take place from the C-terminus towards the N-terminus. It is also shown that homodimers show a single-state unfolding, while heterodimers show a two-state unfolding, suggesting that the dimer first falls apart and the helices then unfold according to the stability of each protein. The findings argue that Geminin-family members form homodimers and heterodimers between them, and this ability is likely to be important for modulating their function in cycling and differentiating cells.
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Affiliation(s)
- Christophe Caillat
- Department of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Alexander Fish
- Department of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | - Stavros Taraviras
- Laboratory of Physiology, School of Medicine, University of Patras, 26505 Rio, Patras, Greece
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, 26505 Rio, Patras, Greece
| | - Anastassis Perrakis
- Department of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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110
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Tarnawski M, Barends TRM, Schlichting I. Structural analysis of an oxygen-regulated diguanylate cyclase. ACTA ACUST UNITED AC 2015; 71:2158-77. [PMID: 26527135 DOI: 10.1107/s139900471501545x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Cyclic di-GMP is a bacterial second messenger that is involved in switching between motile and sessile lifestyles. Given the medical importance of biofilm formation, there has been increasing interest in understanding the synthesis and degradation of cyclic di-GMPs and their regulation in various bacterial pathogens. Environmental cues are detected by sensing domains coupled to GGDEF and EAL or HD-GYP domains that have diguanylate cyclase and phosphodiesterase activities, respectively, producing and degrading cyclic di-GMP. The Escherichia coli protein DosC (also known as YddV) consists of an oxygen-sensing domain belonging to the class of globin sensors that is coupled to a C-terminal GGDEF domain via a previously uncharacterized middle domain. DosC is one of the most strongly expressed GGDEF proteins in E. coli, but to date structural information on this and related proteins is scarce. Here, the high-resolution structural characterization of the oxygen-sensing globin domain, the middle domain and the catalytic GGDEF domain in apo and substrate-bound forms is described. The structural changes between the iron(III) and iron(II) forms of the sensor globin domain suggest a mechanism for oxygen-dependent regulation. The structural information on the individual domains is combined into a model of the dimeric DosC holoprotein. These findings have direct implications for the oxygen-dependent regulation of the activity of the cyclase domain.
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Affiliation(s)
- Miroslaw Tarnawski
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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111
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Abstract
Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein-protein interactions. Coiled-coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled-coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.
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112
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Surkont J, Diekmann Y, Ryder PV, Pereira-Leal JB. Coiled-coil length: Size does matter. Proteins 2015; 83:2162-9. [PMID: 26387794 DOI: 10.1002/prot.24932] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/23/2015] [Accepted: 09/14/2015] [Indexed: 11/09/2022]
Abstract
Protein evolution is governed by processes that alter primary sequence but also the length of proteins. Protein length may change in different ways, but insertions, deletions and duplications are the most common. An optimal protein size is a trade-off between sequence extension, which may change protein stability or lead to acquisition of a new function, and shrinkage that decreases metabolic cost of protein synthesis. Despite the general tendency for length conservation across orthologous proteins, the propensity to accept insertions and deletions is heterogeneous along the sequence. For example, protein regions rich in repetitive peptide motifs are well known to extensively vary their length across species. Here, we analyze length conservation of coiled-coils, domains formed by an ubiquitous, repetitive peptide motif present in all domains of life, that frequently plays a structural role in the cell. We observed that, despite the repetitive nature, the length of coiled-coil domains is generally highly conserved throughout the tree of life, even when the remaining parts of the protein change, including globular domains. Length conservation is independent of primary amino acid sequence variation, and represents a conservation of domain physical size. This suggests that the conservation of domain size is due to functional constraints.
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Affiliation(s)
| | - Yoan Diekmann
- Instituto Gulbenkian de Ciência, Oeiras, 2780-156, Portugal.,Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, 02543
| | - Pearl V Ryder
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, 02543.,Emory University School of Medicine, Atlanta, Georgia, 30322
| | - Jose B Pereira-Leal
- Instituto Gulbenkian de Ciência, Oeiras, 2780-156, Portugal.,Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, 02543
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113
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Joo H, Chavan AG, Fraga KJ, Tsai J. An amino acid code for irregular and mixed protein packing. Proteins 2015; 83:2147-61. [PMID: 26370334 DOI: 10.1002/prot.24929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 11/10/2022]
Abstract
To advance our understanding of protein tertiary structure, the development of the knob-socket model is completed in an analysis of the packing in irregular coil and turn secondary structure packing as well as between mixed secondary structure. The knob-socket model simplifies packing based on repeated patterns of two motifs: a three-residue socket for packing within secondary (2°) structure and a four-residue knob-socket for tertiary (3°) packing. For coil and turn secondary structure, knob-sockets allow identification of a correlation between amino acid composition and tertiary arrangements in space. Coil contributes almost as much as α-helices to tertiary packing. In irregular sockets, Gly, Pro, Asp, and Ser are favored, while in irregular knobs, the preference order is Arg, Asp, Pro, Asn, Thr, Leu, and Gly. Cys, His,Met, and Trp are not favored in either. In mixed packing, the knob amino acid preferences are a function of the socket that they are packing into, whereas the amino acid composition of the sockets does not depend on the secondary structure of the knob. A unique motif of a coil knob with an XYZ β-sheet socket may potentially function to inhibit β-sheet extension. In addition, analysis of the preferred crossing angles for strands within a β-sheet and mixed α-helice/β-sheet identifies canonical packing patterns useful in protein design. Lastly, the knob-socket model abstracts the complexity of protein tertiary structure into an intuitive packing surface topology map.
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Affiliation(s)
- Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
| | - Archana G Chavan
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
| | - Keith J Fraga
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
| | - Jerry Tsai
- Department of Chemistry, University of the Pacific, Stockton, California, 95211
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114
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Gáspári Z, Nyitray L. Coiled coils as possible models of protein structure evolution. Biomol Concepts 2015; 2:199-210. [PMID: 25962029 DOI: 10.1515/bmc.2011.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/01/2011] [Indexed: 01/05/2023] Open
Abstract
Coiled coils are formed by two or more α-helices wrapped around one another. This structural motif often guides di-, tri- or multimerization of proteins involved in diverse biological processes such as membrane fusion, signal transduction and the organization of the cytoskeleton. Although coiled coil motifs seem conceptually simple and their existence was proposed in the early 1950s, the high variability of the motif makes coiled coil prediction from sequence a difficult task. They might be confused with intrinsically disordered sequences and even more with a recently described structural motif, the charged single α-helix. By contrast, the versatility of coiled coil structures renders them an ideal candidate for protein (re)design and many novel variants have been successfully created to date. In this paper, we review coiled coils in the light of protein evolution by putting our present understanding of the motif and its variants in the context of structural interconversions. We argue that coiled coils are ideal subjects for studies of subtle and large-scale structural changes because of their well-characterized and versatile nature.
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115
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Watkins A, Wuo MG, Arora PS. Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. J Am Chem Soc 2015; 137:11622-30. [PMID: 26302018 PMCID: PMC4577960 DOI: 10.1021/jacs.5b05527] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 12/26/2022]
Abstract
The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. Recent success in the inhibition of difficult PPIs by secondary structure mimetics also points to potential limitations, because often, specific cases require tertiary structure mimetics. To streamline protein structure-based inhibitor design, we have previously described the examination of protein complexes in the Protein Data Bank where α-helices or β-strands form critical contacts. Here, we examined coiled coils and helix bundles that mediate complex formation to create a platform for the discovery of potential tertiary structure mimetics. Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. This article identifies critical features of these helical interfaces with respect to coiled coil and other helical PPIs. We expect the analysis to prove useful for the rational design of modulators of this fundamental class of protein assemblies.
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Affiliation(s)
- Andrew
M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael G. Wuo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
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116
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De novo protein design: how do we expand into the universe of possible protein structures? Curr Opin Struct Biol 2015; 33:16-26. [DOI: 10.1016/j.sbi.2015.05.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/15/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
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117
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Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc Natl Acad Sci U S A 2015; 112:E3669-78. [PMID: 26124119 DOI: 10.1073/pnas.1504021112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ∼ 150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. The Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.
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118
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Cook JD, Soto-Montoya H, Korpela MK, Lee JE. Electrostatic Architecture of the Infectious Salmon Anemia Virus (ISAV) Core Fusion Protein Illustrates a Carboxyl-Carboxylate pH Sensor. J Biol Chem 2015; 290:18495-504. [PMID: 26082488 DOI: 10.1074/jbc.m115.644781] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 11/06/2022] Open
Abstract
Segment 5, ORF 1 of the infectious salmon anemia virus (ISAV) genome, encodes for the ISAV F protein, which is responsible for viral-host endosomal membrane fusion during a productive ISAV infection. The entry machinery of ISAV is composed of a complex of the ISAV F and ISAV hemagglutinin esterase (HE) proteins in an unknown stoichiometry prior to receptor engagement by ISAV HE. Following binding of the receptor to ISAV HE, dissociation of the ISAV F protein from HE, and subsequent endocytosis, the ISAV F protein resolves into a fusion-competent oligomeric state. Here, we present a 2.1 Å crystal structure of the fusion core of the ISAV F protein determined at low pH. This structure has allowed us to unambiguously demonstrate that the ISAV entry machinery exhibits typical class I viral fusion protein architecture. Furthermore, we have determined stabilizing factors that accommodate the pH-dependent mode of ISAV transmission, and our structure has allowed the identification of a central coil that is conserved across numerous and varied post-fusion viral glycoprotein structures. We then discuss a mechanistic model of ISAV fusion that parallels the paramyxoviral class I fusion strategy wherein attachment and fusion are relegated to separate proteins in a similar fashion to ISAV fusion.
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Affiliation(s)
- Jonathan D Cook
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hazel Soto-Montoya
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Markus K Korpela
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jeffrey E Lee
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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119
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Terawaki SI, Yoshikane A, Higuchi Y, Wakamatsu K. Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry. Biochem Biophys Res Commun 2015; 460:451-6. [DOI: 10.1016/j.bbrc.2015.03.054] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
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120
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Waldman VM, Stanage TH, Mims A, Norden IS, Oakley MG. Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins. Proteins 2015; 83:1027-45. [PMID: 25664627 DOI: 10.1002/prot.24778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 12/24/2014] [Accepted: 01/20/2015] [Indexed: 11/07/2022]
Abstract
The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans.
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Affiliation(s)
- Vincent M Waldman
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
| | - Tyler H Stanage
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
| | - Alexandra Mims
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
| | - Ian S Norden
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
| | - Martha G Oakley
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405
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121
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Modeling transmembrane domain dimers/trimers of plexin receptors: implications for mechanisms of signal transmission across the membrane. PLoS One 2015; 10:e0121513. [PMID: 25837709 PMCID: PMC4383379 DOI: 10.1371/journal.pone.0121513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/03/2015] [Indexed: 01/01/2023] Open
Abstract
Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.
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Lee M, Sadowska A, Bekere I, Ho D, Gully BS, Lu Y, Iyer KS, Trewhella J, Fox AH, Bond CS. The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation. Nucleic Acids Res 2015; 43:3826-40. [PMID: 25765647 PMCID: PMC4402515 DOI: 10.1093/nar/gkv156] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/18/2015] [Indexed: 12/14/2022] Open
Abstract
SFPQ, (a.k.a. PSF), is a human tumor suppressor protein that regulates many important functions in the cell nucleus including coordination of long non-coding RNA molecules into nuclear bodies. Here we describe the first crystal structures of Splicing Factor Proline and Glutamine Rich (SFPQ), revealing structural similarity to the related PSPC1/NONO heterodimer and a strikingly extended structure (over 265 Å long) formed by an unusual anti-parallel coiled-coil that results in an infinite linear polymer of SFPQ dimers within the crystals. Small-angle X-ray scattering and transmission electron microscopy experiments show that polymerization is reversible in solution and can be templated by DNA. We demonstrate that the ability to polymerize is essential for the cellular functions of SFPQ: disruptive mutation of the coiled-coil interaction motif results in SFPQ mislocalization, reduced formation of nuclear bodies, abrogated molecular interactions and deficient transcriptional regulation. The coiled-coil interaction motif thus provides a molecular explanation for the functional aggregation of SFPQ that directs its role in regulating many aspects of cellular nucleic acid metabolism.
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Affiliation(s)
- Mihwa Lee
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Agata Sadowska
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Indra Bekere
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Diwei Ho
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Benjamin S Gully
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Yanling Lu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - K Swaminathan Iyer
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Archa H Fox
- Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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123
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Liu J, Yang J, Wen J, Yang Y, Wei X, Zhang X, Wang YP. Mutational analysis of dimeric linkers in peri- and cytoplasmic domains of histidine kinase DctB reveals their functional roles in signal transduction. Open Biol 2015; 4:140023. [PMID: 24898140 PMCID: PMC4077058 DOI: 10.1098/rsob.140023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Membrane-associated histidine kinases (HKs) in two-component systems respond to environmental stimuli by autophosphorylation and phospho-transfer. HK typically contains a periplasmic sensor domain that regulates the cytoplasmic kinase domain through a conserved cytoplasmic linker. How signal is transduced from the ligand-binding site across the membrane barrier remains unclear. Here, we analyse two linker regions of a typical HK, DctB. One region connects the first transmembrane helix with the periplasmic Per-ARNT-Sim domains, while the other one connects the second transmembrane helix with the cytoplasmic kinase domains. We identify a leucine residue in the first linker region to be essential for the signal transduction and for maintaining the delicate balance of the dimeric interface, which is key to its activities. We also show that the other linker, belonging to the S-helix coiled-coil family, plays essential roles in signal transduction inside the cell. Furthermore, by combining mutations with opposing activities in the two regions, we show that these two signalling transduction elements are integrated to produce a combined effect on the final activity of DctB.
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Affiliation(s)
- Jiwei Liu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jin Wen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yun Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaolu Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaodong Zhang
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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124
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Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP. Structural plasticity of helical nanotubes based on coiled-coil assemblies. Structure 2015; 23:280-9. [PMID: 25620001 DOI: 10.1016/j.str.2014.12.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/16/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure, in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.
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Affiliation(s)
- E H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
| | - C Xu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - F DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - E Magnotti
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - C Modlin
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - X Yu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - E Wright
- Department of Pediatrics, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - D Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - V P Conticello
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA.
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125
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Li C, Wang XF, Chen Z, Zhang Z, Song J. Computational characterization of parallel dimeric and trimeric coiled-coils using effective amino acid indices. MOLECULAR BIOSYSTEMS 2015; 11:354-60. [DOI: 10.1039/c4mb00569d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RFCoil is a novel predictor for parallel coiled-coil dimer and trimer.
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Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology
- Faculty of Medicine
- Monash University
- Melbourne
- Australia
| | - Xiao-Feng Wang
- State Key Laboratory of Agrobiotechnology
- College of Biological Sciences
- China Agricultural University
- Beijing 100193
- China
| | - Zhen Chen
- State Key Laboratory of Agrobiotechnology
- College of Biological Sciences
- China Agricultural University
- Beijing 100193
- China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology
- College of Biological Sciences
- China Agricultural University
- Beijing 100193
- China
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology
- Faculty of Medicine
- Monash University
- Melbourne
- Australia
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126
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Wang X, Zhou Y, Yan R. AAFreqCoil: a new classifier to distinguish parallel dimeric and trimeric coiled coils. MOLECULAR BIOSYSTEMS 2015; 11:1794-801. [DOI: 10.1039/c5mb00119f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coiled coils are characteristic rope-like protein structures, constituted by one or more heptad repeats.
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Affiliation(s)
- Xiaofeng Wang
- School of Mathematics and Computer Science
- Shanxi Normal University
- Linfen 041004
- China
| | - Yuan Zhou
- College of Biological Sciences
- China Agricultural University
- Beijing 100193
- China
| | - Renxiang Yan
- Institute of Applied Genomics
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
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127
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A fungal sarcolemmal membrane-associated protein (SLMAP) homolog plays a fundamental role in development and localizes to the nuclear envelope, endoplasmic reticulum, and mitochondria. EUKARYOTIC CELL 2014; 14:345-58. [PMID: 25527523 DOI: 10.1128/ec.00241-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/13/2014] [Indexed: 11/20/2022]
Abstract
Sarcolemmal membrane-associated protein (SLMAP) is a tail-anchored protein involved in fundamental cellular processes, such as myoblast fusion, cell cycle progression, and chromosomal inheritance. Further, SLMAP misexpression is associated with endothelial dysfunctions in diabetes and cancer. SLMAP is part of the conserved striatin-interacting phosphatase and kinase (STRIPAK) complex required for specific signaling pathways in yeasts, filamentous fungi, insects, and mammals. In filamentous fungi, STRIPAK was initially discovered in Sordaria macrospora, a model system for fungal differentiation. Here, we functionally characterize the STRIPAK subunit PRO45, a homolog of human SLMAP. We show that PRO45 is required for sexual propagation and cell-to-cell fusion and that its forkhead-associated (FHA) domain is essential for these processes. Protein-protein interaction studies revealed that PRO45 binds to STRIPAK subunits PRO11 and SmMOB3, which are also required for sexual propagation. Superresolution structured-illumination microscopy (SIM) further established that PRO45 localizes to the nuclear envelope, endoplasmic reticulum, and mitochondria. SIM also showed that localization to the nuclear envelope requires STRIPAK subunits PRO11 and PRO22, whereas for mitochondria it does not. Taken together, our study provides important insights into fundamental roles of the fungal SLMAP homolog PRO45 and suggests STRIPAK-related and STRIPAK-unrelated functions.
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128
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Thomson AR, Wood CW, Burton AJ, Bartlett GJ, Sessions RB, Brady RL, Woolfson DN. Computational design of water-soluble α-helical barrels. Science 2014; 346:485-8. [DOI: 10.1126/science.1257452] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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129
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Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S. Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures. J Struct Biol 2014; 188:123-33. [PMID: 25278129 DOI: 10.1016/j.jsb.2014.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023]
Abstract
Coiled coils are widespread protein domains comprising α-helices wound around each other in a regular fashion. Owing to their regularity, coiled-coil structures can be fully described by parametric equations. This in turn makes them an excellent model for studying sequence-structure relationships in proteins. Here, we used computational design to identify sequence features that determine the degree of helix axial rotation in four-helical homo-oligomeric antiparallel coiled coils. We designed 135,000 artificial sequences for a repertoire of backbone models representing all theoretically possible axial rotation states. Analysis of the designed sequences revealed features that precisely define the rotation of the helices. Based on these features we implemented a bioinformatic tool, which given a coiled-coil sequence, predicts the rotation of the helices in its structure. Moreover, we showed that another structural parameter, helix axial shift, is coupled to helix axial rotation and that dependence between these two parameters narrows the number of possible axial rotation states.
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Affiliation(s)
- Krzysztof Szczepaniak
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Bioinformatics and Protein Engineering, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Grzegorz Lach
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Bioinformatics and Protein Engineering, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Bioinformatics and Protein Engineering, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland; Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland.
| | - Stanislaw Dunin-Horkawicz
- International Institute of Molecular and Cell Biology in Warsaw, Laboratory of Bioinformatics and Protein Engineering, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland.
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130
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Yang J, Kopeček J. Macromolecular therapeutics. J Control Release 2014; 190:288-303. [PMID: 24747162 PMCID: PMC4142088 DOI: 10.1016/j.jconrel.2014.04.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 12/13/2022]
Abstract
This review covers water-soluble polymer-drug conjugates and macromolecules that possess biological activity without attached low molecular weight drugs. The main design principles of traditional and backbone degradable polymer-drug conjugates as well as the development of a new paradigm in nanomedicines - (low molecular weight) drug-free macromolecular therapeutics are discussed. To address the biological features of cancer, macromolecular therapeutics directed to stem/progenitor cells and the tumor microenvironment are deliberated. Finally, the future perspectives of the field are briefly debated.
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Affiliation(s)
- Jiyuan Yang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City 84112, USA
| | - Jindřich Kopeček
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City 84112, USA; Department of Bioengineering, University of Utah, Salt Lake City 84112, USA.
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131
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Wood CW, Bruning M, Ibarra AÁ, Bartlett GJ, Thomson AR, Sessions RB, Brady RL, Woolfson DN. CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics 2014; 30:3029-35. [PMID: 25064570 PMCID: PMC4201159 DOI: 10.1093/bioinformatics/btu502] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/ Contact:D.N.Woolfson@bristol.ac.uk or Chris.Wood@bristol.ac.uk
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Affiliation(s)
- Christopher W Wood
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - Marc Bruning
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - Amaurys Á Ibarra
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - Gail J Bartlett
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - Andrew R Thomson
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - Richard B Sessions
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - R Leo Brady
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS and School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, BS8 1TD, Bristol, UK
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132
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Nishikawa Y, Oyama T, Kamiya N, Kon T, Toyoshima YY, Nakamura H, Kurisu G. Structure of the entire stalk region of the Dynein motor domain. J Mol Biol 2014; 426:3232-3245. [PMID: 25058684 DOI: 10.1016/j.jmb.2014.06.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 06/12/2014] [Accepted: 06/24/2014] [Indexed: 01/10/2023]
Abstract
Dyneins are large microtubule-based motor complexes that power a range of cellular processes including the transport of organelles, as well as the beating of cilia and flagella. The motor domain is located within the dynein heavy chain and comprises an N-terminal mechanical linker element, a central ring of six AAA+ modules of which four bind or hydrolyze ATP, and a long stalk extending from the AAA+ring with a microtubule-binding domain (MTBD) at its tip. A crucial mechanism underlying the motile activity of cytoskeletal motor proteins is precise coupling between the ATPase and track-binding activities. In dynein, a stalk region consisting of a long (~15nm) antiparallel coiled coil separates these two activities, which must facilitate communication between them. This communication is mediated by a small degree of helix sliding in the coiled coil. However, no high-resolution structure is available of the entire stalk region including the MTBD. Here, we have reported the structure of the entire stalk region of mouse cytoplasmic dynein in a weak microtubule-binding state, which was determined using X-ray crystallography, and have compared it with the dynein motor domain from Dictyostelium discoideum in a strong microtubule-binding state and with a mouse MTBD with its distal portion of the coiled coil fused to seryl-tRNA synthetase from Thermus thermophilus. Our results strongly support the helix-sliding model based on the complete structure of the dynein stalk with a different form of coiled-coil packing. We also propose a plausible mechanism of helix sliding together with further analysis using molecular dynamics simulations. Our results present the importance of conserved proline residues for an elastic motion of stalk coiled coil and imply the manner of change between high-affinity state and low-affinity state of MTBD.
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Affiliation(s)
- Yosuke Nishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Takuji Oyama
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahide Kon
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoko Y Toyoshima
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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133
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Stathopulos PB, Schindl R, Fahrner M, Zheng L, Gasmi-Seabrook GM, Muik M, Romanin C, Ikura M. STIM1/Orai1 coiled-coil interplay in the regulation of store-operated calcium entry. Nat Commun 2014; 4:2963. [PMID: 24351972 PMCID: PMC3927877 DOI: 10.1038/ncomms3963] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022] Open
Abstract
Orai1 calcium channels in the plasma membrane are activated by stromal interaction molecule-1 (STIM1), an endoplasmic reticulum calcium sensor, to mediate store-operated calcium entry (SOCE). The cytosolic region of STIM1 contains a long putative coiled-coil (CC)1 segment and shorter CC2 and CC3 domains. Here we present solution nuclear magnetic resonance structures of a trypsin-resistant CC1–CC2 fragment in the apo and Orai1-bound states. Each CC1–CC2 subunit forms a U-shaped structure that homodimerizes through antiparallel interactions between equivalent α-helices. The CC2:CC2′ helix pair clamps two identical acidic Orai1 C-terminal helices at opposite ends of a hydrophobic/basic STIM–Orai association pocket. STIM1 mutants disrupting CC1:CC1′ interactions attenuate, while variants promoting CC1 stability spontaneously activate Orai1 currents. CC2 mutations cause remarkable variability in Orai1 activation because of a dual function in binding Orai1 and autoinhibiting STIM1 oligomerization via interactions with CC3. We conclude that SOCE is activated through dynamic interplay between STIM1 and Orai1 helices. When endoplasmic reticulum calcium levels are low, STIM1 binds to and opens Orai1 channels in the plasma membrane to replenish calcium stores. Stathopulos et al. present solution structures of the STIM1 coiled-coil domain in the presence and absence of Orai1, revealing the structural basis for this interaction.
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Affiliation(s)
- Peter B Stathopulos
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Rainer Schindl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Marc Fahrner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Le Zheng
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Geneviève M Gasmi-Seabrook
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Martin Muik
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Christoph Romanin
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Mitsuhiko Ikura
- University Health Network and Department of Medical Biophysics, Campbell Family Cancer Research Institute, Ontario Cancer Institute, University of Toronto, Room 4-804, MaRS TMDT, 101 College Street, Toronto, Ontario, Canada M5G 1L7
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134
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Blocquel D, Habchi J, Durand E, Sevajol M, Ferron F, Erales J, Papageorgiou N, Longhi S. Coiled-coil deformations in crystal structures: the measles virus phosphoprotein multimerization domain as an illustrative example. ACTA ACUST UNITED AC 2014; 70:1589-603. [PMID: 24914970 DOI: 10.1107/s139900471400234x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/31/2014] [Indexed: 01/02/2023]
Abstract
The structures of two constructs of the measles virus (MeV) phosphoprotein (P) multimerization domain (PMD) are reported and are compared with a third structure published recently by another group [Communie et al. (2013), J. Virol. 87, 7166-7169]. Although the three structures all have a tetrameric and parallel coiled-coil arrangement, structural comparison unveiled considerable differences in the quaternary structure and unveiled that the three structures suffer from significant structural deformation induced by intermolecular interactions within the crystal. These results show that crystal packing can bias conclusions about function and mechanism based on analysis of a single crystal structure, and they challenge to some extent the assumption according to which coiled-coil structures can be reliably predicted from the amino-acid sequence. Structural comparison also highlighted significant differences in the extent of disorder in the C-terminal region of each monomer. The differential flexibility of the C-terminal region is also supported by size-exclusion chromatography and small-angle X-ray scattering studies, which showed that MeV PMD exists in solution as a dynamic equilibrium between two tetramers of different compaction. Finally, the possible functional implications of the flexibility of the C-terminal region of PMD are discussed.
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Affiliation(s)
- David Blocquel
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Johnny Habchi
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Eric Durand
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Marion Sevajol
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - François Ferron
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Jenny Erales
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | | | - Sonia Longhi
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
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135
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Franke B, Gasch A, Rodriguez D, Chami M, Khan MM, Rudolf R, Bibby J, Hanashima A, Bogomolovas J, von Castelmur E, Rigden DJ, Uson I, Labeit S, Mayans O. Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1. Open Biol 2014; 4:130172. [PMID: 24671946 PMCID: PMC3971405 DOI: 10.1098/rsob.130172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
MuRF1 is an E3 ubiquitin ligase central to muscle catabolism. It belongs to the TRIM protein family characterized by a tripartite fold of RING, B-box and coiled-coil (CC) motifs, followed by variable C-terminal domains. The CC motif is hypothesized to be responsible for domain organization in the fold as well as for high-order assembly into functional entities. But data on CC from this family that can clarify the structural significance of this motif are scarce. We have characterized the helical region from MuRF1 and show that, contrary to expectations, its CC domain assembles unproductively, being the B2- and COS-boxes in the fold (respectively flanking the CC) that promote a native quaternary structure. In particular, the C-terminal COS-box seemingly forms an α-hairpin that packs against the CC, influencing its dimerization. This shows that a C-terminal variable domain can be tightly integrated within the conserved TRIM fold to modulate its structure and function. Furthermore, data from transfected muscle show that in MuRF1 the COS-box mediates the in vivo targeting of sarcoskeletal structures and points to the pharmacological relevance of the COS domain for treating MuRF1-mediated muscle atrophy.
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Affiliation(s)
- Barbara Franke
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
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136
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Molecular Modeling of PEGylated Peptides, Dendrimers, and Single-Walled Carbon Nanotubes for Biomedical Applications. Polymers (Basel) 2014. [DOI: 10.3390/polym6030776] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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137
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Mechanism of Tc toxin action revealed in molecular detail. Nature 2014; 508:61-5. [DOI: 10.1038/nature13015] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/10/2014] [Indexed: 12/20/2022]
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138
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Bhardwaj A, Casjens SR, Cingolani G. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:342-53. [PMID: 24531468 PMCID: PMC3940195 DOI: 10.1107/s1399004713027685] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/09/2013] [Indexed: 11/10/2022]
Abstract
Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.
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Affiliation(s)
- Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Sherwood R. Casjens
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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139
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Squeglia F, Bachert B, De Simone A, Lukomski S, Berisio R. The crystal structure of the streptococcal collagen-like protein 2 globular domain from invasive M3-type group A Streptococcus shows significant similarity to immunomodulatory HIV protein gp41. J Biol Chem 2013; 289:5122-33. [PMID: 24356966 DOI: 10.1074/jbc.m113.523597] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The arsenal of virulence factors deployed by streptococci includes streptococcal collagen-like (Scl) proteins. These proteins, which are characterized by a globular domain and a collagen-like domain, play key roles in host adhesion, host immune defense evasion, and biofilm formation. In this work, we demonstrate that the Scl2.3 protein is expressed on the surface of invasive M3-type strain MGAS315 of Streptococcus pyogenes. We report the crystal structure of Scl2.3 globular domain, the first of any Scl. This structure shows a novel fold among collagen trimerization domains of either bacterial or human origin. Despite there being low sequence identity, we observed that Scl2.3 globular domain structurally resembles the gp41 subunit of the envelope glycoprotein from human immunodeficiency virus type 1, an essential subunit for viral fusion to human T cells. We combined crystallographic data with modeling and molecular dynamics techniques to gather information on the entire lollipop-like Scl2.3 structure. Molecular dynamics data evidence a high flexibility of Scl2.3 with remarkable interdomain motions that are likely instrumental to the protein biological function in mediating adhesive or immune-modulatory functions in host-pathogen interactions. Altogether, our results provide molecular tools for the understanding of Scl-mediated streptococcal pathogenesis and important structural insights for the future design of small molecular inhibitors of streptococcal invasion.
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Affiliation(s)
- Flavia Squeglia
- From the Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134 Napoli, Italy
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140
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Stathopulos PB, Ikura M. Structural aspects of calcium-release activated calcium channel function. Channels (Austin) 2013; 7:344-53. [PMID: 24213636 DOI: 10.4161/chan.26734] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Store-operated calcium (Ca(2+)) entry is the process by which molecules located on the endo/sarcoplasmic reticulum (ER/SR) respond to decreased luminal Ca(2+) levels by signaling Ca(2+) release activated Ca(2+) channels (CRAC) channels to open on the plasma membrane (PM). This activation of PM CRAC channels provides a sustained cytosolic Ca(2+) elevation associated with myriad physiological processes. The identities of the molecules which mediate SOCE include stromal interaction molecules (STIMs), functioning as the ER/SR luminal Ca(2+) sensors, and Orai proteins, forming the PM CRAC channels. This review examines the current available high-resolution structural information on these CRAC molecular components with particular focus on the solution structures of the luminal STIM Ca(2+) sensing domains, the crystal structures of cytosolic STIM fragments, a closed Orai hexameric crystal structure and a structure of an Orai1 N-terminal fragment in complex with calmodulin. The accessible structural data are discussed in terms of potential mechanisms of action and cohesiveness with functional observations.
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Affiliation(s)
- Peter B Stathopulos
- Princess Margaret Cancer Centre; Department of Medical Biophysics; University of Toronto; Toronto, ON, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre; Department of Medical Biophysics; University of Toronto; Toronto, ON, Canada
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141
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Abstract
The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.
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142
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Hayouka Z, Mortenson DE, Kreitler DF, Weisblum B, Forest KT, Gellman SH. Evidence for phenylalanine zipper-mediated dimerization in the X-ray crystal structure of a magainin 2 analogue. J Am Chem Soc 2013; 135:15738-15741. [PMID: 24102563 PMCID: PMC3928869 DOI: 10.1021/ja409082w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-resolution structure elucidation has been challenging for the large group of host-defense peptides that form helices on or within membranes but do not manifest a strong folding propensity in aqueous solution. Here we report the crystal structure of an analogue of the widely studied host-defense peptide magainin 2. Magainin 2 (S8A, G13A, G18A) is a designed variant that displays enhanced antibacterial activity relative to the natural peptide. The crystal structure of magainin 2 (S8A, G13A, G18A), obtained for the racemic form, features a dimerization mode that has previously been proposed to play a role in the antibacterial activity of magainin 2 and related peptides.
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Affiliation(s)
- Zvi Hayouka
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David E. Mortenson
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Dale F. Kreitler
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Bernard Weisblum
- Department of Medicine, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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143
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Parry DAD. Fifty years of fibrous protein research: a personal retrospective. J Struct Biol 2013; 186:320-34. [PMID: 24148884 DOI: 10.1016/j.jsb.2013.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 02/02/2023]
Abstract
As a result of X-ray fiber diffraction studies on fibrous proteins and crystallographic data on fragments derived from them, new experimental techniques across the biophysical and biochemical spectra, sophisticated computer modeling and refinement procedures, widespread use of bioinformatics and improved specimen preparative procedures the structures of many fibrous proteins have now been determined to at least low resolution. In so doing these structures have yielded insight into the relationship that exists between sequence and conformation and this, in turn, has led to improved methodologies for predicting structure from sequence data alone. In this personal retrospective a selection of progress made during the past 50years is discussed in terms of events to which the author has made some contribution.
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Affiliation(s)
- David A D Parry
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
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144
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Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1. Arch Biochem Biophys 2013; 540:9-18. [PMID: 24113299 DOI: 10.1016/j.abb.2013.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/11/2013] [Accepted: 10/01/2013] [Indexed: 12/30/2022]
Abstract
Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a scavenger receptor that mediates the recognition, the binding and internalization of ox-LDL. A truncated soluble form of LOX-1 (sLOX-1) has been identified that, at elevated levels, has been associated to acute coronary syndrome. Human sLOX-1 is the extracellular part of membrane LOX-1 which is cleaved in the NECK domain with a mechanism that has not yet been identified. Purification of human sLOX-1 has been carried out to experimentally identify the cleavage site region within the NECK domain. Molecular modelling and classical molecular dynamics simulation techniques have been used to characterize the structural and dynamical properties of the LOX-1 NECK domain in the presence and absence of the CTLD recognition region, taking into account the obtained proteolysis results. The simulative data indicate that the NECK domain is stabilized by the coiled-coil heptad repeat motif along the simulations, shows a definite flexibility pattern and is characterized by specific electrostatic potentials. The detection of a mobile inter-helix space suggests an explanation for the in vivo susceptibility of the NECK domain to the proteolytic cleavage, validating the assumption that the NECK domain sequence is composed of a coiled-coil motif destabilized in specific regions of functional significance.
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145
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Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP. Rational Design of Helical Nanotubes from Self-Assembly of Coiled-Coil Lock Washers. J Am Chem Soc 2013; 135:15565-78. [DOI: 10.1021/ja4074529] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chunfu Xu
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Rui Liu
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Ricardo C. Guerrero-Ferreira
- Division
of Pediatric Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Suite 500, Atlanta, Georgia 30322, United States
| | - Elizabeth R. Wright
- Division
of Pediatric Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Suite 500, Atlanta, Georgia 30322, United States
| | - Stanislaw Dunin-Horkawicz
- Laboratory
of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, Warsaw 02-109, Poland
| | - Kyle Morris
- School
of Life Sciences, University of Sussex, Lewes Road, Falmer, East Sussex BN1
9QG, United Kingdom
| | - Louise C. Serpell
- School
of Life Sciences, University of Sussex, Lewes Road, Falmer, East Sussex BN1
9QG, United Kingdom
| | - Xiaobing Zuo
- X-ray
Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Joseph S. Wall
- Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973, United States
| | - Vincent P. Conticello
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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146
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Wong ETC, Na D, Gsponer J. On the importance of polar interactions for complexes containing intrinsically disordered proteins. PLoS Comput Biol 2013; 9:e1003192. [PMID: 23990768 PMCID: PMC3749945 DOI: 10.1371/journal.pcbi.1003192] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 07/06/2013] [Indexed: 11/18/2022] Open
Abstract
There is a growing recognition for the importance of proteins with large intrinsically disordered (ID) segments in cell signaling and regulation. ID segments in these proteins often harbor regions that mediate molecular recognition. Coupled folding and binding of the recognition regions has been proposed to confer high specificity to interactions involving ID segments. However, researchers recently questioned the origin of the interaction specificity of ID proteins because of the overrepresentation of hydrophobic residues in their interaction interfaces. Here, we focused on the role of polar and charged residues in interactions mediated by ID segments. Making use of the extended nature of most ID segments when in complex with globular proteins, we first identified large numbers of complexes between globular proteins and ID segments by using radius-of-gyration-based selection criteria. Consistent with previous studies, we found the interfaces of these complexes to be enriched in hydrophobic residues, and that these residues contribute significantly to the stability of the interaction interface. However, our analyses also show that polar interactions play a larger role in these complexes than in structured protein complexes. Computational alanine scanning and salt-bridge analysis indicate that interfaces in ID complexes are highly complementary with respect to electrostatics, more so than interfaces of globular proteins. Follow-up calculations of the electrostatic contributions to the free energy of binding uncovered significantly stronger Coulombic interactions in complexes harbouring ID segments than in structured protein complexes. However, they are counter-balanced by even higher polar-desolvation penalties. We propose that polar interactions are a key contributing factor to the observed high specificity of ID segment-mediated interactions. Protein-protein interactions are essential to communication and signal integration in cells. For these processes to be precise, interactions between proteins have to be specific and well coordinated. In order to understand the specificity in protein interactions, researches have focused on interfaces between two or more folded proteins. It has been shown that specificity in interactions between folded proteins relies on shape complementarity, hydrogen bonding, and salt-bridge formation. However, many proteins lack a unique folded structure; the so-called intrinsically disordered proteins. These proteins fluctuate between different conformations in isolation but often adopt a single structure when interacting with partner proteins. As many intrinsically disordered proteins are involved in signaling and regulation, their interactions have to be highly specific. The finding that the interaction interfaces of intrinsically disordered proteins are enriched in hydrophobic residues has led to questions regarding the specificity of interactions mediated by this group of proteins. Here, we show that polar and charged residues play a larger role in interfaces that involve intrinsically disordered proteins compared to interfaces that involve only folded proteins. Our results suggest that polar interactions are key contributors to the specificity of interactions that involve intrinsically disordered proteins.
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Affiliation(s)
- Eric T. C. Wong
- Centre for High-Throughput Biology, University of British Columbia, East Mall, Vancouver, Canada
| | - Dokyun Na
- Centre for High-Throughput Biology, University of British Columbia, East Mall, Vancouver, Canada
| | - Jörg Gsponer
- Centre for High-Throughput Biology, University of British Columbia, East Mall, Vancouver, Canada
- * E-mail:
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147
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Pratap JV, Luisi BF, Calladine CR. Geometric principles in the assembly of α-helical bundles. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120369. [PMID: 23690631 DOI: 10.1098/rsta.2012.0369] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
α-Helical coiled coils are usually stabilized by hydrophobic interfaces between the two constituent α-helices, in the form of 'knobs-into-holes' packing of non-polar residues arranged in repeating heptad patterns. Here we examine the corresponding 'hydrophobic cores' that stabilize bundles of four α-helices. In particular, we study three different kinds of bundle, involving four α-helices of identical sequence: two pack in a parallel and one in an anti-parallel orientation. We point out that the simplest way of understanding the packing of these 4-helix bundles is to use Crick's original idea that the helices are held together by 'hydrophobic stripes', which are readily visualized on the cylindrical surface lattice of the α-helices; and that the 'helix-crossing angle'--which determines, in particular, whether supercoiling is left- or right-handed--is fixed by the slope of the lattice lines that contain the hydrophobic residues. In our three examples the constituent α-helices have hydrophobic repeat patterns of 7, 11 and 4 residues, respectively; and we associate the different overall conformations with 'knobs-into-holes' packing along the 7-, 11- and 4-start lines, respectively, of the cylindrical surface lattices of the constituent α-helices. For the first two examples, all four interfaces between adjacent helices are geometrically equivalent; but in the third, one of the four interfaces differs significantly from the others. We provide a geometrical explanation for this non-equivalence in terms of two different but equivalent ways of assembling this bundle, which may possibly constitute a bistable molecular 'switch' with a coaxial throw of about 12 Å. The geometrical ideas that we deploy in this paper provide the simplest and clearest description of the structure of helical bundles. In an appendix, we describe briefly a computer program that we have devised in order to search for 'knobs-into-holes' packing between α-helices in proteins.
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Affiliation(s)
- J V Pratap
- Molecular and Structural Biology Division, Central Drug Research Institute, 10/1 Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226 020, India
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148
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Bicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to coordinate recruitment of cargos to dynein. Genes Dev 2013; 27:1233-46. [PMID: 23723415 DOI: 10.1101/gad.212381.112] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cytoplasmic dynein is the major minus end-directed microtubule motor in eukaryotes. However, there is little structural insight into how different cargos are recognized and linked to the motor complex. Here we describe the 2.2 Å resolution crystal structure of a cargo-binding region of the dynein adaptor Bicaudal-D (BicD), which reveals a parallel coiled-coil homodimer. We identify a shared binding site for two cargo-associated proteins-Rab6 and the RNA-binding protein Egalitarian (Egl)-within a region of the BicD structure with classical, homotypic core packing. Structure-based mutagenesis in Drosophila provides evidence that occupancy of this site drives association of BicD with dynein, thereby coupling motor recruitment to cargo availability. The structure also contains a region in which, remarkably, the same residues in the polypeptide sequence have different heptad registry in each chain. In vitro and in vivo analysis of a classical Drosophila dominant mutation reveals that this heterotypic region regulates the recruitment of dynein to BicD. Our results support a model in which the heterotypic segment is part of a molecular switch that promotes release of BicD autoinhibition following cargo binding to the neighboring, homotypic coiled-coil region. Overall, our data reveal a pivotal role of a highly asymmetric coiled-coil domain in coordinating the assembly of cargo-motor complexes.
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149
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Ihara M, Hamamoto S, Miyanoiri Y, Takeda M, Kainosho M, Yabe I, Uozumi N, Yamashita A. Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel. J Biol Chem 2013; 288:15303-17. [PMID: 23553631 DOI: 10.1074/jbc.m112.434795] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multimodal activation by various stimuli is a fundamental characteristic of TRP channels. We identified a fungal TRP channel, TRPGz, exhibiting activation by hyperosmolarity, temperature increase, cytosolic Ca(2+) elevation, membrane potential, and H2O2 application, and thus it is expected to represent a prototypic multimodal TRP channel. TRPGz possesses a cytosolic C-terminal domain (CTD), primarily composed of intrinsically disordered regions with some regulatory modules, a putative coiled-coil region and a basic residue cluster. The CTD oligomerization mediated by the coiled-coil region is required for the hyperosmotic and temperature increase activations but not for the tetrameric channel formation or other activation modalities. In contrast, the basic cluster is responsible for general channel inhibition, by binding to phosphatidylinositol phosphates. The crystal structure of the presumed coiled-coil region revealed a tetrameric assembly in an offset spiral rather than a canonical coiled-coil. This structure underlies the observed moderate oligomerization affinity enabling the dynamic assembly and disassembly of the CTD during channel functions, which are compatible with the multimodal regulation mediated by each functional module.
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Affiliation(s)
- Makoto Ihara
- Molecular Signaling Research Team, Structural Physiology Research Group, RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
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150
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Malik L, Nygaard J, Christensen NJ, Streicher WW, Thulstrup PW, Arleth L, Jensen KJ. Self-assembly of designed coiled coil peptides studied by small-angle X-ray scattering and analytical ultracentrifugation. J Pept Sci 2013; 19:283-92. [DOI: 10.1002/psc.2497] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/23/2013] [Accepted: 01/24/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Leila Malik
- University of Copenhagen; Thorvaldsensvej 40 DK-1871 Frederiksberg C Denmark
| | - Jesper Nygaard
- University of Copenhagen; Thorvaldsensvej 40 DK-1871 Frederiksberg C Denmark
- University of Lund; Ole Römers väg 1 SE-223 63 Lund Sweden
| | | | - Werner W. Streicher
- Faculty of Health Science; NNF Center for Protein Research; Blegdamsvej 3B DK-2200 Copenhagen N Denmark
| | - Peter W. Thulstrup
- University of Copenhagen; Thorvaldsensvej 40 DK-1871 Frederiksberg C Denmark
| | - Lise Arleth
- University of Copenhagen; Thorvaldsensvej 40 DK-1871 Frederiksberg C Denmark
| | - Knud J. Jensen
- University of Copenhagen; Thorvaldsensvej 40 DK-1871 Frederiksberg C Denmark
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