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Chang TH, Hsieh FL, Gu X, Smallwood PM, Kavran JM, Gabelli SB, Nathans J. Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae. Proc Natl Acad Sci U S A 2023; 120:e2221103120. [PMID: 36996108 PMCID: PMC10083539 DOI: 10.1073/pnas.2221103120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low-molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration-presumably a coiled coil-held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP-i.e., the long dimension of the pore-and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.
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Affiliation(s)
- Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Fu-Lien Hsieh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Xiaowu Gu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Philip M. Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jennifer M. Kavran
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD21205
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2
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Coiled-coil structure of meiosis protein TEX12 and conformational regulation by its C-terminal tip. Commun Biol 2022; 5:921. [PMID: 36071143 PMCID: PMC9452514 DOI: 10.1038/s42003-022-03886-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/24/2022] [Indexed: 11/12/2022] Open
Abstract
Meiosis protein TEX12 is an essential component of the synaptonemal complex (SC), which mediates homologous chromosome synapsis. It is also recruited to centrosomes in meiosis, and aberrantly in certain cancers, leading to centrosome dysfunction. Within the SC, TEX12 forms an intertwined complex with SYCE2 that undergoes fibrous assembly, driven by TEX12’s C-terminal tip. However, we hitherto lack structural information regarding SYCE2-independent functions of TEX12. Here, we report X-ray crystal structures of TEX12 mutants in three distinct conformations, and utilise solution light and X-ray scattering to determine its wild-type dimeric four-helical coiled-coil structure. TEX12 undergoes conformational change upon C-terminal tip mutations, indicating that the sequence responsible for driving SYCE2-TEX12 assembly within the SC also controls the oligomeric state and conformation of isolated TEX12. Our findings provide the structural basis for SYCE2-independent roles of TEX12, including the possible regulation of SC assembly, and its known functions in meiotic centrosomes and cancer. The X-ray crystal structures of C-terminal mutants of the coiled-coil protein cancer testis antigen TEX12 in combination with modeling of the TEX12 wild-type dimer reveal the protein’s control of its oligomeric state, which resembles assembly of its complex with synaptonemal complex central element protein SYCE2.
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3
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Simpkin AJ, Thomas JMH, Keegan RM, Rigden DJ. MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:553-559. [PMID: 35503204 PMCID: PMC9063843 DOI: 10.1107/s2059798322003576] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/29/2022] [Indexed: 11/10/2022]
Abstract
Crystallographers have an array of search-model options for structure solution by molecular replacement (MR). The well established options of homologous experimental structures and regular secondary-structure elements or motifs are increasingly supplemented by computational modelling. Such modelling may be carried out locally or may use pre-calculated predictions retrieved from databases such as the EBI AlphaFold database. MrParse is a new pipeline to help to streamline the decision process in MR by consolidating bioinformatic predictions in one place. When reflection data are provided, MrParse can rank any experimental homologues found using eLLG, which indicates the likelihood that a given search model will work in MR. Inbuilt displays of predicted secondary structure, coiled-coil and transmembrane regions further inform the choice of MR protocol. MrParse can also identify and rank homologues in the EBI AlphaFold database, a function that will also interest other structural biologists and bioinformaticians.
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4
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McCoy AJ, Sammito MD, Read RJ. Implications of AlphaFold2 for crystallographic phasing by molecular replacement. Acta Crystallogr D Struct Biol 2022; 78:1-13. [PMID: 34981757 PMCID: PMC8725160 DOI: 10.1107/s2059798321012122] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/13/2021] [Indexed: 12/11/2022] Open
Abstract
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models.
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Affiliation(s)
- Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
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5
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Morton CR, Rzechorzek NJ, Maman JD, Kuramochi M, Sekiguchi H, Rambo R, Sasaki YC, Davies OR, Pellegrini L. Structural basis for the coiled-coil architecture of human CtIP. Open Biol 2021; 11:210060. [PMID: 34129781 PMCID: PMC8205527 DOI: 10.1098/rsob.210060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The DNA repair factor CtIP has a critical function in double-strand break (DSB) repair by homologous recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here, we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, small-angle X-ray scattering (SAXS) and diffracted X-ray tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during the recombinational repair. The zinc-binding motif in the CtIP N-terminus alters dynamically the coiled-coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.
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Affiliation(s)
- C R Morton
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - N J Rzechorzek
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - J D Maman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - M Kuramochi
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan
| | - H Sekiguchi
- Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - R Rambo
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, UK
| | - Y C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan.,Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - O R Davies
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - L Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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6
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McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ. Phasertng: directed acyclic graphs for crystallographic phasing. Acta Crystallogr D Struct Biol 2021; 77:1-10. [PMID: 33404520 PMCID: PMC7787104 DOI: 10.1107/s2059798320014746] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 11/06/2020] [Indexed: 12/01/2022] Open
Abstract
Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies.
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Affiliation(s)
- Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Duncan H. Stockwell
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Kaushik S. Hatti
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
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7
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Muok AR, Ortega DR, Kurniyati K, Yang W, Maschmann ZA, Sidi Mabrouk A, Li C, Crane BR, Briegel A. Atypical chemoreceptor arrays accommodate high membrane curvature. Nat Commun 2020; 11:5763. [PMID: 33188180 PMCID: PMC7666581 DOI: 10.1038/s41467-020-19628-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended array. Here, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of the histidine kinase CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that Td chemoreceptor arrays assume an unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus. Furthermore, the previously characterized Td oxygen sensor ODP influences CheA ordering. These results suggest a greater diversity of the chemotaxis signaling system than previously thought.
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Affiliation(s)
- Alise R Muok
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Davi R Ortega
- Department of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Kurni Kurniyati
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Zachary A Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Adam Sidi Mabrouk
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
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8
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Sánchez Rodríguez F, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ. Helical ensembles outperform ideal helices in molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:962-970. [PMID: 33021498 PMCID: PMC7543657 DOI: 10.1107/s205979832001133x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/18/2020] [Indexed: 03/21/2023]
Abstract
Helical ensembles solve more structures by MR with AMPLE than do ideal helices and at no greater CPU cost. The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the ‘helical ensembles’ mode.
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Affiliation(s)
- Filomeno Sánchez Rodríguez
- Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Adam J Simpkin
- Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Ronan M Keegan
- UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Daniel J Rigden
- Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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9
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Thomas JMH, Keegan RM, Rigden DJ, Davies OR. Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling. Acta Crystallogr D Struct Biol 2020; 76:272-284. [PMID: 32133991 PMCID: PMC7057219 DOI: 10.1107/s2059798320000443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022] Open
Abstract
The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.
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Affiliation(s)
- Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Owen R. Davies
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, England
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Millán C, Jiménez E, Schuster A, Diederichs K, Usón I. ALIXE: a phase-combination tool for fragment-based molecular replacement. Acta Crystallogr D Struct Biol 2020; 76:209-220. [PMID: 32133986 PMCID: PMC7057212 DOI: 10.1107/s205979832000056x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/15/2020] [Indexed: 11/10/2022] Open
Abstract
Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.
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Affiliation(s)
- Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Antonia Schuster
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
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11
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Combinatorial use of disulfide bridges and native sulfur-SAD phasing for rapid structure determination of coiled-coils. Biosci Rep 2018; 38:BSR20181073. [PMID: 30135143 PMCID: PMC6146289 DOI: 10.1042/bsr20181073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 01/16/2023] Open
Abstract
Coiled-coils are ubiquitous protein-protein interaction motifs found in many eukaryotic proteins. The elongated, flexible and often irregular nature of coiled-coils together with their tendency to form fibrous arrangements in crystals imposes challenges on solving the phase problem by molecular replacement. Here, we report the successful combinatorial use of native and rational engineered disulfide bridges together with sulfur-SAD phasing as a powerful tool to stabilize and solve the structure of coiled-coil domains in a straightforward manner. Our study is a key example of how modern sulfur SAD combined with mutagenesis can help to advance and simplify the structural study of challenging coiled-coil domains by X-ray crystallography.
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12
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Caballero I, Sammito M, Millán C, Lebedev A, Soler N, Usón I. ARCIMBOLDO on coiled coils. Acta Crystallogr D Struct Biol 2018; 74:194-204. [PMID: 29533227 PMCID: PMC5947760 DOI: 10.1107/s2059798317017582] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/08/2017] [Indexed: 11/10/2022] Open
Abstract
ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15-635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i.
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Affiliation(s)
- Iracema Caballero
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Andrey Lebedev
- CCP4, STFC Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, England
| | - Nicolas Soler
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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13
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Keegan RM, McNicholas SJ, Thomas JMH, Simpkin AJ, Simkovic F, Uski V, Ballard CC, Winn MD, Wilson KS, Rigden DJ. Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. Acta Crystallogr D Struct Biol 2018; 74:167-182. [PMID: 29533225 PMCID: PMC5947758 DOI: 10.1107/s2059798318003455] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/27/2018] [Indexed: 01/21/2023] Open
Abstract
Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement. MrBUMP is a CCP4 pipeline which automates all stages of the MR procedure. Its scope covers everything from the sourcing and preparation of suitable search models right through to rebuilding of the positioned search model. Recent improvements to the pipeline include the adoption of more sensitive bioinformatic tools for sourcing search models, enhanced model-preparation techniques including better ensembling of homologues, and the use of phase improvement and model building on the resulting solution. The pipeline has also been deployed as an online service through CCP4 online, which allows its users to exploit large bioinformatic databases and coarse-grained parallelism to speed up the determination of a possible solution. Finally, the molecular-graphics application CCP4mg has been combined with MrBUMP to provide an interactive visual aid to the user during the process of selecting and manipulating search models for use in MR. Here, these developments in MrBUMP are described with a case study to explore how some of the enhancements to the pipeline and to CCP4mg can help to solve a difficult case.
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Affiliation(s)
- Ronan M. Keegan
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Stuart J. McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Adam J. Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ville Uski
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles C. Ballard
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Martyn D. Winn
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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14
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Jenkins HT. Fragon: rapid high-resolution structure determination from ideal protein fragments. Acta Crystallogr D Struct Biol 2018; 74:205-214. [PMID: 29533228 PMCID: PMC5947761 DOI: 10.1107/s2059798318002292] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 02/07/2018] [Indexed: 12/02/2022] Open
Abstract
Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure.
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Affiliation(s)
- Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
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15
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Thomas JMH, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ. Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallogr D Struct Biol 2017; 73:985-996. [PMID: 29199978 PMCID: PMC5713875 DOI: 10.1107/s2059798317016436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/15/2017] [Indexed: 02/06/2023] Open
Abstract
α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.
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Affiliation(s)
- Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Olga Mayans
- Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, Department of Biological Chemistry, Medical School, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, Department of Biological Chemistry, Medical School, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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16
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Abstract
Molecular replacement is a method for solving the crystallographic phase problem using an atomic model for the target structure. State-of-the-art methods have moved the field significantly from when it was first envisaged as a method for solving cases of high homology and completeness between a model and target structure. Improvements brought about by application of maximum likelihood statistics mean that various errors in the model and pathologies in the data can be accounted for, so that cases hitherto thought to be intractable are standardly solvable. As a result, molecular replacement phasing now accounts for the lion's share of structures deposited in the Protein Data Bank. However, there will always be cases at the fringes of solvability. I discuss here the approaches that will help tackle challenging molecular replacement cases.
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Affiliation(s)
- Airlie J McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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17
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Sporny M, Guez-Haddad J, Waterman DG, Isupov MN, Opatowsky Y. Molecular symmetry-constrained systematic search approach to structure solution of the coiled-coil SRGAP2 F-BARx domain. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1241-1253. [PMID: 27917825 DOI: 10.1107/s2059798316016697] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
SRGAP2 (Slit-Robo GTPase-activating protein 2) is a cytoplasmic protein found to be involved in neuronal branching, restriction of neuronal migration and restriction of the length and density of dendritic postsynaptic spines. The extended F-BAR (F-BARx) domain of SRGAP2 generates membrane protrusions when expressed in COS-7 cells, while most F-BARs induce the opposite effect: membrane invaginations. As a first step to understand this discrepancy, the F-BARx domain of SRGAP2 was isolated and crystallized after co-expression with the carboxy domains of the protein. Diffraction data were collected from two significantly non-isomorphous crystals in the same monoclinic C2 space group. A correct molecular-replacment solution was obtained by applying a molecular symmetry-constrained systematic search approach that took advantage of the conserved biological symmetry of the F-BAR domains. It is shown that similar approaches can solve other F-BAR structures that were previously determined by experimental phasing. Diffraction data were reprocessed with a high-resolution cutoff of 2.2 Å, chosen using less strict statistical criteria. This has improved the outcome of multi-crystal averaging and other density-modification procedures.
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Affiliation(s)
- Michael Sporny
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Julia Guez-Haddad
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | | | | | - Yarden Opatowsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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18
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Simkovic F, Thomas JMH, Keegan RM, Winn MD, Mayans O, Rigden DJ. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCRJ 2016; 3:259-70. [PMID: 27437113 PMCID: PMC4937781 DOI: 10.1107/s2052252516008113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/18/2016] [Indexed: 05/05/2023]
Abstract
For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.
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Affiliation(s)
- Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Martyn D. Winn
- Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD, England
| | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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19
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Dauter Z. Solving coiled-coil protein structures. IUCRJ 2015; 2:164-5. [PMID: 25866652 PMCID: PMC4392410 DOI: 10.1107/s2052252515003486] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
The successful approach to solving crystal structures of coiled-coil proteins with the program AMPLE is discussed.
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Affiliation(s)
- Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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