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Kong R, Liu R, Xu X, Zhang D, Xu X, Shi H, Chang S. Template‐based modeling and ab‐initio docking using
CoDock
in
CAPRI. Proteins 2020; 88:1100-1109. [DOI: 10.1002/prot.25892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/21/2019] [Accepted: 03/07/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
| | - Ran‐Ran Liu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
| | - Xi‐Ming Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Da‐Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
| | - Xiao‐Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
| | - Hang Shi
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology Qingdao China
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Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue LC, Honorato RV, Moreira I, Kurkcuoglu Z, Vangone A, Bonvin AMJJ. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins 2019; 88:1029-1036. [PMID: 31886559 DOI: 10.1002/prot.25869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/17/2019] [Accepted: 12/26/2019] [Indexed: 01/18/2023]
Abstract
Our information-driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part, to its ability to integrate data into the modeling process, and to the robustness of its scoring function. We participated in CAPRI both as server and manual predictors. In CAPRI rounds 38-45, we have used various strategies depending on the available information. These ranged from imposing restraints to a few residues identified from literature as being important for the interaction, to binding pockets identified from homologous complexes or template-based refinement/CA-CA restraint-guided docking from identified templates. When relevant, symmetry restraints were used to limit the conformational sampling. We also tested for a large decamer target a new implementation of the MARTINI coarse-grained force field in HADDOCK. Overall, we obtained acceptable or better predictions for 13 and 11 server and manual submissions, respectively, out of the 22 interfaces. Our server performance (acceptable or higher-quality models when considering the top 10) was better (59%) than the manual (50%) one, in which we typically experiment with various combinations of protocols and data sources. Again, our simple scoring function based on a linear combination of intermolecular van der Waals and electrostatic energies and an empirical desolvation term demonstrated a good performance in the scoring experiment with a 63% success rate across all 22 interfaces. An analysis of model quality indicates that, while we are consistently performing well in generating acceptable models, there is room for improvement for generating/identifying higher quality models.
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Affiliation(s)
- Panagiotis I Koukos
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Jorge Roel-Touris
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Francesco Ambrosetti
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.,Department of Physics, Sapienza University, Rome, Italy
| | - Cunliang Geng
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Jörg Schaarschmidt
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.,Multiscale Materials Modelling and Virtual Design, Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Mikael E Trellet
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Adrien S J Melquiond
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Li C Xue
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Rodrigo V Honorato
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Irina Moreira
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.,CNC-Center for Neuroscience and Cell Biology, Rua Larga, FMUC, Polo I, 1° andar, Universidade de Coimbra, Coimbra, Portugal
| | - Zeynep Kurkcuoglu
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Anna Vangone
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands
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Kita S, Matsubara H, Kasai Y, Tamaoki T, Okabe Y, Fukuhara H, Kamishikiryo J, Krayukhina E, Uchiyama S, Ose T, Kuroki K, Maenaka K. Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A. Eur J Immunol 2015; 45:1605-13. [DOI: 10.1002/eji.201545509] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/01/2015] [Accepted: 03/26/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Shunsuke Kita
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Haruki Matsubara
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
- Department of Materials Structure Science; Structural Biology Research Center; Photon Factory; Institute of Materials Structure Science; High Energy Accelerator Research Organization (KEK); The Graduate University for Advanced Studies; Tsukuba Ibaraki Japan
| | - Yoshiyuki Kasai
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Takaharu Tamaoki
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Yuki Okabe
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
- Research Center for Hepatitis and Immunology; National Center for Global Health and Medicine; 1-7-1 Kohnodai Ichikawa Chiba Japan
| | - Hideo Fukuhara
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Jun Kamishikiryo
- Faculty of Pharmacy and Pharmaceutical Sciences; Fukuyama University; Fukuyama Japan
| | - Elena Krayukhina
- Department of Biotechnology; Graduate School of Engineering; Osaka University; Osaka Japan
- U-Medico Corporation; Osaka Japan
| | - Susumu Uchiyama
- Department of Biotechnology; Graduate School of Engineering; Osaka University; Osaka Japan
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Kimiko Kuroki
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science; Faculty of Pharmaceutical Sciences; Hokkaido University; Sapporo Japan
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Skálová T, Bláha J, Harlos K, Dušková J, Koval’ T, Stránský J, Hašek J, Vaněk O, Dohnálek J. Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:578-91. [PMID: 25760607 PMCID: PMC4356368 DOI: 10.1107/s1399004714027928] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/22/2014] [Indexed: 12/03/2022]
Abstract
Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, gene KLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the first N-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5 glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.
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Affiliation(s)
- Tereza Skálová
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jan Bláha
- Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic
| | - Karl Harlos
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jarmila Dušková
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Tomáš Koval’
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
| | - Jan Stránský
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Jindřich Hašek
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, 128 40 Praha, Czech Republic
| | - Jan Dohnálek
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Heyrovského nám. 2, 162 06 Praha 6, Czech Republic
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Rozbeský D, Ivanova L, Hernychová L, Grobárová V, Novák P, Černý J. Nkrp1 family, from lectins to protein interacting molecules. Molecules 2015; 20:3463-78. [PMID: 25690298 PMCID: PMC6272133 DOI: 10.3390/molecules20023463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022] Open
Abstract
The C-type lectin-like receptors include the Nkrp1 protein family that regulates the activity of natural killer (NK) cells. Rat Nkrp1a was reported to bind monosaccharide moieties in a Ca2+-dependent manner in preference order of GalNac > GlcNAc >> Fuc >> Gal > Man. These findings established for rat Nkrp1a have been extrapolated to all additional Nkrp1 receptors and have been supported by numerous studies over the past two decades. However, since 1996 there has been controversy and another article showed lack of interactions with saccharides in 1999. Nevertheless, several high affinity saccharide ligands were synthesized in order to utilize their potential in antitumor therapy. Subsequently, protein ligands were introduced as specific binders for Nkrp1 proteins and three dimensional models of receptor/protein ligand interaction were derived from crystallographic data. Finally, for at least some members of the NK cell C-type lectin-like proteins, the “sweet story” was impaired by two reports in recent years. It has been shown that the rat Nkrp1a and CD69 do not bind saccharide ligands such as GlcNAc, GalNAc, chitotetraose and saccharide derivatives (GlcNAc-PAMAM) do not directly and specifically influence cytotoxic activity of NK cells as it was previously described.
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MESH Headings
- Animals
- Antigens, CD/chemistry
- Antigens, CD/immunology
- Antigens, CD/metabolism
- Antigens, Differentiation, T-Lymphocyte/chemistry
- Antigens, Differentiation, T-Lymphocyte/immunology
- Antigens, Differentiation, T-Lymphocyte/metabolism
- Humans
- Killer Cells, Natural/chemistry
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/chemistry
- Lectins, C-Type/immunology
- Lectins, C-Type/metabolism
- Male
- NK Cell Lectin-Like Receptor Subfamily B/chemistry
- NK Cell Lectin-Like Receptor Subfamily B/immunology
- NK Cell Lectin-Like Receptor Subfamily B/metabolism
- Oligosaccharides/chemistry
- Oligosaccharides/immunology
- Oligosaccharides/metabolism
- Protein Structure, Tertiary
- Rats
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Affiliation(s)
- Daniel Rozbeský
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 414220, Czech Republic.
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 212843, Czech Republic.
| | - Ljubina Ivanova
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 414220, Czech Republic.
| | - Lucie Hernychová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 414220, Czech Republic.
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague 212843, Czech Republic.
| | - Valéria Grobárová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague 212843, Czech Republic.
| | - Petr Novák
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 414220, Czech Republic.
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 212843, Czech Republic.
| | - Jan Černý
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague 212843, Czech Republic.
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Kirkham CL, Carlyle JR. Complexity and Diversity of the NKR-P1:Clr (Klrb1:Clec2) Recognition Systems. Front Immunol 2014; 5:214. [PMID: 24917862 PMCID: PMC4041007 DOI: 10.3389/fimmu.2014.00214] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022] Open
Abstract
The NKR-P1 receptors were identified as prototypical natural killer (NK) cell surface antigens and later shown to be conserved from rodents to humans on NK cells and subsets of T cells. C-type lectin-like in nature, they were originally shown to be capable of activating NK cell function and to recognize ligands on tumor cells. However, certain family members have subsequently been shown to be capable of inhibiting NK cell activity, and to recognize proteins encoded by a family of genetically linked C-type lectin-related ligands. Some of these ligands are expressed by normal, healthy cells, and modulated during transformation, infection, and cellular stress, while other ligands are upregulated during the immune response and during pathological circumstances. Here, we discuss historical and recent developments in NKR-P1 biology that demonstrate this NK receptor–ligand system to be far more complex and diverse than originally anticipated.
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Affiliation(s)
- Christina L Kirkham
- Department of Immunology, University of Toronto, Sunnybrook Research Institute , Toronto, ON , Canada
| | - James R Carlyle
- Department of Immunology, University of Toronto, Sunnybrook Research Institute , Toronto, ON , Canada
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