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Gomez Barroso JA, Miranda MR, Pereira CA, Garratt RC, Aguilar CF. X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure. Acta Crystallogr D Struct Biol 2022; 78:30-42. [PMID: 34981759 DOI: 10.1107/s2059798321011219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
Trypanosoma cruzi is a flagellated protozoan parasite that causes Chagas disease, which represents a serious health problem in the Americas. Nucleoside diphosphate kinases (NDPKs) are key enzymes that are implicated in cellular energy management. TcNDPK1 is the canonical isoform in the T. cruzi parasite. TcNDPK1 has a cytosolic, perinuclear and nuclear distribution. It is also found in non-membrane-bound filaments adjacent to the nucleus. In the present work, X-ray diffraction and in vivo studies of TcNDPK1 are described. The structure reveals a novel, multi-hexameric, left-handed helical oligomer structure. The results of directed mutagenesis studies led to the conclusion that the microscopic TcNDPK1 granules observed in vivo in T. cruzi parasites are made up by the association of TcNDPK1 oligomers. In the absence of experimental data, analysis of the interactions in the X-ray structure of the TcNDPK1 oligomer suggests the probable assembly and disassembly steps: dimerization, assembly of the hexamer as a trimer of dimers, hexamer association to generate the left-handed helical oligomer structure and finally oligomer association in a parallel manner to form the microscopic TcNDPK1 filaments that are observed in vivo in T. cruzi parasites. Oligomer disassembly takes place on the binding of substrate in the active site of TcNDPK1, leading to dissociation of the hexamers. This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1.
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Affiliation(s)
- Juan Arturo Gomez Barroso
- Laboratorio de Biología Molecular Estructural, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Mariana Reneé Miranda
- Laboratorio de Parasitología Molecular, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Claudio Alejandro Pereira
- Laboratorio de Parasitología Molecular, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Richard Charles Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense No. 400, São Carlos, São Paulo 13566-590, Brazil
| | - Carlos Fernando Aguilar
- Laboratorio de Biología Molecular Estructural, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina
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Hummel MH, Yu B, Simmerling C, Coutsias EA. LAGUERRE-INTERSECTION METHOD FOR IMPLICIT SOLVATION. ACTA ACUST UNITED AC 2019; 28:1-38. [PMID: 30853740 DOI: 10.1142/s0218195918500012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Explicit solvent molecular dynamics simulations of a macromolecule are slow as the number of solvent atoms considered typically increases by order of magnitude. Implicit methods introduce surface-dependent corrections to the force field, gaining speed at the expense of accuracy. Properties such as molecular interface surfaces, volumes and cavities are captured by Laguerre tessellations of macromolecules. However, Laguerre cells of exterior atoms tend to be overly large or unbounded. Our method, the inclusion-exclusion based Laguerre-Intersection method, caps cells in a physically accurate manner by considering the intersection of the space-filling diagram with the Laguerre tessellation. We optimize an adjustable parameter, the weight, to ensure the areas and volumes of capped cells exposed to solvent are as close as possible, on average, to those computed from equilibrated explicit solvent simulations. The contact planes are radical planes, meaning that as the solvent weight is varied, interior cells remain constant. We test the consistency of our model using a high-quality trajectory of HIV-protease, a dimer with flexible loops and open-close transitions. We also compare our results with interval-arithmetic Gauss-Bonnet based method. Optimal solvent parameters quickly converge, which we use to illustrate the increased fidelity of the Laguerre-Intersection method over two recently proposed methods as compared to the explicit model.
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Affiliation(s)
- Michelle Hatch Hummel
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bihua Yu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Carlos Simmerling
- Department of Chemistry and Laufer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Evangelos A Coutsias
- Department of Applied Mathematics and Statistics and Laufer Center, Stony Brook University, Stony Brook, NY 11794, USA
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Label-free optical biosensor for target detection based on simulation-assisted catalyzed hairpin assembly. Comput Biol Chem 2018; 78:448-454. [PMID: 30545762 DOI: 10.1016/j.compbiolchem.2018.11.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 12/23/2022]
Abstract
The development of efficient and convenient strategy without involving enzyme or complex nanomaterial for the micro molecules detection has profound meaning in the diagnosis of diseases. Herein, taking the advantages of the strong affinity of aptamer and catalyzed hairpin assembly, we develop a new non-label optical amplified strategy for thrombin detection in this work. To support both biological inquiry and technological innovation, thermodynamic models are introduced to predict the minimum energy secondary structure of interacting nucleic acid strands and calculate the partition function and equilibrium concentration for complexes in our system. Then, the thermodynamics properties of interacting DNA strands and the reactions of toehold strand displacement-driven assembly have been simulated, validating the feasibility of the theory and optimizing the follow-up lab tests. Following that, our strategy for thrombin detection is proved to be feasible and effective in biological experiment. Taken together, such a biosensor has a good potential in bioactive molecules detection and disease diagnosis for future biological research.
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Ismer J, Rose AS, Tiemann JKS, Hildebrand PW. A fragment based method for modeling of protein segments into cryo-EM density maps. BMC Bioinformatics 2017; 18:475. [PMID: 29132296 PMCID: PMC5683378 DOI: 10.1186/s12859-017-1904-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly enhanced the resolution of cryo-EM density maps and broadened the applicability and the circle of users. To facilitate modeling of macromolecules into cryo-EM density maps, fast and easy to use methods for modeling are now demanded. RESULTS Here we investigated and benchmarked the suitability of a classical and well established fragment-based approach for modeling of segments into cryo-EM density maps (termed FragFit). FragFit uses a hierarchical strategy to select fragments from a pre-calculated set of billions of fragments derived from structures deposited in the Protein Data Bank, based on sequence similarly, fit of stem atoms and fit to a cryo-EM density map. The user only has to specify the sequence of the segment and the number of the N- and C-terminal stem-residues in the protein. Using a representative data set of protein structures, we show that protein segments can be accurately modeled into cryo-EM density maps of different resolution by FragFit. Prediction quality depends on segment length, the type of secondary structure of the segment and local quality of the map. CONCLUSION Fast and automated calculation of FragFit renders it applicable for implementation of interactive web-applications e.g. to model missing segments, flexible protein parts or hinge-regions into cryo-EM density maps.
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Affiliation(s)
- Jochen Ismer
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Alexander S Rose
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany.,RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, CA, 92093-0743, USA
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany.,Institute of Medical Physics and Biophysics, University Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany. .,Institute of Medical Physics and Biophysics, University Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
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Lidor O, Al-Quntar A, Pesci EC, Steinberg D. Mechanistic analysis of a synthetic inhibitor of the Pseudomonas aeruginosa LasI quorum-sensing signal synthase. Sci Rep 2015; 5:16569. [PMID: 26593271 PMCID: PMC4655403 DOI: 10.1038/srep16569] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/14/2015] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen responsible for many human infections. LasI is an acyl-homoserine lactone synthase that produces a quorum-sensing (QS) signal that positively regulates numerous P. aeruginosa virulence determinants. The inhibition of the LasI protein is therefore an attractive drug target. In this study, a novel in silico to in vitro complementation was applied to screen thiazolidinedione-type compounds for their ability to inhibit biofilm formation at concentrations not affecting bacterial growth. The compound (z)-5-octylidenethiazolidine-2, 4-dione (TZD-C8) was a strong inhibitor of biofilm formation and chosen for further study. Structural exploration of in silico docking predicted that the compound had high affinity for the LasI activity pocket. The TZD-C8 compound was also predicted to create hydrogen bonds with residues Arg30 and Ile107. Site-directed mutagenesis (SDM) of these two sites demonstrated that TZD-C8 inhibition was abolished in the lasI double mutant PAO-R30D, I107S. In addition, in vitro swarming motility and quorum sensing signal production were affected by TZD-C 8, confirming this compound alters the cell to cell signalling circuitry. Overall, this novel inhibitor of P. aeruginosa quorum sensing shows great promise and validates our mechanistic approach to discovering inhibitors of LuxI-type acyl-homoserine lactone synthases.
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Affiliation(s)
- O. Lidor
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - A. Al-Quntar
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Institute of Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - E. C. Pesci
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, USA
| | - D. Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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