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Miyamoto Y, Nakatsuji M, Yoshida T, Ohkubo T, Inui T. Structural and interaction analysis of human lipocalin-type prostaglandin D synthase with the poorly water-soluble drug NBQX. FEBS J 2023; 290:3983-3996. [PMID: 37021622 DOI: 10.1111/febs.16791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023]
Abstract
Lipocalin-type prostaglandin D synthase (L-PGDS) is a secretory lipid-transporter protein that was shown to bind a wide variety of hydrophobic ligands in vitro. Exploiting this function, we previously examined the feasibility of using L-PGDS as a novel delivery vehicle for poorly water-soluble drugs. However, the mechanism by which human L-PGDS binds to poorly water-soluble drugs is unclear. In this study, we determined the solution structure of human L-PGDS and investigated the mechanism of L-PGDS binding to 6-nitro-7-sulfamoyl-benzo[f]quinoxalin-2,3-dione (NBQX), an α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor antagonist. NMR experiments showed that human L-PGDS has an eight-stranded antiparallel β-barrel structure that forms a central cavity, a short 310 -helix and two α-helices. Titration with NBQX was monitored using 1 H-15 N HSQC spectroscopy. At higher NBQX concentrations, some cross-peaks of the protein exhibited fast-exchanging shifts with a curvature, indicating at least two binding sites. These residues were located in the upper portion of the cavity. Singular value decomposition analysis revealed that human L-PGDS has two NBQX binding sites. Large chemical shift changes were observed in the H2-helix and A-, B-, C-, D-, H- and I-strands and H2-helix upon NBQX binding. Calorimetric experiments revealed that human L-PGDS binds two NBQX molecules with dissociation constants of 46.7 μm for primary binding and 185.0 μm for secondary binding. Molecular docking simulations indicated that these NBQX binding sites are located within the β-barrel. These results provide new insights into the interaction between poorly water-soluble drugs and human L-PGDS as a drug carrier.
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Affiliation(s)
- Yuya Miyamoto
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Masatoshi Nakatsuji
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Takuya Yoshida
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Tadayasu Ohkubo
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Takashi Inui
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
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2
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Pérez-Reytor D, Pavón A, Lopez-Joven C, Ramírez-Araya S, Peña-Varas C, Plaza N, Alegría-Arcos M, Corsini G, Jaña V, Pavez L, Del Pozo T, Bastías R, Blondel CJ, Ramírez D, García K. Analysis of the Zonula occludens Toxin Found in the Genome of the Chilean Non-toxigenic Vibrio parahaemolyticus Strain PMC53.7. Front Cell Infect Microbiol 2020; 10:482. [PMID: 33072618 PMCID: PMC7541967 DOI: 10.3389/fcimb.2020.00482] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Vibrio parahaemolyticus non-toxigenic strains are responsible for about 10% of acute gastroenteritis associated with this species, suggesting they harbor unique virulence factors. Zonula occludens toxin (Zot), firstly described in Vibrio cholerae, is a secreted toxin that increases intestinal permeability. Recently, we identified Zot-encoding genes in the genomes of highly cytotoxic Chilean V. parahaemolyticus strains, including the non-toxigenic clinical strain PMC53.7. To gain insights into a possible role of Zot in V. parahaemolyticus, we analyzed whether it could be responsible for cytotoxicity. However, we observed a barely positive correlation between Caco-2 cell membrane damage and Zot mRNA expression during PMC53.7 infection and non-cytotoxicity induction in response to purified PMC53.7-Zot. Unusually, we observed a particular actin disturbance on cells infected with PMC53.7. Based on this observation, we decided to compare the sequence of PMC53.7-Zot with Zot of human pathogenic species such as V. cholerae, Campylobacter concisus, Neisseria meningitidis, and other V. parahaemolyticus strains, using computational tools. The PMC53.7-Zot was compared with other toxins and identified as an endotoxin with conserved motifs in the N-terminus and a variable C-terminal region and without FCIGRL peptide. Notably, the C-terminal diversity among Zots meant that not all of them could be identified as toxins. Structurally, PMC53.7-Zot was modeled as a transmembrane protein. Our results suggested that it has partial 3D structure similarity with V. cholerae-Zot. Probably, the PMC53.7-Zot would affect the actin cytoskeletal, but, in the absence of FCIGRL, the mechanisms of actions must be elucidated.
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Affiliation(s)
- Diliana Pérez-Reytor
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Alequis Pavón
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Carmen Lopez-Joven
- Facultad de Ciencias Veterinarias, Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
| | - Sebastián Ramírez-Araya
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Carlos Peña-Varas
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Nicolás Plaza
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Melissa Alegría-Arcos
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
| | - Gino Corsini
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Víctor Jaña
- Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago, Chile
| | - Leonardo Pavez
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago, Chile.,Instituto de Ciencias Naturales, Universidad de Las Américas, Santiago, Chile
| | - Talia Del Pozo
- Centro Tecnológico de Recursos Vegetales, Escuela de Agronomía, Universidad Mayor, Huechuraba, Chile
| | - Roberto Bastías
- Laboratorio de Microbiología, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Carlos J Blondel
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile.,Facultad de Medicina y Facultad de Ciencias de la Vida, Instituto de Ciencias Biomédicas, Universidad Andrés Bello, Santiago, Chile
| | - David Ramírez
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Katherine García
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
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Gmelch TJ, Sperl JM, Sieber V. Molecular Dynamics Analysis of a Rationally Designed Aldehyde Dehydrogenase Gives Insights into Improved Activity for the Non-Native Cofactor NAD .. ACS Synth Biol 2020; 9:920-929. [PMID: 32208678 DOI: 10.1021/acssynbio.9b00527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aldehyde dehydrogenase from Thermoplasma acidophilum was previously implemented as a key enzyme in a synthetic cell-free reaction cascade for the production of alcohols. In order to engineer the enzyme's cofactor specificity from NADP+ to NAD+, we identified selectivity-determining residues with the CSR-SALAD tool and investigated further positions based on the crystal structure. Stepwise combination of the initially discovered six point mutations allowed us to monitor the cross effects of each mutation, resulting in a final variant with reduced KM for the non-native cofactor NAD+ (from 18 to 0.6 mM) and an increased activity for the desired substrate d-glyceraldehyde (from 0.4 to 1.5 U/mg). Saturation mutagenesis of the residues at the entrance of the substrate pocket could eliminate substrate inhibition. Molecular dynamics simulations showed a significant gain of flexibility at the cofactor binding site for the final variant. The concomitant increase in stability against isobutanol and only a minor reduction in its temperature stability render the final variant a promising candidate for future optimization of our synthetic cell-free enzymatic cascade.
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Affiliation(s)
- Tobias J. Gmelch
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
| | - Josef M. Sperl
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
- Catalysis Research Center, Technical University of Munich, Garching 85748, Germany
- Bio-, Electro- and Chemocatalysis (BioCat) Branch, Fraunhofer Institute of Interfacial Biotechnology (IGB), Straubing 94315, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
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4
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Baicharoen A, Vijayan R, Pongprayoon P. Structural insights into betaine aldehyde dehydrogenase (BADH2) from Oryza sativa explored by modeling and simulations. Sci Rep 2018; 8:12892. [PMID: 30150624 PMCID: PMC6110774 DOI: 10.1038/s41598-018-31204-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/10/2018] [Indexed: 12/02/2022] Open
Abstract
Betaine aldehyde dehydrogenase 2 (BADH2) plays a key role in the accumulation of 2-acetyl-1-pyrroline (2AP), a fragrant compound in rice (Oryza sativa). BADH2 catalyses the oxidation of aminoaldehydes to carboxylic acids. An inactive BADH2 is known to promote fragrance in rice. The 3D structure and atomic level protein-ligand interactions are currently unknown. Here, the 3D dimeric structure of BADH2 was modeled using homology modeling. Furthermore, two 0.5 µs simulations were performed to explore the nature of BADH2 dimer structurally and dynamically. Each monomer comprises of 3 domains (substrate-binding, NAD+-binding, and oligomerization domains). The NAD+-binding domain is the most mobile. A scissor-like motion was observed between the monomers. Inside the binding pocket, N162 and E260 are tethered by strong hydrogen bonds to residues in close proximity. In contrast, the catalytic C294 is very mobile and interacts occasionally with N162. The flexibility of the nucleophilic C294 could facilitate the attack of free carbonyl on an aldehyde substrate. Key inter-subunit salt bridges contributing to dimerization were also identified. E487, D491, E492, K498, and K502 were found to form strong salt bridges with charged residues on the adjacent monomer. Specifically, the nearly permanent R430-E487 hydrogen bond (>90%) highlights its key role in dimer association. Structural and dynamic insights of BADH2 obtained here could play a role in the improvement of rice fragrance, which could lead to an enhancement in rice quality and market price.
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Affiliation(s)
- Apisara Baicharoen
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, PO Box, 15551, Al Ain, Abu Dhabi, United Arab Emirates.
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. .,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand. .,Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Kasetsart University, Bangkok, 10900, Thailand.
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5
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Bermejo GA, Clore GM, Schwieters CD. Improving NMR Structures of RNA. Structure 2016; 24:806-815. [PMID: 27066747 DOI: 10.1016/j.str.2016.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 01/27/2023]
Abstract
Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA.
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6
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Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations. J Chem Theory Comput 2015; 11:4770-9. [PMID: 26574266 DOI: 10.1021/acs.jctc.5b00662] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments.
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Affiliation(s)
| | - Justin L MacCallum
- Department of Chemistry, University of Calgary , Calgary, AB T2N 1N4, Canada
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7
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Yasri S, Wiwanitkit V. Ramachandran plots of envelope glycoprotein GP2 from Ebola virus. Asian Pac J Trop Biomed 2014. [DOI: 10.12980/apjtb.4.2014apjtb-2014-0465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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8
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Solis AD. Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device. PLoS One 2014; 9:e94334. [PMID: 24896099 PMCID: PMC4045576 DOI: 10.1371/journal.pone.0094334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/12/2014] [Indexed: 11/28/2022] Open
Abstract
The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.
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Affiliation(s)
- Armando D. Solis
- Biological Sciences Department, New York City College of Technology, The City University of New York, Brooklyn, New York, United States of America
- * E-mail:
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9
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Carugo O, Djinović-Carugo K. Half a century of Ramachandran plots. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1333-41. [DOI: 10.1107/s090744491301158x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/27/2013] [Indexed: 11/11/2022]
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10
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Torshin IY, Esipova NG, Tumanyan VG. Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II′ region of the Ramachandran plot. J Biomol Struct Dyn 2013; 32:198-208. [DOI: 10.1080/07391102.2012.759451] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Bermejo GA, Clore GM, Schwieters CD. Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures. Protein Sci 2012; 21:1824-36. [PMID: 23011872 DOI: 10.1002/pro.2163] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/14/2012] [Accepted: 09/17/2012] [Indexed: 11/09/2022]
Abstract
Statistical potentials that embody torsion angle probability densities in databases of high-quality X-ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 10⁶ quality-filtered amino acid residues. Incorporated into the Xplor-NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA
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12
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Koppole S, Schaefer M. A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias. J Comput Chem 2012; 33:791-9. [DOI: 10.1002/jcc.22908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/24/2011] [Accepted: 11/20/2011] [Indexed: 11/12/2022]
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13
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Abstract
More than 50% of RNA secondary structure is estimated to be A-form helices, which are linked together by various junctions. Here we describe a protocol for computing three interhelical Euler angles describing the relative orientation of helices across RNA junctions. 5' and 3' helices, H1 and H2, respectively, are assigned based on the junction topology. A reference canonical helix is constructed using an appropriate molecular builder software consisting of two continuous idealized A-form helices (iH1 and iH2) with helix axis oriented along the molecular Z-direction running toward the positive direction from iH1 to iH2. The phosphate groups and the carbon and oxygen atoms of the sugars are used to superimpose helix H1 of a target interhelical junction onto the corresponding iH1 of the reference helix. A copy of iH2 is then superimposed onto the resulting H2 helix to generate iH2'. A rotation matrix R is computed, which rotates iH2' into iH2 and expresses the rotation parameters in terms of three Euler angles α(h), β(h) and γ(h). The angles are processed to resolve a twofold degeneracy and to select an overall rotation around the axis of the reference helix. The three interhelical Euler angles define clockwise rotations around the 5' (-γ(h)) and 3' (α(h)) helices and an interhelical bend angle (β(h)). The angles can be depicted graphically to provide a 'Ramachandran'-type view of RNA global structure that can be used to identify unusual conformations as well as to understand variations due to changes in sequence, junction topology and other parameters.
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14
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Miyamoto Y, Nishimura S, Inoue K, Shimamoto S, Yoshida T, Fukuhara A, Yamada M, Urade Y, Yagi N, Ohkubo T, Inui T. Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR. J Struct Biol 2009; 169:209-18. [PMID: 19833210 DOI: 10.1016/j.jsb.2009.10.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 10/02/2009] [Accepted: 10/09/2009] [Indexed: 11/25/2022]
Abstract
Lipocalin-type prostaglandin D synthase (L-PGDS) acts as both a PGD(2) synthase and an extracellular transporter for small lipophilic molecules. From a series of biochemical studies, it has been found that L-PGDS has an ability to bind a variety of lipophilic ligands such as biliverdin, bilirubin and retinoids in vitro. Therefore, we considered that it is necessary to clarify the molecular structure of L-PGDS upon binding ligand in order to understand the physiological relevance of L-PGDS as a transporter protein. We investigated a molecular structure of L-PGDS/biliverdin complex by small-angle X-ray scattering (SAXS) and multi-dimensional NMR measurements, and characterized the binding mechanism in detail. SAXS measurements revealed that L-PGDS has a globular shape and becomes compact by 1.3A in radius of gyration on binding biliverdin. NMR experiments revealed that L-PGDS possessed an eight-stranded antiparallel beta-barrel forming a central cavity. Upon the titration with biliverdin, some cross-peaks for residues surrounding the cavity and EF-loop and H2-helix above the beta-barrel shifted, and the intensity of other cross-peaks decreased with signal broadenings in (1)H-(15)N heteronuclear single quantum coherence spectra. These results demonstrate that L-PGDS holds biliverdin within the beta-barrel, and the conformation of the loop regions above the beta-barrel changes upon binding biliverdin. Through such a conformational change, the whole molecule of L-PGDS becomes compact.
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Affiliation(s)
- Yuya Miyamoto
- Laboratory of Protein Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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15
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Amir EAD, Kalisman N, Keasar C. Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities. Proteins 2008; 72:62-73. [PMID: 18186478 DOI: 10.1002/prot.21896] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Rotatable torsion angles are the major degrees of freedom in proteins. Adjacent angles are highly correlated and energy terms that rely on these correlations are intensively used in molecular modeling. However, the utility of torsion based terms is not yet fully exploited. Many of these terms do not capture the full scale of the correlations. Other terms, which rely on lookup tables, cannot be used in the context of force-driven algorithms because they are not fully differentiable. This study aims to extend the usability of torsion terms by presenting a set of high-dimensional and fully-differentiable energy terms that are derived from high-resolution structures. The set includes terms that describe backbone conformational probabilities and propensities, side-chain rotamer probabilities, and an elaborate term that couples all the torsion angles within the same residue. The terms are constructed by cubic spline interpolation with periodic boundary conditions that enable full differentiability and high computational efficiency. We show that the spline implementation does not compromise the accuracy of the original database statistics. We further show that the side-chain relevant terms are compatible with established rotamer probabilities. Despite their very local characteristics, the new terms are often able to identify native and native-like structures within decoy sets. Finally, force-based minimization of NMR structures with the new terms improves their torsion angle statistics with minor structural distortion (0.5 A RMSD on average). The new terms are freely available in the MESHI molecular modeling package. The spline coefficients are also available as a documented MATLAB file.
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Affiliation(s)
- El-Ad David Amir
- Department of Computer Science, Ben-Gurion University of the Negev, Israel
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16
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Saccenti E, Rosato A. The war of tools: how can NMR spectroscopists detect errors in their structures? JOURNAL OF BIOMOLECULAR NMR 2008; 40:251-261. [PMID: 18320330 DOI: 10.1007/s10858-008-9228-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 02/08/2008] [Accepted: 02/13/2008] [Indexed: 05/26/2023]
Abstract
Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to which these tools could be applied to detect flaws in NMR structures. In particular, we investigated the variation in the scores assigned by these programs as a function of the deviation of the structures induced by errors in assignments or in the upper distance limits used. These perturbations did not distort radically the protein fold, but resulted in backbone RMS deviations up to 3 A, which is in line with errors highlighted in the available literature. We found that it is quite difficult to discriminate the structures perturbed because of misassignments from the original ones, also because the spread in score over the conformers of the original bundle is relatively large. varphi-psi distributions and normality scores related to the backbone conformation and to the distribution of side-chain dihedral angles are the most sensitive indicators of flaws.
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Affiliation(s)
- Edoardo Saccenti
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
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Shimamoto S, Yoshida T, Inui T, Gohda K, Kobayashi Y, Fujimori K, Tsurumura T, Aritake K, Urade Y, Ohkubo T. NMR Solution Structure of Lipocalin-type Prostaglandin D Synthase. J Biol Chem 2007; 282:31373-9. [PMID: 17715133 DOI: 10.1074/jbc.m700123200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) catalyzes the isomerization of PGH(2), a common precursor of various prostanoids, to produce PGD(2), an endogenous somnogen and nociceptive modulator, in the brain. L-PGDS is a member of the lipocalin superfamily and binds lipophilic substances, such as retinoids and bile pigments, suggesting that L-PGDS is a dual functional protein acting as a PGD(2)-synthesizing enzyme and a transporter for lipophilic ligands. In this study we determined by NMR the three-dimensional structure of recombinant mouse L-PGDS with the catalytic residue Cys-65. The structure of L-PGDS exhibited the typical lipocalin fold, consisting of an eight-stranded, antiparallel beta-barrel and a long alpha-helix associated with the outer surface of the barrel. The interior of the barrel formed a hydrophobic cavity opening to the upper end of the barrel, the size of which was larger than those of other lipocalins, and the cavity contained two pockets. Molecular docking studies, based on the result of NMR titration experiments with retinoic acid and PGH(2) analog, revealed that PGH(2) almost fully occupied the hydrophilic pocket 1, in which Cys-65 was located and all-trans-retinoic acid occupied the hydrophobic pocket 2, in which amino acid residues important for retinoid binding in other lipocalins were well conserved. Mutational and kinetic studies provide the direct evidence for the PGH(2) binding mode. These results indicated that the two binding sites for PGH(2) and retinoic acid in the large cavity of L-PGDS were responsible for the broad ligand specificity of L-PGDS and the non-competitive inhibition of L-PGDS activity by retinoic acid.
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Affiliation(s)
- Shigeru Shimamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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18
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Babini E, Bertini I, Capozzi F, Chirivino E, Luchinat C. A structural and dynamic characterization of the EF-hand protein CLSP. Structure 2006; 14:1029-38. [PMID: 16765896 DOI: 10.1016/j.str.2006.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Revised: 04/04/2006] [Accepted: 04/06/2006] [Indexed: 11/21/2022]
Abstract
The structure and dynamics of human calmodulin-like skin protein (CLSP) have been characterized by NMR spectroscopy. The mobility of CLSP has been found to be different for the N-terminal and C-terminal domains. The isolated domains were also expressed and analyzed. The structure of the isolated C-terminal domain is presented. The N-terminal domain is characterized by four stable helices, which experience large fluctuations. This is shown to be due to mutations in the hydrophobic core. The overall N-terminal domain behavior is similar both in the full-length protein and in the isolated domain. By exploiting the capability of Tb3+ bound to CLSP to induce partial orientation of the molecule in a magnetic field, restricted motion of one domain with respect to the other was proved. By using NMR, ITC, and ESI-MS, the calcium and magnesium binding properties were investigated. Finally, CLSP is framed into the evolutionary scheme of the calmodulin-like family.
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Affiliation(s)
- Elena Babini
- Centro Risonanze Magnetiche, University of Florence, Via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2006; 2:e9. [PMID: 16462939 PMCID: PMC1359070 DOI: 10.1371/journal.pcbi.0020009] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Accepted: 12/29/2005] [Indexed: 12/04/2022] Open
Abstract
One of the major goals of structural genomics projects is to determine the three-dimensional structure of representative members of as many different fold families as possible. Comparative modeling is expected to fill the remaining gaps by providing structural models of homologs of the experimentally determined proteins. However, for such an approach to be successful it is essential that the quality of the experimentally determined structures is adequate. In an attempt to build a homology model for the protein dynein light chain 2A (DLC2A) we found two potential templates, both experimentally determined nuclear magnetic resonance (NMR) structures originating from structural genomics efforts. Despite their high sequence identity (96%), the folds of the two structures are markedly different. This urged us to perform in-depth analyses of both structure ensembles and the deposited experimental data, the results of which clearly identify one of the two models as largely incorrect. Next, we analyzed the quality of a large set of recent NMR-derived structure ensembles originating from both structural genomics projects and individual structure determination groups. Unfortunately, a visual inspection of structures exhibiting lower quality scores than DLC2A reveals that the seriously flawed DLC2A structure is not an isolated incident. Overall, our results illustrate that the quality of NMR structures cannot be reliably evaluated using only traditional experimental input data and overall quality indicators as a reference and clearly demonstrate the urgent need for a tight integration of more sophisticated structure validation tools in NMR structure determination projects. In contrast to common methodologies where structures are typically evaluated as a whole, such tools should preferentially operate on a per-residue basis. Three-dimensional biomolecular structures provide an invaluable source of biologically relevant information. To be able to learn the most of the wealth of information that these structures can provide us, it is of great importance that the quality and accuracy of the protein structure models deposited in the Protein Data Bank are as high as possible. In this work, the authors describe an analysis that illustrates that this is unfortunately not the case for many protein structures solved using nuclear magnetic resonance spectroscopy. They present an example in which two strikingly different models describing the same protein are analyzed using commonly available structure validation tools, and the results of this analysis show one of the two models to be incorrect. Subsequently, using a large set of recently determined structures, the authors demonstrate that unfortunately this example does not stand on its own. The analyses and examples clearly illustrate that relying solely on the experimental data to evaluate structural quality can provide a false sense of correctness and the combination of multiple sophisticated structure validation tools is required to detect the presence of errors in protein nuclear magnetic resonance structures.
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Affiliation(s)
- Sander B Nabuurs
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Chris A. E. M Spronk
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Geerten W Vuister
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
- * To whom correspondence should be addressed. E-mail: (GWV); (GV)
| | - Gert Vriend
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
- * To whom correspondence should be addressed. E-mail: (GWV); (GV)
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Banci L, Bertini I, Cantini F, Ciofi-Baffoni S, Gonnelli L, Mangani S. Solution structure of Cox11, a novel type of beta-immunoglobulin-like fold involved in CuB site formation of cytochrome c oxidase. J Biol Chem 2004; 279:34833-9. [PMID: 15181013 DOI: 10.1074/jbc.m403655200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c oxidase assembly process involves many accessory proteins including Cox11, which is a copper-binding protein required for Cu incorporation into the Cu(B) site of cytochrome c oxidase. In a genome wide search, a number of Cox11 homologs are found in all of the eukaryotes with complete genomes and in several Gram-negative bacteria. All of them possess a highly homologous soluble domain and contain an N-terminal fragment that anchors the protein to the membrane. An anchor-free construct of 164 amino acids was obtained from Sinorhizobium meliloti, and the first structure of this class of proteins is reported here. The apoform has an immunoglobulin-like fold with a novel type of beta-strand organization. The copper binding motif composed of two highly conserved cysteines is located on one side of the beta-barrel structure. The apoprotein is monomeric in the presence of dithiothreitol, whereas it dimerizes in the absence of the reductant. When copper(I) binds, NMR and extended x-ray absorption fine structure (EXAFS) data indicate a dimeric protein state with two thiolates bridging two copper(I) ions. The present results advance the knowledge on the poorly understood molecular aspects of cytochrome c oxidase assembly.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Florence, Italy
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Kleywegt GJ, Henrick K, Dodson EJ, van Aalten DMF. Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure 2003; 11:1051-9. [PMID: 12962624 DOI: 10.1016/s0969-2126(03)00186-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For the refinement of protein and nucleic acid structures, high-quality geometric restraint libraries are available. Unfortunately, for other compounds, such as physiological ligands, lead compounds, substrate analogs, etc., the situation is not as favorable. As a result, the structures of small molecules found in complexes with biomacromolecules are often less reliable than those of the surrounding amino or nucleic acids. Here, we briefly review the use of geometric restraints in structure refinement (be it against X-ray crystallographic or NMR-derived data) and simulation. In addition, we discuss methods to generate both restraint libraries and (idealized) coordinates for small molecules and provide some practical advice.
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Affiliation(s)
- Gerard J Kleywegt
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden.
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