1
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Grieco A, Boneta S, Gavira JA, Pey AL, Basu S, Orlans J, de Sanctis D, Medina M, Martin‐Garcia JM. Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations. Protein Sci 2024; 33:e4957. [PMID: 38501509 PMCID: PMC10949395 DOI: 10.1002/pro.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/20/2024]
Abstract
The human NQO1 (hNQO1) is a flavin adenine nucleotide (FAD)-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics. Moreover, it is overexpressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH. We have also performed molecular dynamics simulations of free hNQO1 and in complex with NADH. This is the first structural evidence that the hNQO1 functional cooperativity is driven by structural communication between the active sites through long-range propagation of cooperative effects across the hNQO1 structure. Both structural results and MD simulations have supported that the binding of NADH significantly decreases protein dynamics and stabilizes hNQO1 especially at the dimer core and interface. Altogether, these results pave the way for future time-resolved studies, both at x-ray free-electron lasers and synchrotrons, of the dynamics of hNQO1 upon binding to NADH as well as during the FAD cofactor reductive half-reaction. This knowledge will allow us to reveal unprecedented structural information of the relevance of the dynamics during the catalytic function of hNQO1.
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Grants
- P18-RT-2413 Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía
- RTI2018-096246-B-I00 ERDF/Spanish Ministry of Science, Innovation and Universities-State Research Agency
- E35-23R Gobierno de Aragón
- B-BIO-84-UGR20 ERDF/Counseling of Economic Transformation, Industry, Knowledge and Universities
- CNS2022-135713 The European Union NextGenerationEU/PRTR
- 2019-T1/BMD-15552 Comunidad de Madrid
- MCIN/AEI/PID2022-136369NB-I00 MCIN/AEI/10.13039/501100011033/ERDF
- Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía
- ERDF/Spanish Ministry of Science, Innovation and Universities‐State Research Agency
- Gobierno de Aragón
- ERDF/Counseling of Economic Transformation, Industry, Knowledge and Universities
- Comunidad de Madrid
- MCIN/AEI/10.13039/501100011033/ERDF
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Affiliation(s)
- Alice Grieco
- Department of Crystallography and Structural BiologyInstitute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC)MadridSpain
| | - Sergio Boneta
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)Universidad de ZaragozaZaragozaSpain
| | - José A. Gavira
- Laboratory of Crystallographic StudiesIACT (CSIC‐UGR)ArmillaSpain
| | - Angel L. Pey
- Departamento de Química FísicaUnidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de GranadaGranadaSpain
| | - Shibom Basu
- European Molecular Biology LaboratoryGrenobleFrance
| | | | | | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)Universidad de ZaragozaZaragozaSpain
| | - Jose Manuel Martin‐Garcia
- Department of Crystallography and Structural BiologyInstitute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC)MadridSpain
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2
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Monteagudo-Cascales E, Gumerov VM, Fernández M, Matilla MA, Gavira JA, Zhulin IB, Krell T. Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria. bioRxiv 2023:2023.10.26.564149. [PMID: 37961346 PMCID: PMC10634846 DOI: 10.1101/2023.10.26.564149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Purines and their derivatives are key molecules for controlling intracellular energy homeostasis and nucleotide synthesis. In eukaryotes, including humans, purines also act as signaling molecules that mediate extracellular communication and control key cellular processes, such as proliferation, migration, differentiation, and apoptosis. However, the signaling role of purines in bacteria is largely unknown. Here, by combining structural and sequence information, we define a purine-binding motif, which is present in sensor domains of thousands of bacterial receptors that modulate motility, gene expression, metabolism and second messenger turnover. The screening of compound libraries and microcalorimetric titrations of selected sensor domains validated their ability to specifically bind purine derivatives. The physiological relevance of purine sensing was demonstrated in a second messenger signaling system that modulates c-di-GMP levels.
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3
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Matilla MA, Gavira JA, Krell T. Accessing nutrients as the primary benefit arising from chemotaxis. Curr Opin Microbiol 2023; 75:102358. [PMID: 37459734 DOI: 10.1016/j.mib.2023.102358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 09/17/2023]
Abstract
About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.
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Affiliation(s)
- Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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4
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Illescas-Lopez S, Martin-Romera JD, Mañas-Torres MC, Lopez-Lopez MT, Cuerva JM, Gavira JA, Carmona FJ, Álvarez de Cienfuegos L. Short-Peptide Supramolecular Hydrogels for In Situ Growth of Metal-Organic Framework-Peptide Biocomposites. ACS Appl Mater Interfaces 2023. [PMID: 37390355 DOI: 10.1021/acsami.3c06943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
The development of bio-MOFs or MOF biocomposites through the combination of MOFs with biopolymers offers the possibility of expanding the potential applications of MOFs, making use of more environmentally benign processes and reagents and giving rise to a new generation of greener and more bio-oriented composite materials. Now, with the increasing use of MOFs for biotechnological applications, the development of new protocols and materials to obtain novel bio-MOFs compatible with biomedical or biotechnological uses is needed. Herein, and as a proof of concept, we have explored the possibility of using short-peptide supramolecular hydrogels as media to promote the growth of MOF particles, giving rise to a new family of bio-MOFs. Short-peptide supramolecular hydrogels are very versatile materials that have shown excellent in vitro and in vivo biomedical applications such as tissue engineering and drug delivery vehicles, among others. These peptides self-assemble by noncovalent interactions, and, as such, these hydrogels are easily reversible, being more biocompatible and biodegradable. These peptides can self-assemble by a multitude of stimuli, such as changes in pH, temperature, solvent, adding salts, enzymatic activity, and so forth. In this work, we have taken advantage of this ability to promote peptide self-assembly with some of the components required to form MOF particles, giving rise to more homogeneous and well-integrated composite materials. Hydrogel formation has been triggered using Zn2+ salts, required to form ZIF-8, and formic acid, required to form MOF-808. Two different protocols for the in situ MOF growth have been developed. Finally, the MOF-808 composite hydrogel has been tested for the decontamination of water polluted with phosphate ions as well as for the catalytic degradation of toxic organophosphate methyl paraoxon in an unbuffered solution.
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Affiliation(s)
- Sara Illescas-Lopez
- Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
| | - Javier D Martin-Romera
- Departamento de Química Inorgánica, UEQ, Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
| | - Mari C Mañas-Torres
- Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
| | - Modesto T Lopez-Lopez
- Departamento de Física Aplicada, Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Av. De Madrid, 15, 18016 Granada, Spain
| | - Juan M Cuerva
- Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, Consejo Superior de Investigaciones Científicas-UGR, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Francisco J Carmona
- Departamento de Química Inorgánica, UEQ, Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Av. De Madrid, 15, 18016 Granada, Spain
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5
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Gutierrez-Rus LI, Gamiz-Arco G, Gavira JA, Gaucher EA, Risso VA, Sanchez-Ruiz JM. Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes. Mol Biol Evol 2023:7180808. [PMID: 37235753 DOI: 10.1093/molbev/msad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
Enzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.
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Affiliation(s)
- Luis I Gutierrez-Rus
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071-Granada, Spain
| | - Gloria Gamiz-Arco
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071-Granada, Spain
| | - J A Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Avenida de las Palmeras 4, Granada 18100 Armilla, Spain
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA 30303
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071-Granada, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071-Granada, Spain
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6
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Artusio F, Gavira JA, Pisano R. Self-Assembled Monolayers As a Tool to Investigate the Effect of Surface Chemistry on Protein Nucleation. Cryst Growth Des 2023; 23:3195-3201. [PMID: 37159657 PMCID: PMC10162442 DOI: 10.1021/acs.cgd.2c01377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Indexed: 05/11/2023]
Abstract
Modified surfaces like siliconized glass are commonly used to support protein crystallization and facilitate obtaining crystals. Over the years, various surfaces have been proposed to decrease the energetic penalty required for consistent protein clustering, but scarce attention has been paid to the underlying mechanisms of interactions. Here, we propose self-assembled monolayers that are surfaces exposing fine-tuned moieties with a very regular topography and subnanometer roughness, as a tool to unveil the interaction between proteins and functionalized surfaces. We studied the crystallization of three model proteins having progressively narrower metastable zones, i.e., lysozyme, catalase, and proteinase K, on monolayers exposing thiol, methacrylate, and glycidyloxy groups. Thanks to comparable surface wettability, the induction or the inhibition of nucleation was readily attributed to the surface chemistry. For example, thiol groups strongly induced the nucleation of lysozyme thanks to electrostatic pairing, whereas methacrylate and glycidyloxy groups had an effect comparable to unfunctionalized glass. Overall, the action of surfaces led to differences in nucleation kinetics, crystal habit, and even crystal form. This approach can support the fundamental understanding of the interaction between protein macromolecules and specific chemical groups, which is crucial for many technological applications in the pharmaceutical and food industry.
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Affiliation(s)
- Fiora Artusio
- Department
of Applied Science and Technology, Politecnico
di Torino, 24 Corso Duca degli Abruzzi, 10129 Torino, Italy
- E-mail:
| | - José A. Gavira
- Laboratorio
de Estudios Cristalográficos, Instituto
Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones
Científicas-Universidad de Granada), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Roberto Pisano
- Department
of Applied Science and Technology, Politecnico
di Torino, 24 Corso Duca degli Abruzzi, 10129 Torino, Italy
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7
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Krell T, Gavira JA, Roca A, Matilla MA. The emerging role of auxins as bacterial signal molecules: Potential biotechnological applications. Microb Biotechnol 2023. [PMID: 37466451 PMCID: PMC10364314 DOI: 10.1111/1751-7915.14235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 07/20/2023] Open
Abstract
Microorganisms are exposed in their natural niches to a wide diversity of signal molecules. Specific detection of these signals results in alterations in microbial metabolism and physiology. Auxins like indole-3-acetic acid are key phytohormones that regulate plant growth and development. Nonetheless, auxin biosynthesis is not restricted to plants but is ubiquitous in all kingdoms of life. This wide phylogenetic distribution of auxins production, together with the diversity of regulated cellular processes, have made auxins key intra- and inter-kingdom signal molecules in life modulating, for example microbial physiology, metabolism and virulence. Despite their increasing importance as global signal molecules, the mechanisms by which auxins perform their regulatory functions in microorganisms are largely unknown. In this article, we outline recent research that has advanced our knowledge of the mechanisms of bacterial auxin perception. We also highlight the potential applications of this research in aspects such as antibiotic production, biosensor design, plant microbiome engineering and antivirulence therapies.
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Affiliation(s)
- Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Universidad de Granada, Granada, Spain
| | - Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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8
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Gutierrez-Rus LI, Gamiz-Arco G, Gavira JA, Gaucher EA, Risso VA, Sanchez-Ruiz JM. Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes. bioRxiv 2023:2023.03.14.532612. [PMID: 36993774 PMCID: PMC10055001 DOI: 10.1101/2023.03.14.532612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Enzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.
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9
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Savchenko M, Hurtado M, Lopez-Lopez MT, Rus G, Álvarez de Cienfuegos L, Melchor J, Gavira JA. Lysozyme crystallization in hydrogel media under ultrasound irradiation. Ultrason Sonochem 2022; 88:106096. [PMID: 35868210 PMCID: PMC9305616 DOI: 10.1016/j.ultsonch.2022.106096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 05/20/2023]
Abstract
Sonocrystallization implies the application of ultrasound radiation to control the nucleation and crystal growth depending on the actuation time and intensity. Its application allows to induce nucleation at lower supersaturations than required under standard conditions. Although extended in inorganic and organic crystallization, it has been scarcely explored in protein crystallization. Now, that industrial protein crystallization is gaining momentum, the interest on new ways to control protein nucleation and crystal growth is advancing. In this work we present the development of a novel ultrasound bioreactor to study its influence on protein crystallization in agarose gel. Gel media minimize convention currents and sedimentation, favoring a more homogeneous and stable conditions to study the effect of an externally generated low energy ultrasonic irradiation on protein crystallization avoiding other undesired effects such as temperature increase, introduction of surfaces which induce nucleation, destructive cavitation phenomena, etc. In-depth statistical analysis of the results has shown that the impact of ultrasound in gel media on crystal size populations are statistically significant and reproducible.
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Affiliation(s)
- Mariia Savchenko
- Universidad de Granada (UGR), Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Universidad de Granada (UGR), Departamento de Física Aplicada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR), UEQ, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Manuel Hurtado
- Universidad de Granada (UGR), Departamento de Estadística e Investigación Operativa, Spain; Departamento de Mecánica de Estructuras e Ingeniería Hidráulica, Ultrasonics Lab TEP-959, Universidad de Granada, Spain; Unidad de Excelencia Modeling Nature MNAT, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain
| | - Modesto T Lopez-Lopez
- Universidad de Granada (UGR), Departamento de Física Aplicada, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain
| | - Guillermo Rus
- Departamento de Mecánica de Estructuras e Ingeniería Hidráulica, Ultrasonics Lab TEP-959, Universidad de Granada, Spain; Unidad de Excelencia Modeling Nature MNAT, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain
| | - Luis Álvarez de Cienfuegos
- Universidad de Granada (UGR), Departamento de Química Orgánica, Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ), C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain.
| | - Juan Melchor
- Universidad de Granada (UGR), Departamento de Estadística e Investigación Operativa, Spain; Unidad de Excelencia Modeling Nature MNAT, Universidad de Granada, Spain; Instituto de Investigación Biosanitaria Ibs, GRANADA, Granada, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR), UEQ, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain.
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10
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Mañas‐Torres MC, Illescas‐Lopez S, Gavira JA, de Cienfuegos LÁ, Marchesan S. Interactions Between Peptide Assemblies and Proteins for Medicine. Isr J Chem 2022. [DOI: 10.1002/ijch.202200018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mari C. Mañas‐Torres
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - Sara Illescas‐Lopez
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR) Avenida de las Palmeras 4 18100 Armilla, UEQ Granada Spain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
- Instituto de Investigación Biosanitaria ibs Granada Spain
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department University of Trieste Via L. Giorgieri 1 Trieste 34127 Italy
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11
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Gavira JA, Artusio F, Castellví A, Pisano R. Protein crystallisation in agarose gel, a cheap and versatile technique. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321093843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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12
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Krell T, Gavira JA, Velando F, Fernández M, Roca A, Monteagudo-Cascales E, Matilla MA. Histamine: A Bacterial Signal Molecule. Int J Mol Sci 2021; 22:6312. [PMID: 34204625 PMCID: PMC8231116 DOI: 10.3390/ijms22126312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria have evolved sophisticated signaling mechanisms to coordinate interactions with organisms of other domains, such as plants, animals and human hosts. Several important signal molecules have been identified that are synthesized by members of different domains and that play important roles in inter-domain communication. In this article, we review recent data supporting that histamine is a signal molecule that may play an important role in inter-domain and inter-species communication. Histamine is a key signal molecule in humans, with multiple functions, such as being a neurotransmitter or modulator of immune responses. More recent studies have shown that bacteria have evolved different mechanisms to sense histamine or histamine metabolites. Histamine sensing in the human pathogen Pseudomonas aeruginosa was found to trigger chemoattraction to histamine and to regulate the expression of many virulence-related genes. Further studies have shown that many bacteria are able to synthesize and secrete histamine. The release of histamine by bacteria in the human gut was found to modulate the host immune responses and, at higher doses, to result in host pathologies. The elucidation of the role of histamine as an inter-domain signaling molecule is an emerging field of research and future investigation is required to assess its potential general nature.
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Affiliation(s)
- Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
| | - José A. Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Avenida de las Palmeras 4, 18100 Armilla, Spain;
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
| | - Matilde Fernández
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071 Granada, Spain; (M.F.); (A.R.)
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071 Granada, Spain; (M.F.); (A.R.)
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
| | - Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
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13
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Contreras-Montoya R, Arredondo-Amador M, Escolano-Casado G, Mañas-Torres MC, González M, Conejero-Muriel M, Bhatia V, Díaz-Mochón JJ, Martínez-Augustin O, de Medina F, Lopez-Lopez MT, Conejero-Lara F, Gavira JA, de Cienfuegos LÁ. Insulin Crystals Grown in Short-Peptide Supramolecular Hydrogels Show Enhanced Thermal Stability and Slower Release Profile. ACS Appl Mater Interfaces 2021; 13:11672-11682. [PMID: 33661596 PMCID: PMC8479728 DOI: 10.1021/acsami.1c00639] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/19/2021] [Indexed: 05/08/2023]
Abstract
Protein therapeutics have a major role in medicine in that they are used to treat diverse pathologies. Their three-dimensional structures not only offer higher specificity and lower toxicity than small organic compounds but also make them less stable, limiting their in vivo half-life. Protein analogues obtained by recombinant DNA technology or by chemical modification and/or the use of drug delivery vehicles has been adopted to improve or modulate the in vivo pharmacological activity of proteins. Nevertheless, strategies to improve the shelf-life of protein pharmaceuticals have been less explored, which has challenged the preservation of their activity. Herein, we present a methodology that simultaneously increases the stability of proteins and modulates the release profile, and implement it with human insulin as a proof of concept. Two novel thermally stable insulin composite crystal formulations intended for the therapeutic treatment of diabetes are reported. These composite crystals have been obtained by crystallizing insulin in agarose and fluorenylmethoxycarbonyl-dialanine (Fmoc-AA) hydrogels. This process affords composite crystals, in which hydrogel fibers are occluded. The insulin in both crystalline formulations remains unaltered at 50 °C for 7 days. Differential scanning calorimetry, high-performance liquid chromatography, mass spectrometry, and in vivo studies have shown that insulin does not degrade after the heat treatment. The nature of the hydrogel modifies the physicochemical properties of the crystals. Crystals grown in Fmoc-AA hydrogel are more stable and have a slower dissolution rate than crystals grown in agarose. This methodology paves the way for the development of more stable protein pharmaceuticals overcoming some of the existing limitations.
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Affiliation(s)
- Rafael Contreras-Montoya
- Departamento
de Química Orgánica, Universidad
de Granada, (UGR), C.
U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
| | - María Arredondo-Amador
- Departamento
de Farmacología, Centro de Investigación Biomédica
en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), School
of Pharmacy, Instituto de Investigación
Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
| | - Guillermo Escolano-Casado
- Laboratorio
de Estudios Cristalográficos, Instituto
Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones
Científicas-UGR), Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Mari C. Mañas-Torres
- Departamento
de Química Orgánica, Universidad
de Granada, (UGR), C.
U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
| | - Mercedes González
- Departamento
de Farmacología, Centro de Investigación Biomédica
en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), School
of Pharmacy, Instituto de Investigación
Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
| | - Mayte Conejero-Muriel
- Laboratorio
de Estudios Cristalográficos, Instituto
Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones
Científicas-UGR), Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Vaibhav Bhatia
- Lamark
Biotech Pvt. Ltd., VIT-TBI, 632 014 Vellore, Tamil Nadu, India
| | - Juan J. Díaz-Mochón
- Departamento
de Química Farmacéutica y Orgánica, Facultad de Farmacia, UGR, 18011 Granada, Spain
- Centre
for Genomics and Oncological Research, Pfizer/University
of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración
114, 18016 Granada, Spain
| | - Olga Martínez-Augustin
- Departamento
de Bioquímica y Biología Molecular II, Centro de Investigación
Biomédica en Red de Enfermedades Hepáticas y Digestivas
(CIBERehd), School of Pharmacy, Instituto
de Investigación Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
| | - Fermín
Sánchez de Medina
- Departamento
de Farmacología, Centro de Investigación Biomédica
en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), School
of Pharmacy, Instituto de Investigación
Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
| | - Modesto T. Lopez-Lopez
- Departamento
de Física Aplicada, Facultad de Ciencias,
UGR, C. U. Fuentenueva,
Avda. Severo Ochoa s/n, E-18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Facultad de Ciencias, UGR, C. U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
| | - José A. Gavira
- Laboratorio
de Estudios Cristalográficos, Instituto
Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones
Científicas-UGR), Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Luis Álvarez de Cienfuegos
- Departamento
de Química Orgánica, Universidad
de Granada, (UGR), C.
U. Fuentenueva, Avda. Severo Ochoa s/n, E-18071 Granada, Spain
- Instituto
de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain
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14
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Fernández-Penas R, Verdugo-Escamilla C, Martínez-Rodríguez S, Gavira JA. Production of Cross-Linked Lipase Crystals at a Preparative Scale. Cryst Growth Des 2021; 21:1698-1707. [PMID: 34602865 PMCID: PMC8479976 DOI: 10.1021/acs.cgd.0c01608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/10/2021] [Indexed: 05/14/2023]
Abstract
The autoimmobilization of enzymes via cross-linked enzyme crystals (CLECs) has regained interest in recent years, boosted by the extensive knowledge gained in protein crystallization, the decrease of cost and laboriousness of the process, and the development of potential applications. In this work, we present the crystallization and preparative-scale production of reinforced cross-linked lipase crystals (RCLLCs) using a commercial detergent additive as a raw material. Bulk crystallization was carried out in 500 mL of agarose media using the batch technique. Agarose facilitates the homogeneous production of crystals, their cross-linking treatment, and their extraction. RCLLCs were active in an aqueous solution and in hexane, as shown by the hydrolysis of p-nitrophenol butyrate and α-methylbenzyl acetate, respectively. RCLLCs presented both high thermal and robust operational stability, allowing the preparation of a packed-bed chromatographic column to work in a continuous flow. Finally, we determined the three-dimensional (3D) models of this commercial lipase crystallized with and without phosphate at 2.0 and 1.7 Å resolutions, respectively.
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Affiliation(s)
- Raquel Fernández-Penas
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Cristóbal Verdugo-Escamilla
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
| | - Sergio Martínez-Rodríguez
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
- Departamento
de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, Avenida de la Investigación 11, 18071 Granada, Spain
| | - José A. Gavira
- Laboratorio
de Estudios Cristalográficos, Instituto Andaluz de Ciencias
de la Tierra, Consejo Superior de Investigaciones
Científicas-Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
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15
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de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Mörl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C. A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. IUCrJ 2019; 6:454-464. [PMID: 31098026 PMCID: PMC6503916 DOI: 10.1107/s2052252519003622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/14/2019] [Indexed: 05/15/2023]
Abstract
Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.
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Affiliation(s)
- Raphaël de Wijn
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Oliver Hennig
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Jennifer Roche
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | | | - Kevin Rollet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Pablo Fernandez-Millan
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Karl Brillet
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS–Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France
| | - Eric Girard
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Gavin C. Fox
- PROXIMA 2A beamline, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Vincent Olieric
- Paul Scherrer Institute, Swiss Light Source, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC–Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Bernard Lorber
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France
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16
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Martín-Mora D, Ortega Á, Matilla MA, Martínez-Rodríguez S, Gavira JA, Krell T. The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN. mBio 2019; 10:e02334-18. [PMID: 30782655 PMCID: PMC6381276 DOI: 10.1128/mbio.02334-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/07/2019] [Indexed: 12/21/2022] Open
Abstract
Chemotaxis and energy taxis permit directed bacterial movements in gradients of environmental cues. Nitrate is a final electron acceptor for anaerobic respiration and can also serve as a nitrogen source for aerobic growth. Previous studies indicated that bacterial nitrate taxis is mediated by energy taxis mechanisms, which are based on the cytosolic detection of consequences of nitrate metabolism. Here we show that Pseudomonas aeruginosa PAO1 mediates nitrate chemotaxis on the basis of specific nitrate sensing by the periplasmic PilJ domain of the PA2788/McpN chemoreceptor. The presence of nitrate reduced mcpN transcript levels, and McpN-mediated taxis occurred only under nitrate starvation conditions. In contrast to the NarX and NarQ sensor kinases, McpN bound nitrate specifically and showed no affinity for other ligands such as nitrite. We report the three-dimensional structure of the McpN ligand binding domain (LBD) at 1.3-Å resolution in complex with nitrate. Although structurally similar to 4-helix bundle domains, the ligand binding mode differs since a single nitrate molecule is bound to a site on the dimer symmetry axis. As for 4-helix bundle domains, ligand binding stabilized the McpN-LBD dimer. McpN homologues showed a wide phylogenetic distribution, indicating that nitrate chemotaxis is a widespread phenotype. These homologues were particularly abundant in bacteria that couple sulfide/sulfur oxidation with nitrate reduction. This work expands the range of known chemotaxis effectors and forms the basis for the exploration of nitrate chemotaxis in other bacteria and for the study of its physiological role.IMPORTANCE Nitrate is of central importance in bacterial physiology. Previous studies indicated that movements toward nitrate are due to energy taxis, which is based on the cytosolic sensing of consequences of nitrate metabolism. Here we present the first report on nitrate chemotaxis. This process is initiated by specific nitrate binding to the periplasmic ligand binding domain (LBD) of McpN. Nitrate chemotaxis is highly regulated and occurred only under nitrate starvation conditions, which is helpful information to explore nitrate chemotaxis in other bacteria. We present the three-dimensional structure of the McpN-LBD in complex with nitrate, which is the first structure of a chemoreceptor PilJ-type domain. This structure reveals striking similarities to that of the abundant 4-helix bundle domain but employs a different sensing mechanism. Since McpN homologues show a wide phylogenetic distribution, nitrate chemotaxis is likely a widespread phenomenon with importance for the life cycle of ecologically diverse bacteria.
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Affiliation(s)
- David Martín-Mora
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Álvaro Ortega
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Sergio Martínez-Rodríguez
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, Melilla, Spain
- Laboratorio de Estudios Cristalográficos, IACT, Superior de Investigaciones Científicas (CSIC) y la Universidad de Granada (UGR), Armilla, Spain
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, Superior de Investigaciones Científicas (CSIC) y la Universidad de Granada (UGR), Armilla, Spain
| | - Tino Krell
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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17
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Martín-Mora D, Fernández M, Velando F, Ortega Á, Gavira JA, Matilla MA, Krell T. Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges. Int J Mol Sci 2018; 19:ijms19123755. [PMID: 30486299 PMCID: PMC6321045 DOI: 10.3390/ijms19123755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.
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Affiliation(s)
- David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Murcia, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, (CSIC-UGR), Avenida las Palmeras 4, 18100 Armilla, Spain.
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
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18
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Escolano G, Contreras-Montoya R, Díaz-Mochón JJ, de Cienfuegos LÁ, Gavira JA. Synthesis and characterization of cross-linked lysozyme crystals filled with single-walled carbon nanotube bionanomaterials. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Gavira JA, Verdugo-Escamilla C, Martínez-Rodríguez S, Rodríguez-Ruiz I, Conejero-Muriel M. On the versatility of CLECs for biotechnological applications, from micro to macro-fluidics devices. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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20
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Escolano G, Contreras-Montoya R, Díaz-Mochón JJ, Álvarez de Cienfuegos L, Gavira JA. Synthesis and characterization of cross-linked lysozyme crystals filled with single-walled carbon nanotubes – bionanomaterials. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Abstract
Lab-on-a-Chip (LoC), or micro-Total Analysis Systems (μTAS), is recognized as a powerful analytical technology with high capabilities, though end-user products for protein purification are still far from being available on the market. Remarkable progress has been achieved in the separation of nucleic acids and proteins using electrophoretic microfluidic devices, while pintsize devices have been developed for protein isolation according to miniaturized chromatography principles (size, charge, affinity, etc.). In this work, we review the latest advances in the fabrication of components, detection methods and commercial implementation for the separation of biological macromolecules based on microfluidic systems, with some critical remarks on the perspectives of their future development towards standardized microfluidic systems and protocols. An outlook on the current needs and future applications is also presented.
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Affiliation(s)
| | - V Babenko
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain.
| | - S Martínez-Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology. University of Granada, Granada, Spain
| | - J A Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada, Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain.
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22
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Conejero-Muriel M, Rodríguez-Ruiz I, Verdugo-Escamilla C, Llobera A, Gavira JA. Continuous Sensing Photonic Lab-on-a-Chip Platform Based on Cross-Linked Enzyme Crystals. Anal Chem 2016; 88:11919-11923. [DOI: 10.1021/acs.analchem.6b03793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mayte Conejero-Muriel
- Laboratory
for Crystallographic Studies, IACT, CSIC-University of Granada, Avd. de las
Palmeras, 4, Armilla, Spain
| | - Isaac Rodríguez-Ruiz
- Institut de Microelectrònica de Barcelona, CNM/CSIC Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
- CEA, DEN, DTEC,
SGCS, F-30207 Bagnols-sur-Cèze, France
| | - Cristóbal Verdugo-Escamilla
- Laboratory
for Crystallographic Studies, IACT, CSIC-University of Granada, Avd. de las
Palmeras, 4, Armilla, Spain
| | - Andreu Llobera
- Institut de Microelectrònica de Barcelona, CNM/CSIC Campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - José A. Gavira
- Laboratory
for Crystallographic Studies, IACT, CSIC-University of Granada, Avd. de las
Palmeras, 4, Armilla, Spain
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23
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Abstract
UNLABELLED Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. SYNOPSIS Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda. de las Palmeras, 4. 18100 Armilla, Granada, Spain
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Conejero-Muriel M, Gavira JA, Pineda-Molina E, Belsom A, Bradley M, Moral M, García-López Durán JDD, Luque González A, Díaz-Mochón JJ, Contreras-Montoya R, Martínez-Peragón Á, Cuerva JM, Álvarez de Cienfuegos L. Influence of the chirality of short peptide supramolecular hydrogels in protein crystallogenesis. Chem Commun (Camb) 2015; 51:3862-5. [PMID: 25655841 DOI: 10.1039/c4cc09024a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the first time the influence of the chirality of the gel fibers in protein crystallogenesis has been studied. Enantiomeric hydrogels 1 and 2 were tested with model proteins lysozyme and glucose isomerase and a formamidase extracted from B. cereus. Crystallization behaviour and crystal quality of these proteins in both hydrogels are presented and compared.
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Affiliation(s)
- Mayte Conejero-Muriel
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Av. de las Palmeras 4, 18100 Armilla, Granada, Spain.
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Conejero-Muriel M, Rodríguez-Ruiz I, Martínez-Rodríguez S, Llobera A, Gavira JA. McCLEC, a robust and stable enzymatic based microreactor platform. Lab Chip 2015; 15:4083-9. [PMID: 26334474 DOI: 10.1039/c5lc00776c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A microfluidic chip for cross-linked enzyme crystals (McCLEC) is presented and demonstrated to be a stable, reusable and robust biocatalyst-based device with very promising biotechnological applications. The cost-effective microfluidic platform allows in situ crystallization, cross-linking and enzymatic reaction assays on a single device. A large number of enzymatic reuses of the McCLEC platform were achieved and a comparative analysis is shown illustrating the efficiency of the process and its storage stability for more than one year.
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Affiliation(s)
- Mayte Conejero-Muriel
- Laboratorio de Estudios Cristalográficos, Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda de las Palmeras, 4, 18100 Armilla, Granada, Spain.
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Rodríguez-Ruiz I, Conejero-Muriel M, Ackermann TN, Gavira JA, Llobera A. A multiple path photonic lab on a chip for parallel protein concentration measurements. Lab Chip 2015; 15:1133-1139. [PMID: 25537135 DOI: 10.1039/c4lc01332h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We propose a PDMS-based photonic system for the accurate measurement of protein concentration with minute amounts of the sample. As opposed to the state of the art approach, in the multiple path photonic lab on a chip (MPHIL), analyte concentration or molar absorptivity is obtained with a single injection step, by performing simultaneous parallel optical measurements varying the optical path length. Also, as opposed to the standard calibration protocol, the MPHIL approach does not require a series of measurements at different concentrations. MPHIL has three main advantages: firstly the possibility of dynamically selecting the path length, always working in the absorbance vs. concentration linear range for each target analyte. Secondly, a dramatic reduction of the total volume of the sample required to obtain statistically reliable results. Thirdly, since only one injection is required, the measurement time is minimized, reducing both contamination and signal drifts. These characteristics are clearly advantageous when compared to commercial micro-spectrophotometers. The MPHIL concept was validated by testing three commercial proteins, lysozyme (HEWL), glucose isomerase (d-xylose-ketol-isomerase, GI) and Aspergillus sp. lipase L (BLL), as well as two proteins expressed and purified for this study, B. cereus formamidase (FASE) and dihydropyrimidinase from S. meliloti CECT41 (DHP). The use of MPHIL is also proposed for any spectrophotometric measurement in the UV-VIS range, as well as for its integration as a concentration measurement platform in more advanced photonic lab on a chip systems.
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Affiliation(s)
- Isaac Rodríguez-Ruiz
- Institut de Microelectrònica de Barcelona (IMB-CNM, CSIC), Campus UAB, 08193 Bellaterra, Spain.
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Conejero-Muriel M, Contreras-Montoya R, Díaz-Mochón JJ, Álvarez de Cienfuegos L, Gavira JA. Protein crystallization in short-peptide supramolecular hydrogels: a versatile strategy towards biotechnological composite materials. CrystEngComm 2015. [DOI: 10.1039/c5ce00850f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pineda-Molina E, Daddaoua A, Krell T, Ramos JL, García-Ruiz JM, Gavira JA. In situ X-ray data collection from highly sensitive crystals of Pseudomonas putida PtxS in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1307-10. [PMID: 23143237 PMCID: PMC3515369 DOI: 10.1107/s1744309112028540] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 06/23/2012] [Indexed: 11/10/2022]
Abstract
Pseudomonas putida PtxS is a member of the LacI protein family of transcriptional regulators involved in glucose metabolism. All genes involved in this pathway are clustered into two operons, kgu and gad. PtxS controls the expression of the kgu and gad operons as well as its own transcription. The PtxS operator is a perfect palindrome, 5'-TGAAACCGGTTTCA-3', which is present in all three promoters. Crystallization of native PtxS failed, and PtxS-DNA crystals were finally produced by the counter-diffusion technique. A portion of the capillary used for crystal growth was attached to the end of a SPINE standard cap and directly flash-cooled in liquid nitrogen for diffraction tests. A full data set was collected with a beam size of 10×10 µm. The crystal belonged to the trigonal space group P3, with unit-cell parameters a=b=213.71, c=71.57 Å. Only unhandled crystals grown in capillaries of 0.1 mm inner diameter diffracted X-rays to 1.92 Å resolution.
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Affiliation(s)
- E Pineda-Molina
- Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain.
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Stsiapanava A, Dohnalek J, Gavira JA, Kuty M, Koudelakova T, Damborsky J, Kuta Smatanova I. Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels. Acta Crystallogr D Biol Crystallogr 2010; 66:962-9. [PMID: 20823547 DOI: 10.1107/s0907444910027101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 07/08/2010] [Indexed: 11/10/2022]
Abstract
The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on the access tunnels of DhaA produced protein variants with significantly improved activity towards TCP. Three mutants of DhaA named DhaA04 (C176Y), DhaA14 (I135F) and DhaA15 (C176Y + I135F) were constructed in order to study the functional relevance of the tunnels connecting the buried active site of the protein with the surrounding solvent. All three protein variants were crystallized using the sitting-drop vapour-diffusion technique. The crystals of DhaA04 belonged to the orthorhombic space group P2(1)2(1)2(1), while the crystals of DhaA14 and DhaA15 had triclinic symmetry in space group P1. The crystal structures of DhaA04, DhaA14 and DhaA15 with ligands present in the active site were solved and refined using diffraction data to 1.23, 0.95 and 1.22 A, resolution, respectively. Structural comparisons of the wild type and the three mutants suggest that the tunnels play a key role in the processes of ligand exchange between the buried active site and the surrounding solvent.
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Affiliation(s)
- A Stsiapanava
- Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
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Kuznetsov YG, Dowell JJ, Gavira JA, Ng JD, McPherson A. Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus. Nucleic Acids Res 2010; 38:8284-94. [PMID: 20693537 PMCID: PMC3001053 DOI: 10.1093/nar/gkq662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Agarose gel electrophoresis, circular dichroism and differential scanning calorimetry showed that single-stranded RNA from satellite tobacco mosaic virus transforms from a conformationally ‘closed state’ at 4°C to a more conformationally ‘open state’ at 65°C. The transition is reversible and shows no hysteresis. Atomic force microscopy (AFM) allowed visualization of the two states and indicated that the conformationally ‘closed state’ probably corresponds to the native encapsidated conformation, and that the ‘open state’ represents a conformation, characterized as short, thick chains of domains, as a consequence of the loss of tertiary interactions. Heating from 75°C to 85°C in the presence of EDTA was necessary to further unravel the ‘open’ conformation RNA into extended chains of lengths >280 nm. Virus exposed to low concentrations of phenol at 65°C, extruded RNA as distinctive ‘pigtails’ in a synchronous fashion, and these ‘pigtails’ then elongated, as the RNA was further discharged by the particles. Moderate concentrations of phenol at 65°C produced complete disruption of virions and only remains of decomposed particles and disordered RNA were evident. AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains.
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Affiliation(s)
- Yuri G Kuznetsov
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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Nieves-Marrero CA, Ruiz-Martínez CR, Estremera-Andújar RA, González-Ramírez LA, López-Garriga J, Gavira JA. Two-step counterdiffusion protocol for the crystallization of haemoglobin II from Lucina pectinata in the pH range 4-9. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:264-8. [PMID: 20208156 PMCID: PMC2833032 DOI: 10.1107/s1744309109053081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 12/09/2009] [Indexed: 11/11/2022]
Abstract
Lucina pectinata haemoglobin II (HbII) transports oxygen in the presence of H(2)S to the symbiotic system in this bivalve mollusc. The composition of the haem pocket at the distal site includes TyrB10 and GlnE7, which are very common in other haem proteins. Obtaining crystals of oxyHbII at various pH values is required in order to elucidate the changes in the conformations of TyrB10 and GlnE7 and structural scenarios induced by changes in pH. Here, the growth of crystals of oxyHbII using the capillary counterdiffusion (CCD) technique at various pH values using a two-step protocol is reported. In the first step, a mini-screen was used to validate sodium formate as the best precipitating reagent for the growth of oxyHbII crystals. The second step, a pH screen typically used for optimization, was used to produce crystals in the pH range 4-9. Very well faceted prismatic ruby-red crystals were obtained at all pH values. X-ray data sets were acquired using synchrotron radiation of wavelength 0.886 A (for the crystals obtained at pH 5) and 0.908 A (for those obtained at pH 4, 8 and 9) to maximum resolutions of 3.30, 1.95, 1.85 and 2.00 A for the crystals obtained at pH 4, 5, 8 and 9, respectively. All of the crystals were isomorphous and belonged to space group P4(2)2(1)2.
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Affiliation(s)
- Carlos A. Nieves-Marrero
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - Carlos R. Ruiz-Martínez
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - Rafael A. Estremera-Andújar
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - Luis A. González-Ramírez
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Edificio López Neyra, PTCS, Avenida del Conocimiento, s/n 18100 Armilla, Granada, Spain
| | - Juan López-Garriga
- Chemistry Department, PO Box 9019, University of Puerto Rico, Mayagüez Campus, Mayagüez, PR 00681, Puerto Rico
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Edificio López Neyra, PTCS, Avenida del Conocimiento, s/n 18100 Armilla, Granada, Spain
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Ruiz-Martínez CR, Nieves-Marrero CA, Estremera-Andújar RA, Gavira JA, González-Ramírez LA, López-Garriga J, García-Ruiz JM. Crystallization and diffraction patterns of the oxy and cyano forms of the Lucina pectinata haemoglobins complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:25-8. [PMID: 19153450 PMCID: PMC2628858 DOI: 10.1107/s1744309108038542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 11/18/2008] [Indexed: 11/10/2022]
Abstract
The native oxygen-carrier haemoglobins complex (HbII-III) is composed of haemoglobin II (HbII) and haemoglobin III (HbIII), which are found in the ctenidia tissue of the bivalve mollusc Lucina pectinata. This protein complex was isolated and purified from its natural source and crystallized using the vapour-diffusion and capillary counter-diffusion methods. Oxy and cyano derivatives of the complex crystallized using several conditions, but the best crystals in terms of quality and size were obtained from sodium formate pH 5 using the counter-diffusion method in a single capillary. Crystals of the oxy and cyano complexes, which showed a ruby-red colour and nonsingular prismatic shapes, scattered X-rays to resolution limits of 2.15 and 2.20 A, respectively, using a 0.886 A synchrotron-radiation source. The crystals belonged to the tetragonal system, space group P4(2)2(1)2, with unit-cell parameters a = b = 74.07, c = 152.07 and a = b = 73.83, c = 152.49 A for the oxy and cyano complexes, respectively. The asymmetric unit of both crystals is composed of a single copy of the heterodimer, with Matthew coefficients (V(M)) of 3.08 and 3.06 A(3) Da(-1) for the oxy and cyano complexes, respectively, which correspond to a solvent content of approximately 60.0% by volume.
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Affiliation(s)
- Carlos R. Ruiz-Martínez
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Carlos A. Nieves-Marrero
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Rafael A. Estremera-Andújar
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGRA), Avenida del Conocimiento s/n, P. T. Ciencias de la Salud, 18100 Armilla, Granada, Spain
| | - Luis A. González-Ramírez
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGRA), Avenida del Conocimiento s/n, P. T. Ciencias de la Salud, 18100 Armilla, Granada, Spain
| | - Juan López-Garriga
- Departamento de Química, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Juan M. García-Ruiz
- Laboratorio de Estudios Cristalográficos, IACT (CSIC–UGRA), Avenida del Conocimiento s/n, P. T. Ciencias de la Salud, 18100 Armilla, Granada, Spain
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Gavira JA, Camara-Artigas A, De Jesús-Bonilla W, López-Garriga J, Lewis A, Pietri R, Yeh SR, Cadilla CL, García-Ruiz JM. Structure and ligand selection of hemoglobin II from Lucina pectinata. J Biol Chem 2008; 283:9414-23. [PMID: 18203714 PMCID: PMC2431033 DOI: 10.1074/jbc.m705026200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 01/10/2008] [Indexed: 11/06/2022] Open
Abstract
Lucina pectinata ctenidia harbor three heme proteins: sulfide-reactive hemoglobin I (HbI(Lp)) and the oxygen transporting hemoglobins II and III (HbII(Lp) and HbIII(Lp)) that remain unaffected by the presence of H(2)S. The mechanisms used by these three proteins for their function, including ligand control, remain unknown. The crystal structure of oxygen-bound HbII(Lp) shows a dimeric oxyHbII(Lp) where oxygen is tightly anchored to the heme through hydrogen bonds with Tyr(30)(B10) and Gln(65)(E7). The heme group is buried farther within HbII(Lp) than in HbI(Lp). The proximal His(97)(F8) is hydrogen bonded to a water molecule, which interacts electrostatically with a propionate group, resulting in a Fe-His vibration at 211 cm(-1). The combined effects of the HbII(Lp) small heme pocket, the hydrogen bonding network, the His(97) trans-effect, and the orientation of the oxygen molecule confer stability to the oxy-HbII(Lp) complex. Oxidation of HbI(Lp) Phe(B10) --> Tyr and HbII(Lp) only occurs when the pH is decreased from pH 7.5 to 5.0. Structural and resonance Raman spectroscopy studies suggest that HbII(Lp) oxygen binding and transport to the host bacteria may be regulated by the dynamic displacements of the Gln(65)(E7) and Tyr(30)(B10) pair toward the heme to protect it from changes in the heme oxidation state from Fe(II) to Fe(III).
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, CSIC, P.T. Ciencias de la Salud, Granada, Spain
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Gavira JA, González-Ramírez LA, Oliver-Salvador MC, Soriano-García M, García-Ruiz JM. Structure of the mexicain–E-64 complex and comparison with other cysteine proteases of the papain family. Acta Crystallogr D Biol Crystallogr 2007; 63:555-63. [PMID: 17452780 DOI: 10.1107/s0907444907005616] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 02/02/2007] [Indexed: 11/10/2022]
Abstract
Mexicain is a 23.8 kDa cysteine protease from the tropical plant Jacaratia mexicana. It is isolated as the most abundant product after cation-exchange chromatography of the mix of proteases extracted from the latex of the fruit. The purified enzyme inhibited with E-64 [N-(3-carboxyoxirane-2-carbonyl)-leucyl-amino(4-guanido)butane] was crystallized by sitting-drop vapour diffusion and the structure was solved by molecular replacement at 2.1 A resolution and refined to an R factor of 17.7% (R(free) = 23.8%). The enzyme belongs to the alpha+beta class of proteins and the structure shows the typical papain-like fold composed of two domains, the alpha-helix-rich (L) domain and the beta-barrel-like (R) domain, separated by a groove containing the active site formed by residues Cys25 and His159, one from each domain. The four monomers in the asymmetric unit show one E-64 molecule covalently bound to Cys25 in the active site and differences have been found in the placement of E-64 in each monomer.
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Affiliation(s)
- J A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Granada, Spain
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Kutá Smatanová I, Gavira JA, Rezácová P, Vácha F, García-Ruiz JM. New techniques for membrane protein crystallization tested on photosystem II core complex of Pisum sativum. Photosynth Res 2006; 90:255-9. [PMID: 17279440 DOI: 10.1007/s11120-007-9131-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 01/04/2007] [Indexed: 05/13/2023]
Abstract
The crystallization of a given protein is a hard task being even more complicated when the protein shows a hydrophobic behavior. In the case of photosynthetic proteins, the difficulty of the experiments increased due to the high light sensitivity. Aqueous solutions of photosystem II core complex (OEC PSII) of Pisum sativum were screened for crystallization conditions using standard crystallization methods. Crystal improvement was achieved by counter-diffusion technique in single capillaries of 0.2 mm inner diameter with a three-layer configuration. The use of this advanced crystallization technique-for the first time applied to the crystallization of membrane proteins-improves the reproducibility of the experiments allowing the initial crystal characterization, and facilitates the manipulation under light protection.
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Affiliation(s)
- Ivana Kutá Smatanová
- Institute of Physical Biology, University of South Bohemia Ceske Budejovice, Zamek 136, 373 33, Nove Hrady, Czech Republic.
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Gavira JA, de Jesus W, Camara-Artigas A, López-Garriga J, García-Ruiz JM. Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:196-9. [PMID: 16511300 PMCID: PMC2197196 DOI: 10.1107/s1744309106002648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 01/22/2006] [Indexed: 11/11/2022]
Abstract
Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 73.92, c = 152.35 A, and diffracted X-rays to a resolution of better than 2.0 A. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (VM) of 3.15 A3 Da(-1) and a solvent content of 61% by volume.
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Affiliation(s)
- José A. Gavira
- Laboratorio de Estudios Cristalográficos–CSIC, P. T. Ciencias de la Salud, Granada, Spain
| | - Walleska de Jesus
- Departamento de Quimica, PO Box 9019, Universidad de Puerto Rico, Recinto de Mayaguez, Mayaguez PR 00681, Puerto Rico
| | - Ana Camara-Artigas
- Departamento Química-Física, Bioquímica y Química Inorgánica, Universidad de Almería, Carretera Sacramento, Almería 04120, Spain
| | - Juan López-Garriga
- Departamento Química-Física, Bioquímica y Química Inorgánica, Universidad de Almería, Carretera Sacramento, Almería 04120, Spain
| | - Juan M. García-Ruiz
- Laboratorio de Estudios Cristalográficos–CSIC, P. T. Ciencias de la Salud, Granada, Spain
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Pusey ML, Liu ZJ, Tempel W, Praissman J, Lin D, Wang BC, Gavira JA, Ng JD. Life in the fast lane for protein crystallization and X-ray crystallography. Prog Biophys Mol Biol 2005; 88:359-86. [PMID: 15652250 DOI: 10.1016/j.pbiomolbio.2004.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).
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Affiliation(s)
- Marc L Pusey
- Biophysics SD48, NASA/MSFC Huntsville, AL 35812, USA
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Oliver-Salvador MC, González-Ramírez LA, Gavira JA, Soriano-García M, García-Ruiz JM. Purification, crystallization and preliminary X-ray analysis of mexicain. Acta Crystallogr D Biol Crystallogr 2004; 60:2058-60. [PMID: 15502326 DOI: 10.1107/s0907444904021638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Accepted: 09/02/2004] [Indexed: 11/10/2022]
Abstract
Mexicain is a 23.7 kDa papain-like cysteine protease from the tropical plant Jacaratia mexicana. Extracted as a mix of proteases from the latex of the fruit, mexicain is isolated after cation-exchange chromatography as the most abundant product. The purified product inhibited with E-64 was crystallized by sitting-drop vapour diffusion in the presence of ethanolamine. Cryoprotected crystals diffracted X-rays from a home source to 1.98 A and belong to the monoclinic space group P2(1), with unit-cell parameters a = 57.36, b = 90.45, c = 80.39 A, beta = 92.64 degrees . The asymmetric unit contains four molecules of mexicain, with a corresponding crystal volume per protein weight (V(M)) of 2.24 A(3) Da(-1) and a solvent content of 45% by volume. A molecular-replacement model has been determined and refinement is in progress.
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Affiliation(s)
- M C Oliver-Salvador
- Unidad Profesional Interdisciplinaria de Biotecnología, IPN, México DF, México
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Gavira JA, Toh D, Lopéz-Jaramillo J, García-Ruíz JM, Ng JD. Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling. Acta Crystallogr D Biol Crystallogr 2002; 58:1147-54. [PMID: 12077434 DOI: 10.1107/s0907444902006959] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2001] [Accepted: 04/17/2002] [Indexed: 11/10/2022]
Abstract
Insulin crystals suitable for cryogenic data collection and structure determination by single-wavelength anomalous scattering (SAS) were obtained by a self-optimization screening process in a single capillary tube without manipulation of the crystals at any time. Using the counter-diffusion crystallization technique, screening for optimal conditions for crystal growth, incorporation of a strong anomalous scattering halide and cryogenic solution took place simultaneously in a single capillary tube. The crystals in the capillaries can be placed directly in the cryostream for data collection using a conventional home-laboratory X-ray source. High-redundancy data were used to obtain a Patterson solution from the anomalous signal of iodine. As a result, the anomalous scattering-atom position was determined and the phase calculated, giving rise to an initial electron-density map at 2.4 A resolution. This entire procedure from crystal growth to the determination of an initial structure was performed within four weeks.
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Affiliation(s)
- José A Gavira
- Laboratory for Structural Biology and the Department of Biological Sciences, University of Alabama in Huntsville, 35899, USA
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Sauter C, Otálora F, Gavira JA, Vidal O, Giegé R, García-Ruiz JM. Structure of tetragonal hen egg-white lysozyme at 0.94 A from crystals grown by the counter-diffusion method. Acta Crystallogr D Biol Crystallogr 2001; 57:1119-26. [PMID: 11468395 DOI: 10.1107/s0907444901008873] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2001] [Accepted: 05/30/2001] [Indexed: 11/10/2022]
Abstract
Very high quality crystals of tetragonal hen egg-white lysozyme were grown in the Advanced Protein Crystallization Facility (APCF) on board the Space Shuttle using a modified free-interface diffusion (FID) reactor designed ad hoc to have a longer diffusion path. This design allows the performance of true counter-diffusion experiments. Crystals were obtained under the classical chemical conditions defined 50 y ago with NaCl as a crystallizing agent and acetate pH 4.5 as a buffer. Counter-diffusion crystallization allows a "physical" instead of chemical optimization of growth conditions: indeed, this method screens for the best supersaturation conditions in a single trial and yields crystals of very high quality. A complete diffraction data set was collected at atomic resolution from one of these crystals using synchrotron radiation at the DESY-EMBL beamlines. The overall R(merge) on intensities in the resolution range 31-0.94 A was 5.2% and the data were 98.9% complete. Refinement was carried out with the programs CNS and SHELX97 to a final crystallographic R factor of 12.26% for 72 390 reflections. A mean standard uncertainty in the atomic positions of 0.024 A was estimated from inversion of blocked least-squares matrices. 22 side chains show alternate conformations and the loop 59-75 adopts in the same crystal packing two conformations that were observed for either triclinic or tetragonal lysozyme in previous high-resolution studies. In addition to 255 water molecules, the crystallizing agent (one hexacoordinated sodium ion and five chloride anions) participates in the ordered lysozyme hydration shell.
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Affiliation(s)
- C Sauter
- UPR 9002, Département Mécanismes et Molécules de la Synthèse Protéique et Cristallogenèse, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, F-67084 Strasbourg CEDEX, France
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Otálora F, Gavira JA, Capelle B, García-Ruiz JM. In-situ measurement of rocking curves during lysozyme crystal growth. Acta Crystallogr D Biol Crystallogr 1999; 55:650-5. [PMID: 10089461 DOI: 10.1107/s0907444998015005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The rocking curve of protein crystals contains a lot of useful information concerning crystal quality, most of which is lost owing to the superimposition of spurious features appearing in these fragile materials after growth, during handling and mounting. To minimize such data spoiling, an experimental setup to perform in situ X-ray diffraction experiments during crystal growth has been designed. The setup, which includes video observation to allow the correlation of crystal shape, size and growth rate with X-ray data, has been used to assess the mosaicity of tetragonal lysozyme crystals during crystal growth. The full width at half maximum (FWHM) of diffraction peaks collected from these crystals changes during the growth process as a (directly proportional) response to the growth rates and the different development of different domain blocks. These changes in the domain distribution and FWHM with time involve a 'zonation' of the crystals, which show very different rocking curves in different parts of their volume. The rocking curves recorded in situ from growing crystals are easier to understand than those from crystals that have suffered even minor handling.
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Affiliation(s)
- F Otálora
- Laboratorio de Estudios Cristalográficos, -Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Fuentenueva s/n, Granada 18002,
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