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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. ULTRASONICS SONOCHEMISTRY 2022; 88:106096. [PMID: 35868210 PMCID: PMC9305616 DOI: 10.1016/j.ultsonch.2022.106096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [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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2
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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] [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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Campos-Escamilla C, Siliqi D, Gonzalez-Ramirez LA, Lopez-Sanchez C, Gavira JA, Moreno A. X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin. Int J Mol Sci 2021; 22:13392. [PMID: 34948188 PMCID: PMC8705962 DOI: 10.3390/ijms222413392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.
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Affiliation(s)
- Camila Campos-Escamilla
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico;
| | - Dritan Siliqi
- Istitituto di Cristallografia (IC), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Luis A. Gonzalez-Ramirez
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
| | - Carmen Lopez-Sanchez
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
| | - Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico;
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
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Tuning Transport Phenomena in Agarose Gels for the Control of Protein Nucleation Density and Crystal Form. CRYSTALS 2021. [DOI: 10.3390/cryst11050466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Agarose gels provide the ideal environment for studying the nucleation step of complex biomacromolecules under diffusion-controlled conditions. In the present paper, we characterized the influence of agarose on the nucleation of three model proteins, i.e., lysozyme, insulin, and proteinase K, as a function of the agarose concentration using a batch method set-up inside flat capillaries. By using this set-up, we were able to directly count the number of crystals in a given volume and correlate it with the amount of agarose and with the average crystal size. We also studied the crystallization behavior of proteinase K with free-interface diffusion so that batch conditions were achieved through slow diffusion of the precipitant. Thanks to the control over the protein mass transport imposed by the network, a previously unknown crystal form, P212121, was obtained, and the three-dimensional structure was determined at a 1.6 Å resolution. Overall, the versatility of agarose gels makes them ideal candidates for the preparation of microcrystalline suspensions of biopharmaceuticals with precise and reproducible crystal attributes or for the exploration of the existence of different polymorphs.
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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. CRYSTAL GROWTH & DESIGN 2021; 21:1698-1707. [PMID: 34602865 PMCID: PMC8479976 DOI: 10.1021/acs.cgd.0c01608] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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Abstract
Multivariate analysis (MA) is becoming a fundamental tool for processing in an efficient way the large amount of data collected in X-ray diffraction experiments. Multi-wedge data collections can increase the data quality in case of tiny protein crystals; in situ or operando setups allow investigating changes on powder samples occurring during repeated fast measurements; pump and probe experiments at X-ray free-electron laser (XFEL) sources supply structural characterization of fast photo-excitation processes. In all these cases, MA can facilitate the extraction of relevant information hidden in data, disclosing the possibility of automatic data processing even in absence of a priori structural knowledge. MA methods recently used in the field of X-ray diffraction are here reviewed and described, giving hints about theoretical background and possible applications. The use of MA in the framework of the modulated enhanced diffraction technique is described in detail.
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