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Yan Y, Wang J, Lu X, Yuan W, Zhang X. Nucleation-Supersaturation Dual-Drive Crystallization Strategy Enables Efficient Protein Crystallization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307924. [PMID: 38072771 DOI: 10.1002/smll.202307924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/30/2023] [Indexed: 12/21/2023]
Abstract
A rational crystallization strategy is essential to obtain high-quality protein crystals, yet the established methods suffer from different limitations arising from the single regulation on either nucleation or supersaturation. Herein, a nucleation-supersaturation dual-driven crystallization (DDC) strategy that realizes synergistic regulation of heterogeneous nucleation sites and solution supersaturation based on dual surface and confinement effects for efficient protein crystallization is reported. This strategy relies on a p(PEGDA-co-DMAA) hydrogel template with pre-filled NaCl under designed concentrations. Once dropping hen egg white lysozyme (HEWL) protein solution on the hydrogel, the wrinkled surface provides numerous nucleation sites, while the internal structure regulates the solution supersaturation in the crystallization region through diffusion. Finally, DDC strategy can create high-quality HEWL crystals with large sizes (100-300 µm), well-defined morphologies (hexagon and tetragon), and a significantly accelerated nucleation time (9-12 times faster than that achieved using the conventional hanging drop method). It also performs well at wider protein concentrations (10-50 mg mL-1) and categories (e.g., achieving fast crystallization and large-size crystals of trypsin), therefore demonstrating clear advantages and great potential for efficiently fabricating protein crystals desirable for diverse applications.
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Affiliation(s)
- Yizhen Yan
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Junyou Wang
- State Key Laboratory of Chemical Engineering and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xuechun Lu
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Weikang Yuan
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiangyang Zhang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
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2
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Govada L, Chayen NE. Crystallisation and characterisation of muscle proteins: a mini-review. J Muscle Res Cell Motil 2023; 44:209-215. [PMID: 37133758 PMCID: PMC10542657 DOI: 10.1007/s10974-023-09648-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/29/2023] [Indexed: 05/04/2023]
Abstract
The techniques of X-ray protein crystallography, NMR and high-resolution cryo-electron microscopy have all been used to determine the high-resolution structure of proteins. The most-commonly used method, however, remains X-ray crystallography but it does rely heavily on the production of suitable crystals. Indeed, the production of diffraction quality crystals remains the rate-limiting step for most protein systems. This mini-review highlights the crystallisation trials that used existing and newly developed crystallisation methods on two muscle protein targets - the actin binding domain (ABD) of α-actinin and the C0-C1 domain of human cardiac myosin binding protein C (cMyBP-C). Furthermore, using heterogenous nucleating agents the crystallisation of the C1 domain of cMyBP-C was successfully achieved in house along with preliminary actin binding studies using electron microscopy and co-sedimentation assays .
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Affiliation(s)
- Lata Govada
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, W12 0NN, London, UK.
| | - Naomi E Chayen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, W12 0NN, London, UK
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3
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCRJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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4
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Cloning and Characterization of Two Novel PR4 Genes from Picea asperata. Int J Mol Sci 2022; 23:ijms232314906. [PMID: 36499235 PMCID: PMC9737788 DOI: 10.3390/ijms232314906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
Pathogenesis-related (PR) proteins are important in plant pathogenic resistance and comprise 17 families, including the PR4 family, with antifungal and anti-pathogenic functions. PR4 proteins contain a C-terminal Barwin domain and are divided into Classes I and II based on the presence of an N-terminal chitin-binding domain (CBD). This study is the first to isolate two PR4 genes, PaPR4-a and PaPR4-b, from Picea asperata, encoding PaPR4-a and PaPR4-b, respectively. Sequence analyses suggested that they were Class II proteins, owing to the presence of an N-terminal signal peptide and a C-terminal Barwin domain, but no CBD. Tertiary structure analyses using the Barwin-like protein of papaya as a template revealed structural similarity, and therefore, functional similarity between the proteins. Predictive results revealed an N-terminal transmembrane domain, and subcellular localization studies confirmed its location on cell membrane and nuclei. Real-time quantitative PCR (RT-qPCR) demonstrated that PaPR4-a and PaPR4-b expression levels were upregulated following infection with Lophodermium piceae. Additionally, PaPR4-a and PaPR4-b were induced in Escherichia coli, where the recombinant proteins existed in inclusion bodies. The renatured purified proteins showed antifungal activity. Furthermore, transgenic tobacco overexpressing PaPR4-a and PaPR4-b exhibited improved resistance to fungal infection. The study can provide a basis for further molecular mechanistic insights into PR4-induced defense responses.
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Lalchandani DS, Paritala S, Gupta PK, Porwal PK. Application of Supervised and Unsupervised Learning Approaches for Mapping Storage Conditions of Biopharmaceutical Product-A Case Study of Human Serum Albumin. J Chromatogr Sci 2022:6640002. [PMID: 35817343 DOI: 10.1093/chromsci/bmac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 11/14/2022]
Abstract
The stability of biopharmaceutical therapeutics over the storage period/shelf life has been a challenging concern for manufacturers. A noble strategy for mapping best and suitable storage conditions for recombinant human serum albumin (rHSA) in laboratory mixture was optimized using chromatographic data as per principal component analysis (PCA), and similarity was defined using hierarchical cluster analysis. In contrast, separability was defined using linear discriminant analysis (LDA) models. The quantitation was performed for rHSA peak (analyte of interest) and its degraded products, i.e., dimer, trimer, agglomerates and other degradation products. The chromatographic variables were calculated using validated stability-indicating assay method. The chromatographic data mapping was done for the above-mentioned peaks over three months at different temperatures, i.e., 20°C, 5-8°C and at room temperature (25°C). The PCA had figured out the ungrouped variable, whereas supervised mapping was done using LDA. As an outcome result of LDA, about 60% of data were correctly classified with the highest sensitivity for 25°C (Aq), 25°C and 5-8°C (Aq with 5% glucose as a stabilizer), whereas the highest specificity was observed for samples stored at 5-8°C (Aq with 5% glucose as a stabilizer).
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Affiliation(s)
- Dimple S Lalchandani
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Sila Katamur (Halugurisuk), Changsari, Guwahati, Assam 781101, India
| | - Sreeteja Paritala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Sila Katamur (Halugurisuk), Changsari, Guwahati, Assam 781101, India
| | - Pawan Kumar Gupta
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Maharajpura, Gwalior, Madhya Pradesh 474 005, India
| | - Pawan Kumar Porwal
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Sila Katamur (Halugurisuk), Changsari, Guwahati, Assam 781101, India
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6
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Xiouras C, Cameli F, Quilló GL, Kavousanakis ME, Vlachos DG, Stefanidis GD. Applications of Artificial Intelligence and Machine Learning Algorithms to Crystallization. Chem Rev 2022; 122:13006-13042. [PMID: 35759465 DOI: 10.1021/acs.chemrev.2c00141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Artificial intelligence and specifically machine learning applications are nowadays used in a variety of scientific applications and cutting-edge technologies, where they have a transformative impact. Such an assembly of statistical and linear algebra methods making use of large data sets is becoming more and more integrated into chemistry and crystallization research workflows. This review aims to present, for the first time, a holistic overview of machine learning and cheminformatics applications as a novel, powerful means to accelerate the discovery of new crystal structures, predict key properties of organic crystalline materials, simulate, understand, and control the dynamics of complex crystallization process systems, as well as contribute to high throughput automation of chemical process development involving crystalline materials. We critically review the advances in these new, rapidly emerging research areas, raising awareness in issues such as the bridging of machine learning models with first-principles mechanistic models, data set size, structure, and quality, as well as the selection of appropriate descriptors. At the same time, we propose future research at the interface of applied mathematics, chemistry, and crystallography. Overall, this review aims to increase the adoption of such methods and tools by chemists and scientists across industry and academia.
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Affiliation(s)
- Christos Xiouras
- Chemical Process R&D, Crystallization Technology Unit, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Fabio Cameli
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Gustavo Lunardon Quilló
- Chemical Process R&D, Crystallization Technology Unit, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium.,Chemical and BioProcess Technology and Control, Department of Chemical Engineering, Faculty of Engineering Technology, KU Leuven, Gebroeders de Smetstraat 1, 9000 Ghent, Belgium
| | - Mihail E Kavousanakis
- School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, 15780 Zografou, Greece
| | - Dionisios G Vlachos
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Georgios D Stefanidis
- School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, 15780 Zografou, Greece.,Laboratory for Chemical Technology, Ghent University; Tech Lane Ghent Science Park 125, B-9052 Ghent, Belgium
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7
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Link F, Heng JYY. Unraveling the Impact of pH on the Crystallization of Pharmaceutical Proteins: A Case Study of Human Insulin. CRYSTAL GROWTH & DESIGN 2022; 22:3024-3033. [PMID: 35529069 PMCID: PMC9073949 DOI: 10.1021/acs.cgd.1c01463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/15/2022] [Indexed: 05/23/2023]
Abstract
One of the most crucial parameters in protein crystallization is pH, as it governs the protein's electrostatic interactions. However, the fundamental role of pH on crystallization still remains unknown. Here, we systematically investigated the crystallization of human insulin (isoelectric point 5.3) at various pHs between 6.0 and 6.7 at different supersaturation ratios, up to 20.9. Our results demonstrate that the pH has an opposing effect on solubility and nucleation rate as a shift in pH toward a more basic milieu increases the solubility by 5-fold while the onset of nucleation was accelerated by a maximum of 8.6-fold. To shed light on this opposing effect, we evaluated the protein-protein interactions as a function of pH by measuring the second virial coefficient and hydrodynamic radius and showed that a change in pH of less than one unit has no significant impact on the protein-protein interactions. As it is widely understood that the increase in protein solubility as a function of pH is due to the increase in the repulsive electrostatic interactions, we have demonstrated that the increase in insulin solubility and decrease in the onset of nucleation are independent of the protein-protein interactions. We hypothesize that it is the electrostatic interactions between both ions and solvent molecules and the protein residues that are governing the crystallization of human insulin. The findings of this study will be of crucial importance for the design of novel crystallization pathways.
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Affiliation(s)
- Frederik
J. Link
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Jerry Y. Y. Heng
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
- Institute
for Molecular Science and Engineering, Imperial
College London, South Kensington Campus, London SW7 2AZ, U.K.
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8
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Macromolecular protein crystallisation with biotemplate of live cells. Sci Rep 2022; 12:3005. [PMID: 35194113 PMCID: PMC8864025 DOI: 10.1038/s41598-022-06999-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/28/2022] [Indexed: 11/21/2022] Open
Abstract
Macromolecular protein crystallisation was one of the potential tools to accelerate the biomanufacturing of biopharmaceuticals. In this work, it was the first time to investigate the roles of biotemplates, Saccharomyces cerevisiae live cells, in the crystallisation processes of lysozyme, with different concentrations from 20 to 2.5 mg/mL lysozyme and different concentrations from 0 to 5.0 × 107 (cfu/mL) Saccharomyces cerevisiae cells, during a period of 96 h. During the crystallisation period, the nucleation possibility in droplets, crystal numbers, and cell growth and cell density were observed and analysed. The results indicated the strong interaction between the lysozyme molecules and the cell wall of the S. cerevisiae, proved by the crystallization of lysozyme with fluorescent labels. The biotemplates demonstrated positive influence or negative influence on the nucleation, i.e. shorter or longer induction time, dependent on the concentrations of the lysozyme and the S. cerevisiae cells, and ratios between them. In the biomanufacturing process, target proteins were various cells were commonly mixed with various cells, and this work provides novel insights of new design and application of live cells as biotemplates for purification of macromolecules.
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Nemergut M, Škrabana R, Berta M, Plückthun A, Sedlák E. Purification of MBP fusion proteins using engineered DARPin affinity matrix. Int J Biol Macromol 2021; 187:105-112. [PMID: 34298044 DOI: 10.1016/j.ijbiomac.2021.07.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 06/20/2021] [Accepted: 07/18/2021] [Indexed: 11/15/2022]
Abstract
Maltose binding protein (MBP) has a long history as an expression tag with the ability to increase the solubility of fused proteins. A critical step for obtaining a sufficient amount of the MBP fusion protein is purification. Commercially available amylose matrix for the affinity purification of MBP fusion proteins has two main issues: (i) low (micromolar) affinity and (ii) the limited number of uses due to the cleavage of polysaccharide matrix by the amylases, present in the crude cell extract. Here, we present a new affinity purification approach based on the protein-protein interaction. We developed the affinity matrix which contains immobilized Designed Ankyrin Repeat Protein off7 (DARPin off7) - previously identified MBP binder with nanomolar affinity. The functionality of the DARPin affinity matrix was tested on the purification of MBP-tagged green fluorescent protein and flavodoxin. The affinity purification of the MBP fusion proteins, based on the MBP-DARPin off7 interaction, enables the purification of the fusion proteins in a simple two-steps procedure. The DARPin affinity matrix - easy to construct, resistant to amylase, insensitive to maltose contamination, and reusable for multiple purification cycles - provides an alternative approach to commercially available affinity matrices for purification of proteins containing the MBP tag.
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Affiliation(s)
- Michal Nemergut
- Center for Interdisciplinary Biosciences, Technology and Innovation Park of P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia; Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Rostislav Škrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10 Bratislava, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park of P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia.
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10
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Tian W, Rielly C, Yang H. Protein crystallisation with air bubble templates: case of gas–liquid–solid interfaces. CrystEngComm 2021. [DOI: 10.1039/d1ce01034d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Crystal formation on air bubble–liquid interface, as soft template to efficiently prompt nucleation of proteins.
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Affiliation(s)
- Wenqing Tian
- Department of Chemical Engineering, Loughborough University, LE11 3RH, Loughborough, UK
| | - Chris Rielly
- Department of Chemical Engineering, Loughborough University, LE11 3RH, Loughborough, UK
| | - Huaiyu Yang
- Department of Chemical Engineering, Loughborough University, LE11 3RH, Loughborough, UK
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11
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Kagan CR, Bassett LC, Murray CB, Thompson SM. Colloidal Quantum Dots as Platforms for Quantum Information Science. Chem Rev 2020; 121:3186-3233. [DOI: 10.1021/acs.chemrev.0c00831] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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12
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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13
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Pu S, Hadinoto K. Continuous crystallization as a downstream processing step of pharmaceutical proteins: A review. Chem Eng Res Des 2020. [DOI: 10.1016/j.cherd.2020.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Wilson J, Ristic M, Kirkwood J, Hargreaves D, Newman J. Predicting the Effect of Chemical Factors on the pH of Crystallization Trials. iScience 2020; 23:101219. [PMID: 32540772 PMCID: PMC7298652 DOI: 10.1016/j.isci.2020.101219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 01/13/2023] Open
Abstract
In macromolecular crystallization, success is often dependent on the pH of the experiment. However, little is known about the pH of reagents used, and it is generally assumed that the pH of the experiment will closely match that of any buffering chemical in the solution. We use a large dataset of experimentally measured solution pH values to show that this assumption can be very wrong and generate a model that can be used to successfully predict the overall solution pH of a crystallization experiment. Furthermore, we investigate the time dependence of the pH of some polyethylene glycol polymers widely used in protein crystallization under different storage conditions. The overall pH of crystallization solutions can be modeled The model was trained and tested on a set of more than 40,000 measured pH values A pH value can be assigned to a non-buffered crystallization cocktail A 12-month stability study of polyethylene glycol suggests ways to store PEGs
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Affiliation(s)
- Julie Wilson
- Department of Mathematics, University of York, York, UK.
| | - Marko Ristic
- Collaborative Crystallisation Centre, CSIRO, Parkville, VIC, Australia
| | | | - David Hargreaves
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge, UK
| | - Janet Newman
- Collaborative Crystallisation Centre, CSIRO, Parkville, VIC, Australia.
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15
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Dong Z, Fang Q. Automated, flexible and versatile manipulation of nanoliter-to-picoliter droplets based on sequential operation droplet array technique. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115812] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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16
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Applications of X-ray Powder Diffraction in Protein Crystallography and Drug Screening. CRYSTALS 2020. [DOI: 10.3390/cryst10020054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Providing fundamental information on intra/intermolecular interactions and physicochemical properties, the three-dimensional structural characterization of biological macromolecules is of extreme importance towards understanding their mechanism of action. Among other methods, X-ray powder diffraction (XRPD) has proved its applicability and efficiency in numerous studies of different materials. Owing to recent methodological advances, this method is now considered a respectable tool for identifying macromolecular phase transitions, quantitative analysis, and determining structural modifications of samples ranging from small organics to full-length proteins. An overview of the XRPD applications and recent improvements related to the study of challenging macromolecules and peptides toward structure-based drug design is discussed. This review congregates recent studies in the field of drug formulation and delivery processes, as well as in polymorph identification and the effect of ligands and environmental conditions upon crystal characteristics. These studies further manifest the efficiency of protein XRPD for quick and accurate preliminary structural characterization.
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17
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A phase diagram-based toolbox to assess the impact of freeze/thaw ramps on the phase behavior of proteins. Bioprocess Biosyst Eng 2019; 43:179-192. [PMID: 31563976 DOI: 10.1007/s00449-019-02215-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/03/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
Abstract
The influence of process parameters during freeze/thaw (FT) operations is essential for the preservation of the protein stability/activity during production and storage processes in the biopharmaceutical industry. Process parameters, such as FT ramps, the final storage time and temperature, affect the occurring FT stress onto the target protein in different ways. FT stress includes cold denaturation, freeze concentration, and ice crystal formation which can result in protein aggregation. To visualize the impact of variations in FT ramps, descriptors such as solubility, phase behavior and crystal morphology were evaluated. The phase diagram-based toolbox in combination with an HTS-compatible cryo-device allowed the identification of suitable ramping schemes during FT operations. It could be clearly shown that rapid operations are needed above the glass transition temperature of the target protein to circumvent precipitation during FT cycles. Finally, a stability index is introduced which allows ranking of the systems investigated.
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18
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Abstract
We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.
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19
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Bezbakh I, Ginkin V, Safronov V, Strelov V, Zakharov B. Mathematical modeling of lysozyme crystal growth under thermal control field for terrestrial and space conditions. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Abstract
This study reports the first experimental evidence of using DNA as a polymeric additive to enhance protein crystallization. Using three kinds of DNA with different molecular weights—calf DNA, salmon DNA, and herring DNA—this study showed an improvement in the success rate of lysozyme crystallization, as compared to control experiments, especially at low lysozyme concentration. The improvement of crystallization is particularly significant in the presence of calf DNA with the highest molecular weight. Calf DNA also speeds up the induction time of lysozyme crystallization and increases the number of crystals per drop. We hypothesized the effect of DNA on protein crystallization may be due to the combination of excluded volume effect, change of water’s surface tension, and the water competition effect. This work confirms predications of the potential use of DNA as a polymeric additive to enhance protein crystallization, potentially applied to systems with limited protein available or difficult to crystallize.
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21
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Wöll AK, Schütz J, Zabel J, Hubbuch J. Analysis of phase behavior and morphology during freeze-thaw applications of lysozyme. Int J Pharm 2018; 555:153-164. [PMID: 30458258 DOI: 10.1016/j.ijpharm.2018.11.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 11/26/2022]
Abstract
Knowledge of protein behavior/stability during freeze/thaw (FT) operations is essential for storage and production processes in the biopharmaceutical industry. FT stress involves freeze concentration, cold denaturation, and ice crystals formation which can result in protein aggregation. Therefore, it is important to understand the ongoing FT processes, and the influence of different solution parameters. In order to evaluate the ongoing processes during FT (up to -80°C), phase diagrams with lysozyme from chicken egg white and sodium chloride were generated. Thereby, three different buffer systems with varying buffer substances and ionic strengths at pH 3 and pH 5 were investigated. As indicators for the ongoing FT processes, the phase behavior, crystal morphology and solubility were used. An increased number of cycles led, for example, to the formation of micro crystals, sea urchin crystals - indicating LLPS and/or high supersaturation - and precipitate. Furthermore, the buffer substances had a more distinct influence on the phase behavior and morphology compared to the ionic strength differences. The solubility line itself was only shifted when distinct changes in the phase behavior could be observed. In summary, a tool was developed for using the phase behavior and especially the crystal morphology as indicator for underlying processes during FT operations.
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Affiliation(s)
- Anna Katharina Wöll
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Juliane Schütz
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jana Zabel
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jürgen Hubbuch
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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22
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Successful amphiphiles as the key to crystallization of membrane proteins: Bridging theory and practice. Biochim Biophys Acta Gen Subj 2018; 1863:437-455. [PMID: 30419284 DOI: 10.1016/j.bbagen.2018.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Membrane proteins constitute a major group of proteins and are of great significance as pharmaceutical targets, but underrepresented in the Protein Data Bank. Particular reasons are their low expression yields and the constant need for cautious and diligent handling in a sufficiently stable hydrophobic environment substituting for the native membrane. When it comes to protein crystallization, such an environment is often established by detergents. SCOPE OF REVIEW In this review, 475 unique membrane protein X-ray structures from the online data bank "Membrane proteins of known 3D structure" are presented with a focus on the detergents essential for protein crystallization. By systematic analysis of the most successful compounds, including current trends in amphiphile development, we provide general insights for selection and design of detergents for membrane protein crystallization. MAJOR CONCLUSIONS The most successful detergents share common features, giving rise to favorable protein interactions. The hydrophile-lipophile balance concept of well-balanced hydrophilic and hydrophobic detergent portions is still the key to successful protein crystallization. Although a single detergent compound is sufficient in most cases, sometimes a suitable mixture of detergents has to be found to alter the resulting protein-detergent complex. Protein crystals with a high diffraction limit involve a tight crystal packing generally favored by detergents with shorter alkyl chains. GENERAL SIGNIFICANCE The formation of well-diffracting membrane protein crystals strongly depends on suitable surfactants, usually screened in numerous crystallization trials. The here-presented findings provide basic criteria for the assessment of surfactants within the vast space of potential crystallization conditions for membrane proteins.
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23
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Thippeshappa S, George SD, Bankapur A, Chidangil S, Mathur D, Abdul Salam AA. Effect of biocompatible nucleants in rapid crystallization of natural amino acids using a CW Nd:YAG laser. Sci Rep 2018; 8:16018. [PMID: 30375443 PMCID: PMC6207789 DOI: 10.1038/s41598-018-34356-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/12/2018] [Indexed: 11/15/2022] Open
Abstract
Laser-induced crystallization is emerging as an alternative technique to crystallize biomolecules. However, its applications are limited to specific small molecules and some simple proteins, possibly because of the need to use high-intensity, pulsed lasers and relatively long laser irradiation time. Both these factors tend to denature biological molecules. If the laser-intensity and time required to crystallize biomolecules were to be reduced, laser-induced crystallization may well become of widespread utility. We report here the crystallization of nineteen natural amino acids by a laser-induced method in combination with one of three nucleants: aluminum, coconut coir, and peacock feather barbule. We have utilized a low-power, continuous wave (CW) Nd:YAG laser (λ = 1064 nm). The advantages of our method are (i) the use of very small laser powers (60 mW), and (ii) the ability to obtain diffraction quality crystals within a mere few seconds. For most amino acids our method yields several orders of magnitude reduction in crystallization time. The use of biocompatible nucleants like coir fibres and peacock feather barbules are novel; their non-toxic nature may find broad applicability in rapid crystallization of diverse biological molecules.
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Affiliation(s)
- Shilpa Thippeshappa
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Sajan D George
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India.,Centre for Applied Nanosciences, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Aseefhali Bankapur
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Santhosh Chidangil
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Deepak Mathur
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India
| | - Abdul Ajees Abdul Salam
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, Karnataka, India.
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24
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Wu P, Li X, Yang M, Huang Z, Mo H, Li T, Zhang Y, Li H. High-throughput, one-step screening, cloning and expression based on the lethality of DpnI in Escherichia coli. Biochem Biophys Res Commun 2018; 504:177-183. [PMID: 30172375 DOI: 10.1016/j.bbrc.2018.08.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/25/2018] [Indexed: 11/17/2022]
Abstract
The manipulation of recombinant DNA has been an integral step in molecular biology to date. A number of strategies have been developed over the years, as traditional cloning methods are time consuming, have high backgrounds and low efficiency and are often limited by the number of suitable restriction sites available. Here, we constructed a series of new positive-selection-based cloning vectors that overcome most of the above mentioned drawbacks and can be applied in both eukaryotic and prokaryotic systems. This strategy is based on the extreme toxicity of DpnI in wild-type E. coli and the inactivation of this lethality by the introduction of target gene within multiple cloning sites. There are no rapid approaches for identifying soluble proteins for high-throughput screening. In this study, we combined this highly efficient cloning strategy with rapid identification of soluble proteins to construct vectors with multiple fusion tags, such as MBP, GST, CBD, NusA, and Sumo, to generate enzymes with potential diagnostic, industrial or therapeutic applications. Thus, this versatile positive-selection-based technology is appropriate for routine cloning, DNA library construction, and high-throughput screening for the expression of proteins of interest.
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Affiliation(s)
- Peijie Wu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Xiaoyan Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Maocheng Yang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Zhengzhi Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Hongya Mo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Ting Li
- Chinese Academy of Inspection and Quarantine, China
| | - Yuan Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China
| | - Hongtao Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China.
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25
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Bruno AE, Charbonneau P, Newman J, Snell EH, So DR, Vanhoucke V, Watkins CJ, Williams S, Wilson J. Classification of crystallization outcomes using deep convolutional neural networks. PLoS One 2018; 13:e0198883. [PMID: 29924841 PMCID: PMC6010233 DOI: 10.1371/journal.pone.0198883] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/25/2018] [Indexed: 11/19/2022] Open
Abstract
The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.
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Affiliation(s)
- Andrew E. Bruno
- Center for Computational Research, University at Buffalo, Buffalo, New York, United States of America
| | - Patrick Charbonneau
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- Department of Physics, Duke University, Durham, North Carolina, United States of America
| | - Janet Newman
- Collaborative Crystallisation Centre, CSIRO, Parkville, Victoria, Australia
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- SUNY Buffalo, Department of Materials, Design, and Innovation, Buffalo, New York, United States of America
| | - David R. So
- Google Brain, Google Inc., Mountain View, California, United States of America
| | - Vincent Vanhoucke
- Google Brain, Google Inc., Mountain View, California, United States of America
| | | | - Shawn Williams
- Platform Technology and Sciences, GlaxoSmithKline Inc., Collegeville, Pennsylvania, United States of America
| | - Julie Wilson
- Department of Mathematics, University of York, York, United Kingdom
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26
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Schieferstein JM, Pawate AS, Varel MJ, Guha S, Astrauskaite I, Gennis RB, Kenis PJA. X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds. LAB ON A CHIP 2018; 18:944-954. [PMID: 29469138 PMCID: PMC5849577 DOI: 10.1039/c7lc01141e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Crystallization of membrane proteins is a critical step for uncovering atomic resolution 3-D structures and elucidating structure-function relationships. Microseeding, the process of transferring sub-microscopic crystal nuclei from initial screens into new crystallization experiments, is an effective, yet underutilized approach to grow crystals suitable for X-ray crystallography. Here, we report simplified methods for crystallization of membrane proteins that utilize microseeding in X-ray transparent microfluidic chips. First, a microfluidic method for introduction of microseed dilutions into metastable crystallization experiments is demonstrated for photoactive yellow protein and cytochrome bo3 oxidase. As microseed concentration decreased, the number of crystals decreased while the average size increased. Second, we demonstrate a microfluidic chip for microseed screening, where many crystallization conditions were formulated on-chip prior to mixing with microseeds. Crystallization composition, crystal size, and diffraction data were collected and mapped on phase diagrams, which revealed that crystals of similar diffraction quality and size typically grow in distinct regions of the phase diagram.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA.
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27
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Strelov VI, Zakharov BG, Bezbakh IZ, Safronov VV, Chernyshev BV, Dutyshev IN. Implementation of Temperature-Controlled Method of Protein Crystallization in Microgravity. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518010194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Yan B, Ye L, Xu W, Liu L. Recent advances in racemic protein crystallography. Bioorg Med Chem 2017; 25:4953-4965. [DOI: 10.1016/j.bmc.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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29
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Hegde RP, Pavithra GC, Dey D, Almo SC, Ramakumar S, Ramagopal UA. Can the propensity of protein crystallization be increased by using systematic screening with metals? Protein Sci 2017. [PMID: 28643473 DOI: 10.1002/pro.3214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization.
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Affiliation(s)
- Raghurama P Hegde
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
| | - Gowribidanur C Pavithra
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Manipal University, Manipal, 576104, India
| | - Debayan Dey
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - S Ramakumar
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Udupi A Ramagopal
- Division of Biological Sciences, Poornaprajna Institute of Scientific Research, Bangalore, 560080, India
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461
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30
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Shilpa T, George SD, Bankapur A, Chidangil S, Dharmadhikari AK, Mathur D, Madan Kumar S, Byrappa K, Abdul Salam AA. Effect of nucleants in photothermally assisted crystallization. Photochem Photobiol Sci 2017; 16:870-882. [PMID: 28379273 DOI: 10.1039/c6pp00430j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Laser-induced crystallization is emerging as a promising technique to crystallize biomolecules like amino acids and proteins. The use of external materials as nucleants and novel seeding methods open new paths for protein crystallization. We report here the results of experiments that explore the effect of nucleants on laser-based crystallization of microlitre droplets of small molecules, amino acids, and proteins. The role of parameters like solute concentration, droplet volume, type and size of the nucleant, and laser power, are systematically investigated. In addition to crystallization of standard molecules like NaCl, KCl, and glycine, we demonstrate the crystallization of negatively (l-histidine), and positively (l-aspartic acid) charged amino acids and lysozyme protein. Single crystal X-ray diffraction and Raman spectroscopy studies unequivocally indicate that the nucleants do not alter the molecular structure of glycine, hydrogen bonding patterns, and packing. Localized vaporization of the solvent near the nucleant due to photothermal heating has enabled us to achieve rapid crystallization - within 3 s - at laser intensities of 0.1 MW cm-2, significantly lower than those reported earlier, with both saturated and unsaturated solutions. The outcome of the current experiments may be of utility in tackling various crystallization problems during the formation of crystals large enough to perform X-ray crystallography.
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Affiliation(s)
- T Shilpa
- Department of Atomic and Molecular Physics, Manipal University, Manipal 576 104, India.
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31
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Schieferstein JM, Pawate AS, Sun C, Wan F, Sheraden PN, Broecker J, Ernst OP, Gennis RB, Kenis PJA. X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization. BIOMICROFLUIDICS 2017; 11:024118. [PMID: 28469762 PMCID: PMC5403737 DOI: 10.1063/1.4981818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/10/2017] [Indexed: 05/10/2023]
Abstract
Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashtamurthy S Pawate
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chang Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Frank Wan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paige N Sheraden
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jana Broecker
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S IA8, Canada
| | | | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paul J A Kenis
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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32
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Brader ML, Baker EN, Dunn MF, Laue TM, Carpenter JF. Using X-Ray Crystallography to Simplify and Accelerate Biologics Drug Development. J Pharm Sci 2017; 106:477-494. [DOI: 10.1016/j.xphs.2016.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023]
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33
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Bourque AJ, Locker CR, Rutledge GC. Heterogeneous Nucleation of an n-Alkane on Tetrahedrally Coordinated Crystals. J Phys Chem B 2017; 121:904-911. [PMID: 28071905 DOI: 10.1021/acs.jpcb.6b12590] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterogeneous nucleation refers to the propensity for phase transformations to initiate preferentially on foreign surfaces, such as vessel walls, dust particles, or formulation additives. In crystallization, the form of the initial nucleus has ramifications for the crystallographic form, morphology, and properties of the resulting solid. Nevertheless, the discovery and design of nucleating agents remains a matter of trial and error because of the very small spatiotemporal scales over which the critical nucleus is formed and the extreme difficulty of examining such events empirically. Using molecular dynamics simulations, we demonstrate a method for the rapid screening of entire families of materials for activity as nucleating agents and for characterizing their mechanism of action. The method is applied to the crystallization of n-pentacontane, a model surrogate for polyethylene, on the family of tetrahedrally coordinated crystals, including diamond and silicon. A systematic variation of parameters in the interaction potential permits a comprehensive, physically based screening of nucleating agents in this class of materials, including both real and hypothetical candidates. The induction time for heterogeneous nucleation is shown to depend strongly on crystallographic registry between the nucleating agent and the critical nucleus, indicative of an epitaxial mechanism in this class of materials. Importantly, the severity of this registry requirement weakens with decreasing rigidity of the substrate and increasing strength of attraction to the surface of the nucleating agent. Employing this method, a high-throughput computational screening of nucleating agents becomes possible, facilitating the discovery of novel nucleating agents within a broad "materials genome" of possible additives.
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Affiliation(s)
- Alexander J Bourque
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - C Rebecca Locker
- ExxonMobil Research and Engineering Company , Annandale, New Jersey 08801, United States
| | - Gregory C Rutledge
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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34
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Renaissance of protein crystallization and precipitation in biopharmaceuticals purification. Biotechnol Adv 2017; 35:41-50. [DOI: 10.1016/j.biotechadv.2016.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022]
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35
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Meikle T, Drummond C, Separovic F, Conn C. Membrane-Mimetic Inverse Bicontinuous Cubic Phase Systems for Encapsulation of Peptides and Proteins. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/bs.abl.2017.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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36
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Boles MA, Engel M, Talapin DV. Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials. Chem Rev 2016; 116:11220-89. [PMID: 27552640 DOI: 10.1021/acs.chemrev.6b00196] [Citation(s) in RCA: 1049] [Impact Index Per Article: 131.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemical methods developed over the past two decades enable preparation of colloidal nanocrystals with uniform size and shape. These Brownian objects readily order into superlattices. Recently, the range of accessible inorganic cores and tunable surface chemistries dramatically increased, expanding the set of nanocrystal arrangements experimentally attainable. In this review, we discuss efforts to create next-generation materials via bottom-up organization of nanocrystals with preprogrammed functionality and self-assembly instructions. This process is often driven by both interparticle interactions and the influence of the assembly environment. The introduction provides the reader with a practical overview of nanocrystal synthesis, self-assembly, and superlattice characterization. We then summarize the theory of nanocrystal interactions and examine fundamental principles governing nanocrystal self-assembly from hard and soft particle perspectives borrowed from the comparatively established fields of micrometer colloids and block copolymer assembly. We outline the extensive catalog of superlattices prepared to date using hydrocarbon-capped nanocrystals with spherical, polyhedral, rod, plate, and branched inorganic core shapes, as well as those obtained by mixing combinations thereof. We also provide an overview of structural defects in nanocrystal superlattices. We then explore the unique possibilities offered by leveraging nontraditional surface chemistries and assembly environments to control superlattice structure and produce nonbulk assemblies. We end with a discussion of the unique optical, magnetic, electronic, and catalytic properties of ordered nanocrystal superlattices, and the coming advances required to make use of this new class of solids.
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Affiliation(s)
- Michael A Boles
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander University Erlangen-Nürnberg , 91052 Erlangen, Germany.,Department of Chemical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Dmitri V Talapin
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States.,Center for Nanoscale Materials, Argonne National Lab , Argonne, Illinois 60439, United States
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37
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Critical reflections on synthetic gene design for recombinant protein expression. Curr Opin Struct Biol 2016; 38:155-62. [DOI: 10.1016/j.sbi.2016.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/17/2022]
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38
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Gavira JA. Current trends in protein crystallization. Arch Biochem Biophys 2015; 602:3-11. [PMID: 26747744 DOI: 10.1016/j.abb.2015.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 10/24/2022]
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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39
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Staneva I, Frenkel D. The role of non-specific interactions in a patchy model of protein crystallization. J Chem Phys 2015; 143:194511. [DOI: 10.1063/1.4935369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Iskra Staneva
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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40
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A Double Emulsion-Based, Plastic-Glass Hybrid Microfluidic Platform for Protein Crystallization. MICROMACHINES 2015. [DOI: 10.3390/mi6111446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Zhang J, Ferré-D'Amaré AR. Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 2015; 22:1363-1371. [PMID: 25185828 DOI: 10.1016/j.str.2014.07.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/11/2014] [Accepted: 07/28/2014] [Indexed: 12/21/2022]
Abstract
Compared to globular proteins, RNAs with complex 3D folds are characterized by poorly differentiated molecular surfaces dominated by backbone phosphates, sparse tertiary contacts stabilizing global architecture, and conformational flexibility. The resulting generally poor order of crystals of large RNAs and their complexes frequently hampers crystallographic structure determination. We describe and rationalize a postcrystallization treatment strategy that exploits the importance of solvation and counterions for RNA folding. Replacement of Li(+) and Mg(2+) needed for growth of crystals of a tRNA-riboswitch-protein complex with Sr(2+), coupled with dehydration, dramatically improved the resolution limit (8.5-3.2 Å) and data quality, enabling structure determination. The soft Sr(2+) ion forms numerous stabilizing intermolecular contacts. Comparison of pre- and posttreatment structures reveals how RNA assemblies redistribute as quasi-rigid bodies to yield improved crystal packing. Cation exchange complements previously reported postcrystallization dehydration of protein crystals and represents a potentially general strategy for improving crystals of large RNAs.
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Affiliation(s)
- Jinwei Zhang
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
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Maeki M, Pawate AS, Yamashita K, Kawamoto M, Tokeshi M, Kenis PJA, Miyazaki M. A Method of Cryoprotection for Protein Crystallography by Using a Microfluidic Chip and Its Application for in Situ X-ray Diffraction Measurements. Anal Chem 2015; 87:4194-200. [DOI: 10.1021/acs.analchem.5b00151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Masatoshi Maeki
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Division
of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
| | - Ashtamurthy S. Pawate
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kenichi Yamashita
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
| | - Masahide Kawamoto
- Kyushu Synchrotron
Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841−0051, Japan
| | - Manabu Tokeshi
- Division
of Biotechnology and Macromolecular Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Paul J. A. Kenis
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Masaya Miyazaki
- Department
of Molecular and Material Sciences, Interdisciplinary Graduate School
of Engineering Sciences, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka 816-8580, Japan
- Advanced
Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1 Shuku, Tosu, Saga 841-0052, Japan
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Stauber M, Jakoncic J, Berger J, Karp JM, Axelbaum A, Sastow D, Buldyrev SV, Hrnjez BJ, Asherie N. Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:427-41. [PMID: 25760593 PMCID: PMC4356360 DOI: 10.1107/s1399004714025061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/15/2014] [Indexed: 11/10/2022]
Abstract
Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.
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Affiliation(s)
- Mark Stauber
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Jean Jakoncic
- National Synchrotron Light Source, Brookhaven National Laboratory, Building 725D, Upton, NY 11973-5000, USA
| | - Jacob Berger
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Jerome M. Karp
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Ariel Axelbaum
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Dahniel Sastow
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Sergey V. Buldyrev
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Bruce J. Hrnjez
- Collegiate School, 260 West 78th Street, New York, NY 10024-6559, USA
| | - Neer Asherie
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
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45
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Chen RQ, Lu QQ, Cheng QD, Ao LB, Zhang CY, Hou H, Liu YM, Li DW, Yin DC. An ignored variable: solution preparation temperature in protein crystallization. Sci Rep 2015; 5:7797. [PMID: 25597864 PMCID: PMC4297974 DOI: 10.1038/srep07797] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/17/2014] [Indexed: 11/16/2022] Open
Abstract
Protein crystallization is affected by many parameters, among which certain parameters have not been well controlled. The temperature at which the protein and precipitant solutions are mixed (i.e., the ambient temperature during mixing) is such a parameter that is typically not well controlled and is often ignored. In this paper, we show that this temperature can influence protein crystallization. The experimental results showed that both higher and lower mixing temperatures can enhance the success of crystallization, which follows a parabolic curve with an increasing ambient temperature. This work illustrates that the crystallization solution preparation temperature is also an important parameter for protein crystallization. Uncontrolled or poorly controlled room temperature may yield poor reproducibility in protein crystallization.
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Affiliation(s)
- Rui-Qing Chen
- 1] Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China [2] Advanced Materials Test Center, School of Mechanics, Civil Engineering and Architecture, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, People's Republic of China
| | - Qin-Qin Lu
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
| | - Qing-Di Cheng
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
| | - Liang-Bo Ao
- Advanced Materials Test Center, School of Mechanics, Civil Engineering and Architecture, Northwestern Polytechnical University, Xi'an 710129, Shaanxi, People's Republic of China
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
| | - Hai Hou
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
| | - Yong-Ming Liu
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
| | - Da-Wei Li
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
| | - Da-Chuan Yin
- Institute for Special Environmental Biophysics, Key Lab for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, People's Republic of China
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Ielasi FS, Hirtz M, Sekula-Neuner S, Laue T, Fuchs H, Willaert RG. Dip-Pen Nanolithography-Assisted Protein Crystallization. J Am Chem Soc 2014; 137:154-7. [DOI: 10.1021/ja512141k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Francesco S. Ielasi
- Department
of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Michael Hirtz
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Sylwia Sekula-Neuner
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Thomas Laue
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Harald Fuchs
- Institute
of Nanotechnology and Karlsruhe Nano Micro Facility, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
- Physical
Institute and Center for Nanotechnology, Westfälische Wilhelms-Universität, 48149 Münster, Germany
| | - Ronnie G. Willaert
- Department
of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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Wang H, Wang M, Tan H, Li Y, Zhang Z, Song J. PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection. PLoS One 2014; 9:e105902. [PMID: 25148528 PMCID: PMC4141844 DOI: 10.1371/journal.pone.0105902] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/25/2014] [Indexed: 01/14/2023] Open
Abstract
X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed ‘PredPPCrys’ using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor.org/PredPPCrys.
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Affiliation(s)
- Huilin Wang
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Mingjun Wang
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hao Tan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Yuan Li
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail: (JS); (ZZ)
| | - Jiangning Song
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria, Australia
- * E-mail: (JS); (ZZ)
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49
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Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot. Sci Rep 2014; 4:5046. [PMID: 24854085 PMCID: PMC5154416 DOI: 10.1038/srep05046] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/02/2014] [Indexed: 01/09/2023] Open
Abstract
Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programmable and reliable liquid-handling operations for nanoliter-scale protein crystallization experiments. We applied the droplet robot in large-scale screening of crystallization conditions of five soluble proteins and one membrane protein with 35–96 different crystallization conditions, study of volume effects on protein crystallization, and determination of phase diagrams of two proteins. The volume for each droplet reactor is only ca. 4–8 nL. The protein consumption significantly reduces 50–500 fold compared with current crystallization stations.
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50
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Pechkova E, Bragazzi NL, Nicolini C. Advances in nanocrystallography as a proteomic tool. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:163-91. [PMID: 24985772 DOI: 10.1016/b978-0-12-800453-1.00005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to overcome the difficulties and hurdles too much often encountered in crystallizing a protein with the conventional techniques, our group has introduced the innovative Langmuir-Blodgett (LB)-based crystallization, as a major advance in the field of both structural and functional proteomics, thus pioneering the emerging field of the so-called nanocrystallography or nanobiocrystallography. This approach uniquely combines protein crystallography and nanotechnologies within an integrated, coherent framework that allows one to obtain highly stable protein crystals and to fully characterize them at a nano- and subnanoscale. A variety of experimental techniques and theoretical/semi-theoretical approaches, ranging from atomic force microscopy, circular dichroism, Raman spectroscopy and other spectroscopic methods, microbeam grazing-incidence small-angle X-ray scattering to in silico simulations, bioinformatics, and molecular dynamics, has been exploited in order to study the LB-films and to investigate the kinetics and the main features of LB-grown crystals. When compared to classical hanging-drop crystallization, LB technique appears strikingly superior and yields results comparable with crystallization in microgravity environments. Therefore, the achievement of LB-based crystallography can have a tremendous impact in the field of industrial and clinical/therapeutic applications, opening new perspectives for personalized medicine. These implications are envisaged and discussed in the present contribution.
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Affiliation(s)
- Eugenia Pechkova
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy
| | - Nicola Luigi Bragazzi
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Claudio Nicolini
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
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