1
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McCue C, Girard HL, Varanasi KK. Enhancing Protein Crystal Nucleation Using In Situ Templating on Bioconjugate-Functionalized Nanoparticles and Machine Learning. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12622-12630. [PMID: 36853011 PMCID: PMC10020963 DOI: 10.1021/acsami.2c17208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Although protein crystallization offers a promising alternative to chromatography for lower-cost protein purification, slow nucleation kinetics and high protein concentration requirements are major barriers for using crystallization as a viable strategy in downstream protein purification. Here, we demonstrate that nanoparticles functionalized with bioconjugates can result in an in situ template for inducing rapid crystallization of proteins at low protein concentration conditions. We use a microbatch crystallization setup to show that the range of successful crystallization conditions is expanded by the presence of functionalized nanoparticles. Furthermore, we use a custom machine learning-enabled emulsion crystallization setup to rigorously quantify nucleation parameters. We show that bioconjugate-functionalized nanoparticles can result in up to a 7-fold decrease in the induction time and a 3-fold increase in the nucleation rate of model proteins compared to those in control environments. We thus provide foundational insight that could enable crystallization to be used in protein manufacturing by reducing both the protein concentration and the time required to nucleate protein crystals.
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2
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Process Modelling of Protein Crystallisation: A Case Study of Lysozyme. Chem Eng Res Des 2023. [DOI: 10.1016/j.cherd.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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3
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Protein Crystals Nucleated and Grown by Means of Porous Materials Display Improved X-ray Diffraction Quality. Int J Mol Sci 2022; 23:ijms231810676. [PMID: 36142586 PMCID: PMC9504001 DOI: 10.3390/ijms231810676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of crystals. Although the nucleation stage is decisive, it is the subsequent growth of crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is theoretically considered. Due to the low degree of metastability, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as bioglass (“Naomi’s Nucleant”), buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of bioglass and buckypaper yield significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. Our theoretical conclusion is that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.
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4
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Enhancement of Protein Crystallization Using Nano-Sized Metal–Organic Framework. CRYSTALS 2022. [DOI: 10.3390/cryst12050578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein crystallization plays a fundamental role in structural biology and chemistry, drug discovery, and crystallography itself. Determining how to improve the crystal growth is necessary and vital during the whole process. According to the recently published data, crystallizing proteins on nanoporous surfaces (i.e., metal–organic framework, abbreviated as MOF) is faster and demands less protein. However, dispersing micro-sized MOF materials uniformly is still a challenge and limiting process in protein crystallization. Here, we investigate the uniformity of micro-sized MOF under the treatment of the high-pressure homogenizer. At various pressures, the MOF is split into particles of different sizes, including the uniform and stable nano-sized MOF. Crystallization experiments demonstrated its enhancement in protein crystallization, and the number of crystals is significantly increased in the presence of nano-sized MOF. This work explores the use of nano-sized MOF solids to crystallize proteins of limited availability (i.e., insufficient for conventional methods) or of a hard-to-crystallize nature.
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5
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Nikishina MA, Alexandrov DV. Nucleation and growth dynamics of ellipsoidal crystals in metastable liquids. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200306. [PMID: 34275366 DOI: 10.1098/rsta.2020.0306] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 06/13/2023]
Abstract
When describing the growth of crystal ensembles from metastable solutions or melts, a significant deviation from a spherical shape is often observed. Experimental data show that the shape of growing crystals can often be considered ellipsoidal. The new theoretical models describing the transient nucleation of ellipsoidal particles and their growth with and without fluctuating rates at the intermediate stage of bulk phase transitions in metastable systems are considered. The nonlinear transport (diffusivity) of ellipsoidal crystals in the space of their volumes is taken into account in the Fokker-Planck equation allowing for fluctuating growth rates. The complete analytical solutions of integro-differential models of kinetic and balance equations are found and analysed. Our solutions show that the desupercooling dynamics is several times faster for ellipsoidal crystals as compared to spherical particles. In addition, the crystal-volume distribution function is lower and shifted to larger particle volumes when considering the growth of ellipsoidal crystals. What is more, this function is monotonically increasing to the maximum crystal size in the absence of fluctuations and is a bell-shaped curve when such fluctuations are taken into account. This article is part of the theme issue 'Transport phenomena in complex systems (part 1)'.
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Affiliation(s)
- Margarita A Nikishina
- Department of Theoretical and Mathematical Physics, Laboratory of Multi-Scale Mathematical Modeling, Ural Federal University, Ekaterinburg, 620000, Russian Federation
| | - Dmitri V Alexandrov
- Department of Theoretical and Mathematical Physics, Laboratory of Multi-Scale Mathematical Modeling, Ural Federal University, Ekaterinburg, 620000, Russian Federation
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6
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Nanev C, Govada L, Chayen NE. Theoretical and experimental investigation of protein crystal nucleation in pores and crevices. IUCRJ 2021; 8:270-280. [PMID: 33708403 PMCID: PMC7924239 DOI: 10.1107/s2052252521000269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
The nucleation ability of pores is explained using the equilibration between the cohesive energy maintaining the integrity of a crystalline cluster and the destructive energy tending to tear it up. It is shown that to get 3D crystals it is vital to have 2D crystals nucleating in the pores first. By filling the pore orifice, the 2D crystal nuclei are more stable because their peripheries are protected from the destructive action of water molecules. Furthermore, the periphery of the 2D crystal is additionally stabilized as a result of its cohesion with the pore wall. The understanding provided by this study combining theory and experiment will facilitate the design of new nucleants.
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Affiliation(s)
- Christo Nanev
- Rostislaw Kaischew Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 11, Sofia 1113, Bulgaria
| | - Lata Govada
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
| | - Naomi E. Chayen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
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7
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Nanev CN. How to Manage a Crystallization Process Aimed at Obtaining a Desired Combination of Number of Crystals and Their Distribution by Size: Learn Here. CRYSTAL RESEARCH AND TECHNOLOGY 2021. [DOI: 10.1002/crat.202000190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christo N. Nanev
- Rostislaw Kaischew Institute of Physical Chemistry Bulgarian Academy of Sciences Sofia 1113 Bulgaria
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8
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Barlow DA, Gregus J. The kinetics of homogeneous and two‐step nucleation during protein crystal growth from solution. INT J CHEM KINET 2019. [DOI: 10.1002/kin.21313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Jan Gregus
- Department of Science and MathematicsAbraham Baldwin Agricultural CollegeTifton Georgia
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9
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Engilberge S, Wagner T, Santoni G, Breyton C, Shima S, Franzetti B, Riobé F, Maury O, Girard E. Protein crystal structure determination with the crystallophore, a nucleating and phasing agent. J Appl Crystallogr 2019; 52:722-731. [PMID: 31396026 PMCID: PMC6662991 DOI: 10.1107/s1600576719006381] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023] Open
Abstract
Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.
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Affiliation(s)
- Sylvain Engilberge
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Tristan Wagner
- Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cécile Breyton
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Seigo Shima
- Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Bruno Franzetti
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Francois Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Eric Girard
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
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10
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Abstract
This paper reviews investigations on protein crystallization. It aims to present a comprehensive rather than complete account of recent studies and efforts to elucidate the most intimate mechanisms of protein crystal nucleation. It is emphasized that both physical and biochemical factors are at play during this process. Recently-discovered molecular scale pathways for protein crystal nucleation are considered first. The bond selection during protein crystal lattice formation, which is a typical biochemically-conditioned peculiarity of the crystallization process, is revisited. Novel approaches allow us to quantitatively describe some protein crystallization cases. Additional light is shed on the protein crystal nucleation in pores and crevices by employing the so-called EBDE method (equilibration between crystal bond and destructive energies). Also, protein crystal nucleation in solution flow is considered.
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11
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Engilberge S, Riobé F, Wagner T, Di Pietro S, Breyton C, Franzetti B, Shima S, Girard E, Dumont E, Maury O. Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Chemistry 2018; 24:9739-9746. [DOI: 10.1002/chem.201802172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/18/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - François Riobé
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
| | - Tristan Wagner
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10 35043 Marburg Germany
| | - Sebastiano Di Pietro
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
| | - Cécile Breyton
- Univ Grenoble Alpes; CEA; CNRS, IBS; 38000 Grenoble France
| | | | - Seigo Shima
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10 35043 Marburg Germany
| | - Eric Girard
- Univ Grenoble Alpes; CEA; CNRS, IBS; 38000 Grenoble France
| | - Elise Dumont
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
| | - Olivier Maury
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
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12
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Artusio F, Pisano R. Surface-induced crystallization of pharmaceuticals and biopharmaceuticals: A review. Int J Pharm 2018; 547:190-208. [PMID: 29859921 DOI: 10.1016/j.ijpharm.2018.05.069] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 01/18/2023]
Abstract
Despite the wide occurrence of crystallization in the pharmaceutical industry, deep understanding and fine control of the process remain a tricky issue. Nevertheless, the successful manufacturing of finished pharmaceutical products, as well as the structural determination of biopharmaceuticals, depend on the size, form, shape and purity of the crystals. The ability of substrates with precise chemistry and topological features to induce nucleation has been thoroughly assessed during the recent years. This paper reviews the major advances and discoveries in controlling small molecule drug and protein crystallization by means of engineered surfaces. By designing superficial properties and morphology, it has been possible to tune the polymorph outcome, shorten the nucleation induction time, impose specific crystal shapes, control the crystal size and carry out crystallization at very low supersaturation levels. Such achievements underline the potential of surface-induced crystallization to provide an ideal platform for the study of the nucleation process and gain control over its stochastic nature.
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Affiliation(s)
- Fiora Artusio
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy.
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13
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Nanev CN. Crystal Size Distribution Resulting from the Time Dependence of Crystal Nucleation. CRYSTAL RESEARCH AND TECHNOLOGY 2018. [DOI: 10.1002/crat.201700248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christo N. Nanev
- Rostislaw Kaischew Institute of Physical Chemistry; Bulgarian Academy of Sciences; 1113 Sofia Bulgaria
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14
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Zhu JJ, Zangari G. Guided Heterogeneous Nucleation of Sodium Chloride at Self-Assembled Monolayer-Modified Nanoporous Gold Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2420-2424. [PMID: 29376390 DOI: 10.1021/acs.langmuir.7b03274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Drug delivery devices are generally inefficient when releasing the active compound at the targeted position. In this work, we investigate nanoporous gold (np-Au) as the drug eluting device, and we use the precipitation of NaCl as a model of drug sedimentation to evaluate the patterns of solute distribution. Hydrophilic and hydrophobic modifications of np-Au result in different, but both inhomogeneous, release patterns, with most of the precipitate forming outside the device. In contrast, the fabrication of a hydrophobic-hydrophilic-layered architecture allows full penetration through the bicontinuous np-Au network, resulting in a homogeneous release pattern. Similar architectures could be used to enhance the efficacy of drug delivery.
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Affiliation(s)
- Joseph J Zhu
- Department of Mechanical and Aerospace Engineering and ‡Department of Materials Science and Engineering, University of Virginia , Charlottesville, Virginia 22903, United States
| | - Giovanni Zangari
- Department of Mechanical and Aerospace Engineering and ‡Department of Materials Science and Engineering, University of Virginia , Charlottesville, Virginia 22903, United States
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15
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Cheng QD, Chen RQ, He J, Li DW, Yang F, Liu YM, Lu QQ, Dong C, Yin DC. Effect of the weather conditions during solution preparation on lysozyme crystallization. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717011086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Protein crystallization is a delicate process that is always sensitive to environmental factors. When the environmental factors are not well controlled or not controlled at all, identical crystallization droplets from the same mother liquid may yield different crystallization results. One environmental factor, the weather conditions during crystallization solution preparation, is not usually considered as a parameter for protein crystallization. In this paper, it is shown that the weather parameters during preparation of the crystallization experiment, including the ambient temperature, humidity, pressure and particulate matter in the air, can all affect the reproducibility of lysozyme crystallization. An identical lysozyme crystallization experiment was repeated for an entire year, and the weather conditions when each crystallization experiment was set up were recorded along with the crystallization results. Among the parameters recorded, the humidity during the experiment setup showed the strongest effect on lysozyme crystallization. On the basis of these results, it is suggested that the weather conditions during crystallization solution preparation should be considered as a potential factor that can influence protein crystallization.
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16
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Engilberge S, Riobé F, Di Pietro S, Lassalle L, Coquelle N, Arnaud CA, Pitrat D, Mulatier JC, Madern D, Breyton C, Maury O, Girard E. Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence. Chem Sci 2017; 8:5909-5917. [PMID: 29619195 PMCID: PMC5859728 DOI: 10.1039/c7sc00758b] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022] Open
Abstract
Macromolecular crystallography suffers from two major issues: getting well-diffracting crystals and solving the phase problem inherent to large macromolecules. Here, we describe the first example of a lanthanide complex family named "crystallophore" (Xo4), which contributes to tackling both bottlenecks. This terbium complex, Tb-Xo4, is an appealing agent for biocrystallography, combining the exceptional phasing power of the Tb(iii) heavy atom with powerful nucleating properties, providing ready-to-use crystals for structure determination. Furthermore, protein/Tb-Xo4 co-crystals can be easily detected and discriminated from other crystalline by-products using luminescence. We demonstrate the potential of this additive for the crystallisation and structure determination of eight proteins, two of whose structures were unknown.
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Affiliation(s)
| | - François Riobé
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Sebastiano Di Pietro
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Louise Lassalle
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | - Nicolas Coquelle
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | | | - Delphine Pitrat
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Jean-Christophe Mulatier
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Dominique Madern
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | - Cécile Breyton
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
| | - Olivier Maury
- Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France .
| | - Eric Girard
- Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France .
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17
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Chen YW, Lee CH, Wang YL, Li TL, Chang HC. Nanodiamonds as Nucleating Agents for Protein Crystallization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6521-6527. [PMID: 28602087 DOI: 10.1021/acs.langmuir.7b00578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nanodiamond (ND) is a carbon-based nanomaterial with potential for a wide range of biological applications. One of such applications is to facilitate the nucleation of protein crystals in aqueous solution. Here, we show that NDs (nominal diameters of 30 and 100 nm) after surface oxidation in air and subsequent treatment in strong acids are useful as heterogeneous nucleating agents for protein crystallization. Tested with lysozyme, ribonuclease A, proteinase K, and catalase, the nanomaterials in either aggregate or film form are found to be able to increase the crystallization efficiency of all proteins. Particularly, for 30 nm NDs, the films with an area of ∼2 mm2 can effectively induce the crystallization of lysozyme at a concentration as low as 5 mg/mL. The efficiency can be further improved by adding preformed protein clusters (∼300 nm in diameter) as inherent nucleation precursors, as demonstrated for ribonuclease A. This combined approach is easy to implement, highly compatible with existing technologies, and can be applied to other protein samples as well.
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Affiliation(s)
- Yen-Wei Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan
| | - Chien-Hsun Lee
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica , Taipei 106, Taiwan
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
- Department of Chemical Engineering, National Taiwan University of Science and Technology , Taipei 106, Taiwan
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18
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Phenomenological Consideration of Protein Crystal Nucleation; the Physics and Biochemistry behind the Phenomenon. CRYSTALS 2017. [DOI: 10.3390/cryst7070193] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Nanev CN. On some aspects of crystallization process energetics, logistic new phase nucleation kinetics, crystal size distribution and Ostwald ripening. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717007105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nucleation, nucleus number densities, and the respective supersaturation dependence, crystal growth and Ostwald ripening are reconsidered from the energetics perspective. Supersaturation-dependent critical nucleus sizes are calculated accordingly. It is argued that the logistic time-dependent nucleation resembles one period of a harmonic oscillation. The general conclusion is that a crystallizing system adapts to the distorting influence of the supersaturation imposed, and during crystal nucleation and growth, the system gradually consumes this supersaturation to reach a new equilibrium state at the end of Ostwald ripening (completely exhausted supersaturation). This is an indication that the system responds to the change in its energetic status according to the well known Le Châtelier–Braun principle. The extent to which the nucleation process affects the crystal size distribution (CSD) is also discussed. Slightly altered by the crystal growth, the CSD also preserves some trace of the nucleation stage shape during Ostwald ripening.
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20
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Abstract
The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials.
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21
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Zhou RB, Cao HL, Zhang CY, Yin DC. A review on recent advances for nucleants and nucleation in protein crystallization. CrystEngComm 2017. [DOI: 10.1039/c6ce02562e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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22
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Luo Z, Morey JR, McDevitt CA, Kobe B. Heterogeneous nucleation is required for crystallization of the ZnuA domain of pneumococcal AdcA. Acta Crystallogr F Struct Biol Commun 2015; 71:1459-64. [PMID: 26625286 PMCID: PMC4666472 DOI: 10.1107/s2053230x15021330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/10/2015] [Indexed: 01/17/2023] Open
Abstract
Zn(2+) is an essential nutrient for all known forms of life. In the major human pathogen Streptococcus pneumoniae, the acquisition of Zn(2+) is facilitated by two Zn(2+)-specific solute-binding proteins: AdcA and AdcAII. To date, there has been a paucity of structural information on AdcA, which has hindered a deeper understanding of the mechanism underlying pneumococcal Zn(2+) acquisition. Native AdcA consists of two domains: an N-terminal ZnuA domain and a C-terminal ZinT domain. In this study, the ZnuA domain of AdcA was crystallized. The initial crystals of the ZnuA-domain protein were obtained using dried seaweed as a heterogeneous nucleating agent. No crystals were obtained in the absence of the heterogeneous nucleating agent. These initial crystals were subsequently used as seeds to produce diffraction-quality crystals. The crystals diffracted to 2.03 Å resolution and had the symmetry of space group P1. This study demonstrates the utility of heterogeneous nucleation. The solution of the crystal structures will lead to further understanding of Zn(2+) acquisition by S. pneumoniae.
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Affiliation(s)
- Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Jacqueline R. Morey
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Christopher A. McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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Wang G, Mitomo H, Matsuo Y, Niikura K, Maeda M, Ijiro K. DNA-modulated photo-transformation of AgCl to silver nanoparticles: visiting the formation mechanism. J Colloid Interface Sci 2015; 452:224-234. [PMID: 25957236 DOI: 10.1016/j.jcis.2015.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/10/2015] [Indexed: 11/17/2022]
Abstract
Solution-phase synthesis and post-synthetic bio-modification have continued to play a dominant role in preparation of nanostructured biomaterials. Heterogeneous nucleation and growth that occur much more often in nature, however, remain rarely explored in nano-biomaterials research. We have newly developed a DNA-modulated photoconversion approach to uniform silver nanoparticles that afford DNA-directed recognition and multi-mode imaging. The present study was aimed at understanding the rapid heterogeneous nucleation and growth of AgNPs at the solid-liquid interface with the aid of DNA. Dynamic changes in absorbance, size and morphology of silver nanostructures were monitored and analyzed to clarify the growth kinetics, which indicated a synthetic route involving synchronous growth of silver nanostructures and the fragmentation and consumption of AgCl. Various stabilizers, including polymer and amino acids, were assessed and compared with respect to the efficacy in photoconversion of AgCl. DNA was found to offer the best monodispersity and the smallest diameter for the resultant AgNPs, due to its strong interactions to silver species as well as excellent charge dispersion ability. By controlling the physicochemical property of DNA through choice of pH and ionic strength, we have demonstrated tunable structure and composition of the nanoparticles.
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Affiliation(s)
- Guoqing Wang
- Research Institute for Electronic Science, Hokkaido University, Kita21, Nishi10, Kita-Ku, Sapporo 001-0021, Japan; Bioengineering Laboratory, RIKEN, 2-1 Hirosawa Wako, Saitama 351-0198, Japan
| | - Hideyuki Mitomo
- Research Institute for Electronic Science, Hokkaido University, Kita21, Nishi10, Kita-Ku, Sapporo 001-0021, Japan; JST-CREST, Sanban-Cho 5, Chiyoda-Ku, Japan
| | - Yasutaka Matsuo
- Research Institute for Electronic Science, Hokkaido University, Kita21, Nishi10, Kita-Ku, Sapporo 001-0021, Japan; JST-CREST, Sanban-Cho 5, Chiyoda-Ku, Japan
| | - Kenichi Niikura
- Research Institute for Electronic Science, Hokkaido University, Kita21, Nishi10, Kita-Ku, Sapporo 001-0021, Japan; JST-CREST, Sanban-Cho 5, Chiyoda-Ku, Japan
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa Wako, Saitama 351-0198, Japan
| | - Kuniharu Ijiro
- Research Institute for Electronic Science, Hokkaido University, Kita21, Nishi10, Kita-Ku, Sapporo 001-0021, Japan; JST-CREST, Sanban-Cho 5, Chiyoda-Ku, Japan.
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24
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Aich A, Pan W, Vekilov PG. Thermodynamic mechanism of free heme action on sickle cell hemoglobin polymerization. AIChE J 2015. [DOI: 10.1002/aic.14800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Anupam Aich
- Department of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
| | - Weichun Pan
- Department of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering; University of Houston; Houston TX 77204
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Khurshid S, Govada L, El-Sharif HF, Reddy SM, Chayen NE. Automating the application of smart materials for protein crystallization. ACTA ACUST UNITED AC 2015; 71:534-40. [PMID: 25760603 PMCID: PMC4356364 DOI: 10.1107/s1399004714027643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022]
Abstract
The first semi-liquid, non-protein nucleating agent for automated protein crystallization trials is described. This ‘smart material’ is demonstrated to induce crystal growth and will provide a simple, cost-effective tool for scientists in academia and industry. The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as ‘smart materials’) for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials.
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Affiliation(s)
- Sahir Khurshid
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, England
| | - Lata Govada
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, England
| | - Hazim F El-Sharif
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, England
| | - Subrayal M Reddy
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, England
| | - Naomi E Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, England
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Utilisation of adsorption and desorption for simultaneously improving protein crystallisation success rate and crystal quality. Sci Rep 2014; 4:7308. [PMID: 25471817 PMCID: PMC4255177 DOI: 10.1038/srep07308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/11/2014] [Indexed: 11/21/2022] Open
Abstract
High-quality protein crystals of suitable size are an important prerequisite for applying X-ray crystallography to determine the 3-dimensional structure of proteins. However, it is often difficult to obtain protein crystals of appropriate size and quality because nucleation and growth processes can be unsuccessful. Here, we show that by adsorbing proteins onto porous polystyrene-divinylbenzene microspheres (SDB) floating on the surface of the crystallisation solution, a localised high supersaturation region at the surface of the microspheres and a low supersaturation region below the microspheres can coexist in a single solution. The crystals will easily nucleate in the region of high supersaturation, but when they grow to a certain size, they will sediment to the region of low supersaturation and continue to grow. In this way, the probability of crystallisation and crystal quality can be simultaneously increased in a single solution without changing other crystallisation parameters.
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