Porous silicon: an effective nucleation-inducing material for protein crystallization 1 1Edited by R. Huber

Chayen, Naomi E.; Saridakis, Emmanuel; El-Bahar, R.; Nemirovsky, Y.

doi:10.1006/jmbi.2001.4995

Cited by 193 publications

(168 citation statements)

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“…However, the primary motivation behind this work is to better understand the nucleation of protein crystals in solutions that contain a piece of porous medium [8,9]. The nucleation only occurs in the presence of the porous medium and the crystals are found to be stuck to this medium, implying that the protein crystal nucleates on the surface of the porous medium.…”

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confidence: 99%

“…Finally, only disordered porous media were effective; media in which the pores were of uniform size, such as zeolites, did not induce nucleation [9,10]. It was hypothesized [8,9] that there is a pore size at which the nucleation rate was maximal and that as disordered porous media have pores with a range of sizes a disordered porous medium is likely to have pores near this size. A zeolite's pores are all the same size and it is improbable that this size will just happen to be a size at which the nucleation is fast.…”

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confidence: 99%

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Heterogeneous Nucleation in and out of Pores

2006

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We study the nucleation of a new thermodynamic phase in pores and find that the nucleation often proceeds via two steps: nucleation of pore filling, and nucleation out of the pore. These two rates have opposing dependencies on pore size, resulting in a pore size at which the nucleation rate of the new phase is maximal. This finding is relevant to attempts to design and use porous media to crystallize proteins. DOI: 10.1103/PhysRevLett.97.065701 PACS numbers: 64.60.Qb, 68.55.Ac, 82.60.Nh Crystallization and condensation both start with heterogeneous nucleation, which occurs at a surface. The nucleus of the crystal or liquid phase forms in contact with this surface. In both cases nucleation is an activated process [1]. The barrier to formation and hence the rate of crystallization or condensation depends on the properties of the surface. In particular, this rate is known to be very sensitive to the geometry of the surface. Studies of nucleation in pores where the surfaces of the pore may confine the nucleus along one or more directions [2 -5] have found that both the size and shape of the pore strongly effect the nucleation rate. These studies were motivated by the desire to understand the hysteresis of phase transitions inside porous media [6,7]. Here, we study nucleation in pores via computer simulations, and we find that nucleation occurs in the corners of pores. Thus, for example, unless a slit pore is very long we expect condensation in it to occur via nucleation in a corner, not via nucleation far from the pore ends as was studied in earlier work [2,3]. This is consistent with the work of Paul and Rieger [7] who found less hysteresis for a closed pore (which has corners) than for an open pore (without corners).Thus our work is relevant to condensation in porous media. However, the primary motivation behind this work is to better understand the nucleation of protein crystals in solutions that contain a piece of porous medium [8,9]. The nucleation only occurs in the presence of the porous medium and the crystals are found to be stuck to this medium, implying that the protein crystal nucleates on the surface of the porous medium. Surfaces that are not porous have proved less successful at promoting nucleation [9,10]. This is evidence that it is the geometry of the pores that is accelerating nucleation. Finally, only disordered porous media were effective; media in which the pores were of uniform size, such as zeolites, did not induce nucleation [9,10]. It was hypothesized [8,9] that there is a pore size at which the nucleation rate was maximal and that as disordered porous media have pores with a range of sizes a disordered porous medium is likely to have pores near this size. A zeolite's pores are all the same size and it is improbable that this size will just happen to be a size at which the nucleation is fast. We find here that there is indeed a pore size at which the nucleation rate is fastest, supporting the earlier hypothesis.As we are interested in generic features of nucleation from pores, we study...

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Heterogeneous Nucleation in and out of Pores

2006

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“…In order to control heterogeneous nucleation of lysozyme crystals, hair cuticles [8] or ad hoc engineered structured surfaces such as Poly-L-Lysine modified glass substrate [9], chemically modified mica surfaces [10] or other chemically modified patterns [11], xanthenes dyes [12], polystyrene nanospheres [13], porous glass [14], porous silicon [15] and fluorinated layered silicate (which is a phyllosilicate with a parallel two-dimensional lamellar structure; Ino et al, 2011) [16] can be exploited. In the last work, the fluorine atoms were considered responsible for driving the nucleation process.…”

Section: Apa Templatementioning

confidence: 99%

“…In the last work, the fluorine atoms were considered responsible for driving the nucleation process. In the work by Chayen and collaborators [15], the authors found that a porous template with a porosity distribution in the range of 5-10 nm could properly act as a nucleating agent, in that, being the pores of a similar size to the proteins, they would entrap protein molecules, facilitating the formation and aggregation of ordered, crystalline structures [17]. Recently, the porosity distribution and pore size were proven as crucial parameters in induced heterogeneous nucleation of protein crystals in a porous medium by theoretical work using sophisticated mathematical models [18,19] and advanced computational approaches, such as the Metropolis Monte Carlo algorithm [20].…”

Section: Apa Templatementioning

confidence: 99%

Protein Crystallization by Anodic Porous Alumina (APA) Template: The Example of Hen Egg White Lysozyme (HEWL)

Pechkova¹,

Bragazzi²,

Nicolini³

2015

NanoWorld J

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In this communication, we report anodic porous alumina (APA) template induced crystallization. The APA nanotemplate was prepared on the glass substrate for the hen egg white lysozyme (HEWL) crystal growth. The changes in the lysozyme crystals morphology, namely in the a/c axis ratio, were observed in the crystal grown by APA nanotemplate, but not in the crystal obtained with classical hanging drop vapor diffusion method, under the same experimental conditions. The comparison of the diffraction data of the two crystals as well as bioinformatics and data mining approaches and molecular dynamics simulations suggest a possible explanation of the nanotemplate crystallization phenomenon and shed light on the APA-induced nanocrystallography.

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“…In earlier work, we used two types of media with nanoscale pores as nucleants: etched silicon 13 and bio-glass. 4 In both cases the surfaces are composed of pores of typical size a few nanometres across but each pore has a different size and shape.…”

Section: Introductionmentioning

confidence: 99%

Carbon-Nanotube-Based Materials for Protein Crystallization

Asanithi

Saridakis

Govada

et al. 2009

ACS Appl. Mater. Interfaces

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We report on the first use of carbon-nanotube based films to produce crystals of proteins. The crystals nucleate on the surface of the film. The difficulty of crystallising proteins is a major bottleneck in the determination of the structure and function of biological molecules. The crystallisation of two model proteins and two medically relevant proteins was studied. Quantitative data on the crystallisation times of the model protein lysozyme are also presented. Two types of the nanotube film, one made with the surfactant Triton X-100 (TX-100) and one with gelatin, were tested. Both induce nucleation of the crystal phase at supersaturations at which the protein solution would otherwise remain clear, however the gelatin-based film induced nucleation down to much lower supersaturations for the two model proteins with which it was used. It appears that the interactions of gelatin with the protein molecules are particularly favourable to nucleation. Crystals of the C1 domain of the human cardiac myosin-binding protein-C that diffracted to a resolution of 1.6Å, were obtained on the TX-100 film. This is far superior to the best crystals obtained using standard techniques, which only diffracted to 3.0 Å. Thus, both our nanotube-based films are very promising candidates for future work on crystallising difficult-tocrystallise target proteins.3

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Porous silicon: an effective nucleation-inducing material for protein crystallization 1 1Edited by R. Huber

Cited by 193 publications

References 16 publications

Heterogeneous Nucleation in and out of Pores

Heterogeneous Nucleation in and out of Pores

Protein Crystallization by Anodic Porous Alumina (APA) Template: The Example of Hen Egg White Lysozyme (HEWL)

Carbon-Nanotube-Based Materials for Protein Crystallization

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