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13 pages, 4534 KiB

Open AccessArticle

Protein Crystals Nucleated and Grown by Means of Porous Materials Display Improved X-ray Diffraction Quality

by Christo N. Nanev, Emmanuel Saridakis, Lata Govada and Naomi E. Chayen

Int. J. Mol. Sci. 2022, 23(18), 10676; https://doi.org/10.3390/ijms231810676 - 14 Sep 2022

Cited by 4 | Viewed by 2038

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. Full article

(This article belongs to the Section Molecular Biophysics)

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11 pages, 3382 KiB

Open AccessArticle

Time-Resolved Studies of Ytterbium Distribution at Interfacial Surfaces of Ferritin-like Dps Protein Demonstrate Metal Uptake and Storage Pathways

by Kornelius Zeth, Gabriela Pretre and Mitsuhiro Okuda

Biomedicines 2021, 9(8), 914; https://doi.org/10.3390/biomedicines9080914 - 29 Jul 2021

Cited by 2 | Viewed by 2100

Abstract

Cage-shaped protein (CSP) complexes are frequently used in bionanotechnology, and they have a variety of different architectures and sizes. The smallest cage-shaped protein, Dps (DNA binding protein from starved cells), can naturally form iron oxide biominerals in a multistep process of ion attraction, translocation, oxidation, and nucleation. The structural basis of this biomineralization mechanism is still unclear. The aim of this paper is to further develop understanding of this topic. Time-resolved metal translocation of Yb³⁺ ions has been investigated on Dps surfaces using X-ray crystallography. The results reveal that the soak time of protein crystals with Yb³⁺ ions strongly affects metal positions during metal translocation, in particular, around and inside the ion translocation pore. We have trapped a dynamic state with ongoing translocation events and compared this to a static state, which is reached when the cavity of Dps is entirely filled by metal ions and translocation is therefore blocked. By comparison with La³⁺ and Co²⁺ datasets, the time-dependence together with the coordination sphere chemistry primarily determine metal−protein interactions. Our data can allow structure-based protein engineering to generate CSPs for the production of tailored nanoparticles. Full article

(This article belongs to the Special Issue Interfacial Phenomena on Biomedicines)

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23 pages, 4485 KiB

Open AccessReview

Crystal Growth in Gels from the Mechanisms of Crystal Growth to Control of Polymorphism: New Trends on Theoretical and Experimental Aspects

by Omar Velásquez-González, Camila Campos-Escamilla, Andrea Flores-Ibarra, Nuria Esturau-Escofet, Roberto Arreguin-Espinosa, Vivian Stojanoff, Mayra Cuéllar-Cruz and Abel Moreno

Crystals 2019, 9(9), 443; https://doi.org/10.3390/cryst9090443 - 26 Aug 2019

Cited by 22 | Viewed by 10368

Abstract

A gel can be considered to be a two-phase (liquid and solid) system, which lacks flow once it reaches a stationary state. The solid phase is usually a tridimensional polymeric mesh, while the liquid phase is usually found in three forms: contained in great cavities, retained in the capillary pores between micelles, or adsorbed on the surface of a micelle. The influence of the use of gels in crystal growth is diverse and depends on the type of gel being used. A decrease in solubility of any solute in the liquid may occur if the solvent interacts extensively with the polymeric section, hence, the nucleation in gels in these cases apparently occurs at relatively low supersaturations. However, if the pore size is small enough, there is a possibility that a higher supersaturation is needed, due to the compartmentalization of solvents. Finally, this may also represent an effect in the diffusion of substances. This review is divided into three main parts; the first evaluates the theory and practice used for the obtainment of polymorphs. The second part describes the use of gels into crystallogenesis of different substances. The last part is related to the particularities of protein crystal polymorphism, as well as modern trends in gel growth for high-resolution X-ray crystallography. Full article

(This article belongs to the Special Issue Crystal Growth in Gels)

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16 pages, 667 KiB

Open AccessEditor’s ChoiceReview

Peculiarities of Protein Crystal Nucleation and Growth

by Christo N. Nanev

Crystals 2018, 8(11), 422; https://doi.org/10.3390/cryst8110422 - 8 Nov 2018

Cited by 12 | Viewed by 5797

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. Full article

(This article belongs to the Special Issue Biological Crystallization)

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14 pages, 6026 KiB

Open AccessArticle

Electro-Infiltration of Cytochrome C into a Porous Silicon Network, and Its Effect on Nucleation and Protein Crystallization—Studies of the Electrical Properties of Porous Silicon Layer-Protein Systems for Applications in Electron-Transfer Biomolecular Devices

by Laura E. Serrano-De la Rosa, Abel Moreno and Mauricio Pacio

Crystals 2017, 7(7), 194; https://doi.org/10.3390/cryst7070194 - 28 Jun 2017

Viewed by 4269

Abstract

In this work, we report the electrical properties of cytochrome C (Cyt C) inside porous silicon (PSi). We first used two techniques of protein infiltration: classic sitting drop and electrochemical migration methods. The electrochemically assisted cell, used for the infiltration by electro-migration, improved the Cyt C nucleation and the crystallization behavior due to the PSi. We were able to carry out the crystallization thanks to the previous infiltration of proteins inside the Si pores network. We then continued the protein crystal growth through a vapor diffusion set-up. Secondly, we applied both forward and reverse bias currents only to the infiltrated Cyt C. Finally, the electrical characteristics were compared to the control (the protein molecules of which were not infiltrated) and to the samples without protein infiltration. The linker used in the sitting drop method influenced the electrical properties, which showed a modification in the current density. The simple drop method showed a current density of ~42 A/cm²; when employing the electrochemical cell technique, the current density was ~318 A/cm²; for the crystallized structures, it was ~0.908 A/cm². Full article

(This article belongs to the Special Issue Protein Crystallization under the Presence of an Electric Field)

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