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Fulltext Antifreeze Proteins and Their Practical Utilization in Industry, Medicine, and Agriculture

Eskandari A, Leow TC, Rahman MBA, Oslan SN

Biomolecules, 2020 12 09;10(12).
PMID: 33317024 DOI: 10.3390/biom10121649

Antifreeze proteins (AFPs) are specific proteins, glycopeptides, and peptides made by different organisms to allow cells to survive in sub-zero conditions. AFPs function by reducing the water's freezing point and avoiding ice crystals' growth in the frozen stage. Their capability in modifying ice growth leads to the stabilization of ice crystals within a given temperature range and the inhibition of ice recrystallization that decreases the drip loss during thawing. This review presents the potential applications of AFPs from different sources and types. AFPs can be found in diverse sources such as fish, yeast, plants, bacteria, and insects. Various sources reveal different α-helices and β-sheets structures. Recently, analysis of AFPs has been conducted through bioinformatics tools to analyze their functions within proper time. AFPs can be used widely in various aspects of application and have significant industrial functions, encompassing the enhancement of foods' freezing and liquefying properties, protection of frost plants, enhancement of ice cream's texture, cryosurgery, and cryopreservation of cells and tissues. In conclusion, these applications and physical properties of AFPs can be further explored to meet other industrial players. Designing the peptide-based AFP can also be done to subsequently improve its function.

Matched MeSH terms: Crystallization
Profiling of drug crystallization in the skin

Goh CF, Boyd BJ, Craig DQM, Lane ME

Expert Opin Drug Deliv, 2020 09;17(9):1321-1334.
PMID: 32634033 DOI: 10.1080/17425247.2020.1792440

BACKGROUND: Drug crystallization following application of transdermal and topical formulations may potentially compromise the delivery of drugs to the skin. This phenomenon was found to be limited to the superficial layers of the stratum corneum (~7 µm) in our recent reports and tape stripping of the skin samples was necessary. It remains a significant challenge to profile drug crystallization in situ without damaging the skin samples.
METHODS: This work reports the application of an X-ray microbeam via synchrotron SAXS/WAXS analysis to monitor drug crystallization in the skin, especially in the deeper skin layers. Confocal Raman spectroscopy (CRS) was employed to examine drug distribution in the skin to complement the detection of drug crystallization using SAXS/WAXS analysis.
RESULTS: Following application of saturated drug solutions (ibuprofen, diclofenac acid, and salts), CRS depth profiles confirmed that the drugs generally were delivered to a depth of ~15 - 20 µm in the skin. This was compared with the WAXS profiles that measured drug crystal diffraction at a depth of up to ~25 µm of the skin.
CONCLUSION: This study demonstrates the potential of synchrotron SAXS/WAXS analysis for profiling of drug crystallization in situ in the deeper skin layers without pre-treatment for the skin samples. [Figure: see text].

Matched MeSH terms: Crystallization
Fulltext Investigation of struvite crystals formed in palm oil mill effluent anaerobic digester

Ngatiman M, Jami MS, Abu Bakar MR, Subramaniam V, Loh SK

Heliyon, 2021 Jan;7(1):e05931.
PMID: 33490684 DOI: 10.1016/j.heliyon.2021.e05931

The formation of struvite crystals or magnesium ammonium phosphate (MgNH4PO4) in palm oil mill effluent (POME) occurs as early as in the secondary stage of POME treatment system. Its growth continues in the subsequent tertiary treatment which reduces piping diameter, thus affecting POME treatment efficiency. Hypothesis. The beneficial use of the crystal is the motivation. This occurrence is rarely reported in scientific articles despite being a common problem faced by palm oil millers. The aim of this study is to characterize struvite crystals found in an anaerobic digester of a POME treatment facility in terms of their physical and chemical aspects. The compositions, morphology and properties of these crystals were determined via energy dispersive spectroscopy (EDS), elemental analysis, scanning electron microscopy (SEM) and x-ray diffraction (XRD). Solubility tests were carried out to establish solubility curve for struvite from POME. Finally, crystal growth experiment was done applying reaction crystallization method to demonstrate struvite precipitation from POME. Results showed that high phosphorous (P) (24.85 wt%) and magnesium (Mg) (21.33 wt%) content was found in the struvite sample. Elemental analysis detected carbon (C), hydrogen (H), nitrogen (N) and sulfur (S) below 4 wt%. The crystals analysed by XRD in this study were confirmed as struvite with 94.8% struvite mineral detected from its total volume. Having an orthorhombic crystal system, struvite crystals from POME recorded an average density of 1.701 g cm-3. Solubility curve of struvite from POME was established with maximum solubility of 275.6 mg L-1 at pH 3 and temperature 40 °C. Minimum solubility of 123.6 mg L-1 was recorded at pH 7 and temperature 25 °C. Crystal growth experiment utilizing POME as the source medium managed to achieve 67% reduction in phosphorous content. This study concluded that there is a potential of harnessing valuable nutrients from POME in the form of struvite. Struvite precipitation technology can be adapted in the management of POME in order to achieve maximum utilization of the nutrients that are still abundant in POME. At the same time maximization of nutrient extractions from POME will also reduce pollutants loading in the final discharge.

Matched MeSH terms: Crystallization
Multiple crystallization as a potential strategy for efficient recovery of succinic acid following fermentation with immobilized cells

Luthfi AAI, Tan JP, Isa NFAM, Bukhari NA, Shah SSM, Mahmod SS, et al.

Bioprocess Biosyst Eng, 2020 Jul;43(7):1153-1169.
PMID: 32095989 DOI: 10.1007/s00449-020-02311-x

This study aimed to enhance the crystallizability of bio-based succinic acid for its efficient recovery while maintaining the end product at the highest purity. Immobilization of Actinobacillus succinogenes was initially evaluated based on three different carriers: volcanic glass, clay pebbles, and silica particles. The adsorption capacity of metabolites with a low concentration (10 g/L) and a high concentration (40 g/L) was investigated. It was demonstrated that clay pebbles adsorbed the least succinic acid (

Matched MeSH terms: Crystallization
Crystal structure of a compact α-amylase from Geobacillus thermoleovorans

Mok SC, Teh AH, Saito JA, Najimudin N, Alam M

Enzyme Microb Technol, 2013 Jun 10;53(1):46-54.
PMID: 23683704 DOI: 10.1016/j.enzmictec.2013.03.009

A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimally at 70°C and pH 6.0. While enzyme activity was not enhanced by the addition of CaCl2, GTA's thermostability was significantly improved in the presence of CaCl2. The structure, in complex with an acarbose-derived pseudo-hexasaccharide, consists of the typical three domains and binds one Ca(2+) ion. This Ca(2+) ion was strongly bound and not chelated by EDTA. A predicted second Ca(2+)-binding site, however, was disordered. With limited subsites, two novel substrate-binding residues, Y147 and Y182, may help increase substrate affinity. No distinct starch-binding domain is present, although two regions rich in aromatic residues have been observed. GTA, with a smaller domain B and several shorter loops compared to other α-amylases, has one of the most compact α-amylase folds that may contribute greatly to its tight Ca(2+) binding and thermostability.

Matched MeSH terms: Crystallization
Production and characterization of silica nanoparticles from fly ash: conversion of agro-waste into resource

Uda MNA, Gopinath SCB, Hashim U, Halim NH, Parmin NA, Afnan Uda MN, et al.

Prep Biochem Biotechnol, 2021;51(1):86-95.
PMID: 32713293 DOI: 10.1080/10826068.2020.1793174

A chemical method to synthesize amorphous silica nanoparticles from the incinerated paddy straw has been introduced. The synthesis was conducted through the hydrolysis by alkaline-acidic treatments. As a result, silica particles produced with the sizes were ranging at 60-90 nm, determined by high-resolution microscopy. The crystallinity was confirmed by surface area electron diffraction. Apart from that, chemical and diffraction analyses for both rice straw ash and synthesized silica nanoparticles were conducted by X-ray diffraction and Fourier-transform infrared spectroscopy. The percentage of silica from the incinerated straw was calculated to be 28.3. The prominent surface chemical bonding on the generated silica nanoparticles was with Si-O-Si, stretch of Si-O and symmetric Si-O bonds at peaks of 1090, 471, and 780 cm-1, respectively. To confirm the impurities of the elements in the produced silica, were analyzed using X-ray photoelectron spectroscopy and energy dispersive X-ray spectroscopy. The stability of silica nanoparticles was investigated using thermogravimetric analysis and zeta potential. The measured size from zeta potential analysis was 411.3-493 nm and the stability of mass reduction was located at 200 °C with final amount of mass reduced ∼88% and an average polydispersity Index was 0.195-0.224.

Matched MeSH terms: Crystallization
The development of a tool to predict temperature-exposure of incinerated teeth using colourimetric and hydroxyapatite crystal size data

Rahmat RA, Humphries MA, Austin JJ, Linacre AMT, Self P

Int J Legal Med, 2021 Sep;135(5):2045-2053.
PMID: 33655354 DOI: 10.1007/s00414-021-02538-7

This study presents a novel tool to predict temperature-exposure of incinerated pig teeth as a proxy for understanding impacts of fire on human teeth. Previous studies on the estimation of temperature-exposure of skeletal elements have been limited to that of heat-exposed bone. This predictive tool was developed using a multinomial regression model of colourimetric and hydroxyapatite crystal size variables using data obtained from unheated pig teeth and teeth incinerated at 300 °C, 600 °C, 800 °C and 1000 °C. An additional variable based on the observed appearance of the tooth was included in the tool. This enables the tooth to be classified as definitely burnt (600 °C-1000 °C) or uncertain (27 °C/300 °C). As a result, the model predicting the temperature-exposure of the incinerated teeth had an accuracy of 95%. This tool is a holistic, robust and reliable approach to estimate temperature of heat-exposed pig teeth, with high accuracy, and may act as a valuable proxy to estimate heat exposure for human teeth in forensic casework.

Matched MeSH terms: Crystallization
Fulltext Mechanism-based selection of stabilization strategy for amorphous formulations: Insights into crystallization pathways

Edueng K, Mahlin D, Larsson P, Bergström CAS

J Control Release, 2017 06 28;256:193-202.
PMID: 28412224 DOI: 10.1016/j.jconrel.2017.04.015

We developed a step-by-step experimental protocol using differential scanning calorimetry (DSC), dynamic vapour sorption (DVS), polarized light microscopy (PLM) and a small-scale dissolution apparatus (μDISS Profiler) to investigate the mechanism (solid-to-solid or solution-mediated) by which crystallization of amorphous drugs occurs upon dissolution. This protocol then guided how to stabilize the amorphous formulation. Indapamide, metolazone, glibenclamide and glipizide were selected as model drugs and HPMC (Pharmacoat 606) and PVP (K30) as stabilizing polymers. Spray-dried amorphous indapamide, metolazone and glibenclamide crystallized via solution-mediated nucleation while glipizide suffered from solid-to-solid crystallization. The addition of 0.001%-0.01% (w/v) HPMC into the dissolution medium successfully prevented the crystallization of supersaturated solutions of indapamide and metolazone whereas it only reduced the crystallization rate for glibenclamide. Amorphous solid dispersion (ASD) formulation of glipizide and PVP K30, at a ratio of 50:50% (w/w) reduced but did not completely eliminate the solid-to-solid crystallization of glipizide even though the overall dissolution rate was enhanced both in the absence and presence of HPMC. Raman spectroscopy indicated the formation of a glipizide polymorph in the dissolution medium with higher solubility than the stable polymorph. As a complementary technique, molecular dynamics (MD) simulations of indapamide and glibenclamide with HPMC was performed. It was revealed that hydrogen bonding patterns of the two drugs with HPMC differed significantly, suggesting that hydrogen bonding may play a role in the greater stabilizing effect on supersaturation of indapamide, compared to glibenclamide.

Matched MeSH terms: Crystallization
Temperature-induced first-order displacive phase transition of isonicotinamide-4-methoxybenzoic acid co-crystal

Chia TS, Quah CK

Acta Crystallogr B Struct Sci Cryst Eng Mater, 2017 Apr 01;73(Pt 2):285-295.
PMID: 28362293 DOI: 10.1107/S2052520616019405

Isonicotinamide-4-methoxybenzoic acid co-crystal (1), C6H6N2O·C8H8O3, is formed through slow evaporation from methanol solution and it undergoes a first-order isosymmetry (monoclinic I2/a ↔ monoclinic I2/a) structural phase transition at Tc= 142.5 (5) K, which has been confirmed by an abrupt jump of crystallographic interaxial angle β from variable-temperature single-crystal XRD and small heat hysteresis (6.25 K) in differential scanning calorimetry measurement. The three-dimensional X-ray crystal structures of (1) at the low-temperature phase (LTP) (100, 140 and 142 K) and the high-temperature phase (HTP) (143, 150, 200, 250 and 300 K) were solved and refined as a simple non-disordered model with final R[F2> 2σ(F2)] ≃ 0.05. The asymmetric unit of (1) consists of crystallographically independent 4-methoxybenzoic acid (A) and isonicotinamide (B) molecules in both enantiotropic phases. Molecule A adopts a `near-hydroxyl' conformation in which the hydroxyl and methoxy groups are positioned on the same side. Both `near-hydroxyl' and `near-carbonyl' molecular conformations possess minimum conformational energies with an energy difference of

Matched MeSH terms: Crystallization
Influence of citric acid on the physical and biomineralization ability of freeze/thaw poly(vinyl alcohol) hydrogel

Wahid MNA, Abd Razak SI, Abdul Kadir MR, Hassan R, Nayan NHM, Mat Amin KA

J Biomater Appl, 2018 07;33(1):94-102.
PMID: 29716417 DOI: 10.1177/0885328218771195

This work reports the modification of freeze/thaw poly(vinyl alcohol) hydrogel using citric acid as the bioactive molecule for hydroxyapatite formation in simulated body fluid. Inclusion of 1.3 mM citric acid into the poly(vinyl alcohol) hydrogel showed that the mechanical strength, crystalline phase, functional groups and swelling ability were still intact. Adding citric acid at higher concentrations (1.8 and 2.3 mM), however, resulted in physically poor hydrogels. Presence of 1.3 mM of citric acid showed the growth of porous hydroxyapatite crystals on the poly(vinyl alcohol) surface just after one day of immersion in simulated body fluid. Meanwhile, a fully covered apatite layer on the poly(vinyl alcohol) surface plus the evidence of apatite forming within the hydrogel were observed after soaking for seven days. Gel strength of the soaked poly(vinyl alcohol)/citric acid-1.3 mM hydrogel revealed that the load resistance was enhanced compared to that of the neat poly(vinyl alcohol) hydrogel. This facile method of inducing rapid growth of hydroxyapatite on the hydrogel surface as well as within the hydrogel network can be useful for guided bone regenerative materials.

Matched MeSH terms: Crystallization
Preparation of durian skin nanofibre (DSNF) and its effect on the properties of polylactic acid (PLA) biocomposites

Nur Aimi M, Anuar H, Maizirwan M, Sapuan S, Wahit M, Zakaria S

Sains Malaysiana, 2015;44:1551-1559.

Biological fermentation of Rhizopus oryzae was introduced to extract cellulose nanofibre from durian skin fibre (DSF).
The diameter of the extracted durian skin nanofibre (DSNF) was in the range of 49-81 nm. The changes of chemical
composition of DSNF were clearly seen after evaluated via TAPPI standard test methods. Verification via Fourier transform
infrared (FTIR) confirmed the deduction of hemicelluloses and lignin in DSNF in the range of 1200 to 1000 cm-1. X-ray
diffraction (XRD) demonstrated increment in the crystallinity from 58.3 to 72.2% after biological fermentation. DSNF was
then incorporated into polylactic acid (PLA) via extrusion and injection moulding processes. The effect of 1-5 wt. % DSNF
content on PLA biocomposites was investigated for its mechanical and thermal properties. The presence of only 1 wt. %
improved the tensile and impact strength by 14.1 MPa and 33.1 kJ/m2
, respectively. The thermal properties of PLA-1DSNF
biocomposite also recorded higher thermal stability, glass transition temperature (Tg
), crystallization temperature (Tc
)
and melting temperature (Tm). Additionally, from the DMA, it was determined that PLA-1DSNF possessed lower storage
modulus and loss modulus, as well as low energy dissipation.

Matched MeSH terms: Crystallization
Sustainable Dissolution Performance of a Carrier Tailored Electrospun

Teoh XY, Yeoh Y, Yoong LK, Chan SY

Pharm Res, 2020 Jan 07;37(2):28.
PMID: 31912250 DOI: 10.1007/s11095-019-2734-0

PURPOSE: This study aims to conduct an impact investigation in the hydrophobic-hydrophilic balance as an important factor for dissolution improvement of a hydrophilic carrier-based solid dispersion system.
METHODS: Polymeric carriers with different hydrophobic to hydrophilic ratios were used to prepare several electrospun solid dispersion formulations. Physicochemical properties and surface morphology of the samples were assessed using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR), polarized light microscopy, Differential Scanning Calorimetry (DSC), X-ray Powder Diffraction (XRPD) and Scanning Electron Microscopy (SEM). Dissolution study was conducted in a non-sink condition to assess the drug release.
RESULTS: Incorporation of a higher amount of hydrophilic component showed an improvement in formulating a fully amorphous system based on XRPD, yet the dissolution rate increment showed no significant difference from the lower. Hence, the degree of crystallinity is proven not to be the crucial factor contributing to dissolution rate improvement. The presence of a concomitant hydrophobic component, however, showed ability in resisting precipitation and sustaining supersaturation.
CONCLUSION: Hydrophobicity in a binary carrier system plays an important role in achieving and maintaining the supersaturated state particularly for an amorphous solid dispersion. Graphical Abstract.

Matched MeSH terms: Crystallization
Smart electrical bi-layers lipopeptides: Novel peptidic chains like zigzag map esterified with phospho-glyceride as mono-layer moieties capable in forming a meso-sphere- envelop with scaffold- ability to cellular impurities

Saadi S, Saari N, Abdulkarim MS, Ghazali HM, Anwar F

J Control Release, 2018 03 28;274:93-101.
PMID: 29031897 DOI: 10.1016/j.jconrel.2017.10.011

Cell impurities are an emerging nucleating molecular barriers having the capability in disordering the metabolic chain reactions of proteolysis, glycolysis and lipolysis. Their massive effects induced by copolymer crystal growth in compaction with metal and mineral transients are extended as well as in damaging DNA and mRNA structure motif and other molecular assembly e.g. histones structure unites. Their polycrystalline packing modes, polydispersity and their tendency to surface and interface adhesion prompted us in structuring scaffold biomaterials enriched with biopeptides, layered by phospho-glycerides ester-forms. The interface tension of the formed map is flexible and dependent to the surface exposure and its collapse modes to the surrounding molecular ligands. Thus, the attempts in increasing surface exposure e.g. the viscoelastic of structured lipopeptides and types of formed network structures interplays an extra- conjugating biomolecules having a least cytotoxicity effects to cells constituents. Disulfides molecules are selected to be the key regulatory element in rejoining both lipidic and proteic moieties by disordering atoms status via chemical ionization using organic catalyst. The insertion of methionine based peptidic chain at the lateral surfaces of scaffold biomaterials enhances the electron-meta-static motions by raising a molecular disordering status at distinct regions of the map e.g. epimerization into a nonpolar side that helps the chemical conjunction of disulfide groups with the esterified phosphoglycerides mono-layers. These effects in turn are accomplished by the formation of meso-sphere nonpolar- vesicles. The oxidation of disulfide group would alter the ordering of initial molecules by raising a newly molecular disorders to the map with high polarity to surface regions. In the same time indicates a continuation in the crystallization growth factor via a low chemical lesions between the impurities and a supersaturation in the intra-atomic distances with maximum cross linking to the deformed ligand with scaffold biomaterials.

Matched MeSH terms: Crystallization
Functional properties and utilization of Artocarpus heterophyllus Lam seed starch from new species in China

Zhang Y, Hu M, Zhu K, Wu G, Tan L

Int J Biol Macromol, 2018 Feb;107(Pt B):1395-1405.
PMID: 29017887 DOI: 10.1016/j.ijbiomac.2017.10.001

Jackfruit is now receiving extensive attention as a new source of starch. However, jackfruit seeds are discarded as waste, although they are rich in starch. The functional properties of the starches were investigated from new Chinese jackfruit species. All the starches have a high amylose (26.56-38.34%) with a potential to become functional foods rich in resistant starch. The jackfruit starches varied from trigonal and tetragonal, round to semi-oval/bell shapes and showed significant variations in particle sizes (5.53-14.46μm). These variations led to significant differences in their functional properties, and significant correlations were found in their pasting, thermal, crystal and texture parameters. Hierarchical cluster analysis sorted the samples into three groups of 1) Malaysia 8 (M8) and ZhenZhu (ZZ); 2) Malaysia 2, Malaysia 3 and Malaysia 4, (M2, M3, M4); and 3) Xiangyinsuo 11, Xiangyinsuo 4, Xiangyinsuo 3 and Xiangyinsuo 2 (X11, X4, X3, X2). The first group could be used as food thickening or gelling agents. The second group could be applied in glutinous foods. The third group make them suitable for fillings in confectionery or weaning foods.

Matched MeSH terms: Crystallization
Computational docking of L-arginine and its structural analogues to C-terminal domain of Escherichia coli arginine repressor protein (ArgRc)

Kueh R, Rahman NA, Merican AF

J Mol Model, 2003 Apr;9(2):88-98.
PMID: 12707802

The arginine repressor (ArgR) of Escherichia coli binds to six L-arginine molecules that act as its co-repressor in order to bind to DNA. The binding of L-arginine molecules as well as its structural analogues is compared by means of computational docking. A grid-based energy evaluation method combined with a Monte Carlo simulated annealing process was used in the automated docking. For all ligands, the docking procedure proposed more than one binding site in the C-terminal domain of ArgR (ArgRc). Interaction patterns of ArgRc with L-arginine were also observed for L-canavanine and L-citrulline. L-lysine and L-homoarginine, on the other hand, were shown to bind poorly at the binding site. Figure A general overview of the sites found from docking the various ligands into ArgRc ( grey ribbons). Red coloured sticks: residues in binding site H that was selected for docking

Matched MeSH terms: Crystallization
Utilization of red mud waste into mesoporous ZSM-5 for methylene blue adsorption-desorption studies

Tehubijuluw H, Subagyo R, Yulita MF, Nugraha RE, Kusumawati Y, Bahruji H, et al.

Environ Sci Pollut Res Int, 2021 Mar 13.
PMID: 33712959 DOI: 10.1007/s11356-021-13285-y

Red mud as industrial waste from bauxite was utilized as a precursor for the synthesis of mesoporous ZSM-5. A high concentration of iron oxide in red mud was successfully removed using alkali fusion treatment. Mesoporous ZSM-5 was synthesized using cetyltrimethylammonium bromide (CTABr) as a template via dual-hydrothermal method, and the effect of crystallization time was investigated towards the formation of mesopores. Characterization using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), N2 adsorption-desorption, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) indicated the formation of cubic crystallite ZSM-5 with high surface area and mesopore volume within 6 h of crystallization. Increasing the crystallization time revealed the evolution of highly crystalline ZSM-5; however, the surface area and mesoporosity were significantly reduced. The effect of mesoporosity was investigated on the adsorption of methylene blue (MB). Kinetic and thermodynamic analysis of MB adsorption on mesoporous ZSM-5 was carried out at a variation of adsorption parameters such as the concentration of MB solution, the temperatures of solution, and the amount of adsorbent. Finally, methanol, 1-butanol, acetone, hydrochloric acid (HCl), and acetonitrile were used as desorbing agents to investigate the reusability and stability of mesoporous ZSM-5 as an adsorbent for MB removal.

Matched MeSH terms: Crystallization
Fulltext Structures and binding specificity of galactose- and mannose-binding lectins from champedak: differences from jackfruit lectins

Gabrielsen M, Abdul-Rahman PS, Othman S, Hashim OH, Cogdell RJ

Acta Crystallogr F Struct Biol Commun, 2014 Jun;70(Pt 6):709-16.
PMID: 24915077 DOI: 10.1107/S2053230X14008966

Galactose-binding and mannose-binding lectins from the champedak fruit, which is native to South-east Asia, exhibit useful potential clinical applications. The specificity of the two lectins for their respective ligands allows the detection of potential cancer biomarkers and monitoring of the glycosylated state of proteins in human serum and/or urine. To fully understand and expand the use of these natural proteins, their complete sequences and crystal structures are presented here, together with details of sugar binding.

Matched MeSH terms: Crystallization
Fulltext Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the histone-like HU protein from Spiroplasma melliferum KC3

Boyko K, Gorbacheva M, Rakitina T, Korzhenevskiy D, Vanyushkina A, Kamashev D, et al.

Acta Crystallogr F Struct Biol Commun, 2015 Jan 01;71(Pt 1):24-7.
PMID: 25615963 DOI: 10.1107/S2053230X14025333

HU proteins belong to the nucleoid-associated proteins (NAPs) that are involved in vital processes such as DNA compaction and reparation, gene transcription etc. No data are available on the structures of HU proteins from mycoplasmas. To this end, the HU protein from the parasitic mycoplasma Spiroplasma melliferum KC3 was cloned, overexpressed in Escherichia coli and purified to homogeneity. Prismatic crystals of the protein were obtained by the vapour-diffusion technique at 4°C. The crystals diffracted to 1.36 Å resolution (the best resolution ever obtained for a HU protein). The diffraction data were indexed in space group C2 and the structure of the protein was solved by the molecular-replacement method with one monomer per asymmetric unit.

Matched MeSH terms: Crystallization
Fulltext Fragment-based in silico design of SARS-CoV-2 main protease inhibitors

Ahmad S, Usman Mirza M, Yean Kee L, Nazir M, Abdul Rahman N, Trant JF, et al.

Chem Biol Drug Des, 2021 Oct;98(4):604-619.
PMID: 34148292 DOI: 10.1111/cbdd.13914

3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and 7,158 stereoisomers were screened using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. The top 22 hits having conformations approaching the linear combination of their constituent fragments were selected for MD simulation on Desmond. MD simulation suggested 15 of these did adopt conformations very close to their constituent pieces with far higher binding affinity than either constituent domain alone. These structures could provide a starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding, and structures are provided.

Matched MeSH terms: Crystallization
Fulltext Biological pretreatment of rubberwood with Ceriporiopsis subvermispora for enzymatic hydrolysis and bioethanol production

Nazarpour F, Abdullah DK, Abdullah N, Motedayen N, Zamiri R

Biomed Res Int, 2013;2013:268349.
PMID: 24167813 DOI: 10.1155/2013/268349

Rubberwood (Hevea brasiliensis), a potential raw material for bioethanol production due to its high cellulose content, was used as a novel feedstock for enzymatic hydrolysis and bioethanol production using biological pretreatment. To improve ethanol production, rubberwood was pretreated with white rot fungus Ceriporiopsis subvermispora to increase fermentation efficiency. The effects of particle size of rubberwood (1 mm, 0.5 mm, and 0.25 mm) and pretreatment time on the biological pretreatment were first determined by chemical analysis and X-ray diffraction and their best condition obtained with 1 mm particle size and 90 days pretreatment. Further morphological study on rubberwood with 1 mm particle size pretreated by fungus was performed by FT-IR spectra analysis and SEM observation and the result indicated the ability of this fungus for pretreatment. A study on enzymatic hydrolysis resulted in an increased sugar yield of 27.67% as compared with untreated rubberwood (2.88%). The maximum ethanol concentration and yield were 17.9 g/L and 53% yield, respectively, after 120 hours. The results obtained demonstrate that rubberwood pretreated by C. subvermispora can be used as an alternative material for the enzymatic hydrolysis and bioethanol production.

Matched MeSH terms: Crystallization

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