Determination of protein 3-dimensional structure offers very important information in biology researches, especially for understanding protein functions and redundant drug design. The X-ray crystallography is still the main technique for protein structure determination. Obtaining protein crystals is an essential procedure after protein purification in this technique. However, there is only 42% of soluble purified proteins yield crystals by statistics. Experimental verification of protein crystallizability is relatively expensive and time-consuming. Thus it is desired to predict the protein crystallizability by a computational method before starting the experiment. In this paper, combined with our own efforts, some successful in silico methods to predict the protein crystallizability are reviewed.
Crystallization ; methods ; Crystallography, X-Ray ; Protein Structure, Tertiary ; Proteins ; chemistry

Crystallography, X-Ray ; DNA Repair ; Exodeoxyribonucleases ; chemistry ; Humans ; Protein Conformation

OBJECTIVEThe aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied.

METHODSThe three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures.

RESULTSThe crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected.

CONCLUSIONProtein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

Bacterial Proteins ; chemistry ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Dental Caries ; Humans ; Streptococcus mutans ; chemistry ; X-Ray Diffraction

This paper reviews the effects of physical environments (including light, electric field, ultrasound, magnetic field, microgravity, temperature, mechanical vibration, and heterogeneous nucleation interface) on protein crystal nucleation. The research results are summarized and the possible mechanisms of the effects are discussed. In the end of this review, the application prospects of these physical environments (including coupled environments) in protein crystallization are presented.
Crystallization ; Crystallography, X-Ray ; Electromagnetic Fields ; Environment ; Light ; Protein Conformation ; Proteins ; chemistry ; Temperature

AIMTo investigate the lattice mechanisms involved in the increased dissolution effect of polyethylene glycol (PEG 6,000) dispersion system on poorly soluble drug silymarin (SILY).

METHODSFusion method was used to prepare the solid dispersions of SILY with PEG 6,000. Evaluation of the improvement of dissolution was performed with dissolution studies in vitro. X-ray powder diffraction combined with diffraction peak pattern-fitting procedure were applied to quantitatively analyze the changes of lattice parameters. The interaction of SILY and PEG 6,000 was also determined with Fourier transform-infrared (FT-IR) spectroscopy.

RESULTSThe dissolution rate of SILY was considerably increased when formulated in solid dispersion of PEG 6,000 as compared to pure SILY. The datum from the X-ray diffraction showed the changes in the lattic spacings and particular diffraction peaks (position and the intensity) of PEG 6,000 and SILY. These could explain the increased rate of SILY released from solid dispersion system. The information of FT-IR spectroscopy showed the absence of well-defined drug-polymer interaction.

CONCLUSIONThe dissolution improvement of poorly soluble SILY from solid dispersion of PEG 6,000 can be illuminated by the changes of the lattice parameters of PEG 6,000 and the drug.

Chemistry, Pharmaceutical ; Crystallization ; Crystallography, X-Ray ; Drug Carriers ; Polyethylene Glycols ; chemistry ; Silymarin ; administration & dosage ; chemistry ; Solubility

AIMTo study the crystalline characteristics of ceftezole sodium.

METHODSCeftezole sodium crystals were obtained from different solvents. X-ray diffraction, DSC, TGA, etc were used to analyze the crytals.

RESULTSCeftezole sodium crystal was easily obtained in isopropanol-water mixture. It consists of ceftizole sodium monohydrate, which consists of type I and type II two different crystal forms. Powder X-ray diffraction patterns showed differences between type I and the type II crystal forms. Peaks at 8 degrees and 18 degrees in diffractograms of the type I, but at 9 degrees and 18.6 degrees in the type II could be observed. Water molecules in different crystal forms had different combining condition. They lost during 35-117 degrees C in the type I form, but lost during 110-160 degrees C in the type II form.

CONCLUSIONStructure of ceftizole sodium monohydrate crystal obtained in different circumstance could be some vary, which influence upon the thermal stability of the compound. The type I crystal form is more stable than the type II.

Cefazolin ; analogs & derivatives ; chemistry ; classification ; Crystallization ; Crystallography, X-Ray ; Drug Stability ; Molecular Conformation ; Molecular Structure

In pursuit of effective agents for hepatocellular carcinoma derived from the Artemisia species, this study built upon initial findings that an ethanol (EtOH) extract and ethyl acetate (EtOAc) fraction of the aerial parts of Artemisia dubia Wall. ex Bess. exhibited cytotoxicity against HepG2 cells with inhibitory rates of 57.1% and 84.2% (100 μg·mL^-1), respectively. Guided by bioactivity, fourteen previously unidentified sesquiterpenes, artemdubinoids A-N (1-14), were isolated from the EtOAc fraction. Their structural elucidation was achieved through comprehensive spectroscopic analyses and corroborated by the comparison between the experimental and calculated ECD spectra. Single crystal X-ray diffraction provided definitive structure confirmation for artemdubinoids A, D, F, and H. Artemdubinoids A and B (1-2) represented unique sesquiterpenes featuring a 6/5-fused bicyclic carbon scaffold, and their putative biosynthetic pathways were discussed; artemdubinoid C (3) was a novel guaianolide derivative that might be formed by the [4 + 2] Diels-Alder reaction; artemdubinoids D and E (4-5) were rare 1,10-seco-guaianolides; artemdubinoids F-K (6-11) were chlorine-containing guaianolides. Eleven compounds exhibited cytotoxicity against three human hepatoma cell lines (HepG2, Huh7, and SK-Hep-1) with half-maximal inhibitory concentration (IC₅₀) values spanning 7.5-82.5 μmol·L^-1. Artemdubinoid M (13) exhibited the most active cytotoxicity with IC₅₀ values of 14.5, 7.5 and 8.9 μmol·L^-1 against the HepG2, Huh7, and SK-Hep-1 cell lines, respectively, which were equivalent to the positive control, sorafenib.
Humans ; Artemisia/chemistry* ; Sesquiterpenes/chemistry* ; Cell Line ; Hep G2 Cells ; Crystallography, X-Ray ; Molecular Structure

The α3* nAChRs, which are considered to be promising drug targets for problems such as pain, addiction, cardiovascular function, cognitive disorders etc., are found throughout the central and peripheral nervous system. The α-conotoxin (α-CTx) LvIA has been identified as the most selective inhibitor of α3β2 nAChRs known to date, and it can distinguish the α3β2 nAChR subtype from the α6/α3β2β3 and α3β4 nAChR subtypes. However, the mechanism of its selectivity towards α3β2, α6/α3β2β3, and α3β4 nAChRs remains elusive. Here we report the co-crystal structure of LvIA in complex with Aplysia californica acetylcholine binding protein (Ac-AChBP) at a resolution of 3.4 Å. Based on the structure of this complex, together with homology modeling based on other nAChR subtypes and binding affinity assays, we conclude that Asp-11 of LvIA plays an important role in the selectivity of LvIA towards α3β2 and α3/α6β2β3 nAChRs by making a salt bridge with Lys-155 of the rat α3 subunit. Asn-9 lies within a hydrophobic pocket that is formed by Met-36, Thr-59, and Phe-119 of the rat β2 subunit in the α3β2 nAChR model, revealing the reason for its more potent selectivity towards the α3β2 nAChR subtype. These results provide molecular insights that can be used to design ligands that selectively target α3β2 nAChRs, with significant implications for the design of new therapeutic α-CTxs.
Animals ; Aplysia ; Binding Sites ; Conotoxins ; chemistry ; Crystallography, X-Ray ; Humans ; Protein Structure, Quaternary ; Receptors, Nicotinic ; chemistry

Cryoelectron Microscopy ; methods ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; methods ; Models, Molecular ; Molecular Conformation

Alleles ; Crystallography, X-Ray ; HIV Infections ; HIV-1 ; HLA-B Antigens ; chemistry ; immunology ; Humans