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

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

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

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

Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using α-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 Å resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.
Animals ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Mice ; Molecular Dynamics Simulation ; Tyrosine Transaminase ; chemistry