Crystal structure of E. coli lipoprotein diacylglyceryl transferase.

Lipoprotein biogenesis is essential for bacterial survival. Phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) is an integral membrane enzyme that catalyses the first reaction of the three-step post-translational lipid modification. Deletion of the lgt gene is lethal to most Gram-negative bacteria. Here we present the crystal structures of Escherichia coli Lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid at 1.9 and 1.6 Å resolution, respectively. The structures reveal the presence of two binding sites and support the previously reported structure-function relationships of Lgt. Complementation results of lgt-knockout cells with different mutant Lgt variants revealed critical residues, including Arg143 and Arg239, that are essential for diacylglyceryl transfer. Using a GFP-based in vitro assay, we correlated the activities of Lgt with structural observations. Together, the structural and biochemical data support a mechanism whereby substrate and product, lipid-modified lipobox-containing peptide, enter and leave the enzyme laterally relative to the lipid bilayer.

Complete genome sequence of Lactococcus lactis S0, an efficient producer of nisin.

Lactococcus lactis S0 is a nisin Z-producing strain isolated from milk, and the nisin production of the strain can reach 4000 IU/ml under fermenting condition. Here, we present the complete genome sequence of L. lactis S0 which includes a single circular chromosome.

Terahertz spectroscopic investigation of human gastric normal and tumor tissues.

Human dehydrated normal and cancerous gastric tissues were measured using transmission time-domain terahertz spectroscopy. Based on the obtained terahertz absorption spectra, the contrasts between the two kinds of tissue were investigated and techniques for automatic identification of cancerous tissue were studied. Distinctive differences were demonstrated in both the shape and amplitude of the absorption spectra between normal and tumor tissue. Additionally, some spectral features in the range of 0.2~0.5 THz and 1~1.5 THz were revealed for all cancerous gastric tissues. To systematically achieve the identification of gastric cancer, principal component analysis combined with t-test was used to extract valuable information indicating the best distinction between the two types. Two clustering approaches, K-means and support vector machine (SVM), were then performed to classify the processed terahertz data into normal and cancerous groups. SVM presented a satisfactory result with less false classification cases. The results of this study implicate the potential of the terahertz technique to detect gastric cancer. The applied data analysis methodology provides a suggestion for automatic discrimination of terahertz spectra in other applications.

Crystal structure and biochemical studies of Brucella melitensis 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

The prokaryotic 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH), a process that plays a key role in several metabolic pathways. Its absence in all mammalian species has implicated this enzyme as a promising target for antimicrobial drug design. Here, we report the crystal structure of BmMTAN in complex with its product adenine at a resolution of 2.6 Å determined by single-wavelength anomalous dispersion method. 11 key residues were mutated for kinetic characterization. Mutations of Tyr134 and Met144 resulted in the largest overall increase in Km, whereas mutagenesis of residues Glu18, Glu145 and Asp168 completely abolished activity. Glu145 and Asp168 were identified as active site residues essential for catalysis. The catalytic mechanism and implications of this structure for broad-based antibiotic design are discussed.

Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A.

The major facilitator superfamily (MFS) is the largest family of secondary active transporters and is present in all life kingdoms. Detailed structural basis of the substrate transport and energy-coupling mechanisms of these proteins remain to be elucidated. YajR is a putative proton-driven MFS transporter found in many Gram-negative bacteria. Here we report the crystal structure of Escherichia coli YajR at 3.15 Å resolution in an outward-facing conformation. In addition to having the 12 canonical transmembrane helices, the YajR structure includes a unique 65-residue C-terminal domain which is independently stable. The structure is unique in illustrating the functional role of "sequence motif A." This highly conserved element is seen to stabilize the outward conformation of YajR and suggests a general mechanism for the conformational change between the inward and outward states of the MFS transporters.

[Spectral analysis of nitrofurantoin in the terahertz frequency range].

The present article measured the absorption coefficient spectra and refractive index spectra of nitrofurantoin original drug, which is one kind of nitrofuran drugs, in the terahertz frequency range from 0.2 to 1.8 THz using terahertz time-domain spectroscopy. The results showed that there exist a number of characteristic absorption peaks of nitrofurantoin with different intensity in the range and the absorption coefficient spectra can be used to identify nitrofurantoin. The article also simulated absorption coefficient spectra of nitrofurantoin molecule within 0.2 - 1.8 THz using density functional theory by Gaussian software, and vibrational modes of some peaks in the experimental absorption coefficient spectra were analyzed and identified. The results show that the experimental absorption peaks at 1.25 and 1.60 THz correspond with the theoretical peaks at 1.30 and 1.67 THz, and these experimental peaks were caused by intramolecular vibrational modes of nitrofurantoin.

[Terahertz time-domain spectroscopy of alpha endosulfan persistent organic pollutant].

Frequency-dependent absorption coefficient spectrum and refractive index spectrum of alpha endosulfan, a kind of persistent organic pollutants, are presented in the terahertz frequency region by terahertz (THz) time-domain spectroscopy (TDS). The spectral features in the THz region have a number of unique characteristic absorption peaks. The result demonstrates that THz-TDS is a promising method to identify materials. Then we adopted density functional calculation method to analyze theoretic absorption coefficients of single alpha endosulfan molecule within 0.2-2 THz. The results show that absorption peaks at 1.68, 1.91 THz in theoretical calculation correspond to 1.7, 1.88 THz in the experiment. Finally, vibrational modes and approximate assignments were discussed, showing that these matched peaks are caused by intramolecular vibrational modes of alpha endosulfan. Others might be related to intermolecular vibrational modes or combined vibrational modes.

[Terahertz time-domain spectroscopy of ractopamine hydrochloride].

The terahertz spectra of Ractopamine hydrochloride in the range of 0.2 to 2.2 THz was obtained by THz time-domain spectroscopy, and the absorption and refraction spectra of Ractopamine hydrochloride was got meanwhile. The structure and vibrational frequencies of Ractopamine molecule in the THz range were simulated by density functional theory. The difference between experimental and theoretical results was analyzed. And assisted by Gaussian View 3.09, the origin of the vibrational frequencies was recognized. The results show that besides the intramolecular vibrations, THz absorption of Ractopamine hydrochloride originated from the intermolecular hydrogen bond network and Van der Waals force between molecules. This study demonstrated the feasibility of time-domain terahertz spectroscopy for the identification of Ractopamine hydrochloride and provided a new way for the detection of Ractopamine hydrochloride.

[Terahertz time-domain spectroscopy of Clenbuterol hydrochloride].

The terahertz spectra of Clenbuterol hydrochloride in the range of 0.2 to 2.6 THz were obtained by THz time-domain spectroscopy, the absorption and refraction spectra of Clenbuterol hydrochloride was got meanwhile. The structure and vibrational frequencies of Clenbuterol molecule, Clenbuterol hydrochloride molecule and Clenbuterol hydrochloride crystal in the THz range were simulated. Based on the difference between experimental and theoretical results, the origin of the vibrational frequencies was analyzed. This study demonstrated the feasibility of time-domain terahertz spectroscopy for the identification of Clenbuterol hydrochloride and provides a new way for the detection of Clenbuterol hydrochloride.

[Terahertz spectroscopic investigation of elaidic acid].

The optical properties of elaidic acid in the THz band were investigated by using THz time-domain spectroscopy (THZ-TDS). The absorption and refractive index spectra in the frequency range from 0.5 to 2.5 THz were obtained at room temperature under nitrogen atmosphere, and the results show that elaidic acid had some characteristic absorption peaks, and the average refractive index of the sample was 1.43. The structure and vibrational frequencies of elaidic acid molecule in the THz range were simulated by the B3LYP algorithm of density functional theory, and the THz characteristic absorption peaks of elaidic acid molecule were identified by using Gaussian View software. The results show that the experimental and theoretical results agree in general, and the observed absorption peaks in the THz range were mainly caused by the intramolecular and intermolecular vibrations jointly. At the same time, the fingerprint spectra of elaidic acid in the THz band verify that the time-domain terahertz spectroscopy can be used to detect oleic acid, and this study provides a new experimental method for the detection of trans fatty acids in food.

Plant NAC-type transcription factor proteins contain a NARD domain for repression of transcriptional activation.

Plant-specific transcription factor NAC proteins play essential roles in many biological processes such as development, senescence, morphogenesis, and stress signal transduction pathways. In the NAC family, some members function as transcription activators while others act as repressors. In the present study we found that though the full-length GmNAC20 from soybean did not have transcriptional activation activity, the carboxy-terminal activation domain of GmNAC20 had high transcriptional activation activity in the yeast assay system. Deletion experiments revealed an active repression domain with 35 amino acids, named NARD (NAC Repression Domain), in the d subdomain of NAC DNA-binding domain. NARD can reduce the transcriptional activation ability of diverse transcription factors when fused to either the amino-terminal or the carboxy-terminal of the transcription factors. NARD-like sequences are also present in other NAC family members and they are functional repression domain when fused to VP16 in plant protoplast assay system. Mutation analysis of conserved amino acid residues in NARD showed that the hydrophobic LVFY motif may partially contribute to the repression function. It is hypothesized that the interactions between the repression domain NARD and the carboxy-terminal activation domain may finally determine the ability of NAC family proteins to regulate downstream gene expressions.