An approach to quality management in structural biology: biophysical selection of proteins for successful crystallization

Aggregation, incorrect folding and low stability are common obstacles for protein structure determination, and are often discovered at a very late state of protein production. In many cases, however, the reasons for failure to obtain diffracting crystals remain entirely unknown. We report on the contribution of systematic biophysical characterization to the success in structural determination of human proteins of unknown fold. Routine analysis using dynamic light scattering (DLS), differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR) was employed to evaluate fold and stability of 263 purified protein samples (98 different human proteins). We found that FTIR-monitored temperature scanning may be used to detect incorrect folding and discovered a positive correlation between unfolding enthalpy measured with DSC and the size of small, globular proteins that may be used to estimate the quality of protein preparations. Furthermore, our work establishes that the risk of aggregation during concentration of proteins may be reduced through DLS monitoring. In summary, our study demonstrates that biophysical characterization provides an ideal tool to facilitate quality management for structural biology and many other areas of biological research.     

Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold

The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 A resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an alphabetabetaalpha four-layer topology. A metal ion residing between the central beta-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn(2+). Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn(2+) to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and beta-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.     

Structure of the Bet3-Tpc6B core of TRAPP: two Tpc6 paralogs form trimeric complexes with Bet3 and Mum2

The transport protein particle (TRAPP) complexes are involved in the tethering process at different trafficking steps of vesicle transport. We here present the crystal structure of a human Bet3-Tpc6B heterodimer, which represents a core sub-complex in the assembly of TRAPP. We describe a conserved patch of Tpc6 with uncharged pockets, forming a putative interaction interface for an anchoring moiety at the Golgi. The structural and functional comparison of the two paralogs Tpc6A and Tpc6B, only found in some organisms, indicates redundancy and added complexity of TRAPP architecture and function. Both iso-complexes, Bet3-Tpc6A and Bet3-Tpc6B, are able to recruit Mum2, a further TRAPP subunit, and we identify the alpha1-alpha2 loop regions as a binding site for Mum2. Our study reveals similar stability of the iso-complexes and similar expression patterns of the tpc6 variants in different mouse organs. These findings raise the possibility that the Tpc6 paralogs might contribute to the formation of two distinct TRAPP complexes that differ in function.     

南方4种草本植物对铝胁迫生理响应的研究

 不同的植物对铝胁迫的生理响应不同, 因而对铝毒的耐性也不相同。设置5种铝浓度,进行砂培法处理,研究了4种我国南方红壤广泛分布的草本植物——牵牛(Pharbitis nil)、望江南(Cassia occidentlis)、光头稗(Echinochloa colonum)和合萌(Aeschynomene indica)的种子萌发、光合色素、脯氨酸含量、丙二醛(MDA)含量、可溶性糖(SS)含量、质膜透性(MP)、过氧化氢酶 (CAT) 活性以及过氧化物酶 (POD)活性的变化。结果表明铝对4种植物的生理特性都有明显的影响。4种植物的种子在10 000 mg·L－1 Al3+处理条件下都不能萌发。2 000 mg·L－1 Al3+处理都不利于4种植物的生长,与对照相比,2 000 mg·L－1 Al3+处理时4种草本植物叶绿素和叶绿素总含量显著降低(p<0.05);MDA含量和MP显著增加(p<0.05);脯氨酸含量极显著增加(p<0.01);POD和CAT活性极显著降低(p<0.01)。中低铝(80和400 mg·L－1)处理时,牵牛和合萌与对照相比,MP和MDA含量降低,POD和CAT活性升高;望江南的反应与牵牛和合萌的反应相反;光头稗在80 mg·L－1 Al3+处理时,与牵牛和合萌的变化一致,在400 mg·L－1 Al3+处理时,则相反。植物在中低铝处理条件下,通过维持较高的POD和CAT活性和脯氨酸、叶绿素含量,较低的MP和MDA含量来增加其对铝的耐性。     

X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1)

Background  

Human Aortic Preferentially Expressed Protein-1 (APEG-1) is a novel specific smooth muscle differentiation marker thought to play a role in the growth and differentiation of arterial smooth muscle cells (SMCs).     

Optimized variants of the cold shock protein from in vitro selection: structural basis of their high thermostability

The bacterial cold shock proteins (Csp) are widely used as models for the experimental and computational analysis of protein stability. In a previous study, in vitro evolution was employed to identify strongly stabilizing mutations in Bs-CspB from Bacillus subtilis. The best variant found by this approach contained the mutations M1R, E3K and K65I, which raised the midpoint of thermal unfolding of Bs-CspB from 53.8 degrees C to 83.7 degrees C, and increased the Gibbs free energy of stabilization by 20.9 kJ mol(-1). Another selected variant with the two mutations A46K and S48R was stabilized by 11.1 kJ mol(-1). To elucidate the molecular basis of these stabilizations, we determined the crystal structures of these two Bs-CspB variants. The mutated residues are generally well ordered and provide additional stabilizing interactions, such as charge interactions, additional hydrogen bonds and improved side-chain packing. Several mutations improve the electrostatic interactions, either by the removal of unfavorable charges (E3K) or by compensating their destabilizing interactions (A46K, S48R). The stabilizing mutations are clustered at a contiguous surface area of Bs-CspB, which apparently is critically important for the stability of the beta-barrel structure but not well optimized in the wild-type protein.     

Structural and functional characterization of human Iba proteins

Iba2 is a homolog of ionized calcium-binding adapter molecule 1 (Iba1), a 17-kDa protein that binds and cross-links filamentous actin (F-actin) and localizes to membrane ruffles and phagocytic cups. Here, we present the crystal structure of human Iba2 and its homodimerization properties, F-actin cross-linking activity, cellular localization and recruitment upon bacterial invasion in comparison with Iba1. The Iba2 structure comprises two central EF-hand motifs lacking bound Ca2+. Iba2 crystallized as a homodimer stabilized by a disulfide bridge and zinc ions. Analytical ultracentrifugation revealed a different mode of dimerization under reducing conditions that was independent of Ca2+. Furthermore, no binding of Ca2+ up to 0.1 mM was detected by equilibrium dialysis. Correspondingly, Iba EF-hand motifs lack residues essential for strong Ca2+ coordination. Sedimentation experiments and microscopy detected pronounced, indistinguishable F-actin binding and cross-linking activity of Iba1 and Iba2 with induction of F-actin bundles. Fluorescent Iba fusion proteins were expressed in HeLa cells and co-localized with F-actin. Iba1 was recruited into cellular projections to a larger extent than Iba2. Additionally, we studied Iba recruitment in a Shigella invasion model that induces cytoskeletal rearrangements. Both proteins were recruited into the bacterial invasion zone and Iba1 was again concentrated slightly higher in the cellular extensions.     

Heavy metal contamination of water and fish in peri-urban dams around Bulawayo,Zimbabwe

Urban effluents are significant sources of heavy metal pollution in fresh water. Metal contamination in dams around the city of Bulawayo, Zimbabwe, were monitored during October 2014 to assess ecological and public health risks. Heavy metals were measured in water, sediment and fish in dams located downstream of effluent discharge zones in Bulawayo and were compared to those in a pristine upstream dam. Water conductivity indicated pollution of downstream dams. Levels of lead (0.13–0.28 ppm) and cadmium (0.02–0.06 ppm) in water from downstream dams exceeded WHO safe limits for drinking water. Cadmium levels in polluted dams also exceeded the safe limit for agricultural use. Sediments of effluent-polluted dams had metal contamination factors ranging from 8.8 to 31.2 relative to the control, and fish from the dams had higher metal content and were unfit for human consumption. Metal levels were also measured along an urban stream to establish the sources of metals. The city’s industrial zone had the highest levels of metals, suggesting that industrial effluents were major sources of contamination. The environmental consequences and human health risks of the pollution of peri-urban water bodies from urban effluents are discussed.     

Interactions of Cd with Zn, Cu, Mn and Fe for lettuce (Lactuca sativa L.) in hydroponic culture

Abstract. The effect and accumulation of cadmium (Cd) in lettuce grown by means of the hydroponic technique was investigated by multivariate analysis, and was found to be affected by the concentration of other trace elements. Particularly iron acted in a strongly antagonistic way against Cd. Consequently, no absolute toxicity limits for Cd can be drawn without considering other trace elements.