Structural genomics efforts at the Chinese Academy of Sciences and Peking University

Structural genomics efforts at the Chinese Academy of Sciences and Peking University are reported in this article. The major targets for the structural genomics project are targeted proteins expressed in human hematopoietic stem/progenitor cells, proteins related to blood diseases and other human proteins. Up to now 328 target genes have been constructed in expression vectors. Among them, more than 50% genes have been expressed in Escherichia coli, approximately 25% of the resulting proteins are soluble, and 35 proteins have been purified. Crystallization, data collection and structure determination are continuing. Experiences accumulated during this initial stage are useful for designing and applying high-throughput approaches in structural genomics.

[Glucose isomerase gene knock-out by denatured double-stranded DNA]

After Genetic background analysis of Streptomyces diastaticus No. 7 strain M1033, the modified conditions of M1033 protoplasts and transformation were established. Replacement plasmid for homologous recombination was also constructed by inserting tsr gene into glucose isomerase gene. The homologous recombination of GI gene in M1033 chromosomes was achieved by using denatured linearized DNA fragments and glucose isomerase deficient strain M1033LJ was obtained. It is basic for introducing mutation into M1033 chromosome and realizing site-directed molecular reformation.

Characterization, crystallization and preliminary X--ray diffraction analysis of acutohaemolysin, a haemolytic toxin from Agkistrodon acutus venom

Acutohaemolysin, a phospholipase A(2) (PLA(2)) from the venom of the snake Agkistrodon acutus, has been isolated and purified to homogeneity by anion-exchange chromatography on a DEAE-Sepharose column followed by cation-exchange chromatography on a CM-Sepharose column. It is an alkaline protein with an isoelectric point of 10.5 and is comprised of a single polypeptide chain of 13 938 Da. Its N-terminal amino-acid sequence shows very high similarity to Lys49-type PLA(2) proteins from other snake venoms. Although its PLA(2) enzymatic activity is very low, acutohaemolysin has a strong indirect haemolytic activity and anticoagulant activity. Acutohaemolysin crystals with a diffraction limit of 1.60 A were obtained by the hanging-drop vapour-diffusion method. The crystals belong to the space group C2, with unit-cell parameters a = 45.30, b = 59.55, c = 46.13 A, beta = 117.69 degrees. The asymmetric unit contains one molecule.

Increasing the thermostability of D-xylose isomerase by introduction of a proline into the turn of a random coil

Thermostability can be increased by introducing prolines at suitable sites in target proteins. Two single (G138P, G247D) mutants and one double (G138P/G247D) mutant of xylose isomerase from Streptomyces diastaticus No.7, strain M1033 have been constructed by site-directed mutagenesis. With respect to the wild-type enzyme, G138P showed about a 100% increase in thermostability, and G247D showed an increased catalytic activity. Significantly, the double mutant, G138P/G247D displayed even higher activity than G247D and better heat stability than G138P. Its half life was about 2.5-fold greater than the wild-type enzyme, using xylose as a substrate. Molecular modelling suggested that the introduction of a proline residue in the turn of a random coil may cause the surrounding conformation to be tightened by reducing the backbone flexibility. The change in thermostability can, therefore, be explained based on changes in the molecular rigidity. Furthermore, the improvements in the properties of the double mutant indicated that the advantages of two single mutants can be combined effectively.

Protein crystallization with a combination of hard and soft precipitants

Much effort and progress have been made in understanding the nucleation and crystallization of globular proteins, and many techniques have been developed to crystallize proteins in the past decades. The advantages of the use of combined precipitants in protein crystallization have been much appreciated. Unfortunately, there is still no theory or empirical guide on how to combine so many precipitants and how to use combined precipitants, although many proteins have been crystallized successfully using combined precipitants. This report gives a proposal about how to use conventional precipitants to obtain protein crystals, based on a novel idea of hard and soft precipitant combinations.

Purification and characterization of two fibrinogen-clotting enzymes from five-pace snake (Agkistrodon acutus) venom

From the snake venom of Agkistrodon acutus, two proteases, acuthrombin-A and acuthrombin-C, were isolated and purified to homogeneity. They can cleave the human fibrinogen to release the fibrinopeptide A and fibrinopeptide B with specific activity of 120 and 370 NIH units/mg, respectively; the fibrinogen-clotting activity can be inhibited distinctly by PMSF or DFP or EDTA, but not by heparin. The two proteases show also arginine-esterase activity hydrolyzing some synthetic substrates such as TAME and BAEE. Additionally, they are glycoproteins with an average content of 2.4% (acuthrombin-A) and 2.1% (acuthrombin-C) neutral carbohydrates, respectively. Acuthrombin-A has a MW of 13,900 as estimated by SDS-PAGE under reduced or nonreduced conditions and 28,000 as determined by gel filtration. For acuthrombin-C, there were two protein bands corresponding to MW of 13,900 and 14,800 on SDS-PAGE with different darkness under reduced or nonreduced conditions, while its MW was estimated to be 69,000 by gel filtration. The isoelectric points were 7.5 for acuthrombin-A and 5.0 for acuthrombin-C by isoelectric focusing. Neither acuthrombin-A nor acuthrombin-C has haemorrhagic or lethal activity. Acuthrombin-A has also a small amount of activity to activate the Factor XIII.

Purification, characterization, crystallization and preliminary X-ray diffraction of acuthrombin-B, a thrombin-like enzyme from Agkistrodon acutus venom

Acuthrombin-B, a thrombin-like enzyme from Agkistrodon acutus venom, has been isolated and purified to homogeneity by ion-exchange chromatography on DEAE-Sepharose, gel filtration on Sephacryl S-100 and fast performance liquid chromatography on DEAE-8HR. The protease is an acid protein (pI 6.0) consisting of two non-identical polypeptide chains (14.4 and 16 kDa) and there is no disulfide bond between the subunits. Its molecular weight is 27 kDa as estimated by gel filtration on Sephacryl S-100. The protease has arginine-esterase activity and hydrolyzes synthetic substrates such as p-toluenesulfonyl arginine methyl ester and alpha-N-benzoyl-L-arginine amide ethyl ester, and shows clotting activity with human fibrinogen, rabbit citrated plasma and human citrated plasma in vitro. The specific activity with human fibrinogen was estimated to be 230 NIH units mg-1. The protease is considered as a serine-type protease and contains metal ion(s) to some extent, as indicated by the fact that its clotting and arginine-esterase activities could be completely inhibited by PMSF and partially inhibited by the chelating agent EDTA, while the thrombin inhibitor heparin had no effect on its clotting activity towards rabbit citrated plasma. Acuthrombin-B crystals with a resolution limit of 2.06 A were obtained by conventional hanging-drop vapour diffusion. The crystals belong to space group P21 with unit-cell parameters a = 34.97, b = 53.58, c = 67.88 A, beta = 98.89 degrees and contain one molecule per asymmetric unit.

Studies on the crystal structure of (D-Ala)-B0 porcine insulin at 1.9 A resolution

The crystal structure of (D-Ala)-B0 porcine insulin has been determined, using data to 1.9 A and atomic parameters of 2 Zn porcine insulin as a starting model, and through the use of the difference method and the restrained least square method, to a final R-factor of 0.211 and r.m.s. deviation of 0.057 A for the bond lengths. The electron densities of B0 residues were very clear. Introduction of B0 residues into the molecules had reduced the thermal vibration of the N-terminus of B-chain for both molecules I and II and made the molecules pack closer in the crystal. The obvious differences between the crystal structures of 2 Zn and (D-Ala)-B0 porcine insulin were the conformations of partial polar groups around the possible receptor binding surface and the assembly mode of two helixes of A-chain in molecule I. In the local environment of the N-terminus of B-chain there were great differences between the crystal structures of (D-Ala)-B0 porcine insulin, (Trp)-B1 porcine insulin and Des B1(Phe) bovine insulin. In this paper the structure-immunoactivity relationships of insulin molecule have also been discussed briefly.

Molecular structure and absolute configuration of suberogorgin

In the present paper it is reported that the molecular structure and absolute configuration of poisonous suberogorgin are determined by using X-ray diffraction method. The crystal of suberogorgin belongs to orthogonal system with space group D4(2)-P2(1)2(1)2(1). The crystallographic parameters are: a = 16.135A, b = 13.189A, c = 12.901A, Z = 8. The initial model of the crystal structure was solved by the direct method. The refinement of the structure parameters was carried out by using the least square method and led to a final R-factor of 0.056. In accordance with the molecular structure of suberogorgin mentioned above, the solvent effect of NMR has been further discussed and the relationship between the molecular structure of suberogorgin and its toxicity has also been preliminarily investigated.