The Sso7d protein of Sulfolobus solfataricus: in vitro relationship among different activities

The physiological role of the nonspecific DNA-binding protein Sso7d from the crenarchaeon Sulfolobus solfataricus is unknown. In vitro studies have shown that Sso7d promotes annealing of complementary DNA strands (Guagliardi et al. 1997), induces negative supercoiling (Lopez-Garcia et al. 1998), and chaperones the disassembly and renaturation of protein aggregates in an ATP hydrolysis-dependent manner (Guagliardi et al. 2000). In this study, we examined the relationships among the binding of Sso7d to double-stranded DNA, its interaction with protein aggregates, and its ATPase activity. Experiments with 1-anilinonaphthalene-8-sulfonic acid as probe demonstrated that exposed hydrophobic surfaces in Sso7d are responsible for interactions with protein aggregates and double-stranded DNA, whereas the site of ATPase activity has a non-hydrophobic character. The interactions of Sso7d with double-stranded DNA and with protein aggregates are mutually exclusive events, suggesting that the disassembly activity and the DNA-related activities of Sso7d may be competitive in vivo. In contrast, the hydrolysis of ATP by Sso7d is independent of the binding of Sso7d to double-stranded DNA or protein aggregates.     

Local and global anatomy of antibody‐protein antigen recognition

Deciphering antibody‐protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein‐protein complexes. We investigated the physicochemical properties of regions on and away from the antibody‐antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody‐protein antigen recognition is entropy driven, with residues having low side‐chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens. Antibodies prefer charged and polar antigen residues and bridging water molecules. They also prefer positive net charge, presumably to promote interaction with negatively charged protein antigens, which are common in proteomes. Antibody‐antigen interfaces have large percentages of Tyr, Ser, and Asp, but little Lys. Electrostatic and hydrophobic interactions in the Ag binding sites might be coupled with Fab domains through organized charge and residue distributions away from the binding interfaces. Here we describe some features of antibody‐antigen interfaces and of Fab domains as compared with nonantibody protein‐protein interactions. The distributions of interface residues in human and murine antibodies do not differ significantly. Overall, our results provide not only a local but also a global anatomy of antibody structures.     

The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition

Intrinsically disordered proteins (IDPs) are extensively involved in dynamic signaling processes which require a high association rate and a high dissociation rate for rapid binding/unbinding events and at the same time a sufficient high affinity for specific recognition. Although the coupled folding-binding processes of IDPs have been extensively studied, it is still impossible to predict whether an unfolded protein is suitable for molecular signaling via coupled folding-binding. In this work, we studied the interplay between intrinsic folding mechanisms and coupled folding-binding process for unfolded proteins through molecular dynamics simulations. We first studied the folding process of three representative IDPs with different folded structures, that is, c-Myb, AF9, and E3 rRNase. We found the folding free energy landscapes of IDPs are downhill or show low barriers. To further study the influence of intrinsic folding mechanism on the binding process, we modulated the folding mechanism of barnase via circular permutation and simulated the coupled folding-binding process between unfolded barnase permutant and folded barstar. Although folding of barnase was coupled to target binding, the binding kinetics was significantly affected by the intrinsic folding free energy barrier, where reducing the folding free energy barrier enhances binding rate up to two orders of magnitude. This accelerating effect is different from previous results which reflect the effect of structure flexibility on binding kinetics. Our results suggest that coupling the folding of an unfolded protein with no/low folding free energy barrier with its target binding may provide a way to achieve high specificity and rapid binding/unbinding kinetics simultaneously.     

5型肺炎链球菌荚膜多糖结合疫苗的不同糖蛋白比与免疫原性的关系

实验中比较了以不同糖蛋白比结合的5型肺炎链球菌荚膜多糖结合疫苗的免疫原性。以氨还原法制备的不同糖蛋白比的5型多糖结合疫苗分别经腹腔注射NIH小鼠,共免疫3次,间隔2周。末次免疫2周后采血分离血清,以间接ELISA测定血清抗体,t检验统计分析数据。结果显示,生理盐水组(R组)无免疫原性;5型荚膜多糖组(H组)免疫原性低,无免疫加强效应;结合疫苗M组、N组第1、2针有免疫加强效应,第2、3针无免疫加强效应,而F组和Q组的两针次间均有明显的免疫加强效应。说明5型肺炎链球菌荚膜多糖结合疫苗的糖与蛋白比较高时能获得较好的免疫原性。     

牛乳源金黄色葡萄球菌EsxA蛋白的表达及免疫原性分析

为分析牛乳源金黄色葡萄球菌(Staphylococcus aureus)EsxA蛋白的免疫原性,构建EsxA-p ET-28a重组表达质粒,重组质粒经诱导表达后进行SDS-PAGE和Western blotting鉴定。用纯化后重组EsxA蛋白免疫小鼠,用间接ELISA检测免疫小鼠血清中的IgG、IgG1和IgG2a水平;免疫小鼠经S.aureus菌株攻击后,检测小鼠肝、脾、肾组织荷菌数和免疫保护率,观察S.aureus菌株攻击后小鼠肝、脾、肾病理组织学变化。结果表明,成功诱导表达了EsxA重组蛋白,该重组蛋白免疫小鼠后血清抗体效价可达1∶900,与对照相比,重组蛋白免疫后可减少小鼠肝、脾、肾组织的荷菌数,减轻这些脏器的病理损伤,对免疫小鼠保护率达75%。上述结果表明,该重组Esx A蛋白具有良好的免疫原性。     

Treatment of adjuvant arthritis with granulocyte-colony stimulating factor and peptide derived from heat shock protein 65

Adjuvant arthritis in Lewis rats is induced by the subcutaneous injection of Mycobacterium tuberculosis in mineral oil, and the predominant T cell immune reactivity is against the heat shock protein 65 derived peptide 176-190. We treated Lewis rats with human recombinant G-CSF followed by (i.v) administration of peptide 176-190 after induction of adjuvant arthritis (AA), and observed decreased disease severity, joint destruction, new bone formation and joint ankylosis. Treatment with G-CSF alone was also effective, but to a lesser extent. In addition, we found that splenocytes from rats treated with G-CSF had reduced antigen presenting capacity compared with splenocytes from vehicle treated rats. Primed lymph node cells from G-CSF plus peptide treated rats showed a marked reduction in proliferation and secretion of IFN-gamma after stimulation with the heat shock protein peptide in vitro as compared to controls.     

Investigation of the dynamics of the viral immediate-early protein 1 in different conformations and oligomerization states

The viral immediate-early protein 1 (IE1) is crucial for efficient replication of cytomegalovirus (CMV). A recent crystal structure of the IE1 protein from rhesus CMV revealed that the protein exhibits a novel fold and crystallizes in two slightly different dimeric arrangements. Molecular dynamics simulations and energetic analyses performed in this study show that both dimers are stable and allowed us to identify a common set of five residues that appear particularly important for dimer formation. These residues are distributed over the entire dimer interface and do not form a typical hot spot for protein interactions. In addition, the dimer interface of IE1 proved to include a high portion of hydrophilic interactions pointing toward the transient nature of dimer formation. Characterization of monomeric and dimeric IE1 revealed three sequentially discontinuous dynamic domains that exhibit correlated motion within the domain and are simultaneously anti-correlated to the adjacent domains. The hinge motions observed between the dynamic domains increase the shape complementarity to the coiled–coil region of tripartite motif proteins, suggesting that the detected dynamics of IE1 might be physiologically important by enabling a better interaction with its cellular target molecules.     

The influence of molecular variation on protein interactions

We investigated the influence of solvation forces on protein-protein interactions for two forms of lysozyme: hen egg white (HEWL) and turkey egg white (TEWL). Turkey egg white has more surface exposed hydrophobic residues than HEWL and the protein-protein interactions of TEWL are shown to be more attractive than those of HEWL, for the conditions studied. The importance of including a solvation term in the potential of mean force model, to account for molecular variation in protein surface characteristics, is highlighted. We also show that the magnitude of this solvation term can be estimated using readily available data.     

The influence of glycosylation on secretion,stability, and immunogenicity of recombinant HBV pre-S antigen synthesized in Saccharomyces cerevisiae

Three types of recombinant pre-S antigens (i.e., pre-S1S2) of hepatitis B virus (HBV) were synthesized in Saccharomyces cerevisiae and secreted into extracellular medium: wild type (pre-S1S2) and two mutant antigens, pre-S1 degrees S2 (Asn15Gln) and pre-S1 degrees S2 degrees (Asn15Gln and Asn123Gln). An N-terminus sequence (Ser5-Ala28) of human interleukin 1 beta (hIL-1 beta) was used as synthetic prosequence of recombinant HBV surface antigen (pre-S), secreted from S. cerevisiae. The expression cassette comprised the signal peptide of the killer toxin of Kluyveromyces lactis, the synthetic prosequence above, KEX2 dibasic endopeptidase cleavage site (-Lys-Arg-), and the surface antigen. The recombinant pre-S1S2 and pre-S1 degrees S2 were secreted in the hyper-mannosylated form, while the recombinant pre-S1 degrees S2 degrees was produced without N-glycosylation. It has been demonstrated that the two particular N-linked glycans at Asn15 and Asn123 interfered with the B-cell response to the HBV-derived pre-S1S2, resulting in low titers of pre-S1S2-neutralizing antibodies. This problem was overcome by eliminating both of the N-glycosylation signals. Despite enhanced immunogenicity, the recombinant pre-S1 degrees S2 degrees showed two major problems: (1) inefficient Kex2 cleavage process in the secretory pathway and (2) the severe proteolytic degradation by yeast proteases. The efficiency of Kex2 cleavage increased dramatically by removing N-glycosylation signal in the synthetic prosequence, but the proteolysis of pre-S1 degrees S2 degrees was somewhat inevitable. Further systematic approaches including modulation of degree of N-glycosylation or relocation of N-glycosylation sites in the recombinant pre-S1S2 may make it possible to achieve both enhanced immunogenicity and resistance towards proteolytic degradation of the secreted pre-S antigen.     

不同产地冬虫夏草及不同厂家虫草发酵菌丝的可溶性蛋白比较

冬虫夏草〔Ｃｏｒｄｙｃｅｐｓｓｉｎｅｎｓｉｓ (Ｂｅｒｋ .)Ｓａｃｃ.〕为我国滋补名贵出口中药 ,主产于青海、西藏、四川、云南、甘肃等省。因野生资源有限 ,严重脱销。为解决药源问题 ,近年来我国已开发出了虫草菌丝体发酵产品[1] 。由于虫草系真菌寄生在昆虫体上的复合体     

The 18-kDa lectin-binding protein of Chlamydia trachomatis is different from the 18-kDa histone-like protein

Abstract Five proteins of Chlamydia trachomatis at the 18000 (18-kDa) molecular mass region were resolved by two-dimensional electrophoresis. Three proteins at 18.2 kDa, p I 6.9, 18.0 kDa, p I 6.3, and 17.9 kDa, p I 6.4 were shown to bind lectin. A fourth protein of 18.0 kDa at p I 10 was the histone-like protein. The fifth protein at 17.9 kDa, p I 7.0 was not characterized.     

Structural comparison of 26S rRNA-binding ribosomal protein L25 from two different yeast strains and the equivalent proteins from three eubacteria and two chloroplasts

Summary The sequences ofSaccharomyces carlsbergensis ribosomal protein (r-protein) SL25^* and its equivalents fromCandida utilis (CL25),Escherichia coli (EL23),Bacillus stearothermophilus (BL23),Mycoplasma capricolum (ML23),Marchantia polymorpha chloroplasts (McpL23), andNicotiana tabacum chloroplasts (NcpL23) were examined using a computer program that evaluates the extent of sequence similarity by calculating correlation coefficients for each pair of residues in two proteins from a number of physical properties of individual amino acids. Comparison matrices demonstrate that the prokaryotic sequences (including McpL23 and NcpL23) can be aligned unambiguously by introducing small internal deletions/insertions at three specific positions. A similar comparison brought to light a clear evolutionary relationship between the prokaryotic and the yeast proteins despite the fact that visual inspection of these sequences revealed only limited similarity. The alignment deduced from this comparison shows the two yeast r-proteins to have acquired a long (50–60 amino acids) N-terminal extension as well as a 13-amino acid-long deletion near the C-terminus. The significance of these findings in terms of the evolution of r-proteins in general and the biological function of various parts of the SL25 protein in particular is discussed.     

Effect of dextran on protein stability and conformation attributed to macromolecular crowding

Thermally induced transition curves of hen egg-white lysozyme were measured in the presence of several concentrations of dextran at pH 2.0 by near-UV and far-UV CD. The transition curves were fitted to a two-state model by a non-linear, least-squares method to obtain the transition temperature (T(m)), enthalpy change (deltaH(u)(T(m))), and free energy change (deltaG(u)(T)) of the unfolding transition. An increase in T(m) and almost constant deltaH(u)(T(m)) values were observed in the presence of added dextran at concentrations exceeding ca 100 g l(-1). In addition, dextran-induced conformational changes of fully unfolded protein were investigated by CD spectroscopy. Addition of high concentrations of dextran to solutions of acid-unfolded cytochrome c at pH 2.0 results in a shift of the CD spectrum from that characteristic of the fully unfolded polypeptide to that characteristic of the more compact, salt-induced molten globule state, a result suggesting that the molten globule-like state is stabilized relative to the fully unfolded form in crowded environments. Both observations are in qualitative accord with predictions of a previously proposed model for the effect of intermolecular excluded volume (macromolecular crowding) on protein stability and conformation.     

The limit of accuracy of protein modeling: influence of crystal packing on protein structure

The size of the protein database (PDB) makes it now feasible to arrive at statistical conclusions regarding structural effects of crystal packing. These effects are relevant for setting upper practical limits of accuracy on protein modeling. Proteins whose crystals have more than one molecule in the asymmetric unit or whose structures were determined at least twice by X-ray crystallography were paired and their differences analyzed. We demonstrate a clear influence of crystal environment on protein structure, including backbone conformations, hinge-like motions and side-chain conformations. The positions of surface water molecules tend to be variable in different crystal environments while those of ligands are not. Structures determined by independent groups vary more than structures determined by the same authors. The use of different refinement methods is a major source for this effect. Our pair-wise analysis derives a practical limit to the accuracy of protein modeling. For different crystal forms, the limit of accuracy (C(alpha), root-mean-square deviation (RMSD)) is approximately 0.8A for the entire protein, which includes approximately 0.3A due to crystal packing. For organized secondary elements, the upper limit of C(alpha) RMSD is 0.5-0.6A while for loops or protein surface it reaches 1.0A. Twenty percent of exposed side- chains exhibit different chi(1+2) conformations with approximately half of the effect also resulting from crystal packing. A web based tool for analysis and graphic presentation of surface areas of crystal contacts is available (http://ligin.weizmann.ac.il/cryco).     

The influence of proteins and peptides on the phase properties of lipids

This paper reviews model membrane studies on the modulation of the macroscopic structure of lipids by lipid-protein interactions, with particular emphasis on the gramicidin molecule. This hydrophobic peptide has three main effects on lipid polymorphism: (1) in lysophosphatidylcholine it triggers a micellar to bilayer transition, (2) in phosphatidylethanolamine it lowers the bilayer to hexagonal H_II phase transition temperature and (3) in phosphatidylcholine and other bilayer preferring lipids it is able to induce the formation of an H_II phase. From experiments in which the gramicidin molecule was chemically modified it can be concluded that the tryptophan residues play a determining role in the peptide-induced changes in polymorphism. The experimental data lead to the proposal that gramicidin molecules have a tendency to self-associate, possibly mediated by tryptophan-tryptophan interactions and organize into tubular structures such as found in the H_II phase.     

呼吸道合胞病毒融合蛋白F1和截短F1蛋白的表达差异研究

目的构建呼吸道合胞病毒融合蛋白F1和截短F1蛋白的原核表达载体,并对它们在大肠杆菌中的表达差异进行了初步研究。方法用DNAstar软件对呼吸道合胞病毒F1蛋白进行亲疏水性和抗原表位可能性分析后,将其两端的疏水区域截去之后与pET-42b(+)构建表达载体,同时用相同的表达系统构建F1蛋白的表达载体并将2种重组蛋白进行诱导表达。实验对2种蛋白在Rossata/pET-42b(+)菌株中的表达难易度、表达形式及初步洗涤的包涵体纯度进行了比较。结果与F1蛋白相比,截短的F1蛋白相对更容易表达,表达的可溶性蛋白含量更高,洗涤纯化后的包涵体纯度也更高。结论呼吸道合胞病毒F1蛋白截去两端疏水氨基酸后更容易表达,为后期蛋白的大量制备及其免疫原性研究奠定了基础。     

Evaluation of different biological data and computational classification methods for use in protein interaction prediction

Protein–protein interactions play a key role in many biological systems. High‐throughput methods can directly detect the set of interacting proteins in yeast, but the results are often incomplete and exhibit high false‐positive and false‐negative rates. Recently, many different research groups independently suggested using supervised learning methods to integrate direct and indirect biological data sources for the protein interaction prediction task. However, the data sources, approaches, and implementations varied. Furthermore, the protein interaction prediction task itself can be subdivided into prediction of (1) physical interaction, (2) co‐complex relationship, and (3) pathway co‐membership. To investigate systematically the utility of different data sources and the way the data is encoded as features for predicting each of these types of protein interactions, we assembled a large set of biological features and varied their encoding for use in each of the three prediction tasks. Six different classifiers were used to assess the accuracy in predicting interactions, Random Forest (RF), RF similarity‐based k‐Nearest‐Neighbor, Naïve Bayes, Decision Tree, Logistic Regression, and Support Vector Machine. For all classifiers, the three prediction tasks had different success rates, and co‐complex prediction appears to be an easier task than the other two. Independently of prediction task, however, the RF classifier consistently ranked as one of the top two classifiers for all combinations of feature sets. Therefore, we used this classifier to study the importance of different biological datasets. First, we used the splitting function of the RF tree structure, the Gini index, to estimate feature importance. Second, we determined classification accuracy when only the top‐ranking features were used as an input in the classifier. We find that the importance of different features depends on the specific prediction task and the way they are encoded. Strikingly, gene expression is consistently the most important feature for all three prediction tasks, while the protein interactions identified using the yeast‐2‐hybrid system were not among the top‐ranking features under any condition. Proteins 2006. © 2006 Wiley‐Liss, Inc.     

共价交联捕获聚酮合成中的酮基还原酶和酰基载体蛋白结构域的瞬时复合物

【背景】在模块化聚酮合成酶(polyketidesynthase,PKS)的催化过程中,催化结构域与同源酰基载体蛋白(acyl-carrierprotein,ACP)之间的蛋白质-蛋白质相互作用起重要作用,但这种瞬时可逆的相互作用难以捕捉分析。【目的】获得ACP和酮基还原酶(ketoreductase,KR)相互作用的蛋白复合物。【方法】在KR和ACP之间的Linker上插入烟草蚀纹病毒(tobacco etch virus,TEV)蛋白酶切位点,通过双功能马来酰亚胺试剂BMH将KR和ACP共价交联,随后TEV酶切检测交联结果。调整反应条件,使交联效率最大化。根据KR-ACP交联复合物与体系内其他蛋白标签和分子量的差异,通过亲和层析和凝胶过滤等纯化手段,获得纯度较高的KR-ACP稳定交联复合物。【结果】单独表达的KR和ACP结构域交联不成功,融合表达的KR+ACP双结构域可以有效交联,结合使用亲和层析和凝胶过滤等纯化手段成功获得纯度较高的复合物。该策略可运用于多个KR和ACP的共价交联。【结论】建立了捕获并纯化KR和ACP瞬时相互作用复合物的有效方法,为后期晶体结构的解析、KR与ACP相互作用机理的揭示及参与相互作用关键氨基酸的鉴定提供了实验基础。     

The influence of complex biological feedstock on the fluidization and bed stability in expanded bed adsorption

The stability of expanded bed adsorption systems (EBA) was studied in biomass containing culture broth by residence time distribution (RTD) experiments, using pulse inputs of fluorescent molecules as tracers. Different commercial adsorbents (Streamline DEAE, SP, Phenyl, Chelating, and AC) were tested at various biomass concentrations (2.5–12 %, wet weight) of whole (Saccharomyces cerevisiae) yeast, yeast cell homogenate, and Escherichia coli homogenate. Analyzing the RTD according to the PDE model (PDE: axially dispersed plug‐flow exchanging mass with stagnant zones) allowed the calculation of three parameters: the number of transfer units for mass exchange between mobile and stagnant fraction (N), the Peclet number for overall axial dispersion (P), and the mobile fraction of the liquid in axially dispersed plug flow (φ). When fluidization was performed in particle‐free buffer the normalized response signal (after perfect input pulse) was symmetric (N:0; P: 50–100; φ: 1), thus, demonstrating the formation of a homogeneous fluidized (expanded) bed. Upon application of suspended biomass the RTD was skewed, depending on the adsorbent used and the type and level of biomass present in the sample. This situation leads to three different characteristic pictures: the well‐fluidized system (N: ≥ 7–10; P: ≥ 40; φ: 0.80–0.90), the system exhibiting bottom channeling (N: < 1–2; P: ≥ 40; φ: 0.5–0.7) and, the system where extensive agglomeration develops (N: 4–7; P: 20–40; φ: < 0.5). These results demonstrate that changes in the hydrodynamics of EBA already take place in the presence of moderate concentrations of biomass. Furthermore, those changes can be quantitatively described mainly in terms of the fraction of stagnant zones in the system, which are formed due to the interaction of biomass and adsorbent. The technique described here can be used to evaluate a certain combination of adsorbent and biomass with regard to its suitability for expanded bed adsorption from whole broth. © 1999 John Wiley & Sons, Inc. Biotechol Bioeng 64: 484–496, 1999.