Molecular chaperones, folding catalysts, and the recovery of active recombinant proteins fromE. coli

The high-level expression of recombinant gene products in the gramnegative bacteriumEscherichia coli often results in the misfolding of the protein of interest and its subsequent degradation by cellular proteases or its deposition into biologically inactive aggregates known as inclusion bodies. It has recently become clear that in vivo protein folding is an energy-dependent process mediated by two classes of folding modulators. Molecular chaperones, such as the DnaK-DnaJ-GrpE and GroEL-GroES systems, suppress off-pathway aggregation reactions and facilitate proper folding through ATP-coordinated cycles of binding and release of folding intermediates. On the other hand, folding catalysts (foldases) accelerate rate-limiting steps along the protein folding pathway such as thecis/trans isomerization of peptidyl-prolyl bonds and the formation and reshuffling of disulfide bridges. Manipulating the cytoplasmic folding environment by increasing the intracellular concentration of all or specific folding modulators, or by inactivating genes encoding these proteins, holds great promise in facilitating the production and purification of heterologous proteins. Purified folding modulators and artificial systems that mimic their mode of action have also proven useful in improving the in vitro refolding yields of chemically denatured polypeptides. This review examines the usefulness and limitations of molecular chaperones and folding catalysts in both in vivo and in vitro folding processes.     

Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approach

We analyzed ABC transporter solute-binding proteins (SBPs) of the Bacillus subtilis membrane using a proteomic approach. We prepared a washed cell membrane fraction that was insoluble in 134 mM nondetergent sulfobetaine and then extracted proteins using mixtures of detergents in a stepwise manner. The membrane proteins were resolved by three two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) or two one-dimensional (1-D) PAGE procedures, electroblotted, and digested in the presence of 5% or 80% acetonitrile. Thereafter, matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS) identified 637 proteins corresponding to 15.9% of the total cellular proteins. We predicted that among these, 256 were membrane proteins, 101 were lipoproteins or secretory proteins and 280 were soluble proteins containing peripheral proteins that function in both the cytoplasm and the cell membrane such as SecA and FtsY. Among the 637 proteins, we identified 30 SBPs among 38 importers predicted by a bioinformatic search of the genome. We confirmed expression of the genes for the 30 SBPs using DNA microarray analysis. We compared the 2-D gel separation profiles of submembrane fractions solubilized by 1% n-dodecyl-beta-D-maltoside from cells cultured on Luria Bertani (LB), S7, and S7 medium without glutamate as well as DNA microarray data on LB and S7. The results suggested that YcdH, YtmK and YurO are binding proteins for Mn(++), glutamate and glucose, respectively, and that YqiX and YxeM are binding proteins for amino acids (tryptophan in S7 medium).     

RATE OF INTRA-MOLECULAR CONTACT FORMATION IN SHORT TWO-DIMENSIONAL COMPACT POLYMERS CHAINS

It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p(r) of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p(r) of short two-dimensional compact polymers chains may consist of two parts, i.e. p(r) = p1(r) p2(r), where p1(r) and p2(r) are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k(N) ∝ N-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H (hydrophobic) residues in the sequences of compact chains and the energy parameters of εHH, εHP and εPP . Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.     

Lipophilicity in PK design: methyl, ethyl, futile

Lipophilicity, often expressed as distribution coefficients (log D) in octanol/water, is an important physicochemical parameter influencing processes such as oral absorption, brain uptake and various pharmacokinetic (PK) properties. Increasing log D values increases oral absorption, plasma protein binding and volume of distribution. However, more lipophilic compounds also become more vulnerable to P450 metabolism, leading to higher clearance. Molecular size and hydrogen bonding capacity are two other properties often considered as important for membrane permeation and pharmacokinetics. Interrelationships among these physicochemical properties are discussed. Increasing size (molecular weight) often gives higher potency, but inevitably also leads to either higher lipophilicity, and hence poorer dissolution/solubility, or to more hydrogen bonding capacity, which limits oral absorption. Differences in optimal properties between gastrointestinal absorption and uptake into the brain are addressed. Special attention is given to the desired lipophilicity of CNS drugs. In examples using -blockers, Ca channel antagonists and peptidic renin inhibitors we will demonstrate how potency and pharmacokinetic properties need to be balanced.     

Electroactivity of Nonconjugated Proteins and Peptides. Towards Electroanalysis of All Proteins

Present proteomics and biomedicine require sensitive analytical methods for all proteins. Recent progress in electrochemical analysis of peptides and proteins based on their intrinsic electroactivity is reviewed. Tyrosine and/or tryptophan‐containing proteins are oxidizable at carbon electrodes. At mercury electrodes all peptides and proteins (about 13 peptides and >25 proteins were tested) produce chronopotentiometric peak H at nanomolar concentrations. This peak is sensitive to changes in protein structure. Microliter sample volumes are sufficient for the analysis. Electrochemical methods can be used in studies of nucleic acid‐protein interactions and can be applied in biomedicine. Examples of such applications in neurogenerative diseases and cancer are presented.     

Evaluation of soybean seed protein extraction focusing on metalloprotein analysis

Two methods of protein extraction for soybean seeds were evaluated in terms of preservation of the metal ions bound to proteins after the extraction and separation procedures. The proteins were firstly separated according to their molar masses by polyacrylamide gel electrophoresis. Then, the protein bands were mapped by synchrotron radiation X-ray fluorescence in order to establish which metal ions were present in each one. Finally, some mapped protein bands were decomposed by microwave-assisted combustion and Ca, Cu, K, Mg, Mn, and Zn were quantified by inductively coupled plasma mass spectrometry or inductively coupled plasma optical emission spectrometry. The extraction methods studied were Method A (based on the treatment of ground soybean seeds with hexane and their extraction with Tris–HCl and β-mercaptoethanol) and Method B (based on the treatment of ground soybean seeds with petroleum ether and their extraction with Tris–HCl, dithiothreitol, phenylmethanesulfonyl fluoride, sodium dodecyl sulfate and potassium chloride). The best method was Method B, in which a 78% higher extraction efficiency was obtained when compared to Method A. Additionally, the metal-protein interactions were more appropriately preserved when Method B was applied, where the most affected ions were those that are bound weakly to proteins, such as Ca, K, and Mg.     

Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules.

Proteins are key components of biological cells. For example, enzymes catalyze biochemical reactions, membrane transporters are responsible for uptake and release of critical and superfluous components from the cell environment, and structural proteins are responsible for the stability of the cell wall and cytoskeleton. Many of the diverse protein functions involve dynamic transitions ranging from small local atomic displacements up to large allosteric conformational changes. In any conformation, proteins are in contact with the universal solvent medium of cells, water. Water not only surrounds proteins but is often an integral part of proteins and also is involved in key mechanistic steps. This Minireview discusses recent experimental and theoretical results on the role of water for protein dynamics and function.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

Solvation of amino acid residues in water and urea-water mixtures: Volumes and heat capacities of 20 amino acids in water and in 8 molar urea at 25°C

The limiting partial molar volumes V ^o and heat capacities C _p ^o of 20 amino acids have been determined in water and in 8 molar urea at 25.0°C using flow calorimetry and flow densimetry. The side chain contributions to V ^o and C _p ^o were obtained as the difference between the properties of the various amino acids and those of glycine, both in water and in 8M urea. The solvent accessible surface area of the amino acid residues were obtained using a method developed by Hermann, and the total surface areas were separated into their hydrophobic A _Hb and hydrophilic components. In water, C _p ^o values for the various residues C _p ^o (R) were found well correlated with A _Hb , though much less so in the urea solution. Hence, C _p ^o (R) values, in water yield a good estimate of side chain hydrophobicity, but the (waterurea) transfer heat capacities appear strongly affected by specific solvation effects in the urea solution.Presented at the sixth Italian meeting on Calorimetry and Thermal Analysis (AICAT) held in Naples, December 4–7, 1984.     

蛋白芯片法同时检测食品中克伦特罗与莱克多巴胺的残留量

建立了食品中克伦特罗和莱克多巴胺残留含量同时检测的微阵列蛋白芯片法。结果显示:克伦特罗的线性范围为0.07～1.2 ng/g;莱克多巴胺的线性范围为0.05～0.8 ng/g。猪肉、猪肝中上述两种物质的加标回收率为74%～132%,相对标准偏差均小于10%。将所建立的方法与HPLC-MS方法进行对比,两者检测结果一致。该方法简单、快速、通量高,可用于实际样品中克伦特罗和莱克多巴胺残留量的检测。