Electrostatic interaction in the NH2-terminus accelerates inactivation of the Kv1.4 channel

Inactivation of potassium channels plays an important role in shaping the electrical signalling properties of nerve and muscle cells. While it has been assumed that the rapid inactivation of the Kv1.4 channel is controlled by a “ball and chain” inactivation mechanism, the chain structure of the channel has not been well defined. Here, by conducting electrophysiological studies on variants containing mutations of the positively charged and negatively charged segments of the NH₂-terminal of the channel protein, we show that neutralization or deletion of the positively charged segment (residues 83-98) significantly slowed the inactivation process. Replacement of this positively charged segment with the negatively charged segment (residues 123-137), and vice versa, so that both segments were simultaneously positively or negatively charged, also slowed the inactivation process. Furthermore, the inactivation process was not changed when the positively charged and the negatively charged segments were interchanged. In contrast, the voltage dependence of activation and inactivation of the channels was not significantly altered by these mutants. These results indicate that the electrostatic interaction between the positively and negatively charged segments plays a critical role in the inactivation process of the Kv1.4 channel. Taken together, we propose that the electrostatic interaction accelerates the inactivation of the Kv1.4 channel by making it easier for the inactivation ball to access its binding site.     

Role of electrostatic interactions in 2,2,2-trifluoroethanol-induced structural changes and aggregation of alpha-chymotrypsin

It has been recently demonstrated that alpha-chymotrypsin (CT) can be driven toward amyloid aggregation by addition of 2,2,2-trifluoroethanol (TFE), at intermediate concentrations. In the present article, the process of TFE-induced CT aggregation was investigated in more detailed kinetic terms where the effects of medium conditions, such as temperature, presence of kosmotropic and chaotropic salts, pH and chemical modification of lysine residues were examined. Various techniques, including light scattering, fluorescence and circular dichroism spectroscopy, were used to follow and characterize this process. The kinetics of aggregation was found to obey a second-order reaction with respect to protein concentration. The aggregation-prone A-state and aggregation-deficient TFE- or T-state of CT were found to be induced at lower TFE concentrations in the presence of salts. Use of acidic and alkaline conditions and lysine modification also promoted the formation of the T-state. Results presented suggest a role for electrostatic interactions in the aggregation process.     

Local effects in hydrophobicity. Electrostatic interactions in the restructuring of highly polar solvent around less polar solute

Two simplifying assumptions are frequently used in the biophysical chemistry of aqueous solutions: (i) a dielectric mediates the interactions of polar and ionic molecules in aqueous phases and (ii) the dielectric constant of this medium is high and uniform up to molecular surfaces. Because of their great utility in rationalizing simple electrostatic and dielectric effects in such polar systems, it is important to examine whether these assumptions also lead to deductions that are locally consistent with the solvent restructuring observed in hydrophobic phenomena. In this paper, using a model polar fluid system, these macroscopic assumptions are applied to the rigorous, microscopic nonlinear integral equation for Wki, the potential of mean force between two adjacent polar molecules. In systems of high dielectric constant, linearization of Boltzmann exponentials and approximation of three-molecule potentials of mean force by superposition of two-molecule potentials permit reduction to a linear integral equation for Wki. It is shown that the strictly local electrostatic contributions to Wki exert an effect that is qualitatively similar to the global screening effect of a dielectric medium. Through the relation between Wki and configurational probabilities, it is further found that reducing the polarity of a molecule in a polar fluid shifts local pair probability density from energetically unfavorable to energetically favorable two-molecule configurations. This general effect, which clearly promotes local structure, would augment more specific hydrophobic mechanisms in aqueous systems. Thus, the assumptions upon which the highly successful Debye-Hückel and Onsager models are supported lead also to deductions about local structure that are consistent with hydrophobic structure enhancement.     

Role of the basic character of alpha-sarcin's NH2-terminal beta-hairpin in ribosome recognition and phospholipid interaction

Ribotoxins are a family of toxic extracellular fungal RNases that first enter into the cells and then exert a highly specific ribonucleolytic activity on the larger rRNA molecule, leading to protein synthesis inhibition and cell death by apoptosis. α-Sarcin is the best characterized ribotoxin. Previous characterization of a deletion variant of this protein showed that its long NH₂-terminal β-hairpin is essential for its cytotoxicity. Docking, enzymatic, and lipid-protein interaction studies suggested that this β-hairpin establishes specific interactions with ribosomal proteins and that it is a region involved in the interaction with cell membranes. Consequently, in order to assess the influence of the basic character of this NH₂-terminal β-hairpin (there are 1 arginine and 4 lysines along its 16 residues) on the ribotoxins cytotoxic ability, five individual mutants substituting these five basic residues by glutamic acid were produced, purified to homogeneity, and characterized. Regarding ribosomal recognition, all mutants showed a diminished activity in a cell-free reticulocyte lysate, whereas the activity against an oligoribonucleotide mimicking the sarcin/ricin loop rRNA (SRL) or the homopolymer poly(A) remained unaffected, confirming that the mutated basic residues participate in electrostatic interactions with other ribosomal elements apart from this SRL. The study of the interaction with phospholipid vesicles showed that Lys 17, Arg 22, and, most importantly, Lys 14 and Lys 21, are crucial residues in the first stages of the aggregation phenomenon, where protein-vesicle and protein-protein interactions are required. The data obtained reveal that electrostatic interactions involving basic residues of the β-hairpin are required not only for establishing specific interactions with ribosomal regions other than the SRL but also to explain the ability of the protein to interact with acid phospholipid bilayers.     

疏水层析用于大规模纯化重组HBsAg的工艺研究

应用疏水层析法从CHO细胞培养液中纯化HBsAg,每根制备柱每次可处理细胞收液350L,在适宜的上样流速和层析温度条件下,层析后可去除96％的杂蛋白,再经超速离心和凝胶过滤层析,可获HBsAg纯品。经检定,HPLC纯度高于95％,其余各项检定指标均符合《中国生物制品规程》要求。结果表明,此方法纯化效率高、处理样品量大、成本低,适于大规模生产。     

Potential Regulatory Interactions of Escherichia coli RraA Protein with DEAD-box Helicases

Members of the DEAD-box family of RNA helicases contribute to virtually every aspect of RNA metabolism, in organisms from all domains of life. Many of these helicases are constituents of multicomponent assemblies, and their interactions with partner proteins within the complexes underpin their activities and biological function. In Escherichia coli the DEAD-box helicase RhlB is a component of the multienzyme RNA degradosome assembly, and its interaction with the core ribonuclease RNase E boosts the ATP-dependent activity of the helicase. Earlier studies have identified the regulator of ribonuclease activity A (RraA) as a potential interaction partner of both RNase E and RhlB. We present structural and biochemical evidence showing how RraA can bind to, and modulate the activity of RhlB and another E. coli DEAD-box enzyme, SrmB. Crystallographic structures are presented of RraA in complex with a portion of the natively unstructured C-terminal tail of RhlB at 2.8-Å resolution, and in complex with the C-terminal RecA-like domain of SrmB at 2.9 Å. The models suggest two distinct mechanisms by which RraA might modulate the activity of these and potentially other helicases.     

Water and Protein Movements in Ligand-Receptor Interactions

I have recently developed a novel method `mutual repulsion' for simulating ligand unbindingfrom receptor. Combined with adiabatic switching,this method can evaluate the free energy change of unbinding. Mutualrepulsion has been applied to the bovine serum retinol-bindingprotein-retinol complex (1HBP). Large changes in amino acid configurationis observed in only three residues at the mouth of the binding site. Thechange in water structure around the ligand, from bulk-phase tohydrophobic hydration, as retinol unbinds, is also described.     

Protein Stabilization and the Hofmeister Effect: The Role of Hydrophobic Solvation

Using the IGg binding domain of protein L from Streptoccocal magnus (ProtL) as a case study, we investigated how the anions of the Hofmeister series affect protein stability. To that end, a suite of lysine-to-glutamine modifications were obtained and structurally and thermodynamically characterized. The changes in stability introduced with the mutation are related to the solvent-accessible area of the side chain, specifically to the solvation of the nonpolar moiety of the residue. The thermostability for the set of ProtL mutants was determined in the presence of varying concentrations (0-1 M) of six sodium salts from the Hofmeister series: sulfate, phosphate, fluoride, nitrate, perchlorate, and thiocyanate. For kosmotropic anions (sulfate, phosphate, and fluoride), the stability changes induced by the cosolute (encoded in ) are proportional to the surface changes introduced with the mutation. In contrast, the m₃ values measured for chaotropic anions are much more independent of such surface modifications. Our results are consistent with a model in which the increase in the solution surface tension induced by the anion stabilizes the folded conformation of the protein. This contribution complements the nonspecific and weak interactions between the ions and the protein backbone that shift the equilibrium toward the unfolded state.     

Electrostatic interactions and complement activation on the surface of phospholipid vesicle containing acidic lipids: Effect of the structure of acidic groups

Anionic vesicles containing acidic phospholipids are known complement activators. To clarify which negative physicochemical electrostatic charges on vesicles and structural specificities of acidic lipids are critical to complement activation, the electrostatic properties and activity to complement of two anionic vesicles modified with a carboxylic acid derivative or a conventional acidic phospholipid were compared. Electrophoretic mobility measurements indicated that the negative zeta potential and the electrostatic interactivity of these two anionic vesicles were equal at pH 7.4. However, the infusion of vesicles containing acidic phospholipid induced significant complement activation, while vesicles containing the carboxylic acid derivative failed to activate complement. These results indicate that the negative charge on the surface of vesicles is not critical for the activation complement, suggesting that complement activation is specific to the structure of acidic groups. This finding is likely to be important to the design of anionic biointerfaces and may support the promising medical applications of this anionic vesicle modified with a carboxylic acid derivative.     

Hydrophobic interactions mediate binding of the glycine receptor beta-subunit to gephyrin

Glycine receptors (GlyRs) are ligand-gated chloride channel proteins composed of alpha- and beta-subunits. GlyRs are located to and anchored at postsynaptic sites by the receptor-associated protein gephyrin. Previous work from our laboratory has identified a core motif for gephyrin binding in the cytoplasmic loop of the GlyR beta-subunit. Here, we localized amino acid residues implicated in gephyrin binding by site-directed mutagenesis. In a novel transfection assay, a green fluorescent protein-gephyrin binding motif fusion protein was used to monitor the consequences of amino acid substitutions for beta-subunit interaction with gephyrin. Only multiple, but not single, replacements of hydrophobic side chains abolished the interaction between the two proteins. Our data are consistent with gephyrin binding being mediated by the hydrophobic side of an imperfect amphipathic helix.     

Arylsulphatase C and Estrone Sulphatase of Sheep Hypothalamus, Preoptic Area, and Midbrain: Separation by Hydrophobic Interaction Chromatography and Evidence for Differences in Their Lipid Environment

Abstract: Arylsulphatase C and estrone sulphatase activities of sheep hypothalamus-preoptic area-midbrain were examined for their susceptibility to phospholipase action. Russel's viper phospholipase A could completely inactivate estrone sulphatase without affecting arylsulphatase C. The latter was partially inactivated by S. aureus phospholipase C but not by C. welchi phospholipase C. Both arylsulphatase C and estrone sulphatase were inactivated to different extents by sodium deoxycholate, which is known to activate the intrinsic phospholipases of brain. Hydrophobic interaction chromatography on phenyl-Sepharose resulted in the differential elution of arylsulphatase C and estrone sulphatase. The results suggest that one enzyme is not responsible for arylsulphatase C and estrone sulphatase activities.     

Nucleotide Binding to Na,K-ATPase: The Role of Electrostatic Interactions.

The contribution of electrostatic forces to the interaction of Na,K-ATPase with adenine nucleotides was investigated by studying the effect of ionic strength on nucleotide binding. At pH 7.0 and 20 degrees C, there was a qualitative correlation between the equilibrium dissociation constant (K(d)) values for ATP, ADP, and MgADP and their total charges. All K(d) values increased with increasing ionic strength. According to the Debye-Hückel theory, this suggests that the nucleotide binding site and its ligands have "effective" charges of opposite signs. However, quantitative analysis of the dependence on ionic strength shows that the product of the effective electrostatic charges on the ligand and the binding site is the same for all nucleotides, and is therefore independent of the total charge of the nucleotide. The data suggest that association of nucleotides with Na,K-ATPase is governed by a partial charge rather than the total charge of the nucleotide. This charge, interacting with positive charges on the protein, is probably the one corresponding to the alpha-phosphate of the nucleotide. Dissociation rate constants measured in complementary transient kinetic experiments were 13 s(-1) for ATP and 27 s(-1) for ADP, independent of the ionic strength in the range 0.1-0.5 M. This implies similar association rate constants for the two nucleotides (about 40 x 10(6) M(-1) s(-1) at I = 0.1 M). The results suggest that long-range Coulombic forces, affecting association rates, are not the main contributors to the observed differences in affinities, and that local interactions, affecting dissociation rates, may play an even greater role.     

Role of a Hydrophobic Pocket in Polyamine Interactions with the Polyspecific Organic Cation Transporter OCT3

Organic cation transporter 3 (OCT3, SLC22A3) is a polyspecific, facilitative transporter expressed in astrocytes and in placental, intestinal, and blood-brain barrier epithelia, and thus elucidating the molecular mechanisms underlying OCT3 substrate recognition is critical for the rational design of drugs targeting these tissues. The pharmacology of OCT3 is distinct from that of other OCTs, and here we investigated the role of a hydrophobic cavity tucked within the translocation pathway in OCT3 transport properties. Replacement of an absolutely conserved Asp by charge reversal (D478E), neutralization (D478N), or even exchange (D478E) abolished MPP⁺ uptake, demonstrating this residue to be obligatory for OCT3-mediated transport. Mutations at non-conserved residues lining the putative binding pocket of OCT3 to the corresponding residue in OCT1 (L166F, F450L, and E451Q) reduced the rate of MPP⁺ transport, but recapitulated the higher sensitivity pharmacological profile of OCT1. Thus, interactions of natural polyamines (putrescine, spermidine, spermine) and polyamine-like potent OCT1 blockers (1,10-diaminodecane, decamethonium, bistriethylaminodecane, and 1,10-bisquinuclidinedecane) with wild-type OCT3 were weak, but were significantly potentiated in the mutant OCT3s. Conversely, a reciprocal mutation in OCT1 (F161L) shifted the polyamine-sensitivity phenotype toward that of OCT3. Further analysis indicated that OCT1 and OCT3 can recognize essentially the same substrates, but the strength of substrate-transporter interactions is weaker in OCT3, as informed by the distinct makeup of the hydrophobic cleft. The residues identified here are key contributors to both the observed differences between OCT3 and OCT1 and to the mechanisms of substrate recognition by OCTs in general.     

Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family

Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp²⁰² and Phe²⁰³ in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability.     

Role of unique basic residues of human pancreatic ribonuclease in its catalysis and structural stability

Human pancreatic ribonuclease (HPR) and bovine RNase A belong to the RNase A superfamily and possess similar key structural and catalytic residues. Compared to RNase A, HPR has six extra non-catalytic basic residues and high double-stranded RNA (dsRNA) cleavage activity. We mutated four of these basic residues, K6, R32, K62, and K74 to alanine and characterized the variants for function and stability. Only the variant K74A had an altered secondary structure. Whereas R32A and K62A had full catalytic activity, the mutants K6A and K74A had reduced activity on both ssRNA and dsRNA. The mutations of K62 and K74 resulted in reduction in protein stability and DNA double helix unwinding activity of HPR; while substitutions of K6 and R32 did not affect either the stability or helix unwinding activity. The reduced catalytic and DNA melting activities of K74A mutant appear to be an outcome of its altered secondary structure. The basic residues studied here, appear to contribute to the overall stability, folding, and general catalytic activity of HPR.     

Hydrophobic interactions between the secondary structures on the molecular surface reinforce the alkaline stability of serine protease

We employed random mutagenesis to determine the region of the initial unfolding of hyper-alkaline-sensitive subtilisin, ALP I, that precedes the denaturation of the entire protein under highly alkaline conditions. This region comprises two α-helices and a calcium-binding loop. Stabilization of the region caused the stabilization of the entire protein at a high alkaline pH 12. The alkaline stability of this region was most effectively improved by hydrophobic interactions, followed by ionic interactions with Arg residues. The effect of mutations on the improvement was different with regard to the alkaline stability and thermostability. This indicated that different strategies were necessary to improve the alkaline stability and thermostability of the protein.     

Homology Modelling of a Newly Discovered Thioredoxin Protein and Analysis of the Force Field and Electrostatic Properties

Thioredoxin is a small protein (Mr approximately 12,000) found in all living cells from archaebacteria to humans. The active site is highly conserved and has two redox-active cysteine residues in the sequence: -Trp-Cys-Gly-Pro-Cys-. Besides the function of the reduced form as a powerful protein disulfide oxidoreductase, thioredoxin is known to regulate and activate different target enzymes, i.e. ribonucleotide reductase and the mitochondrial 2-oxoacid dehydrogenase multienzyme complexes. Despite the high degree of homology between thioredoxin proteins from different species, there exists a strong variation in the capability of activating target enzymes. This is yet unexplainable, since there still exists no model of a thioredoxin/receptor complex.On the basis of the recently determined amino acid sequence of the thioredoxin Trx2 from rat mitochondria, which is known to be highly efficient in activating mitochondrial 2-oxoacid dehydrogenase multienzyme complexes, we construct the 3-D structure of this protein by homology modelling methods, using the X-ray structures of thioredoxin from E. coli and human as background information. We analyze the differences in the electrostatic properties of the different protein structures and show, that despite the observed homology between the primary sequences, the dipole moment of the protein structures shows significant variations, which might lead to deviations with respect to the binding to the target protein. Using the AMBER 4.0 program package we further investigate and compare the force field energies of the different thioredoxin structures.Electronic Supplementary Material available.     

Native Molecular Forms of Head Acetylcholinesterase from Adult Drosophila melanogaster: Quaternary Structure and Hydrophobic Character

The native molecular forms of acetylcholinesterase (AChE) present in adult Drosophila heads were characterized by sedimentation analysis in sucrose gradients and by nondenaturing electrophoresis. The hydrophobic properties of AChE forms were studied by comparing their migration in the presence of Triton X100, 10-oleyl ether, or sodium deoxycholate, or in the absence of detergent. We examined the polymeric structure of AChE forms by disulfide bridge reduction. We found that the major native molecular form is an amphiphilic dimer which is converted into hydrophilic dimer and monomer on autolysis of the extracts, or into a catalytically active amphiphilic monomer by partial reduction. The latter component exists only as trace amounts in the native enzyme. Two additional minor native forms were identified as hydrophilic dimer and monomer. Although a significant proportion of AChE was only solubilized in high salt, following extractions in low salt, this high salt-soluble fraction contained the same molecular forms as the low salt-soluble fractions: thus, we did not detect any molecular form resembling the asymmetric forms of vertebrate cholinesterases.     

Prediction of Protein-Protein Interactions Using Protein Signature Profiling

Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain inter- actions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as “interacting“. In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis ele- gans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area un- der the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs in- creased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on aver- age 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.