A Single Mutation at Residue 25 Populates the Folding Intermediate of E. coli RNase H and Reveals a Highly Dynamic Partially Folded Ensemble

Understanding the nature of partially folded intermediates transiently populated during protein folding is important for understanding both protein folding and misfolding. These ephemeral species, however, often elude direct experimental characterization. The well-characterized protein ribonuclease H (RNase H) from Escherichia coli populates an on-pathway intermediate identified in both bulk studies and single-molecule mechanical unfolding experiments. Here, we set out to trap the transient intermediate of RNase H at equilibrium by selectively destabilizing the region of the protein known to be unfolded in this species. Surprisingly, a single change at Ile25 (I25A) resulted in the equilibrium population of the intermediate under near-native conditions. The intermediate was undetectable in a series of heteronuclear single quantum coherences, revealing the dynamic nature of this partially unfolded form on the timescale of NMR detection. This result is in contrast to studies in which the structures of trapped intermediates are solved by NMR, indicating that they are well packed and native-like. The dynamic nature of the RNase H intermediate may be important for its role as an on-pathway, productive species that promotes efficient folding.     

A conformational study of N-phenyl-1-naphthylamine and 1-anilino-8-naphthalene sulfonate by the empirical method

Conformational analysis of N-phenyl-1-naphthylamine and 1-anilinonaphthalene-8-sulfonate (ANS) was carried out using the empirical method. Properties such as conformational energies and dipole moments were considered. Furthermore, the effect of solvent medium was examined through the effective dielectic constant. The N-phenyl-1-naphthylamine molecule showed two energy minima which were independent of dielectic constant. The ANS molecule also showed two energy minima but the minima changed positions when the dielectic constant increased from 1.0 (vacuum) to 80.0 (highly polar medium). Hydrogen bonding appeared to play an important role in stabilizing these conformations. The minimum energy conformations may have relevance to the binding of ANS to lipid bilayers and bimembranes. The dipole moment, in contrast to the energy minimum, was found to depend on orientation of the sulfonate group rather than of the benzene ring with respect to the naphthalene ring. Thus binding and fluorescence enhancement of ANS may be attributed to the orientation of the sulfonate group, which to a large extent may determine the magnitude of the dipole moment and the degree of electrostatic interactions between the probe and binding domains. Various dimensions like intra-atomic distances, volume and area of the ANS molecule were calculated.     

SecB-Mediated Protein Export Need Not Occur via Kinetic Partitioning

In Escherichia coli, the cytosolic chaperone SecB is responsible for the selective entry of a subset of precursor proteins into the Sec pathway. In vitro, SecB binds to a variety of unfolded substrates without apparent sequence specificity, but not native proteins. Selectivity has therefore been suggested to occur by kinetic partitioning of substrates between protein folding and SecB association. Evidence for kinetic partitioning is based on earlier observations that SecB blocks the refolding of the precursor form of maltose-binding protein (preMBP)⁵ and slow-folding maltose-binding protein (MBP) mutants, but not faster-folding mature wild-type MBP. In order to quantitatively validate the kinetic partitioning model, we have independently measured each of the rate constants involved in the interaction of SecB with refolding preMBP (a physiological substrate of SecB) and mature MBP. The measured rate constants correctly predict substrate folding kinetics over a wide range of SecB, MBP, and preMBP concentrations. Analysis of the data reveals that, for many substrates, kinetic partitioning is unlikely to be responsible for SecB-mediated protein export. Instead, the ability of SecB-bound substrates to continue folding while bound to SecB and their ability to interact with other components of the secretory machinery such as SecA may be key opposing determinants that inhibit and promote protein export, respectively.     

Changes in microsomal enzyme activities during DAB carcinogenesis

Microsomal fractions were isolated from livers of rats that been fed p-dimethylaminoazobcnzene (DAB) for 2 months sygnificant decreases were noted in the specific activities of four of the membrane-bound enzymes, Sudies on membrane composition and the interactions between membranc components were carried out in an attempt to explain the mechanisms responsable for these decreases. Changes in the lipid components of the membrane were brought about as a result of DAB feeding. No changes were detected in the protein components of the membrane. 1-Anilinonaphthalene-8-Sulfonic acid (ANS) fluorescence enhancement was decreased by 25 % in membranes delived from DAB-fed animals. The response of the membranebound enzymes to pretreatment with NH₄OH and Triton X-100 was examined. The glucose-6-phosphatase of membranes derived from carcinogen-fed animals was more activated by Triton than the enzyme from control. It is concluded that altered membrane conformation is a result of DAB carcinogensus, and that such alterations may be responsible for loss of enzyme activity.     

Binding of thyrotropin releasing hormone and prolactin release by synchronized GH3 rat pituitary cell line.

GH3 cells were synchronized by growing them in a low serum concentration (1%). They were thereafter put back in normal medium (17.5% serum) (time 0 of synchronization). Four parameters were then examined every two hours for up to 40 hours : rate of [³H] thymidine incorporation, cell number, binding of [³H] Thyrotropin Releasing Hormone (TRH) after a 30 min exposure, and prolactin (PRL) content of culture medium and cell extract.The rate of thymidine incorporation presented a 10–20 fold increase in S phase, beginning on 12–16 hours and lasting at 26 hours. The cell population was doubled at 28 hours. [³H] TRH binding to attached cells was observed throughout the cell cycle, but presented a significant increase (40–80%) during the S phase. In contrast, the % increase of PRL release in response to TRH was optimum (300% of control) in G₁ phase. Variations of the PRL cell content as well as of the PRL spontaneous release ability of the cell do not account for the variations of TRH responsiveness. The discrepancy between the two parameters of the TRH-GH3 cells interaction strongly suggest a morphological or functional heterogeneity of the TRH-binding sites.     

Molecularly imprinted poly β-cyclodextrin polymer: Application in protein refolding

Regarding our previous report on refolding of alkaline phosphatase [Yazdanparast and Khodagholi, 2005 Arch. Biochem. Biophys] it was found that in spite of the anti-aggregatory effect of 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS), a zwitteronic detergent, the recovered activity was almost the same as the recovered activity obtained through the unassisted approach. The low recovery yield is probably due to the bulky groups of the detergent that interfere with its entrance into the small cavity of the stripping agent, cyclodextrin, implying that the stripping of detergent molecules from the detergent–protein complexes plays a major role in successful refolding processes. To improve the efficiency of CHAPS stripping, we evaluated, for the first time, the stripping potential of a molecular imprinting polymer designed to replace β-CD. In this approach, CHAPS was used as the template and the refolding of GuHCl denatured alkaline phosphatase was studied. Our results indicated that under the optimally developed refolding environment and similar to stripping by soluble β-CD, a refolding yield of 79% was obtained for denatured alkaline phosphatase using 20 mg/ml of the molecularly imprinted poly (β-CD) polymer. The major advantage of the new stripping agent, besides of its recycling option and ease of separation from the finished product, is its high potential of preventing aggregate formation. Based on these results, it seems that the new stripping strategy can constitute an ideal approach for refolding of proteins at much lower industrial costs compared to stripping with soluble β-cyclodextrin.     

Understanding mAb aggregation during low pH viral inactivation and subsequent neutralization

Monoclonal antibodies (mAbs) and related recombinant proteins continue to gain importance in the treatment of a great variety of diseases. Despite significant advances, their manufacturing can still present challenges owing to their molecular complexity and stringent regulations with respect to product purity, stability, safety, and so forth. In this context, protein aggregates are of particular concern due to their immunogenic potential. During manufacturing, mAbs routinely undergo acidic treatment to inactivate viral contamination, which can lead to their aggregation and thereby to product loss. To better understand the underlying mechanism so as to propose strategies to mitigate the issue, we systematically investigated the denaturation and aggregation of two mAbs at low pH as well as after neutralization. We observed that at low pH and low ionic strength, mAb surface hydrophobicity increased whereas molecular size remained constant. After neutralization of acidic mAb solutions, the fraction of monomeric mAb started to decrease accompanied by an increase on average mAb size. This indicates that electrostatic repulsion prevents denatured mAb molecules from aggregation under acidic pH and low ionic strength, whereas neutralization reduces this repulsion and coagulation initiates. Limiting denaturation at low pH by d -sorbitol addition or temperature reduction effectively improved monomer recovery after neutralization. Our findings might be used to develop innovative viral inactivation procedures during mAb manufacturing that result in higher product yields.