A model for determining the steady state flux of inorganic microfiltration membranes

The present paper provides a model based on dimensional analysis that gives the basis for design of the cross-flow microfiltration processes. This gives the permeate flux f in terms of the pressure drop across the filtration membrane ΔP and the velocity V of cross-flow of the feed fluid in the membrane tubes. The model is compared with an extensive series of experimental results with magnesium hydroxide slurries. The model has certain similarities with previous ones and can be used for unit optimization.     

A PELDOR-based nanometer distance ruler for oligonucleotides

A pulsed electron paramagnetic resonance (EPR) spectroscopic ruler for oligonucleotides was developed using a series of duplex DNAs. The spin-labeling is accomplished during solid-phase synthesis of the oligonucleotides utilizing a palladium-catalyzed cross-coupling reaction between 5-iodo-2'-deoxyuridine and the rigid spin-label 2,2,5,5-tetramethyl-pyrrolin-1-yloxyl-3-acetylene (TPA). 4-Pulse electron double resonance (PELDOR) was then used to measure the intramolecular spin-spin distances via the dipolar coupling, yielding spin-spin distances of 19.2, 23.3, 34.7, 44.8, and 52.5 A. Employing a full-atom force field with explicit water, molecular dynamic (MD) simulations on the same spin-labeled oligonucleotides in their duplex B-form gave spin-spin distances of 19.6, 21.4, 33.0, 43.3, and 52.5 A, respectively, in very good agreement with the measured distances. This shows that the oligonucleotides adopt a B-form duplex structure also in frozen aqueous buffer solution. It also demonstrates that the combined use of site-directed spin-labeling, PELDOR experiments, and MD simulations can yield a microscopic picture about the overall structure of oligonucleotides. The technique is also applicable to more complex systems, like ribozymes or DNA/RNA-protein complexes, which are difficult to access by NMR or X-ray crystallography.     

Method of determining the position of guanosine residues in oligodeoxyribonucleotides

A method is proposed for determining the position of guanosine residues in oligo-deoxyribonucleotides. After limited modification of the oligonucleotide with glyoxal, a mixture of molecules of the initial oligonucleotide with different degrees of modification is formed. In the presence of borate ions, the glyoxal-modified guanosine residues form negatively charged borate complexes which inhibit the action of snake venom phosphodiesterase. The treatment of such a complex with the enzyme forms a mixture of fragments of the initial oligonucleotide the 5-terminal sequences of which are identical while at the 3-end there are modified guanosine residues. The determination of the length of these fragments provides the necessary information on the positions of the guanosine residues in the chain of the initial oligonucleotides. The positions of the guanosine residues in eight synthetic oligodeoxyribonucleotides have been confirmed with the aid of the method developed.A. N. Belozerskii Interfaculty Problem Scientific-Research Laboratory of Molecular Biology and Bioorganic Chemistry of the M. V. Lomonosov Moscow State University. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 570–573, July–August, 1979.     

Method of determining the position of guanosine residues in oligodeoxyribonucleotides

Chemistry of Natural Compounds - A method is proposed for determining the position of guanosine residues in oligo-deoxyribonucleotides. After limited modification of the oligonucleotide with...     

A method for determining the position of tautomeric equilibrium solely from infrared and ultraviolet spectral data

Conclusions A method was described for determining the position of equilibrium in tautomeric systems, using only data from IR and UV spectra.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1887–1888, August, 1968     

New method for determining the concentration of ionic impurities in solvent polymeric membranes

A new method is proposed for ascertaining the amount of ionic impurities in solvent polymeric membranes of ion-selective electrodes. The method is based on determining the selectivity coefficient for ions of different valences as a function of the concentration of a lipophilized tetraphenylborate salt added to the membrane phase. Thus, the concentration of anionic impurities in commercially available poly(vinyl chloride) and of cationic ones in Tecoflex® (a polyurethane) was obtained as 0.063 ± 0.016 and 0.044 ± 0.006 mmol/kg, respectively.     

Factors determining pore shape in polycarbonate track membranes

The formation of pores in polycarbonate films irradiated by accelerated ions upon their treatment with alkali solution containing a surfactant was studied. It was found that the pore shape is determined by both the structure of the initial film and the peculiarities of interaction of a surfactant with a polymer surface and its transfer to a track. Because of the inhomogeneity of the initial material, the track pore cross section varies along the pore length. The presence of a surfactant leads to an additional effect. Being adsorbed onto the film surface and at the entrances of etched tracks of heavy ions, surfactant molecules tend to decrease the etching rate, thus leading to the formation of spindle-shaped pores. Thus, the use of a surfactant as a component of the chemical etching solution makes it possible to vary the pore shape of track membranes in a directional manner, optimizing their efficiency and selectivity.Translated from Kolloidnyi Zhurnal, Vol. 66, No. 6, 2004, pp. 725–732.Original Russian Text Copyright © 2004 by Apel, Blonskaya, Orelovich, Akimenko, Sartowska, Dmitriev.     

A distance ruler for RNA using EPR and site-directed spin labeling

As a basic model study for measuring distances in RNA molecules using continuous wave (CW) EPR spectroscopy, site-directed spin-labeled 10-mer RNA duplexes and HIV-1 TAR RNA motifs with various interspin distances were examined. The spin labels were attached to the 2'-NH2 positions of appropriately placed uridines in the duplexes, and interspin distances were measured from both molecular dynamics simulations (MD) and Fourier deconvolution methods (FD). The 10-mer duplexes have interspin distances ranging from 10 A to 30 A based on MD; however, dipolar line broadening of the CW EPR spectrum is only observed for the RNAs for predicted interspin distances of 10-21 A and not for distances over 25 A. The conformational changes in TAR (transactivating responsive region) RNA in the presence and in the absence of different divalent metal ions were monitored by measuring distances between two nucleotides in the bulge region. The predicted interspin distances obtained from the FD method and those from MD calculations match well for both the model RNA duplexes and the structural changes predicted for TAR RNA. These results demonstrate that distance measurement using EPR spectroscopy is a potentially powerful method to help predict the structures of RNA molecules.     

Importance of native-state topology for determining the folding rate of two-state proteins

Understanding the relationship between amino acid sequences and folding rate of proteins is a challenging task similar to protein folding problem. In this work, we have analyzed the relative importance of protein sequence and structure for predicting the protein folding rates in terms of amino acid properties and contact distances, respectively. We found that the parameters derived with protein sequence (physical-chemical, energetic, and conformational properties of amino acid residues) show very weak correlation (|r| < 0.39) with folding rates of 28 two-state proteins, indicating that the sequence information alone is not sufficient to understand the folding rates of two-state proteins. However, the maximum positive correlation obtained for the properties, number of medium-range contacts, and alpha-helical tendency reveals the importance of local interactions to initiate protein folding. On the other hand, a remarkable correlation (r varies from -0.74 to -0.88) has been obtained between structural parameters (contact order, long-range order, and total contact distance) and protein folding rates. Further, we found that the secondary structure content and solvent accessibility play a marginal role in determining the folding rates of two-state proteins. Multiple regression analysis carried out with the combination of three properties, beta-strand tendency, enthalpy change, and total contact distance improved the correlation to 0.92 with protein folding rates. The relative importance of existing methods along with multiple-regression model proposed in this work will be discussed. Our results demonstrate that the native-state topology is the major determinant for the folding rates of two-state proteins.     

A general method for determining the electron self-exchange rates of blue copper proteins by longitudinal NMR relaxation

A general NMR method is presented that allows a precise determination of the second-order rate constant, k(ese), for the electron self-exchange in blue copper proteins, from the longitudinal relaxation rates of the nuclei in the protein. The method relies on the use of partly oxidized (paramagnetic) samples of the protein. In contrast to previous NMR approaches for the determination of electron self-exchange rates, the applicability of the method extends beyond the slow-exchange limit, k(ese)c < R(ip), i = 1, 2, where c is the protein concentration, and R(ip) is the paramagnetic relaxation enhancement of the observed nuclei.     

Electric field effects in proteins in membranes

Both the organization and function of protein nanostructures in membranes are related to the substructural properties of the lipid portion of the membrane. Potential differences that are established across the membrane and generate electric fields in these very thin portions are shown to modulate the organizational and functional properties of the protein modules. Many protein modules also have nonisotropic distributions of charged sites, including configurations in which there are regions containing predominantly positive fixed charges, juxtaposed with adjacent regions containing predominantly negative fixed charges. In these double fixed charge regions, very large electric fields can manifest in the ionic depletion layer at the junction of the two fixed charge regions.Consideration is also given to the manner in which the intense electric fields that are established in protein modules, such as proton ATPases, can modulate the chemical reactions that are associated with proton transport and dehydration reactions.     

Methodology for determining degree of hydrolysis of proteins in Hydrolysates: a review

Degree of hydrolysis (DH) is defined as the proportion of cleaved peptide bonds in a protein hydrolysate. Several methods exist for determining DH; the most commonly used of these include the pH-stat, trinitrobenzenesulfonic acid (TNBS), o-phthaldialdehyde (OPA), trichloroacetic acid soluble nitrogen (SN-TCA), and formol titration methods. The pH-stat method is based on the number of protons released during hydrolysis; the TNBS, OPA, and formol titration methods are based on the measurement of amino groups generated from hydrolysis. The SN-TCA method measures the amount of TCA-soluble nitrogen, rather than DH. The pH-stat is the simplest and most commonly used method, but does not determine peptide bonds directly. In addition, the accuracy of the method depends on the type of hydrolytic enzymes used, the size of the hydrolyzed peptides, and the reaction temperature. Generally, the TNBS and OPA methods compare well and do directly determine DH. However, the assumption that the response factor for all derivatized N-terminal amino acids is similar may lead to inaccuracies. In conclusion, there is no consensus as to the best method for determining the DH of protein hydrolysates; consequently, there is a need for a standardized approach if interstudy comparisons are to be made.     

Evaluation of membranes used for electroblotting of proteins for direct automated microsequencing

Protein purification and characterisation have been age-old problems for the biochemist. A new era has arisen with the advent of one- and two-dimensional gel electrophoresis and high sensitivity automated protein microsequencing. These two tools along with electroblotting have made it possible to separate and analyse complex protein mixtures. We studied six different membranes compatible with Edman degradation chemistry to determine their efficiencies at binding proteins electroblotted from one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Their overall blotting-sequencing properties were also evaluated. We found that the polyvinylidene difluoride-based membranes out-performed the glass-based and polypropylene-based membranes under our selected experimental conditions. The problems associated with electroblotting and microsequencing are discussed.     

Targeting proteins to liquid-ordered domains in lipid membranes

We demonstrate the construction of novel protein-lipid assemblies through the design of a lipid-like molecule, DPIDA, endowed with tail-driven affinity for specific lipid membrane phases and head-driven affinity for specific proteins. In studies performed on giant unilamellar vesicles (GUVs) with varying mole fractions of dipalymitoylphosphatidylcholine (DPPC), cholesterol, and diphytanoylphosphatidyl choline (DPhPC), DPIDA selectively partitioned into the more ordered phases, either solid or liquid-ordered (L(o)) depending on membrane composition. Fluorescence imaging established the phase behavior of the resulting quaternary lipid system. Fluorescence correlation spectroscopy confirmed the fluidity of the L(o) phase containing DPIDA. In the presence of CuCl(2), the iminodiacetic acid (IDA) headgroup of DPIDA forms the Cu(II)-IDA complex that exhibits a high affinity for histidine residues. His-tagged proteins were bound specifically to domains enriched in DPIDA, demonstrating the capacity to target protein binding selectively to both solid and L(o) phases. Steric pressure from the crowding of surface-bound proteins transformed the domains into tubules with persistence lengths that depended on the phase state of the lipid domains.     

Electrophoretic transfer of proteins across polyacrylamide membranes

The electrophoretic transfer of purified proteins has been examined in a Gradiflow "Babyflow BF100" unit. A number of factors affect protein separation within this preparative electrophoresis system. We established that the rate of protein transfer was proportional to the applied voltage. The transfer is slowest at the isoelectric point (pI) and increased the further away the pH was from the pI of the protein. Protein transfer was found to be independent of the ionic strength of the buffer, for buffers that excluded the addition of strong acids or strong bases or sodium chloride. Transfer decreased as the pore size of the membrane decreased. Finally, transfer was inhibited at high salt concentrations in the protein solution, but remained unaffected when urea and non-ionic detergents were added to the solution. To increase the speed of protein separations, buffers with low conductivity should be used. A pH for the optimal separation should be selected on the basis of the relative pI and size of the target proteins and that of the major contaminants.     

Use of electrophoretic techniques in determining the composition of seed storage proteins in alfalfa

Holoprotein molecular weights and polypeptide composition can be determined for complex mixtures of oligomeric proteins using two-dimensional electrophoretic techniques. The variety of two-dimensional analyses presented here is a reflection of the general usefulness of each method for the identification and characterization of the different classes of seed storage proteins in alfalfa. These techniques can be applied to studies of storage proteins in other seeds as well as non-seed storage proteins. The major seed storage proteins in alfalfa are medicagin (a legumin-like globulin), alfin (a vicilin-like globulin) and a family of lower molecular weight albumins (LMW1-3). These comprise 30%, 10%, and 20%, respectively, of the total extractable protein from cotyledons of mature seeds. Alfin is a heterogeneous oligomeric protein (Mr approximately 150,000) composed of polypeptides ranging in size from Mr 14,000 to 50,000 (alpha 1-alpha 6; 50,000, 38,000, 32,000, 20,000, 16,000 and 14,000, respectively). Medicagin is also a high molecular weight oligomeric protein, but requires high concentrations of salt for solubilisation. It is comprised of a family of individually distinct subunits, each composed of an acidic polypeptide (A1-A9; Mr 49,000 to 39,000) linked via disulphide bond(s) to a basic polypeptide (B1, B2, B3; Mr 24,000, 23,000 and 20,000, respectively). This pairing is highly specific and two families are recognizable on the basis of the B polypeptide (B3 or B1/B2). Subunits (Mr approximately 50,000-65,000) are assembled as trimers (8S) or larger oligomers (12S-15S) in mature seeds. The lower molecular weight albumins (LMW1-3) are acidic (pI less than 6), and consist of sets of disulphide-bonded polypeptides (Mr 15,000 and 11,000).