Thermodynamics of thermal denaturation of ribonuclease A and cytochrome c in the presence of 1,1,1,3,3,3-hexafluoro-2-propanol

The thermal denaturation of ribonuclease A and cytochrome c has been studied by differential scanning calorimetry (d.s.c.) and u.v.-visible spectrophotometry in the presence of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) at pH  =  5.5 and pH  =  4.0, respectively. The quantitative thermodynamic parameters accompanying the thermal transitions from native to denatured state have been evaluated. The results of the reversible thermal denaturations have been fitted with a two-state native-to-denatured mechanism. A comparison has been made of the relative effect of HFIP on the thermal stability of ribonuclease A and cytochrome c. It has been observed that the denaturation capacity of HFIP tends more towards cytochrome c compared with ribonuclease A. The results have been explained on the basis of a fine balance between the preferential exclusion and binding that take place during the course of the denaturation reaction and the structuring of water around the groups of the protein exposed upon denaturation. Using the thermodynamic data obtained from calorimetric and spectroscopic measurements, we have calculated the changes in preferential solvation of ribonuclease A and cytochrome c upon heat denaturation. It is observed that the preferential solvation of these two proteins is specific, indicating that the solvation mechanism is not the same for them.     

Insights into the energetics and mechanism underlying the interaction of tetraethylammonium bromide with proteins

Calorimetry has been employed to investigate the quantitative energetic aspects and mechanism underlying protein–tetraethylammonium bromide (TEAB) interactions. Differential scanning calorimetry and UV–Visible spectroscopy have been used to study the thermal unfolding of three proteins of different structure and function (bovine serum albumin, α-lactalbumin, and bovine pancreatic ribonuclease A). The mode of interaction has been studied by using isothermal titration calorimetry, which demonstrates the absence of appreciable specific binding of TEAB to the protein. This suggests the involvement of solvent mediated effects and, possibly weak non-specific binding. The thermal unfolding transitions were found to be calorimetrically reversible for α-lactalbumin and bovine pancreatic ribonuclease A and partially reversible in the case of bovine serum albumin. The results indicate protein destabilization promoted by the TEAB interaction. The preferential interaction parameters of TEAB with α-lactalbumin and ribonuclease A confirm that an increased interaction of the hydrophobic groups of the TEAB with that of the protein upon denaturation is responsible for the reduced thermal stability of the protein. The decrease in the thermal stability of proteins in the presence of TEAB is well supported by a red shift in the intrinsic fluorescence of these proteins leading to conformational change thereby shifting the native ? denatured equilibrium towards right. The forces responsible for the thermal denaturation of the proteins of different structure and function in the presence of TEAB are discussed.     

Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops

A method has been developed for minimizing the energy of a polypeptide with rigid geometry while keeping all disulfide loops closed exactly. Exact closure of disulfide loops implies that some dihedral angles become implicit functions of the remaining dihedral angles in the polypeptide; the efficacy of the method is related to the manner in which the implicitly defined dihedral angles are chosen. The method has been used to find minimum-energy conformations of bovine pancreatic trypsin inhibitor, ribonuclease A, crambin, the defensin HNP3 dimer, and ω-conotoxin. For the first two proteins, the starting conformations for energy minimization had been derived previously from crystal structures using pseudopotentials to keep the disulfide loops almost closed. Starting conformations for the remaining three proteins were derived from their crystal or NMR structures by similar procedures. In all cases, the energy-minimized structures had a significantly and, in some cases, substantially, lower energy than the starting structures. The RMS deviations between the exactly closed energy- minimized structures and the crystal or NMR structures from which they were derived ranged from 0.9 Å to 1.9 Å, suggesting that the computed structures can serve as “regularized” native structures for these proteins. The energy of a ribonuclease derivative lacking the 65–72 disulfide bridge was minimized using the procedure; the result showed that this derivative has a low-energy structure with a conformation very close to that of native ribonuclease, and is consistent with its postulated role in the folding of ribonuclease. These results offer strong support for the validity of the rigid-geometry model in the studies of the conformational energy of proteins. © 1997 by John Wiley & Sons, Inc.     

Biomimetic total syntheses of (-)-TAN1251A, (+)-TAN1251B, (+)-TAN1251C, and (+)-TAN1251D

[reaction: see text] The muscarinic antagonists (-)-TAN1251A (1), (+)-TAN1251B (2), (+)-TAN1251C (3), and (+)-TAN1251D (4) have been synthesized biomimetically by enamine formation from an amino aldehyde to give TAN1251C ketal 18. Oxidation and reduction lead to TAN1251A (1), which has been hydroxylated to give TAN1251B (2). Stereospecific reduction of TAN1251C ketal 18 leads to TAN1251D (4).     

Combinatorially Designed Lipid‐like Nanoparticles for Intracellular Delivery of Cytotoxic Protein for Cancer Therapy

An efficient and safe method to deliver active proteins into the cytosol of targeted cells is highly desirable to advance protein‐based therapeutics. A novel protein delivery platform has been created by combinatorial design of cationic lipid‐like materials (termed “lipidoids”), coupled with a reversible chemical protein engineering approach. Using ribonuclease A (RNase A) and saporin as two representative cytotoxic proteins, the combinatorial lipidoids efficiently deliver proteins into cancer cells and inhibit cell proliferation. A study of the structure–function relationship reveals that the electrostatic and hydrophobic interactions between the lipidoids and the protein play a vital role in the formation of protein–lipidoid nanocomplexes and intracellular delivery. A representative lipidoid (EC16‐1) protein nanoparticle formulation inhibits cell proliferation in vitro and suppresses tumor growth in a murine breast cancer model.     

Linderstrom-Lang-Schellman's model for protein stabilization revisited

The fact that cleavage of single peptide linkages in proteins often leads to extensive conformational alteration, including regions far removed from the cleavage site is not fully understood. We propose, based on the work of Linderstrom-Lang and Schellman, that disruption primarily occurs within protein structural domains that are stabilized by cooperative interactions and that cleavage of single peptide linkages of the domain perturbs the entire cooperative interaction. For this model we review experimental observations: on fragment complexation (ribonuclease A, staphylococcal nuclease and cytochrome c), destabilized N-terminal large fragments (ribonuclease A and nuclease), cooperative folding and stabilization of proteins (ribonuclease A, nuclease and cytochrome c), the close relationship of the three-dimensional structure between fragment complexes and the original protein (ribonuclease A and nuclease), ligand induced stabilization (nuclease), 3D domain swapping, circular permutation (dihydrofolate reductase), evolutionary conservation (cytochrome c fold). Based on analysis of these observations, we conclude that the cooperative interactions of domains are important for the mechanism of 3D domain swapping as well as for stabilization and thereby, determination of the ground state of native proteins. Furthermore, analysis of the observations reveals that domains generally contain a hydrophobic core. Further, based on studies of cytochrome c and the Tsao, Evans and Wennerstrom model of electrostatic interactions between two hydrophobic monolayers, we propose the model that the hydrophobic core of a domain is polarizable and responds to the surface charges through its polarizability to stabilize the domain, explaining in part the nature of the cooperative interactions.     

The structural determinants that lead to the formation of particular oligomeric structures in the pancreatic-type ribonuclease family

Pancreatic-type ribonucleases are a family of RNA degrading enzymes that share different degrees of sequence identity but a very similar 3D-structure. The prototype of this family is bovine pancreatic ribonuclease or ribonuclease A. This enzyme has been the object of landmark work on the folding, stability, protein chemistry, catalysis, enzyme-substrate interaction and molecular evolution. In the recent years, the interest in the study of pancreatic-type ribonucleases has increased due to the involvement of some members of this family in special biological functions. In addition, dimeric and also higher oligomeric structures can be attained by the members of this family. The oligomers described structurally to date are mainly formed by 3D-domain swapping, a process which consists of the exchange of identical domains (i.e. identical structural elements, usually the N- and C-termini) between the subunits and is considered to be a mechanism for amyloid-type aggregate formation. This review compares the dimeric and oligomeric structures of different members of the pancreatic-type ribonuclease family which are able to acquire these structures, namely, bovine seminal ribonuclease, ribonuclease A and its human counterpart, human pancreatic ribonuclease. A specific focus is placed on what is known about the structural determinants that lead to the acquisition of a particular oligomeric structure and on the proposed mechanism of 3D-swapping.     

Use of 1-(2-thiazolylazo) 2-naphthol in rapid determination of iron in geological matrices

The present work describes the use of 1-(2-thiazolylazo)-2-naphthol (TAN) as a spectrophotomeric reagent for iron determination. TAN reacts with iron(II) forming a brown complex with absorption maximum at 575 and 787 nm. The following parameters were studied: complex stability, pH effect, amount of the TAN, buffer selection, amount of acetate buffer, reductor effect, order of addition of reagents and adherence to Beer's Law. The results demonstrated that iron can be determined with TAN in a pH range of 4.0-6.2 with an apparent molar absorptivity of 1.83 x 10(4) 1 . mol(-1) . cm(-1) (at 787 nm) and 1.41 x 10(4) 1 . mol(-1) . cm(-1) (at 575 nm). Beer's Law is obeyed for at least 3.00 microg/ml. The TAN reacts with other cations, but at 787 nm only the iron(II)-TAN complex absorbs. So, iron can be determined selectively in the presence of several cations. A procedure based on the direct mixture of the sample and a chromogenic solution is proposed, where iron can be determined rapidly and easily. Such procedures were used for the determination of iron in several geological matrices. No significant differences were obtained for TAN method and certificate results.     

Hydrogen bonding in 3-azetidinol—3. Ab initio and experimental spectra of the hydrogen-bonded species

The IR and Raman spectra in the range 4000-10 cm⁻ of 3-azetidinol and the O,N-dideuterated derivative have been recorded in the solid state and in aqueous solution. The interpretation of the vibrational spectra has been based upon ab initio calculations in the STO-3G approximation. A model structure for the calculations has been adopted in which 3-azetidinol binds two molecules of water and two molecules of ammonia. The results obtained for the aqueous solution are in accordance with the occurrence of 3-azetidinol as a hydrated, stacked, intermolecularly hydrogen-bonded chain.     

A NEW DIAZIRINE FOR PROTEIN MODIFICATION BY FLASH PHOTOLYSIS: COMPARISON WITH AN AZIDE

Abstract— A new photolabeling agent, N-[4–(3-chlorodiazirin-3-yl)benzoyl]glycine (CDBG), a carbene generator, was synthesized. The incorporation of its photolytic products into egg white lysozyme was studied using flash photolysis and compared with incorporation of N-(4-azido-2-nitro-phenyl)-2-amino ethane sulfonate (NAPT) products into lysozyme and bovine pancreatic ribonuclease A. There was considerable additional incorporation of photolysis products into ribonuclease and lysozyme after termination of flash photolysis when NAPT was used but no additional incorporation when CDBG was used. Protein labeled with NAPT retained the label poorly during electrophoresis in sodium dodecyl sulfate. Lysozyme labeled with CDBG lost little label upon electrophoresis. Neither label was well retained during electrophoresis in 8 M urea. Peptic and tryptic peptides from CDBG labeled lysozyme were differentially labeled.     

π-Allylic complexes from allene

A series of π-allylic palladium complexes has been prepared directly from allene. The polarity of the solvents used in the preparations has been found to have a significant effect upon the structure and composition of these complexes. NMR data in support of the proposed structure are tabulated.     

Alfileramine : A new zanthoxylum alkaloid structurally related to tetrahydrocannabinol

A new alkaloid, named alfileramine, has been isolated from Zanthoxylum punctatum. It represents the first alkaloid which has a structure closely related to the tetrahydrocannabinols. The structure was assigned based upon ¹H and ¹³C NMR, UV and mass spectroscopy and by relating alfileramine structure to that of the rearranged dihydrobromide salt. The structure of the dihydrobromide was known from X-ray diffraction. A possible biosynthetic pathway from a dehydrocitral equivalent and two molecules of hordenine is suggested.     

Thermodynamic Stability of Ribonuclease B

The thermodynamic stability of pancreatic ribonuclease B (RNase B), which possesses identical protein structure of pancreatic ribonuclease A (RNase A), but differs by the presence of a carbohydrate chain attached to Asn 34, was studied by means of differential scanning calorimetry (DSC) at different pH conditions. The comparison between the two proteins has shown a little but significant stabilization of RNase B with respect to the unglycosylated one at pH values higher than 7.0. The thermodynamic analysis reveals the carbohydrate moiety to have a small stabilization effect of 3 kJ mol^–1 at pH 8.0 and 63°C on the protein. This revised version was published online in July 2006 with corrections to the Cover Date.     

Determination of cadmium, copper, lead and zinc in water samples by flame atomic absorption spectrometry after cloud point extraction

Cloud point extraction (CPE) has been used for the simultaneous pre-concentration of cadmium, copper, lead and zinc after the formation of a complex with 1-(2-thiazolylazo)-2-naphthol (TAN), and later analysis by flame atomic absorption spectrometry (FAAS) using octylphenoxypolyethoxyethanol (Triton X-114) as surfactant. The chemical variables affecting the separation phase and the viscosity affecting the detection process were optimized. At pH 8.6, pre-concentration of only 50 ml of sample in the presence of 0.05% Triton X-114 and 2×10⁻⁵ mol l⁻¹ TAN permitted the detection of 0.099, 0.27, 1.1 and 0.095 ng ml⁻¹ cadmium, copper, lead and zinc, respectively. The enhancement factors were 57.7, 64.3, 55.6 and 63.7 for cadmium, copper, lead and zinc, respectively. The proposed method has been applied to the determination of cadmium, copper, lead and zinc in water samples and a standard reference material (SRM).     

An inimitable and ecological pleasant technique for the assessment of trace amount of copper (II) in tangible samples with new complexing reagent

A simple and rapid spectrophotometric technique has been designed for the trace copper analysis employing 1-(2-Thiazolylazo)-2-naphthol (TAN) reagent in aqueous micellar solution of cetyl trimethylammonium bromide (CTAB) as a surfactant. Copper complexed with 1-(2-Thiazolylazo)-2-naphthol to form bis[1-(2-Thiazolylazo)-2-naphthol]copper. The present spectrophotometric technique was very important since the micellar system was used in place of the toxic, high cost and time-consuming solvent extraction steps. The technique showed an enhanced detection efficiency, specificity, and molar absorptivity. It was found that the molar absorption coefficient and sensitivity of Sandel were ε 2.45 × 10⁴ L mol^?1cm^?1 and 2.6 ngcm^?2 at λ_max 578.4 nm. A linear calibration plot in the range 0.12–5.0 μg mL^?1 was obtained; a stoichiometric metal ligand ratio [M:L] of 1:2 was found for the formation of Cu-[TAN]₂. The complex was formed at pH 9.5 and was stable up to 24 h. The proposed technique has been employed to study copper from different alloys, biological, environmental and pharmaceutical samples.     

Solvent excess entropy at the electrode—solution interface

A model for water molecules in the double layer based upon information from gas-phase adsorption measurements has been used to calculate the configurational entropy of water in the double layer as a function of electric charge. The calculations agree well experimentally both in respect to dependence on charge and particularly in the position of the maximum entropy. The model can also be made consistent with the rest of the solvent excess entropy. The consistency between model and experiment favours models of capacitance humps which are not dependent upon water molecule orientation.     

Binary adsorption of globular proteins on ion-exchange media

Adsorption equilibrium of binary pairs of lysozyme (LYS), cytochrome c (CYC) and ribonuclease A (RNase) has been measured on different cation-exchange media at various solution conditions. Adsorption patterns largely follow the intrinsic protein–surface interactions, but can differ significantly for different pairs or even for one pair at different solution conditions. LYS/CYC adsorption shows similar behavior on all the adsorbents examined, with competitive adsorption dominated by LYS and the presence of LYS reducing the adsorption of CYC significantly. Simultaneous and sequential measurements for LYS/CYC show that the order of adsorption does not have a significant effect on the adsorption equilibrium. For LYS/RNase, LYS is consistently more strongly adsorbed. For CYC/RNase, both proteins can display significant adsorption, depending on the pH and salt concentration. A model based on colloidal energetics is developed to calculate the binary adsorption isotherms using parameter values obtained from single-component isotherms. The calculated adsorption is in good agreement with experimental results, with significantly better representation than for other commonly used binary isotherms.     

3D structure-based protein retention prediction for ion-exchange chromatography

The interest in understanding fundamental mechanisms underlying chromatography drastically increased over the past decades resulting in a whole variety of mostly semi-empirical models describing protein retention. Experimental data about the molecular adsorption mechanisms of lysozyme on different chromatographic ion-exchange materials were used to develop a mechanistical model for the adsorption of lysozyme onto a SP Sepharose FF surface based on molecular dynamic simulations (temperature controlled NVT simulations) with the Amber software package using a force-field based approach with a continuum solvent model. The ligand spacing of the adsorbent surface was varied between 10 and 20 Å. With a 10 Å spacing it was possible to predict the elution order of lysozyme at different pH and to confirm in silico the pH-dependent orientation of lysozyme towards the surface that was reported earlier. The energies of adsorption at different pH values were correlated with isocratic and linear gradient elution experiments and this correlation was used to predict the retention volume of ribonuclease A in the same experimental setup only based on its 3D structure properties. The study presents a strong indication for the validity of the assumption, that the ligand density of the surface is one of the key parameters with regard to the selectivity of the adsorbent, suggesting that a high ligand density leads to a specific interaction with certain binding sites on the protein surface, while at low ligand densities the net charge of the protein is more important than the actual charge distribution.