Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface.

Barnase and barstar are trivial names of the extracellular RNase and its intracellular inhibitor produced by Bacillus amyloliquefaciens. Inhibition involves the formation of a very tight one-to-one complex of the two proteins. With the crystallographic solution of the structure of the barnase-barstar complex and the development of methods for measuring the free energy of binding, the pair can be used to study protein-protein recognition in detail. In this report, we describe the isolation of suppressor mutations in barstar that compensate for the loss in interaction energy caused by a mutation in barnase. Our suppressor search is based on in vivo selection for barstar variants that are able to protect host cells against the RNAse activity of those barnase mutants not properly inhibited by wild-type barstar. This approach utilizes a plasmid system in which barnase expression is tightly controlled to keep the mutant barnase gene silent. When expression of barnase is turned on, failure to form a complex between the mutant barnase and barstar has a lethal effect on host cells unless overcome by substitution of the wild-type barstar by a functional suppressor derivative. A set of barstar suppressors has been identified for barnase mutants with substitutions in two amino acid positions (residues 102 and 59), which are critically involved in both RNase activity and barstar binding. The mutations selected as suppressors could not have been predicted on the basis of the known protein structures. The single barstar mutation with the highest information content for inhibition of barnase (H102K) has the substitution Y30W. The reduction in binding caused by the R59E mutation in barnase can be partly reversed by changing Glu-76 of barstar, which forms a salt bridge with the Arg-59 in the wild-type complex, to arginine, thus completing an interchange of the two charges.

Least activation path for protein folding: investigation of staphylococcal nuclease folding by stopped-flow circular dichroism.

Is the pathway of protein folding determined by the relative stability of folding intermediates, or by the relative height of the activation barriers leading to these intermediates? This is a fundamental question for resolving the Levinthal paradox, which stated that protein folding by a random search mechanism would require a time too long to be plausible. To answer this question, we have studied the guanidinium chloride (GdmCl)-induced folding/unfolding of staphylococcal nuclease [(SNase, formerly EC 3.1.4.7; now called microbial nuclease or endonuclease, EC 3.1.31.1] by stopped-flow circular dichroism (CD) and differential scanning microcalorimetry (DSC). The data show that while the equilibrium transition is a quasi-two-state process, kinetics in the 2-ms to 500-s time range are triphasic. Data support the sequential mechanism for SNase folding: U3 <--> U2 <--> U1 <--> N0, where U1, U2, and U3 are substates of the unfolded protein and N0 is the native state. Analysis of the relative population of the U1, U2, and U3 species in 2.0 M GdmCl gives delta-G values for the U3 --> U2 reaction of +0.1 kcal/mol and for the U2 --> U1 reaction of -0.49 kcal/mol. The delta-G value for the U1 --> N0 reaction is calculated to be -4.5 kcal/mol from DSC data. The activation energy, enthalpy, and entropy for each kinetic step are also determined. These results allow us to make the following four conclusions. (i) Although the U1, U2, and U3 states are nearly isoenergetic, no random walk occurs among them during the folding. The pathway of folding is unique and sequential. In other words, the relative stability of the folding intermediates does not dictate the folding pathway. Instead, the folding is a descent toward the global free-energy minimum of the native state via the least activation path in the vast energy landscape. Barrier avoidance leads the way, and barrier height limits the rate. Thus, the Levinthal paradox is not applicable to the protein-folding problem. (ii) The main folding reaction (U1 --> N0), in which the peptide chain acquires most of its free energy (via van der Waals' contacts, hydrogen bonding, and electrostatic interactions), is a highly concerted process. These energy-acquiring events take place in a single kinetic phase. (iii) U1 appears to be a compact unfolded species; the rate of conversion of U2 to U1 depends on the viscosity of solution. (iv) All four relaxation times reported here depend on GdmCl concentrations: it is likely that none involve the cis/trans isomerization of prolines. Finally, a mechanism is presented in which formation of sheet-like chain conformations and a hydrophobic condensation event precede the main-chain folding reaction.

Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.

Changing nucleosome positions through modification of the DNA rotational information.

The effects of the rotational information of DNA in determining the in vitro localization of nucleosomal core particles (ncps) have been studied in the Saccharomyces cerevisiae 5S rRNA repeat gene. We have altered the distribution of the phased series of flexibility signals present on this DNA by inserting a 25-bp tract, and we have analyzed the effects of this mutation on the distribution and on the frequencies of ncps, as compared with the wild type and a reference 21-bp insertion mutant. The variation of the standard free energy of nucleosome reconstitution was determined. The results show that the DNA rotational information is a major determinant of ncps positioning, define how many rotationally phased signals are required for the formation of a stable particle, and teach how to modify their distribution through the alteration of the rotational signals.

Simple model of protein folding kinetics.

A simple model of the kinetics of protein folding is presented. The reaction coordinate is the "correctness" of a configuration compared with the native state. The model has a gap in the energy spectrum, a large configurational entropy, a free energy barrier between folded and partially folded states, and a good thermodynamic folding transition. Folding kinetics is described by a master equation. The folding time is estimated by means of a local thermodynamic equilibrium assumption and then is calculated both numerically and analytically by solving the master equation. The folding time has a maximum near the folding transition temperature and can have a minimum at a lower temperature.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Effect of lactose solid-state on the aerosolization performance of drug-carrier mixtures

Lactose, in particular α-lactose monohydrate, is the most used carrier for inhalation. Its surface and solid-state properties are of paramount importance in determining drug aerosolization performance. However, these properties may be altered by processing, such as micronization, thus affecting the product performance and stability. The present research project focused on the study of the effect of lactose solid-state on the aerosolization performance of drug-carrier mixtures, giving particular attention to the impact of micronization on lactose physico-chemical properties. The formation of a fraction of hygroscopic anhydrous α-lactose, rather than amorphous lactose, as a consequence of the mechanical stress stemming from micronization was evidenced by 1H NMR, XRPD and DSC analyses performed on samples of micronized lactose. The development of a new DVS method capable to identify and quantify different forms of α-lactose (hygroscopic anhydrous, stable anhydrous and amorphous), even simultaneously present in the same sample, confirmed the results obtained with the above-mentioned techniques. The influence of lactose solid-state on drug respirability was then evaluated through the preparation and in vitro aerodynamic assessment of ternary and binary mixtures containing two different drugs. In particular, the use, as carriers, of anhydrous forms of α-lactose in place of the conventional α-lactose monohydrate resulted in significantly improved respirability in the case of salbutamol sulphate and poorer performance in the case of budesonide. In an attempt to rationalize the obtained results, IGC was selected as a tool to investigate possible variations in the surface energy of the studied lactose carriers and APIs. A direct correlation between the total surface free energy of lactose carriers and drug respirability was not found. However, salbutamol sulphate and budesonide exhibited different specific surface free energy, to which the difference in the aerosolization performance may be, at least in part, ascribed.

Propriedades superficiais de filmes à base de gelatina

O objetivo do presente trabalho foi caracterizar as propriedades superficiais de filmes à base de gelatina. Para o qual foram elaborados filmes de: (i) Gelatina plastificado com glicerol (G) (gelatina: 5 g/100 g SFF; glicerol: 30 g/100 g de gelatina), (ii) Gelatina reforçado com montmorilhonita (G/MMT) (gelatina: 5 g/100 g SFF; glicerol: 30 g/100 g de gelatina; MMT: 5 g/100 g de gelatina) e Gelatina plastificado com citrato de acetiltributila (G/ATB) (gelatina: 5 g/100 g SFF; ATB: 50 g/100 de gelatina; lecitina de soja: 60 g/100 g de ATB; etanol: 20 g/100 g SFF). Os filmes foram produzidos mediante o uso de um aplicador automático de filmes \"Spreading\". Logo, os filmes foram submetidos a testes para determinação da espessura, umidade e propriedades óticas (brilho, cor e opacidade). Também foi caracterizada a microestrutura por microscopia eletrônica de varredura (MEV) e microscopia de força atômica (AFM); às imagens obtidas por MEV foi aplicado um analise de imagem mediante o programa Image J, para obter o valor da dimensão fractal (DF). Depois foram caracterizadas as propriedades superficiais de ângulo de contato (AC), molhabilidade ou coeficiente de espalhamento (Se), e energia livre superficial (ELS) mediante a medida do ângulo de contato pelo método da gota séssil (água: 5 µL e 1-Bromonaftaleno: 3 µL). Para o cálculo da ELS também foi aplicado o método de Owens-Wendt. Estas caracterizações foram feitas em ambos os lados do filme, lado ar e lado placa. A natureza do filme de G/ATB influenciou na umidade e as propriedades óticas, enquanto que os filmes de G e G/MMT apresentaram características similares. Em relação à microestrutura e rugosidade, o filme de G apresentou a superfície mais homogênea e lisa, contrario ao observado no filme de G/MMT, que apresentou a maior rugosidade seguida do filme de G/ATB. Foi observado que houve uma relação entre os valores de rugosidade e DF. De acordo com o valor do AC, os filmes apresentaram um caráter hidrofóbico, pois seus valores foram superiores a 65° (em ambos os lados dos filmes), na seguinte ordem: G/MMT > G > G/ATB; sendo que o Se seguiu a mesma tendência. Cabe mencionar também que não foi encontrada uma correlação significativa entre os valores de AC e rugosidade. Em função dos valores de AC, Se e ELS (especificamente a componente polar), o filme de G/ATB apresentou o menor caráter hidrofóbico, pois apresentou menores valores de AC e maiores valores de Se em comparação com os outros dois filmes. Os valores da componente polar da G/ATB foram os maiores, explicando de melhor maneira o caráter menos hidrofóbico deste filme. Pode-se concluir que os filmes à base de gelatina elaborados no presente trabalho têm propriedades hidrofóbicas (AC>65°), sendo a G/MMT o filme com melhores características hidrofóbicas.

Tethered Monte Carlo: computing the effective potential without critical slowing down

We present Tethered Monte Carlo, a simple, general purpose method of computing the effective potential of the order parameter (Helmholtz free energy). This formalism is based on a new statistical ensemble, closely related to the micromagnetic one, but with an extended configuration space (through Creutz-like demons). Canonical averages for arbitrary values of the external magnetic field are computed without additional simulations. The method is put to work in the two-dimensional Ising model, where the existence of exact results enables us to perform high precision checks. A rather peculiar feature of our implementation, which employs a local Metropolis algorithm, is the total absence, within errors, of critical slowing down for magnetic observables. Indeed, high accuracy results are presented for lattices as large as L = 1024.

Tethered Monte Carlo: computing the effective potential without critical slowing down

We present Tethered Monte Carlo, a simple, general purpose method of computing the effective potential of the order parameter (Helmholtz free energy). This formalism is based on a new statistical ensemble, closely related to the micromagnetic one, but with an extended configuration space (through Creutz-like demons). Canonical averages for arbitrary values of the external magnetic field are computed without additional simulations. The method is put to work in the two-dimensional Ising model, where the existence of exact results enables us to perform high precision checks. A rather peculiar feature of our implementation, which employs a local Metropolis algorithm, is the total absence, within errors, of critical slowing down for magnetic observables. Indeed, high accuracy results are presented for lattices as large as L = 1024.

First-order transition in a three-dimensional disordered system

We present the first detailed numerical study in three dimensions of a first-order phase transition that remains first order in the presence of quenched disorder (specifically, the ferromagnetic-paramagnetic transition of the site-diluted four states Potts model). A tricritical point, which lies surprisingly near the pure-system limit and is studied by means of finite-size scaling, separates the first-order and second-order parts of the critical line. This investigation has been made possible by a new definition of the disorder average that avoids the diverging-variance probability distributions that plague the standard approach. Entropy, rather than free energy, is the basic object in this approach that exploits a recently introduced microcanonical Monte Carlo method.

First Order Phase Transition in a 3D disordered system

We present a detailed numerical study on the effects of adding quenched impurities to a three dimensional system which in the pure case undergoes a strong first order phase transition (specifically, the ferromagnetic/paramagnetic transition of the site-diluted four states Potts model). We can state that the transition remains first-order in the presence of quenched disorder (a small amount of it) but it turns out to be second order as more impurities are added. A tricritical point, which is studied by means of Finite-Size Scaling, separates the first-order and second-order parts of the critical line. The results were made possible by a new definition of the disorder average that avoids the diverging-variance probability distributions that arise using the standard methodology. We also made use of a recently proposed microcanonical Monte Carlo method in which entropy, instead of free energy, is the basic quantity.

Critical behavior of su(1|1) supersymmetric spin chains with long-range interactions

We introduce a general class of su(1|1) supersymmetric spin chains with long-range interactions which includes as particular cases the su(1|1) Inozemtsev (elliptic) and Haldane-Shastry chains, as well as the XX model. We show that this class of models can be fermionized with the help of the algebraic properties of the su(1|1) permutation operator and take advantage of this fact to analyze their quantum criticality when a chemical potential term is present in the Hamiltonian. We first study the low-energy excitations and the low-temperature behavior of the free energy, which coincides with that of a (1+1)-dimensional conformal field theory (CFT) with central charge c=1 when the chemical potential lies in the critical interval (0,E(π)), E(p) being the dispersion relation. We also analyze the von Neumann and Rényi ground state entanglement entropies, showing that they exhibit the logarithmic scaling with the size of the block of spins characteristic of a one-boson (1+1)-dimensional CFT. Our results thus show that the models under study are quantum critical when the chemical potential belongs to the critical interval, with central charge c=1. From the analysis of the fermion density at zero temperature, we also conclude that there is a quantum phase transition at both ends of the critical interval. This is further confirmed by the behavior of the fermion density at finite temperature, which is studied analytically (at low temperature), as well as numerically for the su(1|1) elliptic chain.

The equilibrium between carbon oxysulfide, carbon monoxide and sulfur ...

Thesis t.-p. pasted over the cover of the issue reprinted from the Journal of the American chemical society, vol. XXXVII, no. 9, September, 1915, which has title: The equilibrium between carbon oxysulfide, carbon monoxide and sulfur, by Gilbert N. Lewis and William N. Lacey.

The effects of parabens on the mechanosensitive channels of E. coli

Parabens are alkyl esters of p-hydroxybenzoic acid used as preservatives in a wide range of food, pharmaceutical, and cosmetic products (Soni et al. Food Chem. Toxicol. 39:513-532, 2001). Despite their common use for over 50 years, their mechanism of action is still unclear. In this study we examined the effects of ethyl and propyl paraben, on gating of the E. coli mechanosensitive channel of large conductance (MscL) reconstituted into azolectin liposomes. We found that propyl and ethyl paraben spontaneously activate MscL. Moreover, the addition of propyl paraben caused an increase in MscL activity and the lowering Of P-1/2, the pressure at which the MscL was opened 50% of the time, the AGO, the free energy required to open the MscL, and the parameter a, which describes the channel sensitivity to pressure. In addition, in silico studies showed that propyl paraben binds to the channel gate of the MscL. The mechanosensitive channel of small conductance was also found to be spontaneously activated by parabens. In summary, our study indicates that one of the previously unidentified mechanisms of action of parabens as antimicrobial agents is via an interaction with the mechanosensitive channels to upset the osmotic gradients in bacteria.