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Proteolytic activity of heterogeneous Zr-based nanozymes is a promising technology for the development of selective protein cleavage protocols, which are pivotal in modern proteomics. Here, we repo...

Despite the enormous importance of insoluble proteins in biological processes, their structural investigation remains a challenging task. The development of artificial enzyme-like catalysts would greatly facilitate the elucidation of their structure since currently used enzymes in proteomics largely lose activity in the presence of surfactants, which are necessary to solubilize insoluble proteins. In this study, the hydrolysis of a fully insoluble protein by polyoxometalate complexes as artificial proteases in surfactant solutions is reported for the first time. The hydrolysis of zein as a model protein was investigated in the presence of Zr(IV) and Hf(IV) substituted Keggin-type polyoxometalates (POMs), (Et2 NH2 )10 [M(α-PW11 O39 )2 ] (M = Zr or Hf), and different concentrations of the anionic surfactant sodium dodecyl sulfate (SDS). Selective hydrolysis of the protein upon incubation with the catalyst was observed, and the results indicate that the hydrolytic selectivity and activity of the POM catalysts strongly depends on the concentration of surfactant. The molecular interactions between the POM catalyst and zein in the presence of SDS were explored using a combination of spectroscopic techniques which indicated competitive binding between POM and SDS towards the protein. Furthermore, the formation of micellar superstructures in ternary POM/surfactant/protein solutions has been confirmed by conductivity and Dynamic Light Scattering measurements. ispartof: CHEMISTRY-A EUROPEAN JOURNAL vol:28 issue:8 ispartof: location:Germany status: published

Certain pairs of paramagnetic species generated under conservation of total spin angular momentum are known to undergo magnetosensitive processes. Two prominent examples of systems exhibiting these so-called magnetic field effects (MFEs) are photogenerated radical pairs created from either singlet or triplet molecular precursors, and pairs of triplet states generated by singlet fission. Here, we showcase confocal microscopy as a powerful technique for the investigation of such phenomena. We first characterise the instrument by studying the field-sensitive chemistry of two systems in solution: radical pairs formed in a cryptochrome protein and the flavin mononucleotide/hen egg-white lysozyme model system. We then extend these studies to single crystals. Firstly, we report temporally and spatially resolved MFEs in flavin-doped lysozyme single crystals. Anisotropic magnetic field effects are then reported in tetracene single crystals. Finally, we discuss the future applications of confocal microscopy for the study of magnetosensitive processes with a particular focus on the cryptochrome-based chemical compass believed to lie at the heart of animal magnetoreception., Confocal microscopy is showcased as a powerful technique for the measurement of spatiotemporally-resolved magnetic field effects in both solutions and single crystals.

The development of artificial proteases is challenging, but important for many applications in modern proteomics and biotechnology. The hydrolysis of hydrophobic or unstructured proteins is particularly difficult due to their poor solubility, which often requires the presence of surfactants. Herein, it is shown that a zirconium(IV)-substituted Keggin polyoxometalate (POM), (Et2 NH2 )10 [Zr(α-PW11 O39 )2 ] (1), is able to selectively hydrolyze β-casein, which is an intrinsically unstructured protein at pH 7.4 and 60 °C. Four surfactants (sodium dodecyl sulfate (SDS), N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (ZW3-12), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), and polyethylene glycol tert-octylphenyl ether (TX-100)), which differ in the nature of their polar groups, were investigated for their role in influencing the selectivity and efficiency of protein hydrolysis. Under experimental conditions, β-casein forms micellar structures in which the hydrophilic part of the protein is water accessible and able to interact with 1. Identical fragmentation patterns of β-casein in the presence of 1 were observed through SDS poly(acrylamide) gel electrophoresis both in the presence and absence of surfactants, but the rate of hydrolysis varied, depending on the nature of surfactant. Whereas TX-100 surfactant, which has a neutral polar head, caused only a slight decrease in the hydrolysis rate, stronger inhibition was observed in the presence surfactants with charges in their polar heads (CHAPS, ZW3-12, SDS). These results were consistent with those of tryptophan fluorescencequenching studies, which showed that the binding between β-casein and 1 decreased with increasing repulsion between the POM and the polar heads of the surfactants. In all cases, the micellar structure of β-casein was not significantly affected by the presence of POM or surfactants, as indicated by circular dichroism spectroscopy. ispartof: CHEMISTRY-A EUROPEAN JOURNAL vol:26 issue:49 pages:11170-11179 ispartof: location:Germany status: published

Redox reactions between polyoxometalates (POMs) and biologically relevant molecules have been virtually unexplored but are important, considering the growing interest in the biological applications of POMs. In this work we give a detailed account on the redox behavior of CeIV-substituted polyoxometalates (CeIV-POMs) toward a range of amino acids and peptides. CeIV-POMs have been shown to act as artificial proteases that promote the selective hydrolysis of peptide bonds. In presence of a protein, a concomitant reduction of CeIV to CeIII ion is frequently observed, leading us to examine the origins of this redox reaction by first using amino acid building blocks as simple models. Among all of the examined amino acids, cysteine (Cys) showed the highest activity in reducing CeIV-POMs to CeIII-POMs, followed by the aromatic amino acids tryptophan (Trp), tyrosine (Tyr), histidine (His), and phenylalanine (Phe). While the redox reaction with Cys afforded the well-defined product cystine, no oxidation products were detected for the Trp, His, Tyr, and Phe amino acids after their reaction with CeIV-POMs, suggesting a radical pathway in which the solvent likely regenerates the amino acid. In general, the rate of redox reactions increased upon increasing the pD, temperature, and ionic strength of the reaction. Moreover, the redox reaction is highly sensitive to the type of polyoxometalate scaffold, as complexation of CeIV to a Keggin (K) or Wells-Dawson (WD) polyoxotungstate anion resulted in a large difference in the rate of redox reaction for both Cys and aromatic amino acids. The reduction of CeIVK was at least 1 order of magnitude faster in comparison to CeIVWD, in accordance with the higher redox potential of CeIVK in comparison to CeIVWD. The reaction of CeIVPOMs with a range of peptides containing redox-active amino acids revealed that the redox reaction is influenced by their coordination mode with CeIV ion, but in all examined peptides the redox reaction is favored in comparison to the hydrolytic cleavage of the peptide bond. ispartof: INORGANIC CHEMISTRY vol:59 issue:15 pages:10569-10577 ispartof: location:United States status: published

The physicochemical effects of the solvent DMSO on protein confirmation remain enigmatic despite its diverse applications in the proteomics field. Many attempts to understand the effects of DMSO have focused on the unfolding of alpha-helical-rich proteins; however, the cause of the profound stability of beta-sheets in DMSO remains to be elucidated. Therefore, we designed an octapeptide as a beta-hairpin fold to serve as a model beta-sheet; we then performed combined experimental and simulation studies to investigate the effects of DMSO on the structure and stability of the beta-hairpin. We compared the results of the designed octapeptide with its cognate polyalanine model to directly analyze the side chain interactions responsible for ordering the octapeptide in a specific conformation. NMR and simulation results established the ordering of the octapeptide as a beta-hairpin fold, while simulations manifested the unfolded conformation of the cognate polyalanine in DMSO. It appears that owing to their weaker dielectric and strong dipolar strengths, DMSO abolishes the alpha-conformation as well as the solvated backbone amidic NH groups through hydrogen bonds; therefore, it destabilizes the intramolecular backbone hydrogen bonds, which leads to the unfolding of polyalanine peptides. Furthermore, our results conform to the possibility that DMSO stabilizes electrostatic and quadrupolar interactions among polar side chain atoms due to its low dielectric strength. Accordingly, we propose that the molecular mechanism of DMSO-induced stabilization of beta-sheets is a combination of polar electrostatic interactions among the side chains and backbone desolvation through bulky side chains, which promotes backbone hydrogen bonding.

Hydrolysis of Transferin (Tf), a glycoprotein consisting of 679 amino acids and three glycan chains, has been examined in the presence of Ce(IV)-substituted Keggin polyoxometalate [CeIV(α-PW11O39)2]10− (Ce-K POM). Incubation at pH = 7.4 and at 37 °C resulted in selective fragmentation of the Tf after 24 h, which was followed by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE). After 5 days of incubation nearly 90% of Tf was hydrolyzed, giving 9 fragments with molecular weight (Mw) in the range between 13.7 and 69.5 kDa. Under the same conditions, the sample of Tf which did not contain the Ce-K POM, showed only 7% of background hydrolysis. The interactions between Ce-K and Tf were studied by tryptophan fluorescence, circular dichroism (CD) and 31P Nuclear magnetic resonance (NMR) spectroscopy. The association constant (Ka) for the interaction was calculated to be 3.2 × 104 M−1 from tryptophan quenching studies. CD spectroscopy revealed that binding of Ce-K to Tf resulted in significant secondary structure changes, mainly affecting the alpha-helical content of the protein. 31P NMR spectroscopy showed that in the presence of the Tf partial reduction of Ce(IV) to Ce(III) occurred, which did not affect the overall structure of the Keggin POM. ispartof: Polyhedron vol:170 pages:570-575 status: published

The hydrolysis of the iron-binding blood plasma glycoprotein transferrin (Tf) has been examined at pH = 7.4 in the presence of a series of Zr-substituted polyoxometalates (Zr-POMs) including Keggin (Et2NH2)10[Zr(PW11O39)2]∙7H2O (Zr-K 1:2), (Et2NH2)8[{&alpha, PW11O39Zr-(&mu, OH) (H2O)}2]∙7H2O (Zr-K 2:2), Wells-Dawson K15H[Zr(&alpha, 2-P2W17O61)2]&middot, 25H2O (Zr-WD 1:2), Na14[Zr4(&alpha, P2W16O59)2(&mu, 3-O)2(&mu, OH)2(H2O)4]&middot, 57H2O (Zr-WD 4:2) and Lindqvist (Me4N)2[ZrW5O18(H2O)3] (Zr-L 1:1), (nBu4N)6[(ZrW5O18(&mu, &ndash, OH))2]∙2H2O (Zr-L 2:2)) type POMs. Incubation of transferrin with Zr-POMs resulted in formation of 13 polypeptide fragments that were observed on sodium dodecyl sulfate poly(acrylamide) gel electrophoresis (SDS-PAGE), but the hydrolysis efficiency varied depending on the nature of Zr-POMs. Molecular interactions between Zr-POMs and transferrin were investigated by using a range of complementary techniques such as tryptophan fluorescence, circular dichroism (CD), 31P-NMR spectroscopy, in order to gain better understanding of different efficiency of investigated Zr-POMs. A tryptophan fluorescence quenching study revealed that the most reactive Zr-WD species show the strongest interaction toward transferrin. The CD results demonstrated that interaction of Zr-POMs and transferrin in buffer solution result in significant secondary structure changes. The speciation of Zr-POMs has been followed by 31P-NMR spectroscopy in the presence and absence of transferrin, providing insight into stability of the catalysts under reaction condition.

X-ray crystallography reveals how a calixarene can bind to dimethyllysine to form a complex with features similar to the aromatic cage motif of a chromodomain bound to a histone tail., Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx4) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH3 + to Lys-NH(Me2)+. Of the six possible dimethyllysine sites, sclx4 selected Lys116-Me2 and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me2 residues to form cation–π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me2 in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.

This article covers recent developments in the design and application of activity-based probes (ABPs) for glycosidases, with emphasis on the different enzymes involved in metabolism of glucosylceramide in humans. Described are the various catalytic reaction mechanisms employed by inverting and retaining glycosidases. An understanding of catalysis at the molecular level has stimulated the design of different types of ABPs for glycosidases. Such compounds range from (1) transition-state mimics tagged with reactive moieties, which associate with the target active site-forming covalent bonds in a relatively nonspecific manner in or near the catalytic pocket-to (2) enzyme substrates that exploit the catalytic mechanism of retaining glycosidase targets to release a highly reactive species within the active site of the enzyme, to (3) probes based on mechanism-based, covalent, and irreversible glycosidase inhibitors. Some applications in biochemical and biological research of the activity-based glycosidase probes are discussed, including specific quantitative visualization of active enzyme molecules in vitro and in vivo, and as strategies for unambiguously identifying catalytic residues in glycosidases in vitro.

Amyloid fibrils have recently gained a lot of attention due to their morphology, functionality and mechanical strength, allowing for their application in nanofiber-based materials, biosensors, bioactive membranes and tissue engineering scaffolds. The in vitro production of amyloid fibrils is still a slow process, thus hampering the massive production of nanofibers and its consequent use. This work presents a new and faster (2-3 h) fibrillation method for hen egg white lysozyme (HEWL) using a deep eutectic solvent based on cholinium chloride and acetic acid. Nanofibers with dimensions of 0.5-1 mu m in length and 0.02-0.1 mu m in thickness were obtained. Experimental variables such as temperature and pH were also studied, unveiling their influence in fibrillation time and nanofibers morphology. These results open a new scope for protein fibrillation into nanofibers with applications ranging from medicine to soft matter and nanotechnology. (C) 2016 Elsevier B.V. All rights reserved.

The peculiar chemical properties of metal-based drugs impart innovative pharmacological profiles to this class of therapeutic and diagnostic agents, most likely in relation to novel molecular mechanisms still poorly understood. However, inorganic drugs have been scarcely considered for medicinal applications with respect to classical organic compounds due to the prejudice of the relevant toxic effects evidenced in certain cases. Thus, the development of improved metallodrugs requires clearer understanding of their physiological processing and molecular basis of actions. Among the various issues in the area of medicinal inorganic chemistry, the possibility of target elucidation is essential for the identification of new therapeutic applications for metal compounds or as molecular biological tools. Here we present the results of our recent research in the field, which in our opinion constitute the basis of a systematic and interdisciplinary approach to address some of the critical issues in the study of the molecular mechanisms of metallodrugs’ action via the implementation of high-resolution biophysical techniques coupled with more pharmacological methods.

The peculiar chemical properties of metal-based drugs impart innovative pharmacological profiles to this class of therapeutic and diagnostic agents, most likely in relation to novel molecular mechanisms still poorly understood. However, inorganic drugs have been scarcely considered for medicinal applications with respect to classical organic compounds due to the prejudice of the relevant toxic effects evidenced in certain cases. Thus, the development of improved metallodrugs requires clearer understanding of their physiological processing and molecular basis of actions. Among the various issues in the area of medicinal inorganic chemistry, the possibility of target elucidation is essential for the identification of new therapeutic applications for metal compounds or as molecular biological tools. Here we present the results of our recent research in the field, which in our opinion constitute the basis of a systematic and interdisciplinary approach to address some of the critical issues in the study of the molecular mechanisms of metallodrugs' action via the implementation of high-resolution biophysical techniques coupled with more pharmacological methods. (C) 2011 Elsevier Inc. All rights reserved.

In this paper, we studied the interaction between human unstimulated saliva and lysozyme-stabilized oil-in-water emulsions (10 wt/wt% oil phase, 10 mM NaCl, pH 6.7), to reveal the driving force for flocculation of these emulsions. Confocal scanning laser microscopy (CSLM) showed formation of complexes between salivary proteins and lysozyme adsorbed at the oil-water interface and lysozyme in solution as well. To assess the electrostatic nature of the interaction in emulsion/saliva mixtures, laser-diffraction and rheological measurements were conducted in function of the ionic strength by adding NaCl to the mixture in the range between 0 and 168 mM. Increasing the ionic strength reduced the ability of saliva to induce emulsion flocculation as shown by the decreased floc size and the effect on the viscosity. Turbidity experiments with varying pH (3-7) and ionic strength also showed decreased complex formation in mixtures between saliva and lysozyme in solution upon NaCl addition up to 200 mM. Decreasing the pH increased the turbidity, in line with the increase of the positive net charge on the lysozyme molecule. We conclude that electrostatic attraction is the main driving force for complex formation between saliva components and lysozyme adsorbed at the oil droplets and in solution. (c) 2007 Elsevier Inc. All rights reserved.

A mixture of 4-chloro-1-butanol and 2,2,2-Trifluoroethanol (TFE) has been used to generate Molten globule (MG) state of structurally homologous but functionally different proteins bovine alpha-lactalbumin and hen egg-white lysozyme. The thermal denaturation was done using UV-Visible spectroscopy. From UV-Visible profile, thermal transition was not observed beyond a particular concentration. There was an indication of molten globule state in case of alpha-lactalbumin from circular dichroism experiments. By intrinsic tryptophan fluorescence, acrylamide and potassium iodide quenching, 8-anilino-naphthalene sulfonic acid (ANS) binding and energy transfer studies the presence of molten globule state was confirmed. Quantitative characterization of MG state and determining the binding thermodynamics of ANS to the MG state was done using Isothermal Titration Calorimetry (ITC). Results show that alpha-lactalbumin exists in MG state at a particular concentration but lysozyme does not show features of MG state.

In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.

The incorporation of impurities during protein crystallization is one of the main obstacles that prevents the growth of high quality crystals. Mass transport has been shown to affect the incorporation of impurities. Here we used a special growth configuration that enables the simultaneous investigation of the two main means of mass transport, diffusion and convection, under otherwise identical conditions. Two polymorphic forms of hen egg-white lysozyme were crystallized using this configuration in the presence of different types of impurities at various degrees of contamination. We found that even in the presence of impurities that are not easily segregated, the diffraction quality of crystals grown under diffusion-limited conditions is better than that of those grown in the presence of natural convection. The results also reveal a significant difference in impurity uptake for the different polymorphic forms of the same protein. The combined results show that also in the presence of large fractions of impurities, the more perfect crystals grow when the rate of accretion of molecules is slow and orderly, as accomplished under diffusion-limited conditions.

This article covers recent developments in the design and application of activity-based probes (ABPs) for glycosidases, with emphasis on the different enzymes involved in metabolism of glucosylceramide in humans. Described are the various catalytic reaction mechanisms employed by inverting and retaining glycosidases. An understanding of catalysis at the molecular level has stimulated the design of different types of ABPs for glycosidases. Such compounds range from (1) transition-state mimics tagged with reactive moieties, which associate with the target active site-forming covalent bonds in a relatively nonspecific manner in or near the catalytic pocket-to (2) enzyme substrates that exploit the catalytic mechanism of retaining glycosidase targets to release a highly reactive species within the active site of the enzyme, to (3) probes based on mechanism-based, covalent, and irreversible glycosidase inhibitors. Some applications in biochemical and biological research of the activity-based glycosidase probes are discussed, including specific quantitative visualization of active enzyme molecules in vitro and in vivo, and as strategies for unambiguously identifying catalytic residues in glycosidases in vitro.

This article covers recent developments in the design and application of activity-based probes (ABPs) for glycosidases, with emphasis on the different enzymes involved in metabolism of glucosylceramide in humans. Described are the various catalytic reaction mechanisms employed by inverting and retaining glycosidases. An understanding of catalysis at the molecular level has stimulated the design of different types of ABPs for glycosidases. Such compounds range from (1) transition-state mimics tagged with reactive moieties, which associate with the target active site—forming covalent bonds in a relatively nonspecific manner in or near the catalytic pocket—to (2) enzyme substrates that exploit the catalytic mechanism of retaining glycosidase targets to release a highly reactive species within the active site of the enzyme, to (3) probes based on mechanism-based, covalent, and irreversible glycosidase inhibitors. Some applications in biochemical and biological research of the activity-based glycosidase probes are discussed, including specific quantitative visualization of active enzyme molecules in vitro and in vivo, and as strategies for unambiguously identifying catalytic residues in glycosidases in vitro.

This article covers recent developments in the design and application of activity-based probes (ABPs) for glycosidases, with emphasis on the different enzymes involved in metabolism of glucosylceramide in humans. Described are the various catalytic reaction mechanisms employed by inverting and retaining glycosidases. An understanding of catalysis at the molecular level has stimulated the design of different types of ABPs for glycosidases. Such compounds range from (1) transition-state mimics tagged with reactive moieties, which associate with the target active site-forming covalent bonds in a relatively nonspecific manner in or near the catalytic pocket-to (2) enzyme substrates that exploit the catalytic mechanism of retaining glycosidase targets to release a highly reactive species within the active site of the enzyme, to (3) probes based on mechanism-based, covalent, and irreversible glycosidase inhibitors. Some applications in biochemical and biological research of the activity-based glycosidase probes are discussed, including specific quantitative visualization of active enzyme molecules in vitro and in vivo, and as strategies for unambiguously identifying catalytic residues in glycosidases in vitro.

The temperature dependence of the excess heat capacity and evaluation of thermodynamic parameters of bovine cr-lactalbumin has been studied by high-sensitivity micro differential scanning calorimetry in the presence of 4-chlorobutan-1-ol, n-butanol, 3-chloropropan-1-ol, 3-chloropropan-1,2-diol, propan-1,2-diol, n-propanol, 2,2,2-trifluoroethanol, and ethanol at neutral pH. The chlorosubstituted alcohols are observed to be more effective destabilisers of a-lactalbumin compared with their normal alcohols in the order: 4-chlorobutan-1-ol > n-butanol > 3-chloropropan-1-ol > n-propanol > 2,2,2-trifluorethanol > 3-chloropropan-1,2-diol > ethanol > propan-1,2-diol. A reversible two-state approximation for the unfolding of the protein has been shown in the absence and presence of these alcohols. A second, smaller, endothermic transition, 23 degrees C beyond the main endotherm was observed only in the presence of 0.125 to 0.250 mol dm(-3) 3-chloropropan-1-ol. Concentrations higher than 25 mmol dm(-3) 4-chlorobutan-1-ol resulted in total loss of an observable endotherm. Thermal destabilisation of the protein in these solvent systems is explained on the basis of competing patterns of interactions of the cosolutes with the native versus unfolded states of the protein during the native reversible arrow denatured reaction. These results are supported by intrinsic fluorescence, energy transfer and UV difference measurements.

A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The ''essential dynamics'' procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins.

A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The ''essential dynamics'' procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins.

After an historical introduction and justification of the importance of proteins (as well as other macromolecules or macromolecular assemblies of biological origin) in modern biology but also in physics, this review presents the state of the field of macromolecular crystallogenesis. The basic questions underlying the crystallization of macromolecules will be addressed and discussed in a first part. The still unsolved problems are highlighted. This section also discusses the methodological approaches that can be used. In the second part, some of the recent achievements in the field are presented. We show how physical methods have contributed to a deeper understanding of protein crystallization. Emphasis is given to the parameter microgravity, since the projects concerning crystallizations in this environment have stimulated the physico-chemical research in the field. Finally, the future perspectives are outlined.

The interaction of hen egg white lysozyme (HEWL) with Na- and Cs-exchanged saponite was investigated using sorption, structural, and spectroscopic methods as a model system to study clay-protein interactions. HEWL sorption to Na- and Cs-saponite was determined using the bicinchoninic acid (BCA) assay, thermogravimetric analysis, and C and N analysis. For Na-saponite, the TGA and elemental analysis-derived sorption maximum was 600 mg/g corresponding to a surface coverage of 0.85 ng/mm(2) with HEWL occupying 526 m(2)/g based on a cross-sectional area of 13.5 nm(2)/molecule. HEWL sorption on Na-saponite was accompanied by the release of 9.5 Na(+) ions for every molecule of HEWL sorbed consistent with an ion exchange mechanism between the positively charged HEWL (IEP 11) and the negatively charged saponite surface. The d-spacing of the HEWL-Na-saponite complex increased to a value of 4.4 nm consistent with the crystallographic dimensions of HEWL of 3 × 3 × 4.5 nm. In the case of Cs-saponite, there was no evidence of interlayer sorption; however, sorption of HEWL to the "external" surface of Cs-saponite showed a high affinity isotherm. FTIR and Raman analysis of the amide I region of the HEWL-saponite films prepared from water and D(2)O showed little perturbation to the secondary structure of the protein. The overall hydrophilic nature of the HEWL-Na-saponite complex was determined by water vapor sorption measurements. The clay retained its hydrophilic character with a water content of 18% at high humidity corresponding to 240 H(2)O molecules per molecule of HEWL.

International audience; Understanding the driving forces governing protein assembly requires the characterization of interactions at molecular level. We focus on two homologous oppositely charged proteins, lysozyme and α-lactalbumin, which can assemble into microspheres. The assembly early steps were characterized through the identification of interacting surfaces monitored at residue level by NMR chemical shift perturbations by titrating one 15N-labeled protein with its unlabeled partner. While α-lactalbumin has a narrow interacting site, lysozyme has interacting sites scattered on a broad surface. The further assembly of these rather unspecific heterodimers into tetramers leads to the establishment of well-defined interaction sites. Within the tetramers, most of the electrostatic charge patches on the protein surfaces are shielded. Then, hydrophobic interactions, which are possible because α-lactalbumin is in a partially folded state, become preponderant, leading to the formation of larger oligomers. This approach will be particularly useful for rationalizing the design of protein assemblies as nanoscale devices.View: ACS ActiveView PDF | PDF | PDF w/ Links | Full Text HTMLCiting Articles

This paper describes the preparation and characterization of polymer protein conjugates composed of a synthetic triblock copolymer with a central polypropylene oxide (PPO) block and two terminal polyethylene oxide (PEO) segments, Pluronic F-127, and the antibacterial enzyme lysozyme attached to the telechelic groups of the PEO chains. Covalent conjugation of lysozyme proceeded via reductive amination of aldehyde functionalized PEO blocks (CHO-Pluronic) and the amine groups of the lysine residues in the protein. SDS-PAGE gel electrophoresis together with MALDI-TOF mass spectrometry analysis revealed formation of conjugates of one or two lysozyme molecules per Pluronic polymer chain. The conjugated lysozyme showed antibacterial activity towards Bacillus subtilis. Analysis with a quartz crystal microbalance with dissipation revealed that Pluronic lysozyme conjugates adsorb in a brush conformation on a hydrophobic gold-coated quartz surface. X-ray photoelectron spectroscopy indicated surface coverage of 32% by lysozyme when adsorbed from a mixture of unconjugated Pluronic and Pluronic lysozyme conjugate (ratio 99:1) and of 47% after adsorption of 100% Pluronic-lysozyme conjugates. Thus, bifunctional brushes were created, possessing both anti-adhesive activity due to the polymer brush, combined with the antibacterial activity of lysozyme. The coating having a lower degree of lysozyme coverage proved to be more bactericidal. (C) 2011 Elsevier Ltd. All rights reserved.

The apparent molar volume V2,ϕ, apparent molar isentropic compressibility KS,2,ϕ, and heat of dilution (q) of aqueous glycine, alanine, α-amino butyric acid, valine, leucine, diglycine, triglycine, and hen egg white lysozyme have been determined in aqueous solutions of 3-chloropropano-1-ol and 3-chloropropan-1,2-diol solutions at T = 298.15 K. These data have been used to calculate the infinite dilution standard partial molar volume V 2 , m 0 , partial molar isentropic compressibility K S , 2 , m 0 , and enthalpy of dilution ΔdilH° of the amino acids and peptides in aqueous 3-chloropropano-1-ol and 3-chloropropan-1,2-diol, and the standard partial molar quantities of transfer of the amino acids and peptides to the aqueous alcohol and diol solutions. The linear correlation of V 2 , m 0 for a homologous series of amino acids has been utilized to calculate the contribution of the charged end groups ( NH 3 + , COO - ) , CH2 group and other alkyl chains of the amino acids to the values of V 2 , m 0 . The results on the standard partial molar volumes of transfer, compressibility and enthalpy of dilution from water to aqueous alcohol and diol solutions have been correlated and interpreted in terms of ion–polar, ion–hydrophobic, and hydrophobic–hydrophobic group interactions. The heat of dilution of these amino acids, peptides, and hen egg white lysozyme measured in aqueous solutions of 3-chloropropano-1-ol and 3-chloropropan-1,2-diol by using isothermal titration calorimetry along with the volumetric, compressibility, and calorimetric results on amino acid and peptides have been correlated to understand the nature of interactions operating in these systems.

The application of ion-exchange (IEX) chromatography to protein refolding (IExR) has been successfully proven, as supported by various studies using different model proteins, ion-exchange media and flow configurations. Ion-exchange refolding offers a relatively high degree of process intensification, represented by the possibility of performing protein refolding, product purification and product concentration, in one unit operation. Besides its high degree of process intensification, IExR offers an additional set of key advantages including: spatial isolation of the bound protein molecules and the controllable change in chemical composition using gradients. Despite of the acknowledgement of the former advantages, the lack of mechanistic understanding on how they influence the process performance of the ion-exchange refolding reactor, limits the ability to exploit them in order to optimize the performance of the unit. This paper presents a quantitative analysis that assesses the effect that the spatial isolation and the urea gradient, have on the IExR performance, judged on the basis of the refolding yield (Y(N)) and the fractional mass recovery (f(Prot,Rec)). Additionally, this work discusses the effect of the protein load, the protein loading state (i.e., native, denatured, denatured and reduced (DR)) and the adsorbent type on f(Prot,Rec). The presented work shows: (1) that the protein load has a direct effect on f(Prot,Rec), and the magnitude of this effect depends on the loading state of the protein solution and the adsorbent type; (2) that irrespectively of the type of adsorbent used, the saturation capacity of a denatured protein is less than the native protein and that this difference can be linked to differences in accessible binding surface area; (3) that there is a clear correlation between fractional surface coverage (θ) and f(Prot,Rec), indicating that the former could serve as a good descriptor to assess spatial isolation, and (4) that the urea gradient has a direct link with the variations on the refolding yield, and this link can be quantitatively estimated using as descriptor the urea gradient slope (ξ). Overall, the information provided in this paper aims at the eventual development of rational design or selection strategies of ion-exchange media for the satisfactory and successful refolding of a target protein.

In the present study, the thermal unfolding of lysozyme in D2O and D2O/CH3CH2OD solutions is analyzed by means of FTIR spectroscopy. A detailed investigation of the conformational rearrangement of the protein upon heating is achieved by inspection of the amide bands. The effects of partial and total deuteration on amide groups are also investigated for they suggest important information about exposure to the solvent. Finally, a comparison between the characteristics of the unfolding process of lysozyme in water and in ethanol/water solutions is performed to clarify some misinterpretation about the possible formation of intermediates.

Lactic acid bacteria are of major economic importance, as they occupy a key position in the manufacture of fermented foods. A considerable body of research is currently being devoted to the development of lactic acid bacterial strains with improved characteristics, that may be used to make fermentations pass of more efficiently, or to make new applications possible. Therefore, and because the lactococci are designated 'GRAS' organisms ('generally recognized as safe') which may be used for safe production of foreign proteins, detailed knowledge of homologous and heterologous gene expression in these organisms is desired. An overview is given of our current knowledge concerning gene expression in Lactococcus lactis. A general picture of gene expression signals in L. lactis emerges that shows considerable similarity to those observed in Escherichia coli and Bacillus subtilis. This feature allowed the expression of a number of L. lactis-derived genes in the latter bacterial species. Several studies have indicated, however, that in spite of the similarities, the expression signals from E. coli, B. subtilis and L. lactis are not equally efficient in these three organisms.

Although alcohols are well-known to be protein denaturants when present at high concentrations, their effect on proteins at low concentrations is much less well characterized. In this paper, we present a study of the effects of alcohols on protein stability using Yfh1, the yeast ortholog of the human protein frataxin. Exploiting the unusual property of this protein of undergoing cold denaturation around 0 degrees C without any ad hoc destabilization, we determined the stability curve on the basis of both high and low temperature unfolding in the presence of three commonly used alcohols: trifluoroethanol, ethanol, and methanol. In all cases, we observed an extended temperature range of protein stability as determined by a modest increase of the high temperature of unfolding but an appreciable decrease in the low temperature of unfolding. On the basis of simple thermodynamic considerations, we are able to interpret the literature on the effects of alcohols on proteins and to generalize our findings. We suggest that alcohols, at low concentration and physiological pH, stabilize proteins by greatly widening the range of temperatures over which the protein is stable. Our results also clarify the molecular mechanism of the interaction and validate the current theoretical interpretation of the mechanism of cold denaturation.

Motivation: In the study of the structural flexibility of proteins, crystallographic Debye-Waller factors are the most important experimental information used in the calibration and validation of computational models, such as the very successful elastic network models (ENMs). However, these models are applied to single protein molecules, whereas the experiments are performed on crystals. Moreover, the energy scale in standard ENMs is undefined and must be obtained by fitting to the same data that the ENM is trying to predict, reducing the predictive power of the model. Results: We develop an elastic network model for the whole protein crystal in order to study the influence of crystal packing and lattice vibrations on the thermal fluctuations of the atom positions. We use experimental values for the compressibility of the crystal to establish the energy scale of our model. We predict the elastic constants of the crystal and compare with experimental data. Our main findings are (1) crystal packing modifies the atomic fluctuations considerably and (2) thermal fluctuations are not the dominant contribution to crystallographic Debye-Waller factors. Availability: The programs developed for this work are available as supplementary material at Bioinformatics Online. Contact: hinsen@cnrs-orleans.fr Supplementary information: (1) A full derivation of the normal mode equations in a crystal and in a continuous medium. (2) A movie illustrating the lattice vibrations. Both supplements are available at Bioinformatics Online.

In solution small-angle neutron scattering has been used to study the solvation properties of lysozyme dissolved in water/glycerol mixtures. To detect the characteristics of the protein-solvent interface, 35 different experimental conditions (i.e., protein concentration, water/glycerol fraction in the solvent, content of deuterated compounds) have been considered and a suitable software has been developed to fit simultaneously the whole set of scattering data. The average composition of the solvent in the close vicinity of the protein surface at each experimental condition has been derived. In all the investigated conditions, glycerol resulted especially excluded from the protein surface, confirming that lysozyme is preferentially hydrated. By considering a thermodynamic hydration model based on an equilibrium exchange between water and glycerol from the solvation layer to the bulk, the preferential binding coefficient and the excess solvation number have been estimated. Results were compared with data previously derived for ribonuclease A in the same mixed solvent: even if the investigated solvent compositions were very different, the agreement between data is noticeable, suggesting that a unique mechanism presides over the preferential hydration process. Moreover, the curve describing the excess solvation number as a function of the solvent composition shows the occurrence of a region of maximal hydration, which probably accounts for the changes in protein stability detected in the presence of cosolvents. (c) 2007 American Institute of Physics.

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.

Densities, apparent molar volumes, and surface tension of aqueous 3-chloropropan-1-ol and 3-chloropropan-1,2-diol were determined at temperatures from (283.08 to 308.15) K. The results of the volumetric measurements have been used to calculate the following thermodynamic quantities at T = 298.15 K. For 3-chloropropan-1-ol(aq): V-2,m(o) = (79.79 +/- 0.23) cm(3) . mol(-1); (partial derivative V/(o)(2,m)/partial derivative T)(p) = (10.31 +/- 1.28) . 10(-2) cm(3) . K-1 . mol(-1); (partial derivative(2)V(2,m)(o)/partial derivative T-2)(p) = (4.16 +/- 1.46) . 10(-3) cm(3) . K-2 . mol(-1), and for 3-chloroproan 1,2-diol(aq): V-2,m(o) = (80.62 +/- 0.23) cm(3) . mol(-1); (partial derivative V-2,m(o)/partial derivative T)p = (8.499 +/- 1.080) 10(-2) cm(3) . K-1 . mol(-1); (partial derivative(2)V(2,m)(o)/partial derivative T-2)(p) = (1.610 +/- 0.67) . 10(-3) cm(3) . K-2 . mol(-1). The preferential interaction parameters of the interaction of 3-chloropropan-1-ol and 3-chloropropan-1,2-diol with two structurally homologous proteins then egg-white lysozyme and alpha-lactalbumin) have been calculated by correlating the measured surface tension data to the surface areas of these proteins. The data on the measured apparent molar volumes and surface tension of aqueous 3-chloropropan-1-ol and 3-chlorupropan-1,2-diol, in combination with the thermal denaturation data and surface area values of hen egg-white lysozyme from literature, clearly indicate a parallel trend in changes in the surface tension of water, partial molar volume, and ability to alter the thermal stability of these proteins. (C) 2000

In this study we have investigated the surface rheological properties of oil-water interfaces stabilized by fibrils from lysozyme (long and semi-flexible and short and rigid ones), fibrils from ovalbumin (short and semi-flexible), lysozyme-pectin complexes, or ovalbumin-pectin complexes. We have compared these properties with those of interfaces stabilized by the native proteins. The surface dilatational and surface shear moduli were determined using an automated drop tensiometer and a stress controlled rheometer with biconical disk geometry. Results show that interfaces stabilized by complexes of these proteins with high-methoxyl pectin have higher surface shear and dilatational moduli than interfaces stabilized by the native proteins only. The interfaces stabilized by ovalbumin and lysozyme complexes have comparable shear and dilatational moduli though ovalbumin-pectin complexes are twice as large in radius as lysozyme-pectin complexes. Under most of the experimental conditions, interfaces stabilized by fibrils have the highest surface rheological moduli. The difference between long semi-flexible lysozyme fibrils or short rigid lysozyme fibrils is not pronounced in interfacial dilation rheology but significant in interfacial shear rheology. The complex surface shear moduli of interfaces stabilized by long semi-flexible fibrils are about 10 times higher than those of interfaces stabilized by short rigid fibrils, over a range of bulk concentrations. Interfaces stabilized by short and more flexible ovalbumin fibrils have a significantly higher surface shear modulus than those stabilized by longer and more rigid lysozyme fibrils. This study has shown that the use of such supra-molecular structural building blocks creates a wider range of microstructural features of the interface, with higher surface shear and dilatational moduli and a more complex dependence on strain.

Heavy metals rock! The reactivity of the antimetastatic metallodrug NAMI-A with human carbonic anhydrase II (hCAII) has been investigated using a number of techniques, including X-ray crystallography. The characterization of the interactions between NAMI-A and hCAII provides valuable information on the molecular mechanisms responsible for the activity of this promising anticancer agent.