Native Protein Molecules Research Articles

Impact of nanosilver surface electronic distributions on serum protein interaction and hemocompatibility.

Translation of silver-based nanotechnology "from bench to bedside" requires a deep understanding of the molecular aspects of its biological action, which remains controversial at low concentrations and non-spherical morphologies. Here, we present a hemocompatibility approach based on the effect of the distinctive electronic charge distribution in silver nanoparticles (nanosilver) on blood components. On basis of spectroscopic, volumetric, microscopic, dynamic light scattering measurements, pro-coagulant activity tests and cellular inspection we determine that, at extremely low nanosilver concentrations (0.125 - 2.5 μg mL-1) there is a relevant interaction effect on serum albumin and on red blood cells. The explanation has its origin in the surface charge distribution of nanosilver and their electron-mediated energy transfer mechanism. Prism-shaped nanoparticles, with anisotropic charge distributions, act at the surface level generating a compaction of the native protein molecule, while the spherical nanosilver, by exhibiting isotropic surface charge, generates a polar environment comparable to the solvent. Both morphologies induce aggregation at NPs / BSA ≅ 0.044 molar ratio values without altering the coagulation cascade tests, although the spherical-shaped nanosilver has a negative impact on red blood cells. Overall, our results suggest that the electron distributions of nanosilver, even at extremely low concentrations, are a critical factor influencing the molecular structure of blood proteins and red blood cells' membranes. Isotropic forms of nanosilver should be considered with caution, as they are not always the least harmful.

Co-encapsulation of curcumin and piperine in whey protein isolate fibrils improves their water dispersibility and antioxidant activity

In this study, whey protein isolate (WPI) fibrils prepared by acid heat treatment for different times (5, 10, 15, or 20 h) were used for the co-encapsulation and co-delivery of curcumin (Cur) and piperine (Pip). Co-encapsulation of both nutraceuticals in the fibrils significantly improved their water dispersibility, chemical stability, and antioxidant activity. For instance, the water dispersibility of Cur and Pip in native WPI solutions was around 47.0% and 47.5%, respectively. In contrast, the water dispersibility of the same two nutraceuticals in WPI fibrils (15 h treatment) was 94.3% and 66.6%, respectively. The nutraceutical-loaded WPI fibrils did not undergo significant flocculation or precipitation after 14 d storage at 25 °C. After encapsulation, the DPPH free radical scavenging ability of the Cur-Pip combination experienced a surge, rising from approximately 35.4% to 72.0%. The Stern-Volmer quenching constants (Ksv) of Cur-WPI (3.03 × 104 M−1) and Pip-WPI (7.08 × 104 M−1) were much smaller than those of Cur-WPI fibrils (3.88 × 104–4.69 × 104 M−1) and Pip-WPI fibrils (8.26 × 104–9.41 × 104 M−1), indicating that the nutraceuticals bind stronger to the protein fibrils than to the native protein molecules. In summary, WPI fibrils have the capability to encapsulate, protect, and deliver hydrophobic nutraceuticals, suggesting their suitability for application in functional foods and beverages.

Dynamic Surface Properties of α-Lactalbumin Fibril Dispersions.

The dynamic surface properties of aqueous dispersions of α-lactalbumin (ALA) amyloid fibrils differ noticeably from the properties of the fibril dispersions of other globular proteins. As a result, the protocol of the application of ALA fibrils to form stable foams and emulsions has to be deviate from that of other protein fibrils. Unlike the fibrils of β-lactoglobulin and lysozyme, ALA fibrils can be easily purified from hydrolyzed peptides and native protein molecules. The application of the oscillating barrier method shows that the dynamic surface elasticity of ALA fibril dispersions exceeds the surface elasticity of native protein solutions at pH 2. ALA fibrils proved to be stable at this pH, but the stability breaks at higher pH levels when the fibrils start to release small peptides of high surface activity. As a result, the dynamic surface properties of ALA coincide with those of native protein solutions. The ionic strength strongly influences the adsorption kinetics of both fibril dispersions and native protein solutions but have almost no impact on the structure of the adsorption layers.

Interfacial properties of protein nanofibrils with different morphology prepared using aqueous solvent with ethanol: Part II. Effect of oil phase hydrophobicity

Self assembled β-lactoglobulin nanofibrils of different morphologies (long semi-flexible or short worm-like) were prepared at pH 2 and 85 °C in the aqueous solution containing different amount of ethanol. The effects of fibril morphology and polarity of the hydrophobic sub-phase on the interfacial adsorption kinetics, viscoelasticity, and structuration of the protein fibrils were investigated using dilatational rheology. It was found that the fibrils have three-stage adsorption at all the oil-water interfaces: diffusion-controlled adsorption in early stage, penetration adsorption near the interface and rearrangement within the interface. Diffusion adsorption rate (Kdif) decreases while penetration rate (kads) and rearrangement (kr) increase with increasing oil polarity. The strength and structuration of the interfacical fibril networks decrease with increasing oil polarity. The forces maintaining the stability of the protein fibril interface were mainly hydrophobic interaction. Kdif, kads and kr of the short fibrils are higher than those of the long fibrils due to their smaller size and higher surface hydrophobicity. The long fibril interface displayed strain softening response during both extension and compression, but form stronger interface than short fibrils, and thus demonstrate better foaming and emulsification ability. The short worm-like fibril interface displays strain softening during extension but strain hardening during compression, which is to some degree similar to the behavior of native flexible protein molecules.

Protein adsorption determines pulmonary cell uptake of lipid-based nanoparticles

The inhalable administration of lipid nanoparticles is an effective strategy for localised delivery of therapeutics against various lung diseases. Of this, improved intracellular delivery of pharmaceuticals for infectious disease and cancer management is of high significance. However, the influence of lipid nanoparticle composition and structure on uptake in pulmonary cell lines, especially in the presence of biologically relevant media is poorly understood. Here, the uptake of lamellar (liposomes) versus non-lamellar (cubosomes) lipid nanoparticles in macrophages and lung epithelial cells was quantified and the influence of bronchoalveolar lavage fluid (BALF), containing native pulmonary protein and surfactant molecules is determined. Cubosome uptake in both macrophages and epithelial cells was strongly mediated by a high percentage of molecular function regulatory and binding proteins present within the protein corona. In contrast, the protein corona did not influence the uptake of liposomes in epithelial cells. In macrophages, the proteins mediated a rapid internalisation, followed by exocytosis of liposomes after 6 h incubation. These findings on the influence of biological fluid in regulating lipid nanoparticle uptake mechanisms may guide future development of optimal intracellular delivery systems for therapeutics via the pulmonary route.

Stapled peptides as potential inhibitors of SARS-CoV-2 binding to the hACE2 receptor.

Stapled peptides are synthetic peptidomimetics of bioactive sites in folded proteins which carry chemical links, introduced during peptide synthesis, designed to retain the secondary structure in the native protein molecule. Stapled peptides have been investigated as potential modulators of protein–protein interactions for over two decades. The potential use of stapled peptides as inhibitors of viral entry, and therefore as antiviral therapeutics, has been established for several important viruses causing disease in humans, such as the human immunodeficiency virus type 1 (HIV‐1), respiratory syncytial virus (RSV), and Middle East Respiratory Syndrome (MERS) coronavirus. Several independent research initiatives have investigated the inhibitory effect of stapled peptides on binding of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the causative agent of COVID‐19, to its receptor, angiotensin‐converting‐enzyme 2 (ACE2). These stapled peptides, which mimic Helix 1 of the human ACE2 receptor, have demonstrated mixed ability to prevent infection with SARS‐CoV‐2 in cell‐based studies.

Self-Replication of Prion Protein Fragment 89-230 Amyloid Fibrils Accelerated by Prion Protein Fragment 107-143 Aggregates.

Prion protein amyloid aggregates are associated with infectious neurodegenerative diseases, known as transmissible spongiform encephalopathies. Self-replication of amyloid structures by refolding of native protein molecules is the probable mechanism of disease transmission. Amyloid fibril formation and self-replication can be affected by many different factors, including other amyloid proteins and peptides. Mouse prion protein fragments 107-143 (PrP(107-143)) and 89-230 (PrP(89-230)) can form amyloid fibrils. -sheet core in PrP(89-230) amyloid fibrils is limited to residues ∼160–220 with unstructured N-terminus. We employed chemical kinetics tools, atomic force microscopy and Fourier-transform infrared spectroscopy, to investigate the effects of mouse prion protein fragment 107-143 fibrils on the aggregation of PrP(89-230). The data suggest that amyloid aggregates of a short prion-derived peptide are not able to seed PrP(89-230) aggregation; however, they accelerate the self-replication of PrP(89-230) amyloid fibrils. We conclude that PrP(107-143) fibrils could facilitate the self-replication of PrP(89-230) amyloid fibrils in several possible ways, and that this process deserves more attention as it may play an important role in amyloid propagation.

Induction of peptidylarginine deiminase 2 and 3 by dibutyryl cAMP via cAMP-PKA signaling in human astrocytoma U-251MG cells.

Peptidylarginine deiminases (PADs) are posttranslational modification enzymes that citrullinate (deiminate) protein arginine residues in a calcium-dependent manner, yielding citrulline residues. Enzymatic citrullination abolishes positive charges of native protein molecules, inevitably causing significant alterations in their structure and function. Previously, we reported the abnormal accumulation of citrullinated proteins and an increase of PAD2 content in hippocampi of patients with Alzheimer disease. In this study, we investigated PAD expression by using dibutyryl cAMP (dbcAMP) in human astrocytoma U-251MG cells. Under normal culture conditions, PAD2 and PAD3 mRNA expression is detectable with quantitative PCR in U-251MG cells. The addition of dbcAMP in a dose-dependent manner significantly increased this mRNA expression and protein levels. Moreover, PAD enzyme activity also increased significantly and dose-dependently. Furthermore, the expression of PAD2 and PAD3 mRNA was inhibited by the cAMP-dependent PKA inhibitor KT5720, suggesting that such expression of dbcAMP-induced PAD2 and PAD3 mRNA is mediated by the cAMP-PKA signaling pathway in U-251MG cells. This is the first report to document the PAD2 and PAD3 mRNA expression induced by dbcAMP and to attribute the induction of these genes to mediation by the cAMP-PKA signaling pathway in U-251MG cells. © 2016 Wiley Periodicals, Inc.

Formation of target-specific binding sites in enzymes: solid-phase molecular imprinting of HRP.

Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike complex protein engineering approaches commonly employed to generate affinity proteins, the method proposed can be used to produce protein-based ligands in a short time period using native protein molecules. These affinity materials are potentially useful tools especially for assays since they combine the catalytic properties of enzymes (for signaling) and molecular recognition properties of antibodies. We demonstrate this concept in an ELISA-format assay where HRP imprinted with vancomycin and ampicillin replaced traditional enzyme-antibody conjugates for selective detection of templates at micromolar concentrations. This approach can potentially provide a fast alternative to raising antibodies for targets that do not require high assay sensitivities; it can also find uses as a biochemical research tool, as a possible replacement for immunoperoxidase-conjugates.

Engineered bacterial hydrophobic oligopeptide repeats in a synthetic yeast prion, [REP-PSI (+)

The yeast translation termination factor Sup35p, by aggregating as the [PSI+] prion, enables ribosomes to read-through stop codons, thus expanding the diversity of the Saccharomyces cerevisiae proteome. Yeast prions are functional amyloids that replicate by templating their conformation on native protein molecules, then assembling as large aggregates and fibers. Prions propagate epigenetically from mother to daughter cells by fragmentation of such assemblies. In the N-terminal prion-forming domain, Sup35p has glutamine/asparagine-rich oligopeptide repeats (OPRs), which enable propagation through chaperone-elicited shearing. We have engineered chimeras by replacing the polar OPRs in Sup35p by up to five repeats of a hydrophobic amyloidogenic sequence from the synthetic bacterial prionoid RepA-WH1. The resulting hybrid, [REP-PSI+], (i) was functional in a stop codon read-through assay in S. cerevisiae; (ii) generates weak phenotypic variants upon both its expression or transformation into [psi-] cells; (iii) these variants correlated with high molecular weight aggregates resistant to SDS during electrophoresis; and (iv) according to fluorescence microscopy, the fusion of the prion domains from the engineered chimeras to the reporter protein mCherry generated perivacuolar aggregate foci in yeast cells. All these are signatures of bona fide yeast prions. As assessed through biophysical approaches, the chimeras assembled as oligomers rather than as the fibers characteristic of [PSI+]. These results suggest that it is the balance between polar and hydrophobic residues in OPRs what determines prion conformational dynamics. In addition, our findings illustrate the feasibility of enabling new propagation traits in yeast prions by engineering OPRs with heterologous amyloidogenic sequence repeats.

ChemInform Abstract: Through the Looking Glass —A New World of Proteins Enabled by Chemical Synthesis

AbstractReview: 32 refs.

Effects of guanidinium ions on the conformational structure of glucose oxidase studied by electrochemistry, spectroscopy, and theoretical calculations: towards developing a chemical-induced protein conformation assay

Understanding conformation transitions of proteins in the presence of a chemical denaturant is a topic of great interest because the rich information contained in chemical unfolding is of fundamental importance for proteomic and pharmaceutical research. In this work, the conformational structure changes of glucose oxidase (GOx) induced by guanidinium ions (Gdm(+)) were studied in detail by a combination of electrochemical methods, various spectroscopic techniques including ultraviolet-visible (UV-vis) absorption, fluorescence, Fourier transform infrared (FTIR), and circular dichroism (CD) spectroscopy, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations with the purpose of revealing the mechanism of chemical unfolding of proteins. The results indicated that GOx underwent substantial conformational changes both at the secondary and tertiary structure levels after interacting with Gdm(+) ions. The interaction of GOx with the chemical denaturant resulted in a disturbance of the structure of the flavin prosthetic group (FAD moiety) that induced the moiety to become less exposed to solvent than that in the native protein molecule. The calculation from quantitative second-derivative infrared and CD spectra showed that Gdm(+) ions induced the conversion of α-helix to β-sheet structures. MD simulations and DFT calculations revealed that Gdm(+) ions could enter the active pocket of the GOx molecule and interact with the FAD group, leading to a significant alteration in the structural characteristics and hydrogen bond networks formed between FAD and the surrounding amino acid residues. These alterations in the conformational structure of GOx resulted in a significant decrease in the catalytic activity of the enzyme to glucose oxidation. The study essentially provides an effective way for investigating the mechanism of chemical denaturant-induced protein unfolding, and this approach can be used for assessing the effect of drug molecules on proteins.

Intramolecular cross-linking in the native JHBP molecule

Juvenile hormone binding protein (JHBP) acts as a shuttle, carrying one of the most crucial hormones for insect development to target tissues. We have found that although the JHBP molecule does not contain tryptophan residues, it exhibits a weak fluorescence maximum near 420nm upon excitation at 315nm. Gel filtration experiments performed in denaturing conditions and ESI-MS analyses excluded the possibility that some low molecular ligand was bound to the protein molecules. Further UV and CD spectroscopy studies, as well as immunoblotting, showed that the unusual JHBP optical properties were due to dityrosine intramolecular cross-linking. These bridges were detected both in native and recombinant protein molecules. We believe that in Galleria mellonella hemolymph the DT generation occurs via ROS-mediated oxidation leading to the formation of cross-linked JHBP monomers. MS analyses of peptides generated after JHBP proteolysis indicated, that the dityrosine bridge occurs between the Y128 and Y130 residues.

Importance of research on peptidylarginine deiminase and citrullinated proteins in age‐related disease

Peptidylarginine deiminases (PAD) are a group of post-translational modification enzymes that citrullinate (deiminate) protein arginine residues in a calcium ion-dependent manner. Enzymatic citrullination abolishes positive charges of native protein molecules, inevitably causing significant alterations in their structure and functions. Citrullinated protein has an important physiological purpose; the formation of a cornified layer of skin that covers the human body. Despite this beneficial function, citrullinated protein also has a negative side, because this protein's accumulation in the brain is a possible cause of Alzheimer's disease. In the present review, we introduce PAD and their protein citrullination function, now considered critical for advancing research on aging and disease.

Developmental and age‐related changes of peptidylarginine deiminase 2 in the mouse brain

Peptidylarginine deiminases (PADs) are a group of posttranslational modification enzymes that citrullinate (deiminate) protein arginine residues in a Ca(2+)-dependent manner. Enzymatic citrullination abolishes positive charges of native protein molecules, inevitably causing significant alterations in their structure and functions. Among the five isoforms of PADs, PAD2 and PAD4 are proved occupants of the central nervous system (CNS), and especially PAD2 is a main PAD enzyme expressed in the CNS. We previously reported that abnormal protein citrullination by PAD2 has been closely associated with the pathogenesis of neurodegenerative disorders such as Alzheimer's disease and prion disease. Protein citrullination in these patients is thought to play a role during the initiation and/or progression of disease. However, the contribution of changes in PAD2 levels, and consequent citrullination, during developmental and aging processes remained unclear. Therefore, we used quantitative real-time RT-PCR, Western blot analysis, and immunohistochemical methods to measure PAD2 expression and localization in the brain during those processes. PAD2 mRNA expression was detected in the brains of mice as early as embryonic day 15, and its expression in cerebral cortex, hippocampus, and cerebellum increased significantly as the animals aged from 3 to 30 months old. No citrullinated proteins were detected during that period. Moreover, we found here, for the first time, that PAD2 localized specifically in the neuronal cells of the cerebral cortex and Purkinje cells of the cerebellum. These findings indicate that, despite PAD2's normally inactive status, it becomes active and citrullinates cellular proteins, but only when the intracellular Ca(2+) balance is upset during neurodegenerative changes.

Direct observation of interaction between proteins and blood-compatible polymer surfaces

The adhesion force between blood-compatible polymer (poly(2-methoxyethyl acrylate: PMEA) and proteins (fibrinogen and bovine serum albumin (BSA)) were measured by atomic force microscopy. The PMEA surface showed almost no adhesion to native protein molecules, whereas non-blood-compatible poly(n-butyl acrylate): PBA strongly adhered to proteins. Interestingly, adhesion did appear between PMEA and proteins when the proteins were denatured. In all cases, these trends were not affected by the conditions of the solution. Combining the results with previous reports, the authors conclude that interfacial water molecules play a critical role in the protein resistance of PMEA.

Technological Options for the Production of Health-Promoting Proteins and Peptides Derived from Milk and Colostrum

Milk proteins are known to exert a wide range of nutritional, functional and biological activities. Apart from being a balanced source of valuable amino acids, milk proteins contribute to the consistency and sensory properties of various dairy products. Furthermore, many milk proteins possess specific biological properties which make them potential ingredients of health-promoting foods. These properties are attributed to both native protein molecules and to physiologically active peptides encrypted in the protein molecules. Considerable progress has been made over the last twenty years in technologies aimed at separation, fractionation and isolation in a purified form of many interesting proteins occurring in bovine colostrum and milk. Industrial-scale methods have been developed for native whey proteins such as immunoglobulins, lactoferrin, lactoperoxidase, alpha-lactalbumin and beta-lactoglobulin. Their large-scale manufacture and commercial exploitation is still limited although validated research data about their physiological health benefits is rapidly accumulating. Promising product concepts and novel fields of use have emerged recently, and some of these molecules have already found commercial applications. The same applies to bioactive peptides derived from different milk proteins. Active peptides can be liberated during gastrointestinal digestion or milk fermentation with proteolytic enzymes. Such peptides may exert a number of physiological effects in vivo on the gastrointestinal, cardiovascular, endocrine, immune, nervous and other body systems. However, at present the industrial-scale production of such peptides is limited by a lack of suitable technologies. On the other hand, a number of bioactive peptides have been identified in fermented dairy products, and there are already a few commercial dairy products enriched with blood pressure-reducing milk protein peptides. There is a need to develop methods to optimise the activity of bioactive peptides in food systems and to enable their optimum utilisation in the body. This review highlights existing modern technologies applicable for the isolation of bioactive native proteins and peptides derived from bovine colostrum, milk and cheese whey, and discusses aspects of their current and potential applications for human nutrition and promotion of human health.

HX-ESI-MS and Optical Studies of the Unfolding of Thioredoxin Indicate Stabilization of a Partially Unfolded, Aggregation-Competent Intermediate at Low pH

Hydrogen exchange monitored by mass spectrometry (HX-MS), in conjunction with multiple optical probes, has been used to characterize the unfolding of thioredoxin. Equilibrium and kinetic studies have been carried out at pH 7 and 3. The HX-MS measurements are shown to be capable of distinguishing between native (N) and unfolded (U) protein molecules when both are present together, and their application in kinetic experiments allows the unfolding reaction to be delineated from the proline isomerization reaction to which it is coupled. At pH 7, equilibrium unfolding studies monitored by three optical probes, intrinsic fluorescence at 368 nm, ellipticity at 222 nm, and ellipticity at 270 nm, as well as by HX-MS, indicate that no intermediate is populated at pH 7, the unfolding reaction is slower than the proline isomerization reaction that follows it, and the three optical probes yield identical kinetics for unfolding, which occurs in a single kinetic phase. The fractional change in any of the three optical signals at any time of unfolding predicts the fraction of the molecules that have become U, as determined by HX-MS. Hence, unfolding at pH 7 appears to occur via a two-state N <==> U mechanism. In contrast at pH 3, HX-MS as well as optical measurements indicate that an unfolding intermediate is stabilized and hence accumulates in equilibrium with N and U, at concentrations of denaturant that define the transition zone of the equilibrium unfolding curve. The intermediate has lost the near-UV signal characteristic of N and possesses fewer amide hydrogen sites that are stable to exchange than does N. Kinetic experiments at pH 3, where unfolding is much faster than proline isomerization, show that more than one intermediate accumulates transiently during unfolding. Thus, the unfolding of thioredoxin occurs via an N <==> I <==> U mechanism, where I is a partially unfolded intermediate that is stabilized and hence populated at pH 3 but not at pH 7. It is shown that transient aggregation of this intermediate results in a deceleration of the kinetics of unfolding at high protein concentrations at pH 3 but not at pH 7.

Irreversible Thermal Denaturation of β-Lactoglobulin Retards Adsorption of Carrageenan onto β-Lactoglobulin-Coated Droplets

The influence of isothermal heat treatments on the adsorption of anionic carrageenan molecules to the surfaces of anionic beta-lactoglobulin-coated droplets has been investigated. The zeta-potential, mean particle diameter, microstructure, and creaming stability of emulsions containing beta-lactoglobulin-coated droplets and/or carrageenan molecules that had previously been heat treated at temperatures ranging from 30 to 90 degrees C for 20 min were measured (pH 6.0, 150 mM NaCl). Three different heat treatments were used to establish the physicochemical origin of the influence of thermal history on the adsorption of carrageenan molecules to the protein coated droplets: (i) droplets and carrageenan were mixed at room temperature, then heated together; (ii) droplets were heated, cooled to room temperature, then mixed with carrageenan; (iii) carrageenan was heated, cooled to room temperature, then mixed with droplets. For treatments i and ii appreciably more carrageenan adsorbed to the protein-coated droplet surfaces at temperatures < or = 60 degrees C than at higher temperatures. For treatment iii, carrageenan adsorbed to the droplet surfaces across the whole temperature range. These results suggest that an irreversible thermal denaturation of the adsorbed beta-lactoglobulin molecules inhibited the adsorption of carrageenan molecules to the droplet surfaces. We postulate that there is a patch of positive charge on the surface of the native globular protein molecules which becomes more diffuse upon thermal denaturation. We found that the carrageenan molecules were unable to protect the beta-lactoglobulin-coated droplets at high temperatures (T > 60 degrees C) because they desorbed from the droplet surfaces. Nevertheless, adsorption of iota-carrageenan was capable of protecting the droplets against flocculation caused by surface denaturation of the adsorbed proteins at lower temperatures (T < or = 50 degrees C).

Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein

Phasing of the crystal structures of four standard proteins (lysozyme, trypsin, glucose isomerase and thaumatin) and a novel 69 kDa protein from Thermus thermophilus, TT0570, was performed using the single-wavelength anomalous diffraction of S atoms intrinsically present within the native protein molecules. To utilize the sulfur anomalous diffraction, the data sets were collected using the loopless data-collection method with chromium Kalpha X-rays of wavelength 2.29 A. Three phasing methods, MLPHARE, SHARP and OASIS-2004, were tested in combination with the DM or SOLOMON density-modification method. The results showed that the solvent contents are still an important factor for phasing with the S-SAD method, even when longer wavelength Cr Kalpha radiation is used. Of the three procedures, the improved direct phasing of OASIS-2004 with its implemented fragment feedback to the direct-method probability calculation gave the best results in determining the initial phases. For all five proteins, almost the entire models could be built automatically.