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SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiaeRSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102. Cryo-EM and biochemical analyses of this subcomplex shows that ARP binding induces a helical conformation in the helicase-SANT–associated (HSA) domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to the full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.

Therapeutic antibodies for subcutaneous (SC) injection must be formulated at high concentrations because of the large therapeutic dose and volume restriction. However, concentrated antibody solutions have undesirably high viscosity, which hampers SC injection. In this study, we demonstrated that hydantoin and its derivatives suppressed the viscosity of concentrated antibody and bovine serum albumin solutions. Hydantoin derivatives, in particular 1-methylhydantoin, appeared more effective. Both hydantoin and 1-methylhydantoin suppressed the viscosity of proteins more effectively when combined with a physiological concentration of NaCl. Moreover, hydantoin rings exhibited thermodynamically favorable interactions with hydrophobic amino acids, as demonstrated using solubility measurements. Molecular dynamics simulations indicated planar stacking interaction or T-shaped interaction between the hydantoin ring structure and the aromatic rings of tryptophan. Thus, the effects of hydantoin compounds in the presence of NaCl on the high viscosity of concentrated protein solutions result from the combined effects between hydantoin and NaCl in suppressing multiple interactions (electrostatic, hydrophobic, π–π, and cation−π interactions) between protein molecules. The obtained data here should be useful for developing therapeutic antibody formulations.

MEP (mercapto-ethyl-pyridine) HyperCel is one of the hydrophobic charge induction chromatography (HCIC) resins. Under normal operation, proteins are bound to the MEP resin at neutral pH, at which MEP is not charged, mostly via hydrophobic interaction. MEP has a pyridine group, whose pK is 4.8, and hence is positively charged at acidic pH range. Based on the binding mechanism (i.e., hydrophobic interaction) and the induced positive charge at acidic pH, there may be two ways to elute the bound proteins. One way is to bring the pH down to protonate both MEP resin and the bound protein, leading to charge repulsion and thereby elution. Another way is to use hydrophobic interaction modifiers, which are often used in hydrophobic interaction chromatography, to reduce hydrophobic interaction. Here, we summarize such two possible elution approaches.

Previously, we have reviewed in this journal (Arakawa, T., Kita, Y., Curr. Protein Pept. Sci., 15, 608-620, 2014) the interaction of arginine with proteins and various applications of this solvent additive in the area of protein formulations and downstream processes. In this special issue, we expand the concept of protein-solvent interaction into the analysis of the effects of solvent additives on various column chromatography, including mixed-mode chromatography. Earlier in our research, we have studied the interactions of such a variety of solvent additives as sugars, salts, amino acids, polymers and organic solvents with a variety of proteins, which resulted in mechanistic understanding on their protein stabilization and precipitation effects, the latter known as Hofmeister series. While such a study was then a pure academic research, rapid development of genetic engineering technologies and resultant biotechnologies made it a valuable knowledge in fully utilizing solvent additives in manipulation of protein solution, including column chromatography.

TOYOPEARL particles are cross-linked hydroxylated methacrylic polymers available in different pore and particle sizes. They are conjugated with different ligands to generate ion-exchange, hydrophobic interaction and affinity resins. They have excellent physical and chemical properties. A mixed-mode resin, TOYOPEARL MX-Trp-650M, is made of this particle with tryptophan conjugated via N-terminal amino group and hence has both hydrophobic/aromatic side chain and carboxyl group. In this review, I will summarize the properties of the TOYOPEARL particles and MX-Trp-650M resin and application of this resin for purification of proteins and in some detail the separation of disulfide (SS)- scrambled oligomers of insulin-like growth factor-1 (IGF-1). For this particular application, the intact IGF-1 was used to examine binding and elution conditions of TOYOSCREEN MX-Trp-650M column. Strong binding was obtained at pH 4.0, at which arginine, but not NaCl, resulted in elution. Both NaCl and arginine resulted in elution at pH 6.5. In addition, a pH gradient from 4.0 to 8.5 was effective. When applied to SS-scrambled IGF-1 oligomers, both pH and arginine gradient exhibited an efficient separation of the oligomers.

Proteins often generate structure isoforms naturally or artificially due to, for example, different glycosylation, disulfide scrambling, partial structure rearrangement, oligomer formation or chemical modification. The isoform formations are normally accompanied by alterations in charged state or hydrophobicity. Thus, isoforms can be fractionated by reverse-phase, hydrophobic interaction or ion exchange chromatography. We have applied mixed-mode chromatography for fractionation of isoforms for several model proteins and observed that cation exchange Capto MMC and anion exchange Capto adhere columns are effective in separating conformational isoforms and self-associated oligomers.

Proteins from moderate and extreme halophiles have unique characteristics. They are highly acidic and hydrophilic, similar to intrinsically disordered proteins. These characteristics make the halophilic proteins soluble in water and fold reversibly. In addition to reversible folding, the rate of refolding of halophilic proteins from denatured structure is generally slow, often taking several days, for example, for extremely halophilic proteins. This slow folding rate makes the halophilic proteins a novel model system for folding mechanism analysis. High solubility and reversible folding also make the halophilic proteins excellent fusion partners for soluble expression of recombinant proteins.

As a graduate course student, I studied the aggregation behavior of the wheat protein gluten, induced by changes in pH and ionic strength, thus beginning my research career in the field of solvent effects. The following 5 years were spent as a post-doctoral reseracher in the U.S., focused on protein-solvent interactions, which, according to my advisor, Dr. Timasheff, was too basic to be supported by academic grants. This study, however, answered a number of questions about how different solvents affect behavior of proteins in solution, e.g., a solubility behavior known as Hofmeister series. This research experience landed me an R position at a startup biotech company, Amgen, where knowledge on solvents played a fundamental role in protein refolding, formulation and chromatography. This demonstrates the unanticipated possibility that an un-funded, basic academic science study earlier can be transitioned later into an industrially-significant applied science.

Arginine is widely used in such applications as protein refolding, solubilization of proteins and small molecules, protein and small molecule formulation, column chromatography and viral inactivation as summarized in this review. What makes arginine effective in these applications is largely based on its ability to suppress protein-protein interactions and protein-surface interactions. The mechanism of these widespread effects of arginine on proteins can be explained at least in part from its unique interactions with the protein surface. Here we describe the modes of the interactions of arginine with model compounds and proteins and also water molecules, and then attempt to explain the mechanism of its effect on proteins by comparing with the interactions that occur between protein and protein denaturants or stabilizers.

Unacceptably high viscosity is observed in high protein concentration formulations due to extremely large therapeutic dose of antibodies and volume restriction of subcutaneous route of administration. Here, we show that a protein aggregation suppressor, arginine hydrochloride (ArgHCl), specifically decreases viscosity of antibody formulations. The viscosities of bovine gamma globulin (BGG) solution at 250 mg/mL and human gamma globulin (HGG) solution at 292 mg/mL at a physiological pH were too high for subcutaneous injections, but decreased to an acceptable level (below 50 cP) in the presence of 1,000 mM ArgHCl. ArgHCl also decreased the viscosity of BGG solution at acidic and alkaline pHs. Interestingly, ArgHCl decreased the viscosity of antibody solutions (BGG, HGG, and human immunoglobulin G) but not globular protein solutions (α-amylase and α-chymotrypsin). These results indicate not only high potency of ArgHCl as an excipient to decrease the solution viscosity of high concentration antibodies formulations but also specific interactions between ArgHCl and antibodies.

Recombinant technology has ushered in a new era for the pharmaceutical industry. Protein therapeutics, including plasma-derived products and antibodies obtained from the serum of infected patients, have been successfully adopted and utilized to treat various indications. The development of recombinant technology and the subsequent improvement in expression, purification, and formulation technologies have enabled the generation of highly purified proteins in a scalable and cost-effective manner. The discovery and development of several recombinant proteins, such as growth factors and cytokines, will be described followed by a brief review of monoclonal antibodies and enzyme replacement therapy. Recombinant protein-based vaccine, which is the focus of the current review, is described in detail with particular emphasis on several viral and bacterial infections. Challenges and new approaches in their use as a replacement for the currently available vaccines are discussed.

Short peptides are important biopharmaceuticals as agonistic or antagonistic ligands, aggregation inhibitors, and vaccines, as well as in many other applications. They behave differently from globular proteins in solution. Many short peptides are unstructured and tend to aggregate and undergo structural transition in response to changes in solvent environment, including pH, temperature, ionic strength, presence of organic solvents or surfactants, and exposure to lipid membranes. Such structural transitions are often associated with fibril or β-amyloid formation. These structural characteristics of short peptides have drastic impact on their function, immunogenicity, and storage stability.

One of the hallmarks of halophilic properties is reversibility of thermal unfolding. A nucleoside diphosphate kinase (NDK) from a moderate halophile Halomonas sp. 593 (HaNDK) follows this behavior. His-tagged chimeric NDK (HisPaHaNDK) consisting of an N-terminal half of a non-halophilic Pseuodomonas aeruginosa NDK (PaNDK) and a Cterminal half of HaNDK loses this reversible property, indicating a critical role of the N-terminal portion of PaNDK in determining the reversibility of the chimeric protein. Various mutations were introduced at Arg45 and Lys61, based on the model NDK structure. It appears that having Glu at position 45 is critical in conferring the thermal reversibility to HisPa- HaNDK chimeric protein.

The solubility and structural properties of halophilic proteins are ascribed to their abundant acidic residues, resulting in large net negative charges at neutral pH. This study examined the effects of low pH, i.e., reduction of net negative charges on the structural properties of starch binding domain (SBD) of halophilic Kocuria varians -amylase. Titration to pH 2.1 caused loss of 233 nm peak characteristic of aromatic interactions present in the native SBD at neutral pH and resulted in the spectrum with a 216 nm valley characteristic of -sheet. The low pH -sheet structure was stable against heat treatment. The addition of NaCl and trifluoroethanol resulted in decrease and increase of the 216 nm signal, without altering the spectral shape. These structural properties were significantly different from those of the native protein.

The starch binding domain of -amlylase from moderate halophile was expressed in E. coli with His tag (His- SBD12) and characterized for its halophilic properties. His-SBD12 was stable up to 35°C and showed binding activity, although at reduced level, to amylose even in the absence of NaCl. Both NaCl and specific ligands exhibited insignificant influence on the secondary structure of His-SBD12, but showed significant stabilization effects against thermal unfolding concentration-dependently, showing its halophilic properties. NaCl increased thermal stability of His-SBD12 by 4°C at 0.2 M and 15°C at 2 M, and enhanced refolding rate by ˜7-fold at 0.2 M and ˜170-fold at 2 M. Its specific ligands, - cyclodextrin (at 3 mM) and maltose (at 470 mM), also stabilized the protein by 11° C, most likely reflecting affinity difference between these two ligands. However, they showed marginal effects on refolding rate. These observations suggest that although binding of NaCl and specific ligands to the native structure can explain their stabilization effects on His- SBD12, it is not a sole factor for modulating their effects on folding of His-SBD12.

Since protein function depends on folding, successful development of active pharmaceutical proteins requires in vitro production of functional, properly folded proteins. In vitro protein folding and hence production can be assisted by co-solvents, including osmolytes and arginine. Osmolytes accumulate in the cytoplasm to raise the osmotic pressure against environmental water stresses, resulting in stabilization of proteins. They have shown to enhance in vitro and in vivo protein folding and suppress in vivo protein aggregation, thus called “chemical chaperones”. Requirement of high concentrations, however, eliminates possible applications of chemical chaperones to rescue in vivo misfolded proteins that cause various diseases. More specific ligands can serve a similar function at much lower concentrations and are called “pharmacological chaperones”. We will review here the applications of chemical chaperones for biotechnology product development and of pharmacological chaperones for in vivo protein folding, and the mechanism of their effects on protein folding. A specific case we review here is the mechanism of action of the polar amino acid arginine, which has been widely used in vitro as a chemical chaperone to assist protein folding and suppress aggregation.

Virus infection is one of the major threats to human health and can be avoided by minimizing exposure to infectious viruses. Viral clearance of pharmaceutical products and sanitization of skin and mucosal surfaces would reduce such exposures. Even with such care, virus infection does occur, requiring effective treatments by antiviral or virucidal agents. Natural products, in particular ingredients of foods and drinks we normally consume or metabolites present in human body at low concentrations, would have advantage over synthetic drugs as antiviral agents for safety concerns. For this reason, we have been studying natural products for their effects on virus inactivation and growth. Such natural products, which we have been focusing, include gallate derivatives, caffeine present in coffee, caffeic acid present in coffee and various fruits, ascorbic and dehydroascorbic acids and a cell metabolite, arginine. Here we will review our work on antiviral and virucidal activities of these compounds and the mechanism of their antiviral and virucidal effects.

A novel neuroprotective peptide, Humanin (HN), has a strong tendency to aggregate in phosphate-buffered saline. Here we attempted to reduce aggregation employing an aqueous phosphate solution, without NaCl, at pH 6.0 and low peptide concentrations wherever possible. Such a condition, though not fully physiological, allowed us to determine the secondary structure and molecular weight of the peptides. Comparison of a parent HN peptide, an inactive analog (S7AHN) and a 1000-fold more active analog (S14G-HN) showed no apparent differences in the secondary structure. These peptides were all disordered over the wide range of peptide concentration. Sedimentation analysis was done only for HN and S7A-HN and showed aggregation into soluble oligomers in 20 mM phosphate at pH 6.0. Aggregation was greatly suppressed in 5 mM phosphate at the same pH in terms of aggregate size, with the formation of smaller oligomers. Sedimentation velocity experiments at 60,000 rpm in 5 mM phosphate at pH 6.0 showed that both HN and S7A-HN distributed into soluble aggregates that sedimented to the bottom of the cell and low molecular weight species that approached sedimentation equilibrium. The mass of this low molecular weight species was determined by sedimentation equilibrium to be close to monomers for both peptides. Thus, these results clearly demonstrate that the active HN and inactive S7AHN are identical in structure and hence there is no apparent correlation between solution structure and biological activity.

We have developed a new Western blotting method of native proteins from agarose-based gel electrophoresis using a buffer at pH 6.1 containing basic histidine and acidic 2-(N-morpholino)ethanesulfonic acid. This gel electrophoresis successfully provided native structures for a variety of proteins and macromolecular complexes. This paper is focused on the Western blotting of native protein bands separated on agarose gels. Two blotting methods from agarose gel to PVDF membrane are introduced here, one by contact (diffusion) blotting and another by electroblotting after pre-treating the agarose gels with SDS. The contact blotting resulted in the transfer of native GFP, native human plexin domain containing protein 2 (PLXDC2) and native SARS-CoV-2 spike protein, which were detected by conformation-specific antibodies generated in-house.

A number of approaches are available in minimizing aggregation of the final protein products. This chapter describes one such approach, i.e., an attempt to avoid stressful conditions that may eventually lead to protein aggregation. Affinity chromatography uses specific interaction between protein to be purified and ligand attached to the column. Due to high affinity, dissociation of such interaction and hence elution often require harsh solvent conditions. Ion exchange and hydrophobic interaction chromatography also pose certain stressful conditions on proteins. Here we describe development of mild elution buffer using arginine. This chapter covers Protein-A, dye, Protein-A mimetic and antigen affinity chromatography.

A majority of column chromatographies use only selected salts, e.g., ammonium sulfate, NaCl, Citrate and phosphate in hydrophobic interaction chromatography (HIC) and NaCl in ion exchange and dye affinity chromatographies. Alternatively, a pH range below or above the neutral value is often used to reduce affinity interactions, e.g., in Protein-A or dye affinity column chromatography. Although these parameters are easily manipulated, they are not necessarily the optimal conditions for high recovery and resolution of the proteins. So-called co-solvents have been used, although to a limited extent, to manipulate performance of column chromatography. Here the term co-solvent is used to indicate its relatively high concentrations required for these applications, meaning that it also serves as solvent along with water. Ethylene glycol and MgCl2 have been used to elute specific antibodies from antigen-affinity column. Arginine has also been used for the same purpose. Arginine has much wider applications for various column chromatographies, including size exclusion chromatography (SEC), HIC and affinity chromatography. Polyethylene glycol and glycine have also been used to improve the performance of HIC and hydroxyapatite chromatography. This review summarizes these applications of co-solvents for column chromatographies.

We have examined the structure of two Humanin (HN) analog peptides, HNG and AGA-(C8R)HNG17, in the presence of sodium dodecylsulfate (SDS) and trifluoroethanol (TFE) using CD and sedimentation velocity. Both HNG and AGA-(C8R)HNG17 underwent complex conformational changes with increasing concentrations of SDS and TFE, in contrast to general trend of increasing -helix with their concentration. To our surprise, both peptides appear to converge into a similar structure in SDS and TFE at higher concentrations; e.g., above 0.05 SDS or 30-40 TFE. Sedimentation velocity analysis showed extensive aggregation of HNG at 0.1 mg/ml in PBS in the absence of SDS, but a highly homogeneous solution in 0.1 SDS, indicating formation of a uniform structure by SDS. These two peptides also formed an intermediate structure both in SDS and TFE at lower concentrations, which appeared to be associated with extensive aggregation. It is interesting that the structure changes of these peptides occur well below the critical micelle concentration of SDS, suggesting that conformational changes are mediated through molecular, not micellar, interactions with SDS.

Arginine has been used to suppress aggregation of proteins during refolding and purification. We have further studied in this paper the aggregation-suppressive effects of arginine on two commercially important proteins, i.e., interleukine- 6 (IL-6) and a monoclonal antibody (mAb). These proteins show extensive aggregation in aqueous buffers when subjected to thermal unfolding. Arginine suppresses aggregation concentration-dependently during thermal unfolding. However, this effect was not specific to arginine, as guanidine hydrochloride (GdnHCl) at identical concentrations also was effective. While equally effective in aggregation suppression during thermal unfolding, arginine and GdnHCl differed in their effects on the structure of the native proteins. Arginine showed no apparent adverse effects on the native protein, while GdnHCl induced conformational changes at room temperature, i.e., below the melting temperature. These additives affected the melting temperature of IL-6 as well; arginine increased it concentration-dependently, while GdnHCl increased it at low concentration but decreased at higher concentration. These results clearly demonstrate that arginine suppresses aggregation via different mechanism from that conferred by GdnHCl.

We report the successful expression and detection of a phosphorylated form of human T cell tyrosine kinase, Lck, in Saccharomyes cerevisiae, which leads to growth suppression of the yeast cells. Expression of an inactive Lck mutant resulted in no phosphorylation and no growth suppression, indicating that cell growth inhibition by Lck is due to the activity of the kinase, consistent with the observed tyrosine-phosphorylation of the Lck and yeast host cell proteins. The addition of a known inhibitor of Lck to the cell culture resulted in recovery of cell growth expressing the active Lck, suggesting that the growth inhibition by lck gene expression can be used to screen inhibitors for the gene product. We have extended such approach to Tob, another potential therapeutic target.

A halophilic nucleoside diphosphate kinase from a moderate halophile, Halomonas sp. 593 (593NDK), was found to be resistant to heat treatment, as indicated by the high level of activity recovery after heating at high temperatures. This is due to reversibility of thermal unfolding, not the high melting temperature, of the protein. The highly homologous NDK from non-halophilic organism, Pseudomonas aeruginosa, showed instability against heat treatment. Chimeric molecules consisting of each half of these two NDKs were constructed and characterized for their heat stability. The results showed that the N-terminal half of 593NDK contributes to the heat stability of the proteins. We discuss the possible reason for the observed difference in resistance to heat treatment between the 593NDK and PaNDK and between two chimeric proteins.

Native sequence keratinocyte growth factor (KGF) is fairly unstable, as manifested by the loss of the monomeric native protein accompanied by the accumulation of aggregated species during storage at moderate temperatures. Several different types of analogs were generated and the storage stability of the protein assessed. In the first type of analog one or more of the five cysteinyl residues in KGF were replaced; in the second class the N-terminal residues that included the first disulfide bond were deleted. Both of these types of analogs involved removal of the disulfide bond between cysteines 1 and 15. The third group involved mutating one of the basic amino acids located in a cluster of positive charges (involved in heparin binding) around Arg144 to a neutral or acidic amino acyl residue. Among the cysteine replacement analogs, the double mutation of Cys1 and 15 to Ser resulted in significantly increased stability without compromising the mitogenic activity, while Cys to Ser mutations at other positions were either destabilizing or had no effect. Deletion of the 15, 23 or 27 N-terminal amino acyl residues also increased the stability of the protein. The activity of the analogs was not affected by the deletion of 15 or 23 amino acids, but it was significantly decreased upon removal of the 27 N-terminal amino acyl residues. Much greater stability was achieved by mutation of the basic amino acids, especially Arg144, to Glu or Gln, but this increase in stability was accompanied by large decrease in activity. The analog with the 23 N-terminal amino acyl residues deleted represents one of the best compromises between increased stability and retention of activity.

Arginine suppresses the aggregation of proteins. However, little is known about its mechanism. Here we have used HsNDK (Halobacterium salinarum nucleoside diphosphate kinase) to examine the solvent property of arginine. After exposure to 2 M arginine, HsNDK was diluted to a low salt buffer, resulting in fully active protein. Since unfolded HsNDK cannot refold in such low salt buffer, the observed activity indicates that HsNDK was in the native state in 2 M arginine. Enzyme activity was also examined directly in the presence of arginine, showing that it was active in the presence of 1 M arginine and, to less extent, 2 M arginine. Arginine, however, could not support refolding of heatdenatured HsNDK. HsNDK was stable at 40 C for 19 h incubation in the presence of 1M arginine.

Arginine is finding a wide range of applications in production of proteins. Arginine has been used for many years to assist protein refolding. This effect was ascribed to aggregation suppression by arginine of folding intermediates during protein refolding. Recently, we have observed that arginine facilitates elution of antibodies during Protein-A chromatography and solubilizes insoluble proteins from inclusion bodies, which both can be ascribed to weakening of protein-protein interactions. In order to gain understanding on why arginine is effective in reducing protein-protein interactions and suppressing aggregation, the effects of arginine on stability and solubility of pure proteins have been examined, which showed that arginine is not a protein-stabilizer, but is an aggregation suppressor. However, there is no explanation proposed so far on why arginine suppresses aggregation of proteins. This review addresses such question and then attempts to show differences between arginine and strong denaturants, which are also known as an aggregation suppressor.

In general, halophilic proteins are stable only in the presence of salts at high concentrations. Not only is high salt concentration important for structural stability of halophilic proteins, but also refolding of a denatured halophilic protein requires high salt concentration. This review summarizes the importance of electrostatic charge shielding and hydrophobic interactions in the stability and refolding of halophilic proteins.

Previously we reported that halobacterial nucleoside diphosphate kinase can be refolded in the presence of concentrated trimethylamine N-oxide (TMAO) as well as NaCl, indicating that enhancement of compact structure formation by TMAO is sufficient for folding. Here we showed that the refolding effect of MgCl2 is maximal at 1 M and declines to zero at 2 M, indicating that charge shielding effect of MgCl2 is offset by its salting-in effect.

Recombinant microbial transglutaminase has been expressed in Escherichia colias insoluble inclusion bodies. After we searched for refolding conditions, refolding of the protein could be done by first dilution of the unfolded enzyme in a buffer at pH 4.0, and then by titration of the pH from 4.0 to 6.0. CD analysis showed that a burst of secondary structure formation occurred within the dead time of the experiment and accounted for 75% of the signal change in the far UV CD, with little tertiary structure being formed. This burst was followed by slow rearrangement of the secondary structure accompanied by formation of tertiary structure. The secondary and tertiary structures of the final sample at pH 4.0, corresponding to the folding intermediate, were different from these structures at pH 6.0. Once the native structure was obtained, acidification of the native protein to pH 4.0 did not lead to a structure like that of the folding intermediate. Sedimentation velocity analysis showed that the folding intermediate had an expanded structure and contained no other structure species including large aggregates.

Glial cell line-derived neurotrophic factor (GDNF) is a member of the TGF-β superfamily of proteins. It exists as a covalent dimer in solution, with the 15 kDa monomers linked by an interchain disulfide bond through the Cys101 residues. Sedimentation equilibrium and velocity experiments demonstrated that, after removal of the interchain disulfide bond, GDNF remains as a non-covalent dimer and is stable at pH 7.0. To investigate the effect of the intermolecular disulfide on the structure and stability of GDNF, we compared the solution structures of the wild-type protein and a cysteine-101 to alanine (C101A) mutant using Fourier transform infrared (FTIR), FT-Raman and circular dichroism (CD) spectroscopy and sedimentation analysis. The elimination of the intermolecular disulfide bond causes only minor changes (∼4%) in the secondary structures of GDNF. The far- and near-UV CD spectra demonstrated that the secondary and tertiary structures were similar for both wild-type and C101A GDNF. Heparin binding and sedimentation velocity experiments also indicated that the folded structure of the wild-type and C101A GDNF are indistinguishable. The thermal stability of GDNF does not appear to be affected by the absence of the interchain disulfide bond and the biological activity of the C101A mutant is identical with that of the wild-type protein. However, small but significant changes in side chain conformations of tyrosine and aliphatic residues were observed by FT-Raman spectroscopy upon removal of the intermolecular disulfide bond, which may reflect structural changes in the area of dimeric contact. By comparing the Raman spectrum of wild-type GDNF with that of the C101A analog, we identified the conformation of the intermolecular disulfide as trans–gauche–trans geometry. These results indicate that GDNF is an active, properly folded molecule in the absence of the interchain disulfide bond.

The interactions of brain-derived neurotrophic factor (BDNF) with the extracellular domain of its receptor (trkB) are investigated by employing isotope-edited Fourier transform IR (FTIR) spectroscopy. The protein secondary structures of individual BDNF and trkB in solutions are compared with those in their complex. The temperature dependence of the secondary structures of BDNF, trkB, and their complex is also investigated. Consistent with the crystal structure, we observe by FTIR spectroscopy that BDNF in solution contains predominantly β strands (~53%) and relatively low contents of other secondary structures including β turns (~16%), disordered structures (~12%), and loops (~18%) and is deficient in α helix. We also observe that trkB in solution contains mostly β strands (52%) and little α helix. Conformational changes in both BDNF and trkB are observed upon complex formation. Specifically, upon binding of BDNF, the conformational changes in trkB appear to involve mostly β turns and disordered structures while the majority of the β-strand conformation remains unchanged. The IR data indicate that some of the disordered structures in the loop regions are likely converted to β strands upon complex formation. The FTIR spectral data of BDNF, trkB, and their complex indicate that more amide NH groups of trkB undergo H–D exchange within the complex than those of the ligand-free receptor and that the thermal stability of trkB is decreased slightly upon binding of BDNF. The FT-Raman spectra of BDNF, trkB, and their complex show that the six intramolecular disulfide bonds of trkB undergo significant conformational changes upon binding of BDNF as a result of changes in the tertiary structure of trkB. Taken together, the FTIR and Raman data are consistent with the loosening of the tertiary structure of trkB upon binding of BDNF, which leads to more solvent exposure of the amide NH group and decreased thermal stability of trkB. This finding reveals an intriguing structural property of the neurotrophin ligand–receptor complex that is in contrast to other ligand–receptor complexes such as a cytokine–receptor complex that usually shows protection of the amide NH group and increased thermal stability upon complex formation. © 2002 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 67: 10–19, 2002; DOI 10.1002/bip.10038

In the light scattering technique, glycosylation gives rise to excess light scattering for glycoproteins. Assuming additivity of refractive index and using an appropriate refractive index increment for carbohydrate, one can determine the degree of glycosylation from the excess light scattering. Here we have used size-exclusion chromatography in combination with online light scattering, UV absorbance, and refractive index. The results show that the technique accurately determines the carbohydrate content of recombinant stem cell factor. ©2001 Elsevier Science.

Enzymes from extremely halophilic archaea are readily denatured in the absence of a high salt concentration. However, we have observed here that a nucleoside diphosphate kinase prepared from Halobacterium salinarumwas active and stable in the absence of salt, though it has the amino acid composition characteristic of halophilic enzymes. Recombinant nucleoside diphosphate kinase expressed in Escherichia colirequires salt for activation in vitro, but once it acquires the proper folding, it no longer requires the presence of salts for its activity and stability.

We succeeded in the expression, purification, and refolding of the immunoglobulin-like (Ig) domain of human granulocyte-colony-stimulating factor (G-CSF) receptor with amino-terminal His-tag in Escherichia coli. The refolded Ig domain bound to a G-CSF affinity column and could be eluted with free G-CSF as a receptor-ligand complex, demonstrating that the Ig domain has the information necessary for binding its ligand, G-CSF. The eluted His-Ig/G-CSF complex could be separated from excess G-CSF by Ni-NTA column chromatography. The yield of this active recombinant His-Ig protein is about 0.72 mg per liter of culture. Its small size and the ease of production make this receptor fragment a useful reagent for the structural analysis of its complex with G-CSF.

Direct expression of the cytokine receptor homology (CRH) domain of granulocyte-colony-stimulating factor (G-CSF) receptor is lethal to Escherichia coli.For the efficient and stable production of an active CRH domain in E. coli,we fused the CRH domain with different proteins, such as maltose-binding protein (MalE), glutathione S-transferase, and thioredoxin (Trx). Among these, Trx appeared to be the best in terms of the protein expression level, purification efficiency by affinity chromatography, and binding activity to its ligand, G-CSF. The yield of active Trx–CRH fusion protein increased about 200-fold compared to that of previously reported MalE–CRH fusion.

Erythropoietin (EPO) derived from Escherichia coli is unstable to elevated temperature and tends to aggregate with time, making it unsuitable for high-resolution structure analysis. The mammalian EPO contains about 40% carbohydrate, which makes this protein more stable and less prone to aggregate than non-glycosylated E.coli-derived EPO, but makes it unsuitable for high-resolution analysis owing to its size and flexibility. In an attempt to decrease the aggregation of E.coli-derived EPO, the three asparagine residues at positions 24, 38 and 83 were mutated to lysine residues. In the native protein, these residues are the sites of N-linked glycosylation, which suggests that they should be located on the surface of the protein and should not be involved in interactions in the hydrophobic protein core. Therefore, the substitution of basic amino acids for these neutral asparagine residues is not expected to affect the protein structure, but should increase the isoelectric point of the protein and its net positive charge, decreasing its tendency to aggregate at or below neutral pH due to electrostatic interactions. No apparent alterations in receptor binding, as determined by both cell-surface receptor competition assay and in vitro receptor dimerization experiments, were observed when these mutations were introduced into the EPO sequence. However, this mutant protein displayed a significant increase in stability to heat treatment and to storage, relative to the wild-type molecule. This resulted in a greater number of observable cross peaks in the mutant EPO in 2D NOESY experiments. However, the mutant was similar to the wild-type in stability when urea was used as a denaturant. This indicates that the introduced mutations resulted in a decrease in aggregation with heating or with prolonged incubation at ambient temperature, without changing the conformational stability or the receptor binding affinity of the mutant protein. This approach of placing charged residues at sites where N-glycosylation occurs in vivo could be applied to other systems as well.

The groESL locus of a protein-hypersecreting bacterium, Bacillus brevis, was cloned by PCR using primers designed based on the DNA sequence of a B. subtilis homolog. GroEL protein was purified to apparent homogeneity and its ATPase activity was characterized: it hydrolyzed ATP, CTP, and TTP in this order of reaction rate, and its specific activity for ATP was 0.1 μmole/min/mg protein. Purified GroEL forms a tetradecamer. GroEL was estimated to contain 22% α-helix, 24% β-sheet, and 19% turn structures, by CD measurement. GroES protein was also highly purified to examine its chaperonin activity. GroEL protected from thermal inactivation of and showed refolding-promoting activity for malate dehydrogenase, strictly depending on the presence of ATP and GroES.

Thermal stress was used to assess the stability of recombinant human erythropoietin (EPO) derived from Chinese hamster ovary cells. In 20 mM phosphate at pH 7.0, this protein had a highly reversible thermal unfolding as observed by far UV circular dichroism (CD) and native gel analysis, with no indication of protein aggregation. It had a relatively low melting temperature at 53°C. Assuming a two-state transition, the observed reversibility permits thermodynamic analysis of the unfolding of EPO, which shows that the free energy of unfolding at 25°C is only 6-7 kcal/mol. Upon heating to 79°C over 30 min, however, this protein does undergo aggregation as assessed by native gel. In 20 mM phosphate and citrate at pH 7.0, the results are similar, i.e., EPO suffered a substantial aggregation, while it showed little aggregation in 20 mM Tris or histidine at pH 7.0 and 20 mM glycine at pH 6.3 under identical heat treatment.

An attempt was made to make protein bands visible on native gel using copper staining, since such a mild staining procedure would make the entire native gel electrophoresis process non-denaturing. Copper staining not only was able to detect various proteins on native gel with reasonable sensitivity, but also made extraction and recovery of active proteins possible from the gel using a gentle procedure.

Enzymes from extremely halophilic archaea are readily denatured in the absence of a high salt concentration. However, we have observed here that a nucleoside diphosphate kinase prepared from Halobacterium salinarumwas active and stable in the absence of salt, though it has the amino acid composition characteristic of halophilic enzymes. Recombinant nucleoside diphosphate kinase expressed in Escherichia colirequires salt for activation in vitro, but once it acquires the proper folding, it no longer requires the presence of salts for its activity and stability.

In an attempt to explain the mechanism of protein stabilization conferred by detergents, we investigated the effect of Tween 80 on aggregation of bovine serum albumin (BSA) using circular dichroism (CD) and native gel electrophoresis. CD thermal scans showed that BSA denatures at about 54°C in 20mMTris, pH 7.2, forming soluble aggregates. Because of this aggregation, thermal unfolding of BSA under these conditions was only partially reversible, as indicated by reduced signal changes in the second scan. On the basis of this observation, BSA was thermally stressed by incubating at 50, 60, or 70°C for 15min and then analyzed by native gel electrophoresis. There was no change at 50°C before and after heating, whereas at 60°C the intensity of the original monomer and dimer bands decreased and that of aggregate bands increased, with much greater changes at 70°C. Addition of Tween 80 before heating reduced aggregation and increased the monomer content. These effects of Tween 80 were greater as its concentration was increased from 0.001 to 1%. There was no correlation between the protective effects and the critical micelle concentration (CMC) of Tween 80. Addition of Tween 80 after 15min incubation at 70°C, or after 70°C heating followed by cooling to room temperature, had no effect, demonstrating that Tween 80 must be present during the 70°C heating step to be protective. Native gel electrophoresis run at 60°C showed multiple aggregate bands and new bands migrating around the dimer and monomer positions, which may correspond to precursors of aggregates. Tween 80 reduced formation of these new bands and aggregates, further demonstrating that it must be present during heating. Finally, CD thermal scans showed that 0.1% Tween 80 only slightly increased the apparent melting temperature. The observed stabilization of BSA against heat treatment is, therefore, due to Tween 80 altering aggregation behavior rather than inducing significant stabilization of the native state. © 2000 Wiley‐Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 89: 646–651, 2000

In an attempt to explain the mechanism of protein stabilization conferred by detergents, we investigated the effect of Tween 80 on aggregation of bovine serum albumin (BSA) using circular dichroism (CD) and native gel electrophoresis. CD thermal scans showed that BSA denatures at about 54°C in 20 mM Tris, pH 7.2, forming soluble aggregates. Because of this aggregation, thermal unfolding of BSA under these conditions was only partially reversible, as indicated by reduced signal changes in the second scan. On the basis of this observation, BSA was thermally stressed by incubating at 50, 60, or 70°C for 15 min and then analyzed by native gel electrophoresis. There was no change at 50°C before and after heating, whereas at 60°C the intensity of the original monomer and dimer bands decreased and that of aggregate bands increased, with much greater changes at 70°C. Addition of Tween 80 before heating reduced aggregation and increased the monomer content. These effects of Tween 80 were greater as its concentration was increased from 0.001 to 1%. There was no correlation between the protective effects and the critical micelle concentration (CMC) of Tween 80. Addition of Tween 80 after 15 min incubation at 70°C, or after 70°C heating followed by cooling to room temperature, had no effect, demonstrating that Tween 80 must be present during the 70°C heating step to be protective. Native gel electrophoresis run at 60°C showed multiple aggregate bands and new bands migrating around the dimer and monomer positions, which may correspond to precursors of aggregates. Tween 80 reduced formation of these new bands and aggregates, further demonstrating that it must be present during heating. Finally, CD thermal scans showed that 0.1% Tween 80 only slightly increased the apparent melting temperature. The observed stabilization of BSA against heat treatment is, therefore, due to Tween 80 altering aggregation behavior rather than inducing significant stabilization of the native state. © 2000 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 89: 646–651, 2000

Purpose. The present study was performed to examine the effect of solution conditions on the reversibility of the thermal denaturation of megakaryocyte growth and development factor (rHuMGDF). Methods. Changes in the far U V CD spectra of rHuMGDF with temperature were used to monitor the thermal denaturation of the protein, and the recovery of folded protein following a return to room temperature. The effect of protein concentration, scan rate, and buffer composition on thermal denaturation and on the reversibility were determined. Surface tension measurements were used to determine the effect of this unfolding reaction on the surface adsorption of the protein. Sedimentation velocity was used to assess recovery of native monomer and the size of soluble aggregates. In addition, monomeric protein remaining in solution after incubation at 37°C for 2 weeks in either 10 mM imidazole of 10 mM phosphate was determined. Results. In phosphate buffer the rHuMGDF irreversibly precipitates upon unfolding under all the conditions examined. In imidazole the unfolding is at least partially reversible, with no visible precipitate seen; the degree of reversibility increased by lowering both protein and salt concentrations, and the amount of time spent at elevated temperature. In order to compare thermal unfolding occuring with different degrees of reversibility, the melting temperature was defined as the temperature at which melting begins. The melting temperature itself is relatively independent of the buffer composition, or experimental conditions. At low protein concentrations the protein stabilizer sucrose had a marginal effect on the thermal transition of rHuMGDF, while at protein concentrations of about 2 mg/ml the inclusion of sucrose increased the apparent melting temperature by about 4°C, to that seen at low protein concentrations, but had little effect on the reversibility of denaturation. Inclusion of 1 or 2 M urea did not affect the reaction. Surface tension measurements of rHuMGDF solutions showed little difference before and after melting, and in the presence or absence of sucrose. When unfolding is irreversible, the MGDF appears to form soluble aggregates of tetramers to 14-mers, while under reversible conditions native monomer is recovered. More monomeric MGDF remained in solution following storage for 2 weeks at 37°C in imidazole than in phosphate, in both the presence and absence of sucrose. Conclusions. These results can be explained by assuming that thermal denaturation proceeds as a two-step reaction, the first step being the equilibrium between folded and unfolded states, while the second step is a slow irreversible aggregation. The different buffer systems affect the rate of the aggregation step, but not the intrinsic thermal stability nor the rate of the unfolding step.

Fibroblast growth factor-16 (FGF-16) is the most recent member of the FGF family to be cloned. Since the biologic activity of rat FGF-16 (rFGF-16) was unknown, and this protein has no apparent signal sequence, we transformed its entire cDNA intoEscherichia colifor high-level expression and further characterization of this novel protein. An attempt was made to purify the expressed protein from the supernatant of mechanically lysed cells using sequential cation-exchange chromatography. This resulted in a gradual loss of the protein as precipitate throughout the purification process. In addition to precipitation during purification, sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed that the partially purified materials showed a cluster of protein bands around 20k to 29k. Sequence analysis of the major bands indicated that two N-terminal truncations had occurred, duringE. colifermentation, purification, or both. The largest truncation resulted in the removal of the 34 N-terminal amino acids, including the initiation codon methionine. We cloned d34 rFGF-16, expressed the gene inE. coli,and developed a purification process for this form. Even with this truncated form, precipitation was a problem. We were largely able to overcome this problem, however, by including EDTA throughout the purification process. We have characterized the structure of purified d34 rFGF-16 extensively using circular dichroism, Fourier transform infrared spectroscopy, and sedimentation velocity analysis. These studies revealed that the protein has a distinct tertiary structure, consists primarily of β-strands, has a weak tendency to self-associate, and is fairly extended. We then performed biologic assays which showed that d34 rFGF-16 induces oligodendrocyte proliferationin vitro,and induces hepatocellular proliferation and increased liver weightin vivo.In summary, FGF-16, a novel FGF family member, has both unique structural and biological properties.

The levels of synthesis of six proteins were increased at elevated growth temperature of the extremely halophilic archaebacterium Halobacterium cutirubrum. One of these proteins, with an apparent molecular mass of 97 kDa on sodium dodecylsulfate–polyacrylamide gel electrophoresis (SDS–PAGE), bound to an ATP-agarose column in the presence of 4 M NaCl, but not in the absence of salt, indicating that this protein retained its ATP-binding activity only at high salt concentration. The NH2-terminal sequence of this protein and the internal sequences of the tryptic peptides covering 1/3 of the total number of residues coincided with that deduced from the nucleotide sequence of the dnaKgene isolated from H. cutirubrum. The results strongly suggest that this apparent 97-kDa protein is the gene product of dnaK,although the molecular mass calculated from the nucleotide sequence is only 68,495, much smaller than the value of this protein determined by SDS–PAGE. Ferguson plot analysis indicated that this protein showed anomalous mobility on SDS–PAGE. We have purified DnaK homologue to greater than 90% homogeneity with stepwise elution from an ATP-agarose column.

Recombinant human keratinocyte growth factor (rhKGF) is prone to aggregation at elevated temperatures. Its aggregation pathway is proposed to proceed initially with a conformational change which perhaps results from repulsion between positively charged residues in clusters forming heparin binding sites. Unfolding of the protein leads to formation of large soluble aggregates. These soluble aggregates then form disulfide cross-linked precipitates. Finally these precipitates are converted to scrambled disulfides and/or non-disulfide cross-linked precipitates. Stabilizers such as heparin, sulfated polysaccharides, anionic polymers and citrate can greatly decrease the rate of aggregation of rhKGF at elevated temperatures. These molecules may all act by reducing charge repulsion on the protein thus stabilizing the native conformation. EDTA, on the other hand, is found to inhibit disulfide formation in aggregates and has only a moderate stabilizing effect on rhKGF.

The stability of recombinant consensus α‐interferon (rConIFN) to air‐jet and ultrasonic nebulization was evaluated. Volumes of 10 mL of 0.5mg/mL rConIFN in phosphate‐buffered saline (PBS) at pH 6.3 were nebulized with a Collison three‐jet nebulizer at 40 psig (10 L/min) for up to 25 min. The effects of pH (3.0, 6.3, and 9.0), additive (0.1% w/v Tween 80, 0.1% w/v Tween 20, and 1% w/v PEG 8000), and ionic strength (0, 0.25, and 1.0) were examined. The effects of ultrasonic nebulization were studied using three devices (DeVilbiss “Aerosonic”; Mountain Medical “Microstat”, and Medix “Easimist”). Stability of rConIFN was assessed by size exclusion chromatography and native and sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE). Structural effects were examined by circular dichroism spectroscopy and bioactivity was assessed by anin vitromitogenic inhibition bioassay. rConIFN is destabilized by air‐jet nebulization. Insoluble noncovalent aggregates are produced rapidly, and only ≈25% of the initial monomeric protein remains after 25 min of nebulization. This correlates with a decrease inin vitrobioactivity. Aggregation during nebulization is influenced by pH (9.0<6.3<3.0) but even at the highest pH, >25% aggregation is observed. Ionic strength does not appear to influence aggregation. rConIFN is also seen to adhere to glass after nebulization. Samples from a rinse of the emptied reservoir with 0.1% w/v SDS, after thorough rinsing with water (three times), show a strong rConIFN band on SDS–PAGE gels. The use of PEG 8000 and Tween mitigate aggregate formation and adhesion (<20%). The cumulative output collected as a wet or dry aerosol is not aggregated to the same extent as the residual protein remaining in the nebulizer. Ultrasonic nebulization also results in aggregation, but the extent of denaturation is dependent upon the nebulizer used and is related to the heating of nebulizer solutions. Cooling of the nebulizer solution during operation (<30 °C) minimizes aggregation (<5%), and bioactivity is retained.