Sodium Dodecyl Sulfate Analogs as a Potential Molecular Biology Reagent.

In this study, we review the properties of three anionic detergents, sodium dodecyl sulfate (SDS), Sarkosyl, and sodium lauroylglutamate (SLG), as they play a critical role in molecular biology research. SDS is widely used in electrophoresis and cell lysis for proteomics. Sarkosyl and, more frequently, SDS are used for the characterization of neuropathological protein fibrils and the solubilization of proteins. Many amyloid fibrils are resistant to SDS or Sarkosyl to different degrees and, thus, can be readily isolated from detergent-sensitive proteins. SLG is milder than the above two detergents and has been used in the solubilization and refolding of proteins isolated from inclusion bodies. Here, we show that both Sarkosyl and SLG have been used for protein refolding, that the effects of SLG on the native protein structure are weaker for SLG, and that SLG readily dissociates from the native proteins. We propose that SLG may be effective in cell lysis for functional proteomics due to no or weaker binding of SLG to the native proteins.

Successful removal of an accidentally swallowed press-through package sheet using a detachable snare: A case report.

Accidental swallowing of press-through package (PTP) sheets that could cause esophageal perforation is commonly encountered in emergency departments requiring early detection and removal. We report a case in which an accidentally swallowed PTP sheet was removed from the esophagus using a detachable snare after usual endoscopic methods proved ineffective. A Japanese woman in her 60s visited the emergency department with a persistent sore throat. Cervicothoracic computed tomography revealed presence of a PTP sheet in the cervical esophagus, and emergency endoscopy was performed. Pre-endoscopy simulations using a sheet identical to the one swallowed by the patient indicated that the sheet would not have been retrievable using an overtube (its inner diameter was smaller than the sheet's diameter) and grasping forceps (they slipped off the sheet). It was successfully removed using a detachable snare, a device normally employed in colorectal polypectomy, allowing us to ligate the end of the sheet and pull it into the overtube. To the best of our knowledge, this is the first report of endoscopic removal of a PTP sheet from the esophagus using a detachable snare. We suggest that this novel method would facilitate removal of esophageal PTP sheets.

Survival Rate and Shunt Infection Incidence Following Gastrostomy in Adult Patients with an Existing Ventriculoperitoneal Shunt.

Ventriculoperitoneal shunts (VPS) and gastrostomies are frequently provided in daily practice. This study investigated the incidence of VPS infection and the survival rate among adult patients who underwent gastrostomy at least 1 month after VPS placement. This single-center retrospective cohort study was conducted among patients with a VPS, who underwent a gastrostomy. This procedure was performed on a standby basis after a period of at least 1 month had elapsed since VPS placement. Subsequent VPS infection and survival rates were assessed over a period of at least 6 months. We reviewed 31 patients who had a VPS at the time of gastrostomy. Gastrostomy was performed endoscopically in 29 cases and via open surgery in 2 cases. The average interval between VPS insertion and gastrostomy was 1135.5 ± 1717.1 days. A single case of VPS infection (3.2%) was diagnosed during the study. This infection rate was not significantly different than that among 230 patients who underwent their first VPS placement (without gastrostomy) at our institution during the same time period (P = .57); there was also no significant difference in the survival rate, compared to 38 age-matched patients (with cerebrovascular disease, but without a VPS) who underwent gastrostomy (P = .73). Gastrostomy performed after an interval of at least 1 month after VPS placement was extremely safe in adult patients, and their prognosis was excellent. Additional studies are required to develop appropriate nutritional interventions for patients with a VPS.

Structure Analysis of Proteins and Peptides by Difference Circular Dichroism Spectroscopy.

Difference circular dichroism (CD) spectroscopy was used here to characterize changes in structure of flexible peptides upon altering their environments. Environmental changes were introduced by binding to a large target structure, temperature shift (or concentration increase) or so-called membrane-mimicking solvents. The first case involved binding of a largely disordered peptide to its target structure associated with chromatin remodeling, leading to a transition into a highly helical structure. The second example was a short 8HD (His-Asp) repeat peptide that can bind metal ions. Both Zn and Ni at µM concentrations resulted in different type of changes in secondary structure, suggesting that these metal ions provide different environments for the peptide to assume unique secondary structures. The third case is related to a few short neuroprotective peptides that were largely disordered in aqueous solution. Increased temperature resulted in induction of significant, though small, ß-sheet structures. Last example was the induction of non-helical structures for short neuroprotective peptides by membrane-mimicking solvents, including trifluoroethanol, dodecylphosphocholine and sodium dodecylsulfate. While these agents are known to induce α-helix, none of the neuropeptides underwent transition to a typical helical structure. However, trifluoroethanol did induce α-helix for the first peptide involved in chromatin remodeling described above in the first example.

Procedure-Related Complications and Survival after Gastrostomy: Results from a Japanese Cohort.

INTRODUCTION: In 2010, a large-scale multi-institutional study in Japan showed a good prognosis for percutaneous endoscopic gastrostomy (PEG). However, the function and efficacy of PEG are not fully understood by patients, families, and health-care professionals; thus, the number of PEG treatments in Japan has declined. Therefore, we aimed to investigate the safety of the PEG procedure and subsequent survival after PEG. METHODS: In total, 249 PEGs were performed at Juzenkai Hospital from 2005 to 2017. PEG was originally performed using the pull method and then by a modified introducer method from mid-2011. We examined procedure-related complications and survival rates after PEG. RESULTS: Fifty-one (20.5%) procedure-related complications occurred; emergency surgery was required in 4 cases. Infections accounted for 76.5% (39/51) of complications. More infections occurred with the pull method than with the modified introducer method. The 1-year survival rate was 66.8%; the median survival time was 678 days. Nine patients (3.6%) died within 30 days; no deaths were directly related to PEG. Sex, age, and albumin level before surgery significantly influenced the prognosis. CONCLUSION: Due to changes in the PEG insertion method and other factors, PEG has become a safer treatment method. Additionally, PEG-based nutritional supplementation is associated with adequate survival.

Protein Solvent Interaction: Transition of Protein-solvent Interaction Concept from Basic Research into Solvent Manipulation of Chromatography.

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.

Capto MMC mixed-mode chromatography of murine and rabbit antibodies.

Murine antibodies have weak affinity for Protein-A. Here, we have tested binding of murine monoclonal antibody (mAb) to Protein-A or Protein-A/Protein-G mixture under salting-out conditions. The addition of ammonium sulfate to HEK conditioned medium (CM) expressing murine mAb resulted in complete binding, leading to its elution by low pH or neutral arginine solution. Alternatively, a mixed-mode chromatography using Capto MMC resin was developed as a capture step. Binding of murine mAb occurred at neutral pH. The bound mAb was eluted with a gradient from 0.3 M NaCl to 0.3 M arginine/0.3 M NaCl at pH 7.0. The Capto MMC-purified murine mAb was further purified by hydroxyl apatite chromatography. Similarly, rabbit mAb was processed with some modifications. Binding of rabbit mAb to Capto MMC required a lower pH. Elution of the bound rabbit mAb was achieved by a gradient to 0.3 M NaCl, pH 7.0.

SUMO3 modification accelerates the aggregation of ALS-linked SOD1 mutants.

Mutations in superoxide dismutase 1 (SOD1) are a major cause of familial amyotrophic lateral sclerosis (ALS), whereby the mutant proteins misfold and aggregate to form intracellular inclusions. We report that both small ubiquitin-like modifier (SUMO) 1 and SUMO2/3 modify ALS-linked SOD1 mutant proteins at lysine 75 in a motoneuronal cell line, the cell type affected in ALS. In these cells, SUMO1 modification occurred on both lysine 75 and lysine 9 of SOD1, and modification of ALS-linked SOD1 mutant proteins by SUMO3, rather than by SUMO1, significantly increased the stability of the proteins and accelerated intracellular aggregate formation. These findings suggest the contribution of sumoylation, particularly by SUMO3, to the protein aggregation process underlying the pathogenesis of ALS.

Multi-faceted arginine: mechanism of the effects of arginine on protein.

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.

Inactive C8A­humanin analog is as stable as a potent S14G­humanin analog.

We have previously shown that the structural stability of humanin (HN), a neuroprotective peptide ligand, is one of the attributes to the observed activity differences between HN analogs. It has been observed that the activity increased consecutively in the S7A­HN analog, the parent HN and the S14G­HN analog, consistent with the increased stability observed in that order. In the present study, the structure and stability of another inactive analog, C8A­HN, was measured, which has been revealed to have no neuroprotective activity similar to that of the S7A­HN analog and hence may have compromised stability. While all these analogs of HN demonstrated a similar disordered secondary structure in phosphate-buffered saline at 5˚C, as determined by circular dichroism spectroscopy, they revealed different structures at 37˚C. At 37˚C, less active HN and inactive S7A­HN revealed a structure with a valley at ~217 nm, indicating a conversion from the disordered structure to a ß­sheet. Such a conversion was largely irreversible. By contrast, C8A­HN and S14G­HN demonstrated a similar structure at 37˚C and at 5˚C and remained largely disordered. The observed small structural changes of the C8A­HN analog at 37˚C and its reversibility upon cooling do not support a hypothesis that the instability at 37˚C may have caused the reduced activity of this analog. Therefore an alternative explanation for its activity loss is required.

Structural characteristics of short peptides in solution.

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 ß-amyloid formation. These structural characteristics of short peptides have drastic impact on their function, immunogenicity, and storage stability.

Interactions of formulation excipients with proteins in solution and in the dried state.

A variety of excipients are used to stabilize proteins, suppress protein aggregation, reduce surface adsorption, or to simply provide physiological osmolality. The stabilizers encompass a wide variety of molecules including sugars, salts, polymers, surfactants, and amino acids, in particular arginine. The effects of these excipients on protein stability in solution are mainly caused by their interaction with the protein and the container surface, and most importantly with water. Some excipients stabilize proteins in solution by direct binding, while others use a number of fundamentally different mechanisms that involve indirect interactions. In the dry state, any effects that the excipients confer to proteins through their interactions with water are irrelevant, as water is no longer present. Rather, the excipients stabilize proteins through direct binding and their effects on the physical properties of the dried powder. This review will describe a number of mechanisms by which the excipients interact with proteins in solution and with various interfaces, and their effects on the physical properties of the dried protein structure, and explain how the various interaction forces are related to their observed effects on protein stability.

The biological activity of Humanin analogs correlates with structure stabilities in solution.

A single mutation has resulted in large differences in neuroprotective activity of a 24 amino acid Humanin (HN). A mutation of Ser7Ala (S7A-HN) resulted in loss of activity, while a mutation of Ser14Gly (S14G-HN) resulted in about 1000-fold increase. The mechanism of the effects conferred by these mutations have been totally unclear, although our recent structure analysis suggested a possibility of the effect of mutation on the structure stability. Here, we have studied the effects of buffer and temperature on the structure of these three HN peptides. These peptides showed a similar disordered structure at 10°C in 10mM phosphate, pH 6.0. They were also similar in phosphate-buffered saline (PBS) as long as the temperature was kept low at 10°C. However, a large difference was observed in both phosphate buffer and PBS between the peptides, when the temperature was raised to a physiological temperature of 37°C. While S14G-HN showed small changes in both solutions at 37°C, the less active HN and inactive S7A-HN showed much larger changes under the identical conditions. In addition, it appeared that structure change at 37°C was faster for S7A-HN than HN. These results show that the structure stability at 37°C increases in the order of S7A-HN, HN and S14G-HN, in correlation with their neuroprotective activities.

Structure of three Humanin peptides with different activities upon interaction with liposome.

We have recently shown that a 24 amino acid Humanin (HN) adopts an anti-parallel ß-sheet structure in the presence of a negatively charged 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG) and suggested a possibility that it interacts with lipid membranes and thereby exerts neuroprotective effects through the target cell surface receptors or the intracellular signaling molecules following membrane interaction events. The structures of two HN analogs, having either a S7A mutation or a S14G mutation, were examined under the identical conditions, as the S7A analog is inactive and the S14G analog is 1000-fold more active than the wild type HN. These analogs showed a secondary structure indistinguishable from the structure of HN in the presence of DOPG liposome, while unrelated peptides were disordered with and without DOPG. It thus appeared that HN and the analogs, regardless of the biological activities, have an ability to interact with DOPG liposome and form an anti-parallel ß-sheet structure. While the wild type HN and the S7A and S14G analogs were largely disordered in buffer, the S14G analog showed greater stability as a disordered structure in the buffer at a physiological temperature, suggesting that it maintains the disordered structure presumably required for the interaction with the DOPG liposome and thereby greater neuroprotective activity.

Chemical and pharmacological chaperones: application for recombinant protein production and protein folding diseases.

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.

Structure changes of natively disordered Humanin in the presence of lipid.

While neuroprotective activities of Humanin peptides have been clearly demonstrated, the functional mechanism has not been fully understood. Humanin and a majority of Humanin analogs showed a disordered structure at low peptide concentrations and aggregation at higher concentrations in aqueous solution at pH 7.0. Here we have examined the structure in lipid environments, i.e., in the presence of liposome by circular dichroism. Humanin underwent a large structure change into a typical beta-sheet structure at neutral pH in the presence liposome made of a negatively charged 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG), but not an electrically neutral 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC). As Humanin possesses a positive charge at neutral pH, the observed structure changes with DOPG suggest electrostatic binding of the peptide with the lipid. No effect of NaCl on the Humanin structure was observed in neutral solution and in the presence of DOPC liposome. Increasing temperature resulted in changes in the structure due to aggregation. On the other hand, the effects of temperature on the Humanin structure showed that it has a relatively stable structure in the presence of DOPG liposome independent of the presence of NaCl.

Stabilizing and destabilizing effects of arginine on deoxyribonucleic acid.

Aqueous arginine solution now finds a wide range of applications in biotechnology fields, including protein refolding, chromatography and virus inactivation. While progress has been made for mechanistic understanding of the effects of arginine on proteins, we have little understanding on how arginine inactivates viruses. One of the viral components is nucleic acid. We have examined the effects of arginine on the structure and thermal stability of calf thymus deoxyribonucleic acid (DNA) using circular dichroism (CD). Both NaCl and arginine reduced CD intensity. At low concentrations, arginine showed a stronger effect on CD intensity than NaCl. Both NaCl and arginine sharply increased the melting temperature at low concentrations (below 0.25 M). However, they had an opposite effect at higher concentrations. Above this concentration, NaCl gradually increased the melting temperature, leading to the onset melting temperature above 90 degrees C. On the other hand, the thermal stability in the presence of arginine reached a maximum at 0.2-0.5 M, after which further addition of arginine caused decreased melting temperature. It is most likely that the increased melting temperature at low concentration is due to electrostatic stabilization of DNA structure by both NaCl and arginine and that the opposite effects at higher salt concentration are due to salt-specific effects, i.e., stabilizing (salting-out) effects of NaCl and destabilizing (salting-in) effects of arginine. Solubility measurements of nucleic acid bases showed that arginine, but not NaCl, increases the solubilities of the bases, supporting their effects on DNA stability at higher concentration.

MEP HyperCel chromatography II: binding, washing and elution.

Binding, washing and elution conditions for MEP HyperCel chromatography were examined using two conditioned media (CM) containing monoclonal antibodies (humanized IgG1) and bovine serum albumin (BSA). Monoclonal antibodies derived from mammalian expression system bound to the column without pretreatment, although a majority of contaminating proteins present in the CM also showed binding. Inorganic salts, ethanol and glycerol were ineffective in eluting proteins under the conditions examined, suggesting that electrostatic or hydrophobic interactions are not a major factor for antibody binding to the MEP resin. Ethylene glycol, 2-propanol, urea and arginine were effective, to varying degrees, in elution of the bound proteins. The bound contaminating proteins and BSA were effectively eluted with ethylene glycol and the bound antibodies were finally eluted with aqueous arginine solutions at neutral pH. MEP showed selectivity toward BSA and hence utility for removing BSA from the samples. Interestingly, Fc-fusion proteins derived from silkworm larvae showed no detectable binding. Serum proteins present in silkworm larvae strongly competed with the Fc-fusion proteins and monoclonal antibody for binding to MEP resin, while the same Fc-fusion proteins can be readily purified in one-step by Protein-A resin, again confirming weak selectivity of the MEP resin.

Stress-free chromatography: affinity chromatography.

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.