Len Ito

High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine

While biotechnological applications of arginine (Arg) as a solution additive that prevents protein aggregation are increasing, the molecular mechanism of its effects remains unclear. In this study, we investigated the Arg-lysozyme complex by high-resolution crystallographic analysis. Three Arg molecules were observed to be in close proximity to aromatic amino acid residues of the protein surface, and their occupancies gradually increased with increasing Arg concentration. These interactions were mediated by electrostatic, hydrophobic and cation-π interactions with the surface residues. The binding of Arg decreased the accessible surface area of aromatic residues by 40%, but increased that of charged residues by 10%. These changes might prevent intermolecular hydrophobic interactions by shielding hydrophobic regions of the lysozyme surface, resulting in an increase in protein solubility.

Enzyme switch by complementary polymer pair system (CPPS)

Manipulation of enzyme activity at will presents various research and industrial applications. Herein we describe development of a technology for inactivation and reactivation of enzyme activities using a polyanionic poly(acrylic acid) (PAAc) and a polycationic poly(allylamine) (PAA). Enzyme activities of ribonuclease A (RNase A), lysozyme, cellulase, and α-amylase were lost through addition of PAAc or PAA because of their binding to the enzymes. The activity of these enzymes except for α-amylase was then fully restored from the complex by the addition of oppositely charged polymers. Such manipulation of enzyme activity using a complementary polymer pair system (CPPS) enables the expansion of biomedical and biotechnological applications of the enzymes, including realization of protein delivery and intelligent bioreactors.

Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A.

The effect of the addition of amino acids and amino acid derivatives on the crystallization of hemoglobin and ribonuclease A has been evaluated. The results showed that certain types of additives expand the concentration conditions in which crystals are formed.

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

A new crystal-mounting method has been developed that involves a combination of controlled humid air and polymer glue for crystal coating. This method is particularly useful when applied to fragile protein crystals that are known to be sensitive to subtle changes in their physicochemical environment.

Glycine amide shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation

Glycine amide (GlyAd), a typically amidated amino acid, is a versatile additive that suppresses protein aggregation during refolding, heat treatment, and crystallization. In spite of its effectiveness, the exact mechanism by which GlyAd suppresses protein aggregation remains to be elucidated. Here, we show the crystal structure of the GlyAd–lysozyme complex by high resolution X‐ray crystallographic analysis at a 1.05 Å resolution. GlyAd bound to the lysozyme surface near aromatic residues and decreased the amount of bound waters and increased the mobility of protein. Arg and GlyAd molecules are different in binding sites and patterns from glycerol and related compounds, indicating that decreasing hydrophobic patches might be involved in suppression of protein aggregation.

Inhibition of the functional interplay between endoplasmic reticulum (ER) oxidoreduclin-1α (Ero1α) and protein-disulfide isomerase (PDI) by the endocrine disruptor bisphenol A.

Background: Protein-disulfide isomerase (PDI) has previously been identified to bind bisphenol A (BPA), an endocrine disrupter. Results: BPA inhibited Ero1α-PDI-mediated disulfide bond formation. Conclusion: BPA significantly inhibited the Ero1α and PDI oxidative cycle, probably through closure of the substrate- and Ero1α-binding pocket in the PDI b′ domain. Significance: BPA may have inhibitory effects on oxidative folding of secretory and membrane proteins. Bisphenol A (BPA) is an endocrine disruptor that may have adverse effects on human health. We recently isolated protein-disulfide isomerase (PDI) as a BPA-binding protein from rat brain homogenates and found that BPA markedly inhibited PDI activity. To elucidate mechanisms of this inhibition, detailed structural, biophysical, and functional analyses of PDI were performed in the presence of BPA. BPA binding to PDI induced significant rearrangement of the N-terminal thioredoxin domain of PDI, resulting in more compact overall structure. This conformational change led to closure of the substrate-binding pocket in b′ domain, preventing PDI from binding to unfolded proteins. The b′ domain also plays an essential role in the interplay between PDI and ER oxidoreduclin 1α (Ero1α), a flavoenzyme responsible for reoxidation of PDI. We show that BPA inhibited Ero1α-catalyzed PDI oxidation presumably by inhibiting the interaction between the b′ domain of PDI and Ero1α; the phenol groups of BPA probably compete with a highly conserved tryptophan residue, located in the protruding β-hairpin of Ero1α, for binding to PDI. Consistently, BPA slowed down the reoxidation of PDI and caused the reduction of PDI in HeLa cells, indicating that BPA has a great impact on the redox homeostasis of PDI within cells. However, BPA had no effect on the interaction between PDI and peroxiredoxin-4 (Prx4), another PDI family oxidase, suggesting that the interaction between Prx4 and PDI is different from that of Ero1α and PDI. These results indicate that BPA, a widely distributed and potentially harmful chemical, inhibits Ero1-PDI-mediated disulfide bond formation.

Comparative analysis of amino acids and amino-acid derivatives in protein crystallization

Optimal conditions for protein crystallization are difficult to determine because proteins tend to aggregate in saturated solutions. This study comprehensively evaluates amino acids and amino-acid derivatives as additives for crystallization. This fourth component of the solution increases the probability of crystallization of hen egg-white lysozyme in various precipitants owing to a decrease in aggregation. These results suggest that the addition of certain types of amino acids and amino-acid derivatives, such as Arg, Lys and esterified and amidated amino acids, is a simple method of improving the success rate of protein crystallization.

Amino acids and glycine ethyl ester as new crystallization reagents for lysozyme

Several amino acids and their derivatives are prominent additives in the field of protein chemistry. This study reports the use of charged amino acids and glycine ethyl ester as precipitants in protein crystallization, using hen egg-white lysozyme (HEWL) as a model. A discussion of the crystallization of HEWL using these reagents as precipitating agents is given.

Glutathione Ethylester, a Novel Protein Refolding Reagent, Enhances both the Efficiency of Refolding and Correct Disulfide Formation

Protein refolding constitutes a crucial process for recombinant proteins. We report here on the development of a multifunctional refolding additive, glutathione ethyl ester (GSHEE), prepared from a redox reagent glutathione and an amino acid ethyl ester, an aggregation suppressor. Compared to glutathione, GSHEE showed 3.2-fold higher efficiency for the refolding yield of hen egg lysozyme. More importantly, a low concentration of GSHEE is more effective for refolding than conventional additives, such as amino acid ethyl esters by two orders of magnitude. The high potency of GSHEE makes it a candidate for use as a refolding additive for use in conjunction with reduced and denatured proteins.

Crystallization and preliminary X-ray structural studies of human prouroguanylin.

Uroguanylin, which serves as an endogenous ligand of guanylyl cyclase C, is initially secreted in the form of a precursor, prouroguanylin. The N-terminal region of prouroguanylin interacts with the mature portion of prouroguanylin during the folding pathway. Here, a preliminary X-ray crystallographic study of prouroguanylin is presented. Prouroguanylin was refolded, purified and crystallized using the hanging-drop vapour-diffusion method. Prouroguanylin crystals were cryocooled and used for data collection. The diffraction data showed that the crystals belonged to space group P6(1)22, with unit-cell parameters a = b = 55.6, c = 157.7 A, and diffracted to 2.5 A resolution. The structure is currently being analyzed.