The effect of Cu2+ on arginine kinase from Euphausia superba: A computational simulation integrating unfolding and aggregation studies

Characterization and activity-folding relationship of serine protease from Antarctic krill (Euphausia superba)

Euphausia superba (Antarctic krill) serine protease (ESP) was investigated to gain insights into the activity-structural relationship, folding behavior, and regulation of the catalytic function. We purified ESP from the krill muscle and characterized biochemical distinctions via enzyme kinetics. Studies of inhibition kinetics and unfolding in the presence of a serine residue modifier, such as phenylmethanesulfonyl fluoride, were conducted. Structural characterizations were measured by spectrofluorimetry, including 1-anilinonaphthalene-8-sulfonate dye labeling for hydrophobic residues. The computational simulations such as docking and molecular dynamics were finally conducted to detect key residues and folding behaviors in a nano-second range. The kinetic parameters of ESP were measured as K_m^BANH = 0.97 ± 0.15 mM and k_cat/K_m^BANH = 4.59 s^-1/mM. The time-interval kinetics measurements indicated that ESP inactivation was transformed from a monophase to a biphase process to form a thermodynamically stable state. Spectrofluorimetry measurements showed that serine is directly connected to the regional folding of ESP. Several osmolytes such as proline and glycine only partially protected the inactive form of ESP by serine modification. Computational molecular dynamics and docking simulations showed that three serine residues (Ser183, Ser188, and Ser207) and Cys184, Val206, and Gly209 are key residues of catalytic functions. Our study revealed the functional roles of serine residues as key residues of catalytic function at the active site and of the structural conformation as key folding factors, where ESP displays a flexible property of active site pocket compared to the overall structure.Communicated by Ramaswamy H. Sarma.

Biochemical Study of Fibrinolytic Protease from Euphausia superba Possessing Multifunctional Serine Protease Activity

BACKGROUND

Fibrinolytic protease from Euphausia superba (EFP) was isolated.

OBJECTIVE

Biochemical distinctions, regulation of the catalytic function, and the key residues of EFP were investigated.

METHODS

The serial inhibition kinetic evaluations coupled with measurements of fluorescence spectra in the presence of 4-(2-aminoethyl) benzene sulfonyl fluoride hydrochloride (AEBSF) was conducted. The computational molecular dynamics (MD) simulations were also applied for a comparative study.

RESULTS

The enzyme behaved as a monomeric protein with a molecular mass of about 28.6 kD with K_m ^BApNA = 0.629 ± 0.02 mM and k_cat/K_m ^BApNA = 7.08 s-1/mM. The real-time interval measurements revealed that the inactivation was a first-order reaction, with the kinetic processes shifting from a monophase to a biphase. Measurements of fluorescence spectra showed that serine residue modification by AEBSF directly caused conspicuous changes of the tertiary structures and exposed hydrophobic surfaces. Some osmolytes were applied to find protective roles. These results confirmed that the active region of EFP is more flexible than the overall enzyme molecule and serine, as the key residue, is associated with the regional unfolding of EFP in addition to its catalytic role. The MD simulations were supportive to the kinetics data.

CONCLUSION

Our study indicated that EFP has an essential serine residue for its catalyst function and associated folding behaviors. Also, the functional role of osmolytes such as proline and glycine that may play a role in defense mechanisms from environmental adaptation in a krill's body was suggested.

Effect of Cd2+ on muscle type of creatine kinase: Inhibition kinetics integrating computational simulations

Creatine kinase (EC 2.7.3.2, CK) plays an important role in cellular energy metabolism and homeostasis by catalyzing the transfer of phosphate between ATP and creatine phosphate. We investigated the effects of Cd2+ on muscle type of creatine kinase from Pelodiscus sinensis (PSCKM). Cd2+ conspicuously inactivated the activity of PSCKM (IC50=0.062 mM) in a first-order kinetic process and exhibited non-competitive inhibition with creatine and ATP. A conformational study showed that Cd2+ induced tertiary structure changes in PSCKM with exposure of hydrophobic surfaces. The addition of osmolytes, such as glycine and proline, partially reactivated the Cd2+-mediated inactive PSCKM. Additionally, molecular dynamics and docking simulations between PSCKM and Cd2+ were conducted to show that Cd2+ blocked the entrance of ATP to the active site, and this result is consistent with the experimental results showing Cd2+-induced inactivation of PSCKM. Our study demonstrates the effect of Cd2+ on PSCKM enzymatic function and unfolding, including the protective effects of osmolytes on PSCKM inactivation. This study provides important insights into the changes in the PSCKM metabolic enzyme of ectothermic animals in response to the environment.