Native-State Heterogeneity of β2-Microglobulin as Revealed by Kinetic Folding and Real-Time NMR Experiments

The kinetic folding of β₂-microglobulin from the acid-denatured state was investigated by interrupted-unfolding and interrupted-refolding experiments using stopped-flow double-jump techniques. In the interrupted unfolding, we first unfolded the protein by a pH jump from pH 7.5 to pH 2.0, and the kinetic refolding assay was carried out by the reverse pH jump by monitoring tryptophan fluorescence. Similarly, in the interrupted refolding, we first refolded the protein by a pH jump from pH 2.0 to pH 7.5 and used a guanidine hydrochloride (GdnHCl) concentration jump as well as the reverse pH jump as unfolding assays. Based on these experiments, the folding is represented by a parallel-pathway model, in which the molecule with the correct Pro32 cis isomer refolds rapidly with a rate constant of 5–6 s^? 1, while the molecule with the Pro32 trans isomer refolds more slowly (pH 7.5 and 25 °C). At the last step of folding, the native-like trans conformer produced on the latter pathway isomerizes very slowly (0.001–0.002 s^? 1) into the native cis conformer. In the GdnHCl-induced unfolding assays in the interrupted refolding, the native-like trans conformer unfolded remarkably faster than the native cis conformer, and the direct GdnHCl-induced unfolding was also biphasic, indicating that the native-like trans conformer is populated at a significant level under the native condition. The one-dimensional NMR and the real-time NMR experiments of refolding further indicated that the population of the trans conformer increases up to 7–9% under a more physiological condition (pH 7.5 and 37 °C).     

Dynamics of thermodynamically stable, kinetically trapped, and inhibitor-bound states of pepsin

The pepsin folding mechanism involves a prosegment (PS) domain that catalyzes folding, which is then removed, resulting in a kinetically trapped native state. Although native pepsin (Np) is kinetically stable, it is irreversibly denatured due to a large folding barrier, and in the absence of the PS it folds to a more thermodynamically stable denatured state, termed refolded pepsin (Rp). This system serves as a model to understand the nature of kinetic barriers and folding transitions between compact states. Quasielastic neutron scattering (QENS) was used to characterize and compare the flexibility of Np, as a kinetically trapped state, with that of Rp, as a thermodynamically stable fold. Additionally, the dynamics of Np were compared with those of a partially unfolded form and a thermally stabilized, inhibitor-bound form. QENS revealed length-scale-dependent differences between Np and Rp on a picosecond timescale and indicated greater flexibility in Np, leading to the conclusion that kinetic stabilization likely does not correspond to reduced internal dynamics. Furthermore, large differences were observed upon inhibition, indicating that QENS of proteins in solution may prove useful for examining the role of conformational entropy changes in ligand binding.     

Recombinant prosegment peptide acts as a folding catalyst and inhibitor of native pepsin

Porcine pepsin A, a gastric aspartic peptidase, is initially produced as the zymogen pepsinogen that contains an N-terminal, 44 residue prosegment (PS) domain. In the absence of the PS, native pepsin (Np) is irreversibly denatured and when placed under refolding conditions, folds to a thermodynamically stable denatured state. This denatured, refolded pepsin (Rp) state can be converted to Np by the exogenous addition of the PS, which catalyzes the folding of Rp to Np. In order to thoroughly study the mechanism by which the PS catalyzes pepsin folding, a soluble protein expression system was developed to produce recombinant PS peptide in a highly pure form. Using this system, the wild-type and three-mutant PS forms, in which single residue substitutions were made (V4A, R8A and K36A), were expressed and purified. These PS peptides were characterized for their ability to inhibit Np enzymatic activity and to catalyze the folding of Rp to Np. The V4A, R8A and K36A mutant PS peptides were found to have nanomolar inhibition constants, K_i, of 82.4, 58.3 and 95.6 nM, respectively, approximately a two-fold increase from that of the wild-type PS (36.2 nM). All three-mutant PS peptides were found to catalyze Np folding with a rate constant of 0.06 min^? 1, five-fold lower than that of the wild-type. The observation that the mutant PS peptides retained their inhibition and folding-catalyst functionality suggests a high level of resilience to mutations of the pepsin PS.     

Folding and aggregation of a multi-domain engineered immunotoxin

Engineered immunotoxins with specific targeting mechanisms have potential applications for the treatment of cancer and other diseases; however, their folding behavior is often poorly understood and this presents challenges during process development, manufacturing, and formulation. Folding thermodynamics of an antibody variable domain (V_H/V_L) genetically fused to a biological toxin payload were characterized at pH 6.0 and pH 8.0 in order to assess the relative domain stabilities, along with time scales on which they fold, and the competition between aggregation and folding. The toxin and V_H/V_L domains had considerably different unfolding free energies (ΔG_UNF), leading to a thermodynamically-distinct intermediate species, with the toxin domain unfolded and the V_H/V_L folded. The intermediate is the majority species over a range of denaturant concentrations (∼4–6 M urea; ∼2–4 M guanidine HCl). Thermal unfolding resulted in reversible unfolding of the toxin domain at pH 8, but at pH 6 thermal unfolding was convoluted with aggregation due to irreversible unfolding and aggregation for the V_H/V_L domain. Chemical unfolding of both domains was more easily reversible, provided that the refold was done stepwise, allowing the antibody domain to fold first at intermediate denaturant concentration, as folding of the V_H/V_L domain played a key role in aggregation of this antibody fusion protein.     

The interplay between protein stability and dynamics in conformational diseases: The case of hPGK1 deficiency

Conformational diseases often show defective protein folding efficiency in vivo upon mutation, affecting protein properties such as thermodynamic stability and folding/unfolding/misfolding kinetics as well as the interactions of the protein with the protein homeostasis network. Human phosphoglycerate kinase 1 (hPGK1) deficiency is a rare inherited disease caused by mutations in hPGK1 that lead to loss-of-function. This disease offers an excellent opportunity to explore the complex relationships between protein stability and dynamics because of the different unfolding mechanisms displayed towards chemical and thermal denaturation. This work explores these relationships using two thermostable mutants (p.E252A and p.T378P) causing hPGK1 deficiency and WT hPGK1 using proteolysis and chemical denaturation. p.T378P is degraded ~ 30-fold faster at low protease concentrations (here, the proteolysis step is rate-limiting) and ~ 3-fold faster at high protease concentrations (where unfolding kinetics is rate-limiting) than WT and p.E252A, indicating that p.T378P is thermodynamically and kinetically destabilized. Urea denaturation studies support the decrease in thermodynamic stability and folding cooperativity for p.T378P, as well as changes in folding/unfolding kinetics. The present study reveals changes in the folding landscape of hPGK1 upon mutation that may affect protein folding efficiency and stability in vivo, also suggesting that native state stabilizers and protein homeostasis modulators may help to correct folding defects in hPGK1 deficiency. Moreover, detailed kinetic proteolysis studies are shown to be powerful and simple tools to provide deep insight into mutational effects on protein folding and stability in conformational diseases.     

The Molten Globule of β2-Microglobulin Accumulated at pH 4 and Its Role in Protein Folding

The acid transition of β₂-microglobulin (β2m) was studied by tryptophan fluorescence, peptide circular dichroism, and NMR spectroscopy. The protein exhibits a three-state transition with an equilibrium intermediate accumulated at pH 4 (25 °C). The pH 4 intermediate has typical characteristics of the molten globule (MG) state; it showed a native-like secondary structure without specific side-chain tertiary structure, and the hydrodynamic radius determined by pulse field gradient NMR was only 20% larger than that of the native state. The accumulation of the pH 4 intermediate is very analogous to the behavior of apomyoglobin, for which the pH 4 MG has been well characterized, although β2m, a β-protein, is structurally very different from α-helical apomyoglobin. NMR pH titration of histidine residues of β2m has also indicated that His84 has an abnormally low pK_a value in the native state. From the pH dependence of the unfolding transition, the protonations of this histidine and 10 weakly abnormal carboxylates triggered the transition from the native to the MG state. This behavior is again analogous to that of apomyoglobin, suggesting a common mechanism of production of the pH 4 MG. In contrast to the folding of apomyoglobin, in which the MG was equivalent to the burst-phase kinetic folding intermediate, the burst-phase refolding intermediate of β2m, detected by stopped-flow circular dichroism, was significantly more structured than the pH 4 intermediate. It is proposed that the folding of β2m from its acid-denatured state takes place in the following order: denatured state → MG → burst-phase intermediate → native state.     

The differential stability of the left and right domains of papain

We have investigated the differential stability of the two domains of papain, a broad specific cysteine protease, which is one of the most commonly used enzyme in various industries. The denaturant induced equilibrium unfolding of this enzyme has been investigated by different spectroscopic techniques. By site specific fluorescent labeling of one of the domain, we observed that during the unfolding process, L domain unfolds first and the R domain unfolds at a later stage. Spectroscopic studies reveal a biphasic unfolding transition, suggesting the presence of an intermediate during the unfolding process. The intermediate is observed between 1.5 and 2.5 M GuHCl and between 3 and 5 M in the case of urea induced unfolding. The unfolding process for both native to intermediate and intermediate to unfolded species is reversible in the case of urea unfolding, with a ΔG of ?2.4 and ?5.5 kcal/mole respectively where as for GuHCl unfolding only native to intermediate species is reversible indicating the predominance of hydrophobic interactions in the stability of the molecule.     

A novel organic solvent-stable alkaline protease from organic solvent–tolerant Bacillus licheniformis YP1A

An organic solvent-stable alkaline protease producing bacterium was isolated from the crude oil contaminant soil and identified as Bacillus licheniformis. The enzyme retained more than 95% of its initial activity after pre-incubation at 40 °C for 1 h in the presence of 50% (v/v) organic solvents such as DMSO, DMF, and cyclohexane. The protease was active in a broad range of pH from 8.0 to 12.0 with the optimum pH 9.5. The optimum temperature for this protease activity was 60 °C, and the enzyme remained active after incubation at 50–60 °C for 1 h. This organic solvent-stable protease could be used as a biocatalyst for organic solvent-based enzymatic synthesis.     

Activation of human biliverdin-IXα reductase by urea: Generation of kinetically distinct forms during the unfolding pathway

Activation of enzymes by low concentrations of denaturants has been reported for a limited number of enzymes including lipocalin-type prostaglandin D synthase (L-PGDS) and adenylate kinase. During unfolding studies on human biliverdin-IXα reductase it was discovered that the enzyme is activated at low concentrations of urea. Under standard assay conditions the native enzyme displays pronounced substrate inhibition with biliverdin as variable substrate; however in the presence of 3 M urea, the substrate inhibition is abolished and the enzyme exhibits Michaelian kinetics. When the initial rate kinetics with NADPH as variable substrate are conducted in 3 M urea, the V_max is increased 11-fold to 1.8 μmol/min/mg and the apparent K_m for biliverdin increases from 1 to 3 μM. We report the existence of two kinetically distinct folded intermediates between the native and unfolded forms. When the period of incubation with urea was varied prior to measuring enzyme activity, the apparent V_max was shown to decay to half that seen at zero time with a half life of 5.8 minutes, while the apparent K_m for NADPH remains constant at approximately 5 μM. With NADH as cofactor the half life of the activated (A) form was 2.9 minutes, and this form decays in 3 M urea to a less active (LA) form. The apparent K_m for NADH increases from 0.33 mM to 2 mM for the A and LA forms. These kinetically distinct species are reminiscent of the activity-enhanced and inactive forms of L-PGDS observed in the presence of urea and guanidine hydrochloride.     

Influence of chemical denaturants on the activity,fold and zinc status of anthrax lethal factor

Anthrax lethal factor (LF) is a zinc-dependent endopeptidase which, through a process facilitated by protective antigen, translocates to the host cell cytosol in a partially unfolded state. In the current report, the influence of urea and guanidine hydrochloride (GdnHCl) on LF?s catalytic function, fold and metal binding was assessed at neutral pH. Both urea and GdnHCl were found to inhibit LF prior to the onset of unfolding, with the inhibition by the latter denaturant being a consequence of its ionic strength. With the exception of demetallated LF (apoLF) in urea, unfolding, as monitored by tryptophan fluorescence spectroscopy, was found to follow a two-state (native to unfolded) mechanism. Analysis of the metal status of LF with 4-(2-pyridylazoresorcinol) (PAR) following urea or GdnHCl exposure suggests the enzyme to be capable of maintaining its metal ion passed the observed unfolding transition in a chelator-inaccessible form. Although an increase in the concentration of the denaturants eventually allowed the chelator access to the protein?s zinc ion, such process is not correlated with the release of the metal ion. Indeed, significant dissociation of the zinc ion from LF was not observed even at 6 M urea, and only high concentrations of GdnHCl (>3 M) were capable of inducing the release of the metal ion from the protein. Hence, the current study demonstrates not only the propensity of LF to tightly bind its zinc ion beyond the spectroscopically determined unfolding transition, but also the utility of PAR as a structural probe.     

Gel properties and molecular forces of lamb myofibrillar protein during heat induction at different pH values

The gel properties and molecular forces of the Aohan Merino lamb myofibrillar protein (MP) were investigated during heat induction at different pH levels. The effects of pH values (from 5.0 to 8.5) on the lamb MP gel textures and water-holding capacities were analyzed. The protein gels had the lowest water-holding capacity and a disordered microstructure at pH 5.5 (P < 0.05) and had the lowest level of hardness at pH 6.5 (P < 0.05). The hardness and water-holding capacity were found to be the highest at pH 8.0 (P < 0.05), which coincided with a compact and ordered microstructure. At these three representative pH values, hydrophobic interactions were the main forces that were observed during gel formation, but the pH level also influenced the formation of ionic and hydrogen bonds. Different mechanisms of gel formation were therefore observed at different pH values. In conclusion, the formation of heat-induced gels with different properties was a result of the dominant molecular forces that are regulated by pH. These findings provide a theoretical basis for the innovation of heat-induced gel lamb products.     

Demineralization of crab shell waste by Pseudomonas aeruginosa F722

Crab shell (CS) waste samples (particle size 3–10 and 20–35 mm) were inoculated with the newly isolated Pseudomonas aeruginosa F722 to study the efficiency of microbial demineralization (DM) and deproteinization (DP) in the process of extracting chitin. The inoculated waste was incubated for 7 days at 25, 30 and 35 °C. Various concentrations of glucose were supplemented as carbon source. At the optimal temperature of 30 °C, DM was 92% and DP was 63% DP, whereas the pH dropped from initial pH 8.0 to 4.1. In comparative experiments with different amounts of CS waste, 5% CS waste treatment was shown to be the optimal amount for efficient DM. A positive relationship is correlated between DM and glucose concentration (r² = 0.821), whereas a negative relationship is correlated between DM and pH (r² = 0.793). DP and protease activity were little affected by different crab shell sizes.     

Isolation,purification and biochemical characterization of dipeptidyl peptidase-III from germinated Vigna radiata seeds

Genome analysis of plants indicated majority of putative protease genes that need characterization at enzymatic and molecular level. Proteases execute important role in seed development but knowledge of dipeptidylpeptidases in seeds is limited. A dipeptidylpeptidase-III that cleaves Arg-Arg from Arg-Arg-4mβNA was purified from germinated Mung bean seeds. Screening of cereals and legumes for DPP-III revealed highest activity in Phaseolus vulgaris and Vigna radiata (variety P.9531) seeds germinated for 48 h. Homogenate (10%) was acid precipitated upto pH 4.2 and then subjected to 0–55% ammonium sulphate precipitation followed by successive chromatographies on cation exchanger, gel filtration and anion exchanger. Enzyme purity was confirmed by native polyacrylamide gel electrophoresis and in situ gel assays. DPP-III is a heterodimer of ～60 kDa with two subunits of 32.8 kDa and 27 kDa on SDS-PAGE. DPP-III worked optimally at pH 8.0 and at 37 °C with pH stability between 7.5 to 9.5. Arg-Arg-4mβNA was preferred substrate and none of endopeptidase and monopeptidase substrates were hydrolysed. Inhibitors studies revealed it as thiol protease with involvement of metals at active site. The enzyme might be involved in plant's development by generating/deactivating bioactive peptides. Further studies on functional characterization and molecular structure are in progress in our laboratory.     

Degradation of chitin and production of bioactive materials by bioconversion of squid pens

Serratia marcescens TKU011, a protease- and chitosanase-producing bacterium, the optimized condition for protease and chitosanase production was found after the media were heated at 121 °C for 120 min and the culture was shaken at 25 °C for 5 days in 100 mL of medium containing 1% squid pen powder (SPP) (w/v), 0.1% K₂HPO₄, and 0.05% MgSO₄. An extracellular metalloprotease with novel properties of solvent stable, and alkaline was purified from the culture supernatant of S. marcescens TKU011 with squid pen wastes as the sole carbon/nitrogen source. The enzyme was a monomeric protease with a molecular mass of 48–50 kDa by SDS–PAGE and gel filtration chromatography. The optimum pH, optimum temperature, pH stability, and thermal stability of TKU011 protease were 8, 50 °C, pH 5–11, and <40 °C, respectively. Besides protease and chitosanase, with this method, deproteinization of squid pen for β-chitin, the production of peptide and reducing sugar may be useful for biological applications.     

Production of novel halo-alkali-thermo-stable xylanase by a newly isolated moderately halophilic and alkali-tolerant Gracilibacillus sp. TSCPVG

An aerobic xylanolytic Gracilibacillus sp. TSCPVG growing at moderate to extreme salinity (1–30%) and neutral to alkaline pH (6.5–10.5) was isolated from the salt fields near Sambhar district of Rajasthan, India. β-xylanase (18.44 U/ml) and β-xylosidase (1.01 U/ml) were produced in 60 h in the GSL-2 mineral base medium with additions of (in g/l) Birchwood xylan (7.5), yeast extract (10.0), tryptone (8.0), proline (2.0), thiamine (2.0), Tween-40 (2.0) and NaCl (35) at pH 7.5, 30 °C and 180 rpm. The β-xylanase was active within a broad salinity range (0–30% NaCl), pH (5.0–10.5) and temperature (50–70 °C). It exhibited maximal activity with 3.5% NaCl, pH 7.5 at 60 °C. It was extremely halotolerant retaining more than 80% of activity at 0 and 30% NaCl and alkali-tolerant retaining 76% of activity at pH 10.5. The acetone precipitated xylanase was highly stable (100%) at variable salinities of 0–30% NaCl, pH of 5.0–10.5 and temperatures of 0–60 °C for 48 h. HPLC analysis showed xylose, arabinose and xylooligosaccharides as hydrolysis products of xylan. This is the first report on hemi-cellulose degrading halo-alkali-thermotolerant enzyme from a moderately halophilic Gram-positive Gracilibacillus species.     

Iron containing keratinolytic metallo-protease produced by Chryseobacterium gleum

Chryseobacterium gleum exhibited complete dissolution of whole chicken-feathers (10 g l^?1, pH 8) after 72 h at 30 °C through synthesis of keratinolytic protease when inoculated at 1% (v/v). This enzyme was purified to 67-fold with yield of 2.25% having a specific activity of 1670 U mg^?1 and ～36 kDa Mw. MALDI-TOF MS of this keratinase showed some similarity with the keratinase peptides of Bacillus subtilis (BOFXJ2). The keratinase action was inhibited by EDTA, iodoacetamide and metal ions like mercury, copper and zinc (1 mM each), while it was enhanced by iron and calcium. Keratinase showed presence of 3 mM of Fe M^?1 as tested by atomic absorption spectroscopy and addition of Fe in its apoenzyme retained about 79% of original residual feather degradation activity which portrayed it to be metalloprotease. Purified keratinase revealed significant degradation (85%) of feather concentrate (20 g l^?1) to 3.9 μM ml^?1 of free amino groups in 24 h at an initial pH of 8.0, 30 °C and 120 rpm shaking. This keratinase activity can be controlled precisely by presence of chemical or metal ions which could be of use in biotechnology industry while the culture can be used in poultry waste management.     

Purification and characterization of two thermostable protease fractions from Bacillus megaterium

Protease enzyme from Bacillus megaterium was successively purified by ammonium sulfate precipitation, ion exchange chromatography on DEAE-cellulose and gel filtration chromatography on Sephadex G-200. The purification steps of protease resulted in the production of two protease fractions namely protease P1 and P2 with specific activities of 561.27 and 317.23 U mg^?1 of protein, respectively. The molecular weights of B. megaterium P1 and P2 were 28 and 25 KDa, respectively. The purified fractions P1 and P2 were rich in aspartic acid and serine. Relatively higher amounts of alanine, leucine, glycine, valine, thereonine valine and glutamic acid were also present. The maximum protease activities for both enzyme fractions were attained at 50 °C, pH 7.5, 1% of gelatine concentration and 0.5 enzyme concentrations. P1 and P2 fractions were more stable over pH 7.0–8.5 and able to prolong their thermal stability up to 80 °C. The effect of different inhibitors on the protease activity of both enzyme fractions was also studied. The enzyme was found to be serine active as it had been affected by lower concentrations of phenylmethylsulfonyl fluoride (PMSF). Complete dehairing of the enzyme-treated skin was achieved in 12 h, at room temperature.     

Purification,characterization and secondary structure elucidation of a detergent stable,halotolerant, thermoalkaline protease from Bacillus cereus SIU1

A thermoalkaline protease with a molecular weight of 22 kDa was purified from the Bacillus cereus SIU1 strain using a combination of Q-Sepharose and Sephadex G-75 chromatography. The kinetic analyses revealed the K_m, V_max and k_cat to be 1.09 mg ml^?1, 0.909 mg ml^?1 min^?1 and 3.11 s^?1, respectively, towards a casein substrate. The protease was most active and stable at pH 9.0 and between a temperature range of 45–55 °C. It was fully stable at 0.0–2.0% and moderately stable at 2.5–10.0% (w/v) sodium chloride. Phenyl methyl sulfonyl fluoride, ethylene diamine tetra acetic acid and ascorbic acid were inhibitory with regard to enzyme activity, whereas cysteine, β-mercaptoethanol, calcium, magnesium, manganese and copper at concentration of 1.0 mM increased enzyme activity. Sodium dodecyl sulfate, Triton X-100, Tween 80, hydrogen peroxide and sodium perborate significantly enhanced protease activity at 0.1 and 1.0% concentrations. In the presence of 0.1 and 1.0% (w/v) detergents, the protease was fairly stable and retained 50–76% activity. Therefore, it may have a possible application in laundry formulations. An initial analysis of the circular dichroism (CD) spectrum in the ultraviolet range revealed that the protease is predominantly a β-pleated structure and a detailed structural composition showed ～50% β-sheets. The CD-based conformational evaluation of the protease after incubation with modulators, metal ions, detergents and at different pH values, revealed that the change in the β-content directly corresponded to the altered enzyme activity. The protease combined with detergent was able to destain blood stained cloth within 30 min.     

The effect of Zn2+ on Euphausia superba arginine kinase: Unfolding and aggregation studies

Arginine kinase plays an important role in the cellular energy metabolism of invertebrates. We investigated the effects of Zn²⁺ on the enzymatic activity and unfolding and aggregation of Euphausia superba arginine kinase (ESAK). Zn²⁺ inhibited the activity of ESAK (IC₅₀ = 0.027 ± 0.002 mM) following first-order kinetics consistent with the transition from a mono-phasic to a bi-phasic reaction. Double-reciprocal Lineweaver–Burk plots indicated that Zn²⁺ induced non-competitive inhibition of arginine and ATP. Circular dichroism spectra and spectrofluorometry results showed that Zn²⁺ induced secondary and tertiary structural changes in ESAK with exposure of hydrophobic surfaces and directly induced ESAK aggregation. The addition of osmolytes such as glycine and proline successfully blocked ESAK aggregation, recovering the conformation and activity of ESAK. Our study demonstrates the effect of Zn²⁺ on ESAK enzymatic function and folding and unfolding mechanisms, and might provide important insights into other metabolic enzymes of invertebrates in extreme climatic marine environments.     

Towards alpha-glucosidase folding induced by trifluoroethanol: Kinetics and computational prediction

Alpha-glucosidase (EC 3.2.1.20) is an enzyme, which is related with diabetes mellitus type 2 clinically, and is also generally used to convert starch to fermentable sugars in the industry. Therefore, study on this enzyme structures and functions is important. In this study, we investigated structural changes in the alpha-glucosidase during trifluoroethanol (TFE)-induced unfolding. The activity of alpha-glucosidase was significantly inactivated by TFE in a dose-dependent manner. The inactivation was composed of two-phases. TFE inhibited alpha-glucosidase in a parabolic mixed-type reaction (K_i = 0.72 ± 0.08 M). TFE directly induced the unfolding and hydrophobic exposure of alpha-glucosidase. We also simulated the docking between alpha-glucosidase and TFE, as well as molecular dynamics. The computational simulations suggested that several residues, such as ASP68, TYR71, VAL108, HIS111, PHE177, ASP214, THR215, GLU276, HIS348, ASP349, and ARG439, interact with TFE. The molecular dynamics simulation confirmed the binding mechanisms, between the alpha-glucosidase and TFE, and suggested that TFE inhibits the glucose binding site. Our study provides insights into the alpha-glucosidase folding behaviors, and cosolvent binding under a 3D structural simulation.