The effect of putrescine on stability and structural properties of bovine serum albumin.

Serum albumins are the abounding proteins in plasma. Their most important characteristic is that they act as carriers for a type of compound, for example, different drugs. Bovine Serum Albumin (BSA) is a single-chain polypeptide with 583 amino acids. Polyamines such as putrescine can interact with negatively charged molecules. The effect of putrescine on the structure of bovine serum albumin has been surveyed utilizing the method of UV-Vis spectroscopy, Thermal stability, fluorescence spectroscopy, and molecular docking at temperature 298 K and 308 K at pH 7.4 using Tris-HCl as a buffer. The complex formation between putrescine and bovine serum albumin was discovered as alter in the absorbance at 280 nm. The amount of absorption increases with the addition of putrescine. The adding of putrescine alters the bovine serum albumin and decrements the hydrophobicity of the micro-environment of the Trp residues in the inner hydrophobic zone. The static kind of quenching process was chiefly contained within the quenching of intrinsic emission of the protein. The fluorescence quenching details (Ksv) for complex bovine serum albumin-putrescine revealed one binding site for putrescine. The negative amount of Gibbs free energy change (ΔG°) suggested the binding operation was spontaneous.Communicated by Ramaswamy H. Sarma.

Experimental and theoretical investigations on the interaction of glucose molecules with myoglobin in the aqueous solution using theoretical and experimental methods.

Osmolytes are generally well-known for the stabilization of proteins. The stabilizing impact of glucose on the dynamics and structure of myoglobin was probed through molecular simulation' docking and spectroscopic procedures. Using thermal stability examinations, the thermodynamic folding properties, point of melting temp. (Tm), thermodynamic enthalpy change (ΔH°) and thermodynamic entropy change (ΔS°) were determined to find out the depiction of myoglobin folding. Glucose operated as an enhancer relative to myoglobin stabilization. The quenching static model was demonstrated by fluorescence spectroscopy. There was one binding site. According to the spectroscopy analysis, glucose was capable of protecting the native structural conformation of protein as well as preventing from protein unfolding. The fluorescence spectroscopy together with simulation through molecular docking method revealed that definitely hydrogen bonding plus van der Waals forces had major contributions to the stabilization of the myoglobin-glucose complex. Hence, the direct interactions contributed slightly to the stabilization impact whereas indirect interactions resulted from the hydration arise from a molecular mechanism primarily inducing the glucose stabilizing impacts. An elevation occurred in the Tm of the myoglobin-glucose complex because of the greater H-bond creation and limited surface hydrophobic activity. Our findings indicate that glucose was capable of protecting the native conformation of myoglobin, clearly describing that glucose stabilization is preferred to be omitted from myoglobin surface. This is because water is more inclined to provide desirable interacting with myoglobin functional groups as compared to glucose. Also, MD results confirmed that the structural changes of myoglobin is the effect of complex formation with glucose.Communicated by Ramaswamy H. Sarma.

Insight into the binding of glycerol with myoglobin: Spectroscopic and MD simulation approach.

Stability of proteins plays a significant role not only in their biological function but also in medical science and protein engineering. Since proteins are only stable in special conditions, maintaining their stability and function in biological and biotechnological applications may pose serious challenges. Osmolytes provide a general method of shielding proteins from the unfolding and aggregation caused by extreme stress on the environment. In such studies, the researchers used spectroscopic and simulation approaches to study the alterations of the myoglobin structure and stability in glycerol presence. Experimental results showed a stability improvement of the complex myoglobin-glycerol. After the addition of glycerol resulting in the initiation of hydrogen bonds and higher levels of hydrophobicity, the increase of the Tm was observed. The static mode quenching observed in this study. Van der Waals forces and hydrogen bindings had a decisive and significant role concerning the stability of protein which was consistent with the modeling results. Molecular dynamics simulation showed that the glycerol presence could enhance myoglobin stability. The consistency between the theoretical studies and experimental findings demonstrates that the method proposed in this study could provide a useful method for protein-ligand complex investigations.

Noncovalent interactions of bovine trypsin with curcumin and effect on stability, structure, and function.

The structural studies of trypsin with curcumin in Tris-hydrochloride (Tris-HCl) buffer solution (pH 8.0) was explored by UV-vis spectroscopic and fluorescence quenching method, kinetic reaction, circular dichroism (CD), Thermal denaturation, molecular docking, and molecular dynamic simulation. The curcumin could decrease trypsin absorbance. It was showed that curcumin could quench the fluorescence of trypsin by static quenching mechanism. This is in agreement with UV-vis results and CD studies in which the α-helix becomes more, and ß-sheet becomes less than trypsin without ligand. The binding constant, the number of binding sites and thermodynamic parameters (ΔH°, ΔS°, and ΔG°) at two temperatures were calculated. The hydrogen bond and Van der Waals interaction were found as the main forces, which is in congruence with docking results. The outcome of the kinetic reaction indicates an uncompetitive inhibition by curcumin on trypsin. Molecular Dynamic simulation and Thermal denaturation results demonstrate that curcumin makes trypsin unstable and more flexible.

Evaluation of maltose on conformation and activity parameters of trypsin.

Communicated by Ramaswamy H. Sarma.

A molecular simulation and spectroscopic approach to the binding affinity between trypsin and 2-propanol and protein conformation.

Increasing the stability and activity of enzymes is one of the most popular ideas in biochemistry studies. The current study focused on the interactions between 2-propanol as an osmolyte and trypsin to increase the enzyme thermal stability by the modification of the solvent environment. To determine the binding mechanism of 2-propanol with trypsin, fluorescence emission quenching was observed as a static mode of quenching upon the binding of 2-propanol to trypsin. With the formation of hydrogen bonds and lower hydrophobicity levels after the addition of 2-propanol, Tm of complexes were increased. Also, the α-helix content of trypsin was increased as obtained by far-UV CD. CD results analysis showed that there was no significant perturbation in the structure of trypsin upon an increase in the concentration of 2-propanol. Molecular docking results also indicated that 2-propanol could bind to trypsin and hydrophobic interactions and hydrogen bond contributions played the major role in this binding. Consequently, the results of the molecular dynamics simulation showed that the stability of trypsin-2 propanol was obtained to be about 2.5 nm in the equilibrium state, indicating the stability and rigidity of the trypsin-2 propanol complex. Upon 2-propanol conjugation, the residual activity of the enzyme was increased. 2-propanol, therefore, acted as a stabilizer and activator for trypsin.

Insights into the molecular interaction between sucrose and α-chymotrypsin.

One of the most important purposes of enzyme engineering is to increase the thermal and kinetic stability of enzymes, which is an important factor for using enzymes in industry. The purpose of the present study is to achieve a higher thermal stability of α-chymotrypsin (α-Chy) by modification of the solvent environment. The influence of sucrose was investigated using thermal denaturation analysis, fluorescence spectroscopy, circular dichroism, molecular docking and molecular dynamics (MD) simulations. The results point to the effect of sucrose in enhancing the α-Chy stability. Fluorescence spectroscopy revealed one binding site that is dominated by static quenching. Molecular docking and MD simulation results indicate that hydrogen bonding and van der Waals forces play a major role in stabilizing the complex. Tm of this complex was enhanced due to the higher H-bond formation and the lower surface hydrophobicity after sucrose modification. The results show the ability of sucrose in protecting the native structural conformation of α-Chy. Sucrose was preferentially excluded from the surface of α-Chy which is explained by the higher tendency of water toward favorable interactions with the functional groups of α-Chy than with sucrose.

The functional and structural stabilization of trypsin by sucrose.

Docking and spectroscopic techniques were performed to probe the stabilizing effect of sucrose on the dynamics, structure and activity of trypsin. The thermodynamic folding properties, melting temperature (Tm), enthalpy change (ΔH°) and entropy change (ΔS°) were measured by thermal stability studies to understand the picture of trypsin folding. Sucrose acted as an enhancer for trypsin stability. Fluorescence spectroscopy revealed the static model of the quenching. The number of binding sites was 1. The Absorption, Fluorescence and circular dichroism spectral analysis illustrated that sucrose could protect the native structural conformation of enzyme and prevent the enzyme unfolding. Fluorescence spectroscopy and the molecular docking technique simulation displayed that the hydrogen bonding and Vander Waals forces played a main role in stabilizing the trypsin-sucrose complex, and the number of direct H-bonds between sucrose and trypsin was low; thus, the direct interactions had little contribution in the stabilizing effect and the indirect interactions caused by the preferential hydration were resulting from a molecular mechanism principally causing the stabilizing effects of sucrose.Upon sucrose conjugation, the kcat/Km value of the enzyme was increased. Tm of the trypsin-sucrose complex was increased due to the higher H-bond formation and the lower surface hydrophobicity after sucrose modification. Sucrose acted as enhancers for trypsin stability and activity. The result shows the ability of sucrose to protect the native structural conformation of trypsin. These results explicitly describe that stabilizing sucrose is preferentially excluded from the surface of trypsin, since water has a higher tendency toward favorable interactions with functional groups of trypsin than with sucrose.

A spectroscopic and thermal stability study on the interaction between putrescine and bovine trypsin.

The interaction of putrescine with bovine trypsin was investigated using steady state thermal stability, intrinsic fluorescence, UV-vis spectroscopy, far and near- UV circular dichroism and kinetic techniques, as well as molecular docking. The Stern-Volmer quenching constants for the trypsin- putrescine complex were calculated revealing that putrescine interacted with trypsin via the static fluorescence quenching. The enthalpy and entropy change values and the molecular docking technique revealed that hydrogen bonds and van der Waals forces play a major role in the binding process. Upon putrescine conjugation, the Vmax value and the kcat/Km values of the enzyme was increased. The results of UV absorbance, circular dichroism and fluorescence techniques demonstrated that the micro environmental changes in trypsin were induced by the binding of putrescine, leading to changes in its secondary structure. The thermal stability of trypsin- putrescine complex was enhanced more significantly, as compared to that of the native trypsin. The increased thermal stability of trypsin- putrescine complex might be due to the lower surface hydrophobicity and the higher hydrogen bond formation after putrescine modification, as reflected in the increase of UV absorbance and the quenching of fluorescence spectra. It was concluded that the binding of putrescine changed trypsin structure and function.

Comparative Studies on the Interaction of Spermidine with Bovine Trypsin by Multispectroscopic and Docking Methods.

The effect of spermidine on the kinetics, conformation, and dynamics of native trypsin was studied by steady-state thermal stability, intrinsic fluorescence, circular dichroism (CD), ultraviolet-visible (UV-vis) spectroscopy, and kinetic techniques, as well as molecular docking, at the temperatures of 298 and 308 K. The Stern-Volmer quenching constants (Ksv) for the trypsin-spermidine complex were obtained at two temperatures, revealing that spermidine quenched the intensity of trypsin through the static mode of the quenching mechanism. The corresponding thermodynamic parameters, Gibbs free-energy, enthalpy, and entropy changes, showed that the binding process was spontaneous. These values and the molecular docking technique revealed that the hydrogen bonding and van der Waals forces played a major role in stabilizing the complex. CD, absorption, and fluorescence results also indicated that spermidine binding had a partial effect on trypsin structure. Spermidine could also influence the activity of trypsin. Upon spermidine binding, the Vmax value of the enzyme was increased and the kcat/Km values were enhanced slightly. The Tm of the trypsin-spermidine complex was enhanced probably due to the higher H-bond formation and lower surface hydrophobicity after spermidine modification, as confirmed by UV-vis spectroscopy and fluorescence spectra. UV absorption and CD studies also indicated that the binding of spermidine to trypsin had induced microenvironmental changes around the enzyme, leading to changes in its secondary structure.