Homology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase

Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach

The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of polysaccharides such as glycogen and starch. Many of these enzymes also perform transglycosylation in various degrees, ranging from secondary to predominant reactions. Identifying structural determinants associated with GH13 family reaction specificity is key to modifying and designing enzymes with increased specificity towards individual reactions for further applications in industrial, chemical, or biomedical fields. This work proposes a computational approach for decoding the determinant structural composition defining the reaction specificity. This method is based on the conservation of coevolving residues in spatial contacts associated with reaction specificity. To evaluate the algorithm, mutants of α-amylase (TmAmyA) and glucanotransferase (TmGTase) from Thermotoga maritima were constructed to modify the reaction specificity. The K98P/D99A/H222Q variant from TmAmyA doubled the transglycosydation/hydrolysis (T/H) ratio while the M279N variant from TmGTase increased the hydrolysis/transglycosidation ratio five-fold. Molecular dynamic simulations of the variants indicated changes in flexibility that can account for the modified T/H ratio. An essential contribution of the presented computational approach is its capacity to identify residues outside of the active center that affect the reaction specificity.

Graphite/gold nanoparticles electrode for direct protein attachment: characterization and gas sensing application

In this work, graphite/gold nanoparticles (G/AuNPs) were synthesized through a facile chemical method, and its potential application for direct protein attachment for electrochemical detection of carbon monoxide (CO) was investigated. The preparation of G/AuNPs electrodes was optimized by synthesizing the nanoparticles in different concentration of HAuCl₄.3H₂O at various temperatures. The G/AuNPs electrode was subsequently modified by four types of mercaptopropionic acid, including 1-mercaptopropionic, 3-mercaptopropionic, 6-mercaptopropionic, and 11-mercaptopropionic acid, to achieve the best structure for protein attachment. Visible absorption and electrochemical studies showed that 3-mercaptopropionic acid possesses the best performance regarding the electrical conductivity between electrode and protein redox center. The cyclic voltammetry results revealed that the modified electrode has an appropriate performance for CO detection at very low concentrations while keeping a linear response. The limit of detection for the modified electrode was calculated to be about 0.2 ppb. Finally, the interactions of cytochrome C and carbon monoxides were simulated using molecular dynamics (MD), and the effect of protein conformation changes on the electrochemical signal was thoroughly examined. The simulation results suggested that the proposed electrochemical sensor has an acceptable performance for the detection of CO due to less fluctuation of amino acids near the protein chain in the presence of CO molecules.

Cloning, expression, homology modelling and molecular dynamics simulation of four domain-containing α-amylase from Streptomyces griseus

In the present study, α-amylase from Streptomyces griseus TBG19NRA1 was amplified, cloned and successfully expressed in E. coli BL21/DE3. Sequence analysis of S. griseus α-amylase (SGAmy) revealed the presence of four domains (A, B, C and E). Alpha-amylases with E domain (also known as carbohydrate binding module 20 (CBM20)) are capable of degrading raw starch and this property holds great potential for application in starch processing industries. Though α-amylase is a well-studied and characterized enzyme, there is no experimental structure available for this four domain-containing α-amylases. To gain more insight about SGAmy structure and function, homology modelling was performed using a multi-template method. The template α-amylase from Pseudoalteromonas haloplanktis (PDB ID 1AQH) and E domain of Cyclodextrin glucanotransferase from Bacillus circulans (PDB ID 1CGY) was found to have significant similarity with the complete target sequence of SGAmy. Therefore, homology model for SGAmy was generated from the crystal structure of 1AQH and 1CGY and the resulting structure was subjected to 10 ns molecular dynamics (MD) simulation. Remarkably, CBM20 domain of SGAmy showed greater flexibility in MD simulation than other three domains. This observation is highly rational as this part of SGAmy is strongly implicated in substrate (raw starch) binding. Thus, conformational plasticity at CBM20 is functionally beneficial.Communicated by Ramaswamy H. Sarma.

Colloidal graphene oxide enhances the activity of a lipase and protects it from oxidative damage: Insights from physicochemical and molecular dynamics investigations

Physical adsorption of lipase from Thermomyces lanuginosus onto single-layer sheets of graphene oxide (GO) was studied using the response surface methodology to evaluate the physicochemical factors - temperature, pH, ionic strength, and concentration - affecting the enzymatic activity and the immobilization efficiency. The immobilization efficiency and the activity of the enzyme were inversely proportional to each other. Specifically, higher pH values increased the immobilization efficacy, but produced changes in the aggregation state and secondary structure of the enzyme, thus decreasing its activity. Lower pH values, in turn, reduced the immobilization efficacy, but increased the activity of the adsorbed lipase. The adsorbed and the free lipase were followed during 600 ns and 3.5 μs, respectively, in molecular dynamics (MD) simulations. MD trajectories showed that irreversible adsorption freezes the enzyme in a state with a correctly opened catalytic cavity, while the active site remains without a direct interaction with the GO adsorbent. In contrast to the interfacial activation of lipases in a hydrophobic environment, where the catalytic pocket attaches to the hydrophobic surface, the adsorption onto GO made the active site of the lipase accessible by altering the tertiary structure of the enzyme, leading to a higher catalytic efficiency. Experimental investigations confirmed that the physical adsorption onto GO induces tertiary structure changes in the lipase and protects it from H₂O₂ by accepting the oxidative damage upon itself. In summary, the physical adsorption of the lipase onto GO is mainly affected by pH and could possibly provide a spreadable and robust catalytic interface for biotechnological applications.

An isolate of Potato Virus X capsid protein from N. benthamiana: Insights from homology modeling and molecular dynamics simulation

Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate. The capsid protein (CP) structure were modeled based on homology and subjected to three independent 80 ns molecular dynamics minimization (GROMACS, OPLS force field) in the SPC water box. The RMSD, RMSF, SASA, and electrostatic properties were retrieved from the trajectories. Flexibility and hydrophilic nature of the N-terminal residues (1-34) of solvated CP could be observed in conformational changes upon minimization. The obtained structure was then docked with NbPCIP1 using ClusPro 2.0. The strong binding affinity of these two proteins (≈-16.0 Kcal mol-1) represents the formation of inclusion body and hence appearance of the symptoms.

Effect of size and chemical composition of graphene oxide nanoparticles on optical absorption cross-section

Photothermal therapy with various nanoparticles, as photothermal transducers, is a widely researched technique. A continuous wave (CW) laser is employed during this procedure. The therapeutic setup is slightly modified to measure the optical absorption cross-section of the graphene oxide (GO), by mitigating the effects of heat diffusion and light scattering. With an 808-nm CW laser setup modulated by a waveform modulation setup, the effect of nanoparticle size and composition of GO in water on optical absorption cross section is characterized.

Role of Trace Elements as Cofactor: An Efficient Strategy toward Enhanced Biobutanol Production

Metabolic engineering has the potential to steadily enhance product titers by inducing changes in metabolism. Especially, availability of cofactors plays a crucial role in improving efficacy of product conversion. Hence, the effect of certain trace elements was studied individually or in combinations, to enhance butanol flux during its biological production. Interestingly, nickel chloride (100 mg L^-1) and sodium selenite (1 mg L^-1) showed a nearly 2-fold increase in solvent titer, achieving 16.13 ± 0.24 and 12.88 ± 0.36 g L^-1 total solvents with yields of 0.30 and 0.33 g g^-1, respectively. Subsequently, the addition time (screened entities) was optimized (8 h) to further increase solvent production up to 18.17 ± 0.19 and 15.5 ± 0.13 g L^-1 by using nickel and selenite, respectively. A significant upsurge in butanol dehydrogenase (BDH) levels was observed, which reflected in improved solvent productions. Additionally, a three-dimensional structure of BDH was also constructed using homology modeling and subsequently docked with substrate, cofactor, and metal ion to investigate proper orientation and molecular interactions.

Sequence-dependent dynamical instability of the human prion protein: a comparative simulation study

The present study aimed to explore the most probable regions of the human prion protein backbone for which the initial steps of conformational transitions as a result of intrinsic and extrinsic perturbing factors on the protein structure can be assigned. A total of 0.3-μs molecular dynamics simulations on several analog structures of the protein have been performed. To mimic the impact of the extrinsic and intrinsic destructive parameters on the dynamical characteristics of the protein, mild acidic conditions and R208H mutation have been simulated. The findings indicated that distribution of conformational flexibilities along the protein chain was almost independent of the induced perturbing factors, and was mostly centralized on certain distinct parts of the structure comprising residues 132-145 and 187-203. Analyses also revealed that the segment comprising residues 187-203 may be considered as a peptide sequence, possessing high potential to start the initial steps of conformational rearrangements due to the induced physicochemical alterations. Sequence alignment and molecular dynamics data also revealed that segment 178-203 prefers to accommodate in extended structures rather than α-helices. Region 178-203 may be considered as a peptide switch capable of initiating the conformational transitions due to the introduced modifications and perturbing parameters.

Insights into unbound-bound states of GPR142 receptor in a membrane-aqueous system using molecular dynamics simulations

G protein coupled receptors (GPCRs) are source machinery in signal transduction pathways and being one of the major therapeutic targets play a significant in drug discovery. GPR142, an orphan GPCR, has been implicated in the regulation of insulin, thereby having a crucial role in Type II diabetes management. Deciphering of the structures of orphan, GPCRs (O-GPCRs) offer better prospects for advancements in research in ion translocation and transduction of extracellular signals. As the crystallographic structure of GPR142 is not available in PDB, therefore, threading and ab initio-based approaches were used for 3D modeling of GPR142. Molecular dynamic simulations (900 ns) were performed on the 3D model of GPR142 and complexes of GPR142 with top five hits, obtained through virtual screening, embedded in lipid bilayer with aqueous system using OPLS force field. Compound 1, 3, and 4 may act as scaffolds for designing potential lead agonists for GPR142. The finding of GPR142 MD simulation study provides more comprehensive representation of the functional properties. The concern for Type II diabetes is increasing worldwide and successful treatment of this disease demands novel drugs with better efficacy.