Molecular dynamics of the membrane interaction and localisation of prodigiosin.

The tripyrrolic antibiotic prodigiosin causes diverse reactions on its targets like energy spilling, membrane leakage, loss of motility and phototoxicity. It has bacteriostatic, bactericidal, anti-fungal, anti-cancer and immunosuppressive properties. Most of the functions suggest the role of prodigiosin in membrane disruption but the exact mechanism remains unknown. A molecular dynamics study was performed to understand the interactions of prodigiosin with the membrane. It was seen that prodigiosin from the solvent enters the membrane immediately either individually or as small clusters. Prodigiosin clusters with more than eight molecules do not appear to enter the membrane. Upon entry, the molecules orient themselves along the membrane-water interface with the pyrrole rings interacting with lipid head groups and with water. This orientation is stabilised by hydrogen bonding and hydrophobic interactions. The presence of prodigiosin molecules in the membrane changes the local lipid architecture and reduces the solvent accessibility of the membrane. The membrane fluidity, thickness or area per lipid head are largely unaffected. This suggests that prodigiosin could cause most damage in the vicinity of a membrane protein and thus could also explain the reason for varied effects on the targets.

Improvement in biochemical characteristics of cross-linked enzyme aggregates (CLEAs) with magnetic nanoparticles as support matrix.

Recent developments in novel carriers for enzyme immobilization have led to improvement in the stability and cost-effectiveness of the biocatalysts for their enhanced suitability in the industrial applications. Cross-linked enzyme aggregates (CLEAs), a recent technique developed in the carrier-free type of enzyme immobilization is a simple and straightforward method. Moreover, the magnetic property and the higher surface-to-volume ratio of the maghemite nanoparticles have also been utilized in the present immobilization technique as magnetic nanoparticle-supported CLEAs (Mgnp-CLEAs). The stability studies of the free and immobilized enzyme revealed the Mgnp-CLEAs to have enhanced enzyme stability with an increase in the reusability cycle. The physical characterization of the nanoparticles and immobilized enzymes by the Scanning Electron Microscopy (SEM), Fourier-Transform Infrared spectroscopy (FT-IR) and X-ray diffraction analysis (XRD) showed the successful immobilization of the enzyme for its improved stability.

Enhanced stability of immobilized keratinolytic protease on electrospun nanofibers.

Feathers from poultry industries are considered a major pollutant and its degradation is a challenging problem due to its recalcitrant nature. The high cost of energy and loss of essential amino acids by conventional methods have paved a way for an environmentally benign approach using microbial keratinolytic proteases. The widespread application of keratinolytic proteases is limited due to autolysis and denaturation of the enzyme upon storage. Immobilization overcomes these disadvantages by adsorbing the enzyme onto a solid support. Recently, electrospun nanofibers have been used due to their increased surface area and porous structure. The biocompatible and hydrophilic polyvinyl alcohol (PVA) has been blended with biodegradable chitosan for immobilization in electrospinning. The present study focuses on feather degradation by immobilized keratinolytic proteases on electrospun nanofibers. The keratinolytic protease production was enhanced by using a media containing hydrolyzed feather under optimized conditions. The immobilized keratinolytic protease on electrospun PVA chitosan (PVA-Ch) nanofibers (100-150 nm diameter) degraded the chicken feathers with 88% efficiency at the end of 72 hr.

Phylogenetic Studies on the Prodigiosin Biosynthetic Operon.

Prodigiosin and undecylprodigiosin are tripyrrolic red pigmented antibiotics produced by certain bacteria. Many strains of Serratia and certain other Gammaproteobacteria produce prodigiosin and undecylprodigiosin is produced by certain strains of Streptomyces. This is a multistage process which involves the synthesis of a bipyrrolic compound from L-proline and its subsequent condensation with a mono pyrrole synthesized from 2-octenal in the case of prodigiosin and malonyl-CoA in the case of undecylprodigiosin respectively. We have carried out sequence analysis of the genes involved in the pathway and identified the distribution of the prodigiosin producing genes amongst the various bacteria which have been fully sequenced. The presence of the operon was clearly seen in certain clustered branches suggesting inheritance from a common ancestor. This was further confirmed by the absence of traits observed in horizontally acquired genes like, GC content variation, codon bias or the presence of mobile elements. Multiple sequence alignment of the promoter of the prodigiosin operon in seven fully sequenced Serratia marcescens strains showed excellent homology. Putative regulatory elements in this region were identified by sequence analysis studies and many of them have been found to influence pigment production. The undecylprodigiosin gene cluster on the other hand, shows homology to other gene clusters involved in the production of other pyrrole-containing antibiotics of the genus Streptomyces. This coupled with the presence of ORFs with three different promoters could indicate lateral gene transfer. Hence the evolution of undecylprodigiosin operon could be an example of convergent evolution.

Cross-linked esterase aggregates (CLEAs) using nanoparticles as immobilization matrix.

The present study focusses on the enhancement of the catalytic activity and stability of an acetylesterase enzyme isolated from Staphylococcus spp. as Cross-Linked Enzyme Aggregates (CLEAs). The various parameters governing the activity of CLEAs were optimized. The magnetite and graphene oxide nanoparticles were successfully prepared via the chemical co-precipitation and Hummer's method, respectively. These nanoparticles supported the preparation as magnetite nanoparticle-supported cross-Linked Enzyme Aggregates (MGNP-CLEAs) and graphene oxide-supported Cross-Linked Enzyme Aggregates (GO-CLEAs). The activity and stability of these immobilized CLEAs were compared with the free enzyme at various temperature, pH, and organic solvents along with its storage stability and reusability. The immobilized preparations were analyzed by Scanning Electron Microscopy (SEM) and Fourier Transform Infrared spectroscopy (FT-IR) techniques. Acetylesterase precipitated with 60% saturated ammonium sulfate salt (SAS) solution and cross-linked with 100 mM glutaraldehyde for 4 h at 30 °C was found to be optimal to produce CLEAs with highest activity recovery of 99.8%. The optimal pH at 8.0 and temperature at 30 °C remained the same for both the free and immobilized enzyme, respectively. Storage stability significantly improved for the immobilized enzyme as compared to free enzyme. SEM showed type-I aggregate and FT-IR revealed the successful immobilization of the enzyme. MGNP-CLEAs were found to have better activity and stability in comparison to other immobilized preparations.

Understanding domain movements and interactions of Pseudomonas aeruginosa lipase with lipid molecule tristearoyl glycerol: A molecular dynamics approach.

Lipases are biocatalysts which exhibit optimal activity at the aqueous-lipid interface. Molecular Dynamics (MD) Simulation studies on lipases have revealed the structural changes occurring in the enzyme, at the loop-helix-loop, often designated as the "lid", which is responsible for its interfacial activation. In recent years, MD simulation of lipases at molecular level have been studied in detail, whereas very few studies are carried over on its interaction with lipid molecules. Hence, in the current study we have investigated molecular interaction of bacterial lipase (Pseudomonas aeruginosa lipase, PAL) with a lipid molecule (tristearoyl glycerol, TGL). This provides an insight into the interfacial activation of the enzyme. The lipid molecule was placed near the lids of the enzyme and MD simulations were performed for 100 ns to understand the nature and site of the interaction. The results clearly indicate that, the presence of a lipid molecule near the lids affects the motion of the enzyme through changes in conformation. Lipid molecule near the lids reduces the movements of both lids, and the TGL molecule was observed moving towards the active site. The movement of the lids, surface accessibility and the domain movements of PAL are discussed and the results provide valuable insight in to the role played by the two lids in the interfacial activation of PAL with TGL.

Crystal Structure Analysis of Great Cormorant (Phalacrocorax carbo) Hemoglobin to Understand its High Oxygen Affinity Characteristics by Special Structural Features.

BACKGROUND: Hemoglobin (Hb) subunits are composed of the specific functional prosthetic group "heme'' and a protein moiety "globin". Bird Hbs are functionally similar to mammalian Hbs but they are structurally dissimilar with mammalian. The insufficient structural studies on avian Hbs limit us to understand their degree of adaptation to such critical environments. The Great Cormorant (GCT) can fly and swim, the dual characteristic of GCT leads to study the sturcture of hemoglobin. OBJECTIVE: To determine the crystal structure of Great Cormorant Hemoglobin and to compare its three dimensional structure with other high and low oxygen affinity hemoglobin species to understand its characteristic features of high oxygen affinity. METHOD: The GCT hemoglobin has been purified, crystallized and data sets were processed using iMosflm. The integrated data has been solved using Molecular replacement method using Graylag hemoglobin (1FAW) as the template. The structure has been deposited in Protein Data Bank with PDB code: 3WR1. RESULTS: In order to characterize the tertiary and quaternary structural differences, the structure of cormorant hemoglobin is compared with GLG, BHG and human Hb. The larger variation observed between GCT and human Hb indicates that GCT Hb differs remarkably from human. The α1ß1 interface of Great cormorant Hb is similar to bar-headed goose Hb with few amino acid substitutions. It has been found that the interaction which is common among avian hemoglobins (α119 Pro- ß55Leu) is altered by Ala 119 in GCT. This intra-dimer contact (α119 Pro - ß 55 Leu) disruption leads to high oxygen affinity in BGH Hb. In cormorant, GLG and human the proline is unchanged but interestingly, in cormorant Hb, the ß55 position was found to be Thr instead of Leu. Similar kind of substitutions (ß 55 Leu - Ser) observed in Andean goose Hb structure leads to elevated oxygen affinity between Hb-O2. To our surprise, such type of substitution at ß 55 (Thr) in cormorant Hb confirms that it is comparable with Andean goose Hb structure. Thus the sequence, structural differences at alpha, beta heme pocket and interface contacts confirms that GCT adopts high oxygen affinity conformation. CONCLUSION: The three dimensional structure of Great cormorant hemoglobin has been investigated to understand its unique structural features to adopt during hypoxia condition. By comparing the sequence and overall structural similarities with high and low oxygen affinity species, it appears that GCT has more possibilities to subsist with low oxygen demand.

Structural insights into a multifunctional inhibitor, 'AMTIN' from tubers of Alocasia macrorrhizos and its possible role in dengue protease (NS2B-NS3) inhibition.

Protease inhibitors from plants play major role in defensive mechanism against various pathogenic organisms. AMTIN from the tubers of Alocasia macrorrhiza has been purified and characterized as multi-functional Kunitz type protease inhibitor. AMTIN is varied from other KTIs by having three different loops specific for binding to trypsin/amylase and subtilisin that are located approximately 30Ǻ away from one another as evidenced from crystallographic efforts. Biochemical studies on AMTIN reveal simultaneous binding of protease/amylase and have been cross validated using in-silico tools to model Amylase - AMTIN - Trypsin complex without any steric clashes. Apart from multi functionality, the remarkable structural and functional stability of AMTIN at high temperature, presence of many phosphorylation, myristoylation and glycosylation sites and molecular docking studies with dengue viral protease (NS2B-NS3) makes this protein interesting. Hence AMTIN can be considered as a template to design effective antivirals against dengue virus.

Improved stability and catalytic activity of graphene oxide/chitosan hybrid beads loaded with porcine liver esterase.

Graphene oxide/chitosan and reduced graphene oxide/chitosan (GO/CS and RGO/CS) beads were prepared by precipitation with NaOH. Porcine liver esterase was immobilized on these beads to give GO/CS/E and RGO/CS/E beads. The optimum conditions for the maximum activity of RGO/CS/E beads were pH 8 and 50°C. The stability of the enzyme immobilized on GO/CS/E and RGO/CS/E was high in the pH range of 5-8. The GO/CS/E beads showed superior stability compared to that of the free enzyme and CS/E beads between 20 and 50°C. Kinetic analysis showed that GO/CS/E was a better catalyst than the RGO/CS/E beads with a lower Km value of 0.9 mM. The hybrid beads also retained more than 95% activity after 10 consecutive cycles. The GO/CS/E and RGO/CS/E beads retained 84% and 87% activity after 40 days at 4°C. The GO/CS/E beads were used for the successful hydrolysis of methyl 4-hydroxy benzoate.

Enhancing the stability of a carboxylesterase by entrapment in chitosan coated alginate beads.

A carboxylesterase isolated from Aeromonas caviae MTCC 7725 was immobilized by entrapping it in chitosan coated calcium alginate beads. This was characterized by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and Fourier transform infrared spectroscopy (FTIR). The activity of the native and immobilized enzyme was measured at various temperatures, pH levels, and organic solvents. The optimum temperature for activity of the native enzyme was found to be 40 °C and this increased to 50 °C on immobilization. The immobilized enzyme showed enhanced stability and high residual activity in various organic solvents as compared to the free enzyme. An environmentally benign approach was used for the synthesis of ethyl salicylate using the immobilized enzyme. The product obtained was confirmed by GC-MS. The kinetic parameters, such as K m and Vmax, were also determined for the native and immobilized enzyme. The immobilized enzyme retained 50% of its activity after vfie cycles. The immobilized enzyme retained 80% and 40% of its activity at 4 °C and at 37 °C, respectively, at the end of 40 days. The results obtained from our study show that the immobilized enzyme can serve as a robust catalyst for industrial applications.

Automatic classification of protein structures using physicochemical parameters.

Protein classification is the first step to functional annotation; SCOP and Pfam databases are currently the most relevant protein classification schemes. However, the disproportion in the number of three dimensional (3D) protein structures generated versus their classification into relevant superfamilies/families emphasizes the need for automated classification schemes. Predicting function of novel proteins based on sequence information alone has proven to be a major challenge. The present study focuses on the use of physicochemical parameters in conjunction with machine learning algorithms (Naive Bayes, Decision Trees, Random Forest and Support Vector Machines) to classify proteins into their respective SCOP superfamily/Pfam family, using sequence derived information. Spectrophores™, a 1D descriptor of the 3D molecular field surrounding a structure was used as a benchmark to compare the performance of the physicochemical parameters. The machine learning algorithms were modified to select features based on information gain for each SCOP superfamily/Pfam family. The effect of combining physicochemical parameters and spectrophores on classification accuracy (CA) was studied. Machine learning algorithms trained with the physicochemical parameters consistently classified SCOP superfamilies and Pfam families with a classification accuracy above 90%, while spectrophores performed with a CA of around 85%. Feature selection improved classification accuracy for both physicochemical parameters and spectrophores based machine learning algorithms. Combining both attributes resulted in a marginal loss of performance. Physicochemical parameters were able to classify proteins from both schemes with classification accuracy ranging from 90-96%. These results suggest the usefulness of this method in classifying proteins from amino acid sequences.

Understanding the lid movements of LolA in Escherichia coli using molecular dynamics simulation and in silico point mutation.

The Lol system in Escherichia coli is involved in localization of lipoproteins and hence is essential for growth of the organism. LolA is a periplasmic chaperone that binds to outer-membrane specific lipoproteins and transports them from inner membrane to outer membrane through LolB. The hydrophobic lipid-binding cavity of LolA consists of α-helices which act as a lid in regulating the transfer of lipoproteins from LolA to LolB. The current study aims to investigate the structural changes observed in LolA during the transition from open to closed conformation in the absence of lipoprotein. Molecular dynamics (MD) simulations were carried out for two LolA crystal structures; LolA(R43L), and in silico mutated MsL43R for a simulation time of 50 ns in water environment. We have performed an in silico point mutation of leucine to arginine in MsL43R to evaluate the importance of arginine to induce structural changes and impact the stability of protein structure. A complete dynamic analysis of open to closed conformation reveals the existence of two distinct levels; closing of lid and closing of entrance of hydrophobic cavity. Our analysis reveals that the structural flexibility of LolA is an important factor for its role as a periplasmic chaperone.

Resonance Energy Transfer between protein and rhamnolipid capped ZnS quantum dots: application in in-gel staining of proteins.

The interaction of proteins with quantum dots is an interesting field of research. These interactions occur at the nanoscale. We have probed the interaction of Bovine Serum Albumin (BSA) and Candida rugosa lipase (CRL) with rhamnolipid capped ZnS (RhlZnSQDs) using absorption and fluorescence spectroscopy. Optical studies on mixtures of RhlZnSQDs and proteins resulted in Förster's Resonance Energy Transfer (FRET) from proteins to QDs. This phenomenon has been exploited to detect proteins in agarose gel electrophoresis. The activity of the CRL was unaffected on the addition of QDs as revealed by zymography.

Molecular dynamics simulations of human and dog gastric lipases: insights into domain movements.

Mammalian gastric lipases are stable and active under acidic conditions and also in the duodenal lumen. There has been considerable interest in acid stable lipases owing to their potential application in the treatment of pancreatic exocrine insufficiency. In order to gain insights into the domain movements of these enzymes, molecular dynamics simulations of human gastric lipase was performed at an acidic pH and under neutral conditions. For comparative studies, simulation of dog gastric lipase was also performed at an acidic pH. Analyses show, that in addition to the lid region, there is another region of high mobility in these lipases. The potential role of this novel region is discussed.

Investigations on domain movements of N-acetyltransferase in nano scale.

Molecular Dynamics simulations were performed on aminoglycoside N-acetyltransferase ((AAC) (2')-Ic) of Mycobacterium tuberculosis, to gain insight into enzyme flexibility and conformation around the ligand and acetyl-CoA binding sites in nano scale. Simulations were performed in water and methanol to further study the effect of solvation on the enzyme. AAC(2')-Ic of M. tuberculosis consists of negatively charged residues of aspartic and glutamic acids, which are believed to form a docking platform for the positively charged aminoglycosides. The acetyl-CoA binding site involves a wide groove surrounded by helices alphal, alpha3, alpha4 and strand beta4. Simulation results revealed the enzyme to be stable in water and the enzyme was found to be flexible around the docking platform (ligand binding site) with Asp 35, Asp 40 and Asp 179 exhibiting maximum movement. An interesting observation was the flexibility and conformational change at beta4, hydrophobic pocket of the acetyl-CoA binding site a prerequisite for catalysis to occur with Leu 95 exhibiting maximum displacement with a root mean square fluctuation of 0.18 nm. The enzyme was found to be very unstable in methanol with root mean square deviation not stabilizing even at 10 ns.

Distribution of tripeptides in MHC binding peptides.

Major Histocompatibility Complex (MHC) molecules are cell surface glycoproteins that are central to the process of immunity. MHC Class I and II molecules differ in their peptide binding specificity. In this study we have analyzed a non redundant set of MHC binding peptides derived from MHCPEP database, in terms of tripeptides and their positional preference. Results indicate that certain tripeptides have a preference to appear at a particular position for a specific allele. Further, the distribution of rigid tripeptides across all binding sequences was also analyzed and their positions were correlated with anchor residue positions.

In silico identification of putative metal binding motifs.

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. In this study, we have performed an in silico analysis of metal binding proteins and have identified putative metal binding motifs for the ions of cadmium, cobalt, zinc, arsenic, mercury, magnesium, manganese, molybdenum and nickel. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high-specificity of the motifs. Motifs were also validated against PDB structures and site directed mutagenesis studies.

Understanding mutations and protein stability through tripeptides.

A novel methodology to predict the local conformational changes in a protein as a consequence of missense mutations is proposed. A pentapeptide at the locus of mutation plays the dominant role and it is analyzed in terms of tripeptides. A measure for spatial and temporal fluctuations in a pentapeptide is devised and validated. The method does not involve any prior knowledge of structural templates from sequence homology studies. Structural deformations can be predicted with about 70-80% reliability in any protein. Disease causing mutations and benign mutations have been addressed. In particular, p53, retinoblastoma protein and lipoprotein lipase are studied in detail.

Role of hydrophobic interactions and salt-bridges in beta-hairpin folding.

Beta-hairpins are the simplest form of beta-sheets which, due to the presence of long-range interactions, can be considered as tertiary structures. Molecular dynamics simulation is a powerful tool that can unravel whole pathways of protein folding/unfolding at atomic resolution. We have performed several molecular dynamics simulations, to a total of over 250 ns, of a beta-hairpin peptide in water using GROMACS. We show that hydrophobic interactions are necessary for initiating the folding of the peptide. Once formed, the peptide is stabilized by hydrogen bonds and disruption of hydrophobic interactions in the folded peptide does not denature the structure. In the absence of hydrophobic interactions, the peptide fails to fold. However, the introduction of a salt-bridge compensates for the loss of hydrophobic interactions to a certain extent.

Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis.

The emergence of multidrug resistant varieties of Mycobacterium tuberculosis has led to a search for novel drug targets. We have performed an insilico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen M. tuberculosis. Enzymes from the biochemical pathways of M. tuberculosis from the KEGG metabolic pathway database were compared with proteins from the host H. sapiens, by performing a BLASTp search against the non-redundant database restricted to the H. sapiens subset. The e-value threshold cutoff was set to 0.005. Enzymes, which do not show similarity to any of the host proteins, below this threshold, were filtered out as potential drug targets. We have identified six pathways unique to the pathogen M. tuberculosis when compared to the host H. sapiens. Potential drug targets from these pathways could be useful for the discovery of broad spectrum drugs. Potential drug targets were also identified from pathways related to lipid metabolism, carbohydrate metabolism, amino acid metabolism, energy metabolism, vitamin and cofactor biosynthetic pathways and nucleotide metabolism. Of the 185 distinct targets identified from these pathways, many are in various stages of progress at the TB Structural Genomics Consortium. However, 67 of our targets are new and can be considered for rational drug design. As a case study, we have built a homology model of one of the potential drug targets MurD ligase using WHAT IF software. The model could be further explored for insilico docking studies with suitable inhibitors. The study was successful in listing out potential drug targets from the M. tuberculosis proteome involved in vital aspects of the pathogen's metabolism, persistence, virulence and cell wall biosynthesis. This systematic evaluation of metabolic pathways of host and pathogen through reliable and conventional bioinformatic methods can be extended to other pathogens of clinical interest.