Management of maxillary first molar with six canals using operating microscope.

The purpose of this article was to highlight the importance of having a thorough knowledge about the root canal morphology. This case report highlights the unusual anatomy of a maxillary first molar with three mesiobuccal (MB) canals, two palatal canals, and one distobuccal canal which is extremely rare. The use of operating microscope was crucial, both for the detection and for the management of the additional canals. The use of surgical operating microscope and digital radiograph showed that MB root had Type 3-1 of Gulabivala classification and palatal canal showed Vertucci's Type II canal morphology This report describes and discusses the identification of variation in canal morphology of maxillary first molar and the use of latest adjuncts in successfully diagnosing and negotiating them.

Management of palato radicular groove in a maxillary lateral incisor.

This study is to report the rare localization of a radicular groove on the palatal aspect of the maxillary lateral incisor and to discuss the pathology and management of the concomitant endo-periodontal defect. Unilateral palato-radicular groove was located on the Maxillary right lateral incisor of an 18-year-old female patient. The groove was associated with deep local periodontal pocket resulting in pulp necrosis and the formation of a large periapical lesion. A collaborative management was carried out using a combination of endodontic therapy, surgical enucleation, odontoplasty, and periodontal regenerative procedure resulting the successful healing of the periapical lesion.

Serine protease inhibitor mediated peptide bond re-synthesis in diverse protein molecules.

Protease inhibitors have been extensively used in research to prevent unwanted degradation of proteins during purification and analysis. Here, we report a remarkable discovery of protease inhibitor mediated reformation of peptide bonds by the serine protease inhibitor, PMSF in a diverse set of proteolyzed molecules. Interestingly, the religation reaction in the presence of PMSF occurs in a very short time period and with very high yields of the religated product. We also investigate the plausible mechanism of such a reaction and demonstrate through biochemical studies and X-ray crystallography that proximity of reacting termini is essential for the feasibility of this reaction.

Carboxylated lysine is required for higher activities in Hydantoinases.

Hydantoinases are industrial enzymes with varying degree of activities on variable substrates to form different products. Although, few of the hydantoinase structures were known recently, the functional details and active site mechanism were not clearly understood yet. In a structure determination effort we reported that Bacillus sp. AR9 hydantoinase contains uncarboxylated lysine in the active site, whereas all the other hydantoinases have a carboxylated active site lysine. Here we describe the importance of carboxylated lysine for differential activities by making lysine mutations as well as carboxylating the lysine in a D-hydantoinase from Bacillus sp. AR9. The lysine to alanine and lysine to arginine mutations showed reduced activities whereas carboxylation of the lysine has enhanced the activity. Theoretical studies involving the calculation of electrostatic potentials for the hydroxide ion between the two metal ions present in the active site suggest that the presence of carboxylated lysine increases the nucleophilicity of the hydroxide.

Salt-assisted religation of proteolyzed Glutathione-S-transferase follows Hofmeister series.

Proteases have been used not only for proteolysis but also in organic solvent-assisted religation processes. Here, we demonstrated the effect of salts on peptide bond resynthesis in Glutathione-S-transferase (GST) and have found it to be in the purview of the Hofmeister phenomena. Our results show that the efficiency and ease of religation increases with an increase in the surface charge densities of the cations used in the study. Thus, the yield of religated GST follows the order: Mg2(+)>Li(+)>Na(+)>K(+). Characteristics of the salt-religated GST were studied using size exclusion chromatography, CD spectroscopy, mass spectrometry and CDNB activity assay. Results show that the properties of salt-religated GST are in close agreement with those of the native GST. Additionally, we also assessed the specific activity of the protease, Subtilisin Carlsberg, used in this study. Contrary, to aqueous-organic systems, wherein there is a remarkable decrease in the proteolytic activity, the activity in the presence of salts is only minimally changed. Our studies suggest that salt-assisted peptide bond formation is favoured primarily due to changes in the ionic environment of the nicked termini of GST, and that there is no role played by the protease.

Database systems for knowledge-based discovery.

Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis.

Aspartate semialdehyde dehydrogenase from Mycobacterium tuberculosis (Asd, ASADH, Rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in Escherichia coli. The enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form A and of one or two monomers in the cubic crystal form B.

Creation of salt-insensitive 3'(2'),5'-bisphosphate nucleotidase by modeling and mutagenesis approach.

3'(2'),5'-Bisphosphate nucleotidase, (EC 3.1.3.7) (BPntase) is a ubiquitous enzyme. Recently, these enzymes have drawn considerable attention as in vivo targets of salt toxicity as well as therapeutic targets of lithium that is used for the treatment of manic-depressive disorders. They belong to the Mg2+-dependent Li+-sensitive phosphomonoesterase super-family and are highly sensitive to lithium and sodium ions. However, the molecular mechanism of inhibition of this group of enzymes by monovalent cations has not been completely understood. Previously we have identified a BPntase (Dhal2p) from a highly halotolerant yeast Debaryomyces hansenii. Molecular characterization revealed a number of unique features in Dhal2p, indicating this is an extraordinary member of the family. In this study, we have carried out the structure-function analysis of Dhal2p through the combination of molecular modeling and in vitro mutagenesis approach. We have not only provided the explanation for the role played by the functionally important elements that are conserved among the members of this family but also identified important, novel structural elements in this enzyme. Our study for the first time unraveled the role of a flap as well as a loop region in the functioning of this enzyme. Most importantly, mutations in the loop region resulted in the creation of a BPntase that was insensitive to salt.

Structural biology, protein conformations and drug designing.

Structure based drug designing is now a popular technique used for increasing the speed of drug designing process. This was made possible by the availability of many protein structures which helped in developing tools to understand the structure function relationships, automated docking and virtual screening. Knowledge of structure based functional properties of a drug target is very essential for a successful in silico designing of drugs. However, some problems associated with the structure determination process and lack of knowledge of conformational freedom associated with available protein structures are the hurdles involved in structure based drug designing. Docking and virtual screening processes depend on the active site structure of the receptor molecule and subtle differences in the conformations of these molecules due to flexibility pose a serious threat to the drug designing process. In this review problems associated with the conformations of proteins and homology models was reviewed.

Characterization of Mycobacterium tuberculosis WhiB1/Rv3219 as a protein disulfide reductase.

WhiB family of protein is emerging as one of the most fascinating group and is implicated in stress response as well as pathogenesis via their involvement in diverse cellular processes. Surprisingly, available in vivo data indicate an organism specific physiological role for each of these proteins. The WhiB proteins have four conserved cysteine residues where two of them are present in a C-X-X-C motif. In thioredoxins and similar proteins, this motif works as an active site and confers thiol-disulfide oxidoreductase activity to the protein. The recombinant WhiB1/Rv3219 was purified in a single step from Escherichia coli using Ni(2+)-NTA affinity chromatography and was found to exist as a homodimer. Mass spectrometry of WhiB1 shows that the four cysteine residues form two intramolecular disulfide bonds. Using intrinsic tryptophan fluorescence as a measure of redox state, the redox potential of WhiB1 was calculated as -236+/-2mV, which corresponds to the redox potential of many cytoplasmic thioredoxin-like proteins. WhiB1 catalyzed the reduction of insulin disulfide thus clearly demonstrating that it functions as a protein disulfide reductase. Present study for the first time suggests that WhiB1 may be a part of the redox network of Mycobacterium tuberculosis through its involvement in thiol-disulfide exchange with other cellular proteins.

Expression and characterization of alpha-(1,4)-glucan branching enzyme Rv1326c of Mycobacterium tuberculosis H37Rv.

Glycogen branching enzyme (GlgB, EC 2.4.1.18) catalyzes the third step of glycogen biosynthesis by the cleavage of an alpha-(1,4)-glucosidic linkage and subsequent transfer of cleaved oligosaccharide to form a new alpha-(1,6)-branch. A single glgB gene Rv1326c is present in Mycobacterium tuberculosis. The predicted amino acid sequence of GlgB of M. tuberculosis has all the conserved regions of alpha-amylase family proteins. The overall amino acid identity to other GlgBs ranges from 48.5 to 99%. The glgB gene of M. tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein was purified to homogeneity using metal affinity and ion exchange chromatography. The recombinant protein is a monomer as evidenced by gel filtration chromatography, is active as an enzyme, and uses amylose as the substrate. Enzyme activity was optimal at pH 7.0, 30 degrees C and divalent cations such as Zn2+ and Cu2+ inhibited activity. CD spectroscopy, proteolytic cleavage and mass spectroscopy analyses revealed that cysteine residues of GlgB form structural disulfide bond(s), which allow the protein to exist in two different redox-dependent conformational states. These conformations have different surface hydrophobicities as evidenced by ANS-fluorescence of oxidized and reduced GlgB. Although the conformational change did not affect the branching enzyme activity, the change in surface hydrophobicity could influence the interaction or dissociation of different cellular proteins with GlgB in response to different physiological states.

SH3-like fold proteins are structurally conserved and functionally divergent.

The folding space for all the protein sequences is limited. Therefore it was observed that many proteins, whose sequences are not related, have similar fold characteristics. The fold databases like SCOP and CATH have classified various protein folds. However, in-depth analysis of the functional features of these folds was not done. We analyzed about twenty unique SH3-like folded proteins in their structural environment and functional characteristics. From our analysis it is apparent that the SH3-like folds could carry out various functions by modulation of loops and the functional region is restricted to one side of a particular sheet helped by two or three loops. The functions vary from oligonucleotide-binding to peptide-binding and other ligand binding. Although certain degree of sequence similarity was observed among the SH3-fold proteins, the similarity was restricted to the beta-strand regions of the proteins.

Molecular structure of D-hydantoinase from Bacillus sp. AR9: evidence for mercury inhibition.

Stereospecific conversion of hydantoins into their carbamoyl acid derivatives could be achieved by using the enzyme hydantoinase. Specific hydantoinases convert either the D-form or the L-form of the hydantoin and the amino acids responsible for stereospecificity have not been identified. Structural studies on hydantoinases from a few bacterial species were published recently. The structure of a thermostable D-hydantoinase from Bacillus sp. AR9 (bar9HYD) was solved to 2.3 angstroms resolution. The usual modification of carboxylation of the active-site residue Lys150 did not happen in bar9HYD. Two manganese ions were modelled in the active site. Through biochemical studies, it was shown that mercury inhibits the activity of the enzyme. The mercury derivative provided some information about the binding site of the mercuric inhibitors and a possible reason for inhibition is presented.

Amino acid residues involved in autophosphorylation and phosphotransfer activities are distinct in nucleoside diphosphate kinase from Mycobacterium tuberculosis.

Nucleoside diphosphate kinase (NdK) is a ubiquitous enzyme in both prokaryotes and eukaryotes and is primarily involved in the maintenance of cellular nucleotide pools. We have cloned ndk from Mycobacterium tuberculosis strain H37Ra and expressed it in Escherichia coli as a fusion protein with glutathione S-transferase. The purified protein, following thrombin cleavage and gel permeation chromatography, was found to be hexameric with a monomeric unit molecular mass of approximately 16.5 kDa. The protein exhibited nucleotide binding, divalent cation-dependent autophosphorylation, and phosphate transfer ability from nucleoside triphosphate to nucleoside diphosphate. Although UDP inhibited the catalytic activity of the recombinant protein, the classic inhibitors, like cromoglycate, 5'-adenosine 3'-phosphate, and adenosine 3'-phosphate 5'-phosphosulfate, had no effect on the activity. Among three histidine residues in the protein, His-117 was found to be essential for autophosphorylation. However, in subsequent phosphate transfer, we observed that His-53 had a significant contribution. Consistent with this observation, substitution of His-53 with either Ala or Gln affected the ability of the recombinant protein to complement NdK function in Pseudomonas aeruginosa. Furthermore, mutational analysis established critical roles for Tyr-50 and Arg-86 of the M. tuberculosis protein in maintaining phosphotransfer ability.

A novel UV laser-induced visible blue radiation from protein crystals and aggregates: scattering artifacts or fluorescence transitions of peptide electrons delocalized through hydrogen bonding?

Proteins lacking prosthetic groups and/or cofactors are known to undergo electronic excitation transitions only upon exposure to UV-C (< 280 nm) and UV-B (280-320 nm), but not UV-A (320-400 nm) photons. Here, we report the discovery of a novel excitation that peaks at approximately 340 nm and yields visible violet-blue radiation with apparent band maxima at approximately 425, 445, 470, and 500 nm. All proteins and large polypeptides examined in solid form, and in solutions, display this quenchable and photobleachable radiation which can be established not owing to aromatic sidechains. As a note of caution, we wish to state that we have not been able to completely eliminate the possibility that the radiation may be an artifact owing to second order effects such as, e.g., Raman scattering of Raman-scattered photons; however, we assert that all our experiments indicate that the radiation actually owes to some form of fluorescence. We propose that peptide electrons that have been delocalized through intramolecular or intermolecular hydrogen bond formation display these long-wavelength electronic transitions. If confirmed by future studies, this preliminary discovery may turn out to have important implications for biomolecular spectroscopy, protein crystallography, and materials science.

OB-fold: growing bigger with functional consistency.

It was predicted that the folding space for various protein sequences is restricted and a maximum of 1000 protein folds could be expected. Although, there were about 648 folds identified, general functional features of individual folds is not thoroughly studied. We selected OB-fold, which is supposed to be an oligonucleotide and oligosaccharide binding fold to study the general functional features. OB-fold is a small beta-barrel fold formed from 5 strands connected by modulating loops. We observed consistently 2 or 3 loops on the same face of barrel acting as clamps to bind to their ligands. Depending on the ligand, which could be a single or double stranded DNA/RNA or an oligosaccharide, and their conformational properties the loops change in length and sequence to accommodate various ligands. Different classes of OB-folded proteins were analyzed and found that the functional features are retained in spite of negligible sequence homology among various proteins studied.

Crystallization and preliminary X-ray diffraction analysis of a thermostable D-hydantoinase from the mesophilic Bacillus sp. AR9.

D-hydantoinase catalyzes the conversion of DL-hydantoin derivatives to the corresponding optically pure N-carbamoyl amino acids, the first step in the industrial preparation of optically pure amino acids using biological catalysts. A thermostable D-hydantoinase from the mesophilic bacteria Bacillus sp. AR9 has been crystallized in three different crystal forms. The hexagonal faced crystals were the best looking, but did not diffract. One of the crystal forms is star-shaped and appeared to be twinned, but diffracted as a single crystal to a resolution of 2.3 A. These crystals belong to space group P6(4) and have unit-cell parameters a = b = 129.55, c = 102.86 A, alpha = beta = 90, gamma = 120 degrees.

Promiscuous binding nature of SH3 domains to their target proteins.

SH3 domains are small but important domains in cell-signaling and function through protein-protein interactions. Their promiscuous nature in binding to polyproline peptides makes them much more important because many SH3 domains from different proteins bind to different proteins having polyproline template on their surface. Very subtle changes in the sequence of SH3 domains and the binding peptides determine the specificity of the peptide binding. Recent observation that SH3 domains bind to non- proline peptides makes the scenario of peptide binding involving SH3 domains complicated. If domain swapped dimerization as observed in Eps8-SH3 domain also binds different peptides, it proves the versatility of the SH3 domains in binding to peptides in various ways. An overview of the promiscuity of SH3 domains has been discussed.

Effect of pH and salt bridges on structural assembly: molecular structures of the monomer and intertwined dimer of the Eps8 SH3 domain.

The SH3 domain of Eps8 was previously found to form an intertwined, domain-swapped dimer. We report here a monomeric structure of the EPS8 SH3 domain obtained from crystals grown at low pH, as well as an improved domain-swapped dimer structure at 1.8 A resolution. In the domain-swapped dimer the asymmetric unit contains two "hybrid-monomers." In the low pH form there are two independently folded SH3 molecules per asymmetric unit. The formation of intermolecular salt bridges is thought to be the reason for the formation of the dimer. On the basis of the monomer SH3 structure, it is argued that Eps8 SH3 should, in principle, bind to peptides containing a PxxP motif. Recently it was reported that Eps8 SH3 binds to a peptide with a PxxDY motif. Because the "SH3 fold" is conserved, alternate binding sites may be possible for the PxxDY motif to bind. The strand exchange or domain swap occurs at the n-src loops because the n-src loops are flexible. The thermal b-factors also indicate the flexible nature of n-src loops and a possible handle for domain swap initiation. Despite the loop swapping, the typical SH3 fold in both forms is conserved structurally. The interface of the acidic form of SH3 is stabilized by a tetragonal network of water molecules above hydrophobic residues. The intertwined dimer interface is stabilized by hydrophobic and aromatic stacking interactions in the core and by hydrophilic interactions on the surface.

The SH3 domain of Eps8 exists as a novel intertwined dimer.

SH3 domains are structurally well-characterized as monomeric modular units of protein structure that mediate protein-protein recognition in numerous signal transduction proteins. The X-ray crystallographic structure of the Eps8 SH3 domain reveals a novel variation of the canonical SH3 fold: the SH3 domain from Eps8 is a dimer formed by strand interchange. In addition, co-immunoprecipitation experiments show that intact Eps8 is multimeric in vivo. Hence, the SH3 domain of Eps8 may represent a dimerization motif.