PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Enantiospecific synthesis of functionalised bicyclo[3.3.1] nonanes from 10-bromocarvones via tandem intermolecular alkylation-intramolecular Michael addition sequence

A simple and convenient tandem methodology for the enantiospecific generation of functionalised bicyclo[3.3.1] nonanes 9,14-18, via intermolecular alkylation of Michael donors with 10-bromocarvones 7, 10 and 11, followed by intramolcular Michael addition, is achieved. An unsuccessful attempt for the extension of the methodology for a possible short enantiospecific approach to AB-ring system 22 of taxanes via the allyl bromide 21, is also described.

Two new families of low-correlation interleaved QAM sequence

Two families of low correlation QAM sequences are presented here. In a CDMA setting, these sequences have the ability to transport a large amount of data as well as enable variable-rate signaling on the reverse link. The first family Á2SQ - B2− is constructed by interleaving 2 selected QAM sequences. This family is defined over M 2-QAM, where M = 2 m , m ≥ 2. Over 16-QAM, the normalized maximum correlation [`(q)]maxmax is bounded above by <~1.17 ÖNUnknown control sequence '\lesssim' , where N is the period of the sequences in the family. This upper bound on [`(q)]maxmax is the lowest among all known sequence families over 16-QAM.The second family Á4SQ4 is constructed by interleaving 4 selected QAM sequences. This family is defined over M 2-QAM, where M = 2 m , m ≥ 3, i.e., 64-QAM and beyond. The [`(q)]maxmax for sequences in this family over 64-QAM is upper bounded by <~1.60 ÖNUnknown control sequence '\lesssim' . For large M, [`(q)]max <~1.64 ÖNUnknown control sequence '\lesssim' . These upper bounds on [`(q)]maxmax are the lowest among all known sequence families over M 2-QAM, M = 2 m , m ≥ 3.

Integer Sequence window based Reconfigurable FIR filters

Conventional hardware implementation techniques for FIR filters require the computation of filter coefficients in software and have them stored in memory. This approach is static in the sense that any further fine tuning of the filter requires computation of new coefficients in software. In this paper, we propose an alternate technique for implementing FIR filters in hardware. We store a considerably large number of impulse response coefficients of the ideal filter (having box type frequency response) in memory. We then do the windowing process, on these coefficients, in hardware using integer sequences as window functions. The integer sequences are also generated in hardware. This approach offers the flexibility in fine tuning the filter, like varying the transition bandwidth around a particular cutoff frequency.

Single-machine scheduling with past-sequence-dependent setup times and learning effects: a parametric analysis

In this article, we consider the single-machine scheduling problem with past-sequence-dependent (p-s-d) setup times and a learning effect. The setup times are proportional to the length of jobs that are already scheduled; i.e. p-s-d setup times. The learning effect reduces the actual processing time of a job because the workers are involved in doing the same job or activity repeatedly. Hence, the processing time of a job depends on its position in the sequence. In this study, we consider the total absolute difference in completion times (TADC) as the objective function. This problem is denoted as 1/LE, (Spsd)/TADC in Kuo and Yang (2007) ('Single Machine Scheduling with Past-sequence-dependent Setup Times and Learning Effects', Information Processing Letters, 102, 22-26). There are two parameters a and b denoting constant learning index and normalising index, respectively. A parametric analysis of b on the 1/LE, (Spsd)/TADC problem for a given value of a is applied in this study. In addition, a computational algorithm is also developed to obtain the number of optimal sequences and the range of b in which each of the sequences is optimal, for a given value of a. We derive two bounds b* for the normalising constant b and a* for the learning index a. We also show that, when a < a* or b > b*, the optimal sequence is obtained by arranging the longest job in the first position and the rest of the jobs in short processing time order.

Structural Annotation of Mycobacterium tuberculosis Proteome

Of the similar to 4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for similar to 2877 ORFs, covering similar to 70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.

Oneand twodimensional single quantumand multiplequantumNMR methodologies: tools for chiral analyses

It is well known that enantiomers cannot be distinguished by NMR spectroscopy unless diastereomorphic interactions are imposed. Several chiral aligning media have therefore been reported for their visualization, although extensive studies are carried out using the liquid crystal made of polypeptide poly-γ-benzyl-L-glutamate (PBLG) in organic solvent. In PBLG medium the spin systems are weakly coupled and the first order analyses of the spectra are generally possible. But due to large number of pair wise interactions of nuclear spins resulting in many degenerate transitions the 1H NMR spectra are not only complex but also broad and featureless, in addition to an indistinguishable overlap of the spectra of enantiomers. This enormous loss of resolution severely hinders the analyses of proton spectra, even for spin systems with 5–6 interacting protons, thereby restricting itsroutine application. In this review we discuss our recently developed several one and multidimensional NMR experiments to circumvent these difficulties taking specific examples of the molecules containing a single chiral centre.

Development of novel multiple quantummethodologies for the analyses of complex protonNMR spectra of scalar coupled spins

One of the significant advancements in Nuclear Magnetic Resonance spectroscopy (NMR) in combating the problem of spectral complexity for deriving the structure and conformational information is the incorporation of additional dimension and to spread the information content in a two dimensional space. This approach together with the manipulation of the dynamics of nuclear spins permitted the designing of appropriate pulse sequences leading to the evolution of diverse multidimensional NMR experiments. The desired spectral information can now be extracted in a simplified and an orchestrated manner. The indirect detection of multiple quantum (MQ) NMR frequencies is a step in this direction. The MQ technique has been extensively used in the study of molecules aligned in liquid crystalline media to reduce spectral complexity and to determine molecular geometries. Unlike in dipolar coupled systems, the size of the network of scalar coupled spins is not big in isotropic solutions and the MQ 1H detection is not routinely employed,although there are specific examples of spin topology filtering. In this brief review, we discuss our recent studies on the development and application of multiple quantum correlation and resolved techniques for the analyses of proton NMR spectra of scalar coupled spins.

Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

C2 domain is responsible for targeting rice phosphoinositide specific phospholipase C

Phosphoinositide-specific phospholipase C (PLC) is involved in Ca2+ mediated signalling events that lead to altered cellular status. Using various sequence-analysis methods, we identified two conserved motifs in known PLC sequences. The identified motifs are located in the C2 domain of plant PLCs and are not found in any other protein. These motifs are specifically found in the Ca2+ binding loops and form adjoining beta strands. Further, we identified certain conserved residues that are highly distinct from corresponding residues of animal PLCs. The motifs reported here could be used to annotate plant-specific phospholipase C sequences. Furthermore, we demonstrated that the C2 domain alone is capable of targeting PLC to the membrane in response to a Ca2+ signal. We also showed that the binding event results from a change in the hydrophobicity of the C2 domain upon Ca2+ binding. Bioinformatic analyses revealed that all PLCs from Arabidopsis and rice lack a transmembrane domain, myristoylation and GPI-anchor protein modifications. Our bioinformatic study indicates that plant PLCs are located in the cytoplasm, the nucleus and the mitochondria. Our results suggest that there are no distinct isoforms of plant PLCs, as have been proposed to exist in the soluble and membrane associated fractions. The same isoform could potentially be present in both subcellular fractions, depending on the calcium level of the cytosol. Overall, these data suggest that the C2 domain of PLC plays a vital role in calcium signalling.

Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.