Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

Hantzsch 1,4-dihydropyridine esters and analogs: candidates for generating reproducible one-dimensional packing motifs

Examination of the symmetric Hantzsch 1,4-dihydropyridine ester derivatives of the prototypical nifedipine molecule indicates the tendency of this class of molecule to form a common packing motif. Crystal structure analysis of 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic diesters and analogs reveals that they form extended chains, characterized as the C(6) packing motif, via intermolecular (amine) N-H...O=C (C3,C5 carbonyl) hydrogen bonds. In addition, all the prepared derivatives also satisfy the basic structural requirements for their high binding efficiency to the receptor. The reproducible C(6) packing motif observed among these compounds has a use in the design of solid-state materials.

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.

Orthogonal beta-beta motifs in proteins

A super-secondary structural motif comprising two orthogonally oriented beta-strands connected by short linking segments of <5 residues has been identified from a data set of 65 independent protein crystal structures. Of the 42 examples from 14 proteins, a vast majority have only a single residue as the linking element. Analysis of the conformational angles at the junction reveals that the recently described type VIII beta-turn occurs frequently at the connecting hinge, while the type II beta-turn is also fairly common.

Mammalian spermatid specific protein, TP2, is a zinc metalloprotein with two finger motifs

An analysis of the recently reported cDNA derived amino acid sequences of mouse (Kleene and Flynn, J. Biol. Chem. , 17272–17277, 1987) and rat (Luersson Image ,Nucl. Acids Res. Image , 3585, 1989). TP2 has revealed the presence of two potential zinc finger motifs involving cysteine and histidine residues. TP2, as purified from rat elongating spermatids, is shown here to contain 0.2 atoms of zinc bound per molecule of the protein by atomic absorption spectroscopy. On incubation with 10 μM ZnCl2, Image , and subsequent exhaustive dialysis, TP2 had 2 atoms of zinc bound per molecule. The involvement of cysteine residues of TP2 in coordination with zinc was also suggested by the observation that TP2 could be labeled, Image , with iodoacetamidofluorescein only after preincubation of spermatid nuclei with EDTA. The zinc finger domains of TP2 may play an important role in initiation of chromatin condensation and /or cessation of transcriptional activity during mammalian spermiogenesis. DTT, Dithiothreitol; IAF, Iodoacetamido-fluorescein; SDS, Sodium dodecyl sulfate; PAGE, Polyacrylamide gel electrophoresis; PMSF, Phynyl methyl sulfonyl fluoride

SSMBS: a web server to locate sequentially separated motifs in biological sequences

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server, SSMBS, which can locate anddisplay the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.

A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS)

Sequence motifs occurring in a particular order in proteins or DNA have been proved to be of biological interest. In this paper, a new method to locate the occurrences of up to five user-defined motifs in a specified order in large proteins and in nucleotide sequence databases is proposed. It has been designed using the concept of quantifiers in regular expressions and linked lists for data storage. The application of this method includes the extraction of relevant consensus regions from biological sequences. This might be useful in clustering of protein families as well as to study the correlation between positions of motifs and their functional sites in DNA sequences.

Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Functional analysis of conserved motifs in EcoP15I DNA methyltransferase

EcoP15I DNA methyltransferase recognizes the sequence 5'-CAGCAG-3' and transfers a methyl group to N-6 of the second adenine residue in the recognition sequence. All N-6 adenine methyltransferases contain two highly conserved sequences, FxGxG (motif I), postulated to form part of the S-adenosyl-L-methionine binding site and (D/N/S)PP(Y/F) (motif IV) involved in catalysis. We have altered the second glycine residue in motif I to arginine and serine, and substituted tyrosine in motif IV with tryptophan in EcoP15I DNA methyltransferase, using site-directed mutagenesis. The mutant enzymes were overexpressed, purified and characterized by biochemical methods. The mutations in motif I completely abolished AdoMet binding but left target DNA recognition unaltered. Although the mutation in motif IV resulted in loss of enzyme activity, we observed enhanced crosslinking of S-adenosyl-L-methionine and DNA. This implies that DNA and AdoMet binding sites are close to motif IV. Taken together, these results reinforce the importance of motif I in AdoMet binding and motif IV in catalysis. Additionally, limited proteolysis and UV crosslinking experiments with EcoP15I DNA methyltransferase imply that DNA binds in a cleft formed by two domains in the protein. Methylation protection analysis provides evidence for the fact that EcoP15I DNA MTase makes contacts in the major groove of its substrate DNA. Interestingly, hypermethylation of the guanine residue next to the target adenine residue indicates that the protein probably flips out the target adenine residue. (C) 1996 Academic Press Limited

Twisted aromatics, 9-anthryl and 1-pyrenyl terpyridines organize into novel multi-directional 'ladder-like' motifs in the solid state

9-Anthryl and 1-pyrenyl terpyridines (1 and 2, respectively), key precursors for the design of novel fluorescent sensors have been synthesized and characterized by H-1 NMR, mass spectroscopy and X-ray crystallography. Twisted molecular conformations for each 1 and 2 were observed in their single crystal structures. Energy minimization calculations for the 1 and 2 using the semi-empirical AM1 method show that the 'twisted' conformation is intrinsic to these systems. We observe interconnected networks of edge-to-face CH...pi interactions, which appear to be cooperative in nature, in each of the crystal structures. The two twisted molecules, although having differently shaped polyaromatic hydrocarbon substituents, show similar patterns of edge-to-face CH...pi interactions.The presently described systems comprise of two aromatic surfaces that are almost orthogonal to each other. This twisted or orthogonal nature of the molecules leads to the formation of interesting multi-directional ladder like supramolecular organizations. A combination of edge-to-face and face-to-face packing modes helps to stabilize these motifs. The ladder like architecture in 1 is helical in nature. (C) 2002 Published by Elsevier Science B.V.

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C–H⋯F and C–H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C–H⋯F and C–H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O–H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Spatial Data Mining and Modeling for visualisation of Rapid Urbanisation

Rapid urbanisation in India has posed serious challenges to the decision makers in regional planning involving plethora of issues including provision of basic amenities (like electricity, water, sanitation, transport, etc.). Urban planning entails an understanding of landscape and urban dynamics with causal factors. Identifying, delineating and mapping landscapes on temporal scale provide an opportunity to monitor the changes, which is important for natural resource management and sustainable planning activities. Multi-source, multi-sensor, multi-temporal, multi-frequency or multi-polarization remote sensing data with efficient classification algorithms and pattern recognition techniques aid in capturing these dynamics. This paper analyses the landscape dynamics of Greater Bangalore by: (i) characterisation of direct impervious surface, (ii) computation of forest fragmentation indices and (iii) modeling to quantify and categorise urban changes. Linear unmixing is used for solving the mixed pixel problem of coarse resolution super spectral MODIS data for impervious surface characterisation. Fragmentation indices were used to classify forests – interior, perforated, edge, transitional, patch and undetermined. Based on this, urban growth model was developed to determine the type of urban growth – Infill, Expansion and Outlying growth. This helped in visualising urban growth poles and consequence of earlier policy decisions that can help in evolving strategies for effective land use policies.

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

Deoxythiosugar Derivatives with Furano, Pyrano, and Septano Motifs from L-Gulono-1,4-lactone and D-Glycero-D-gulo-heptono-1,4-lactone

A short synthesis of thiosugar derivatives mimicking furanose, pyranose, and septanose structures has been achieved starting from L-gulono-1,4-lactone and D-glucoheptono-1,4-lactone. Different strategies used in the synthesis are: (1) a nucleophilic displacement and Michael addition; (2) epoxide ring opening and Michael addition; (3) epoxide ring opening and nucleophilic displacement process; and (4) double nucleophilic displacement. All of these reactions used benzyltriethylammonium tetrathiomolybdate, (BnEt3N)(2)MoS4 as the sulfur-transfer reagent.

Steric and Electronic Interactions Controlling the cis/trans Isomer Equilibrium at X-Pro Tertiary Amide Motifs in Solution

A systematic understanding of the noncovalent interactions that influence the structures of the cis conformers and the equilibrium between the cis and the trans conformers, of the X-Pro tertiary amide motifs, is presented based on analyses of H-1-, C-13-NMR and FTIR absorption spectra of two sets of homologous peptides, X-Pro-Aib-OMe and X-Pro-NH-Me (where X is acetyl, propionyl, isobutyryl and pivaloyl), in solvents of varying polarities. First, this work shows that the cis conformers of any X-Pro tertiary amide motif, including Piv-Pro, are accessible in the new motifs X-Pro-Aib-OMe, in solution. These conformers are uniquely observable by FTIR spectroscopy at ambient temperatures and by NMR spectroscopy from temperatures as high as 273 K. This is made possible by the persistent presence of n(i-1i)* interactions at Aib, which also influence the disappearance of steric effects at these cis X-Pro rotamers. Second, contrary to conventional understanding, the energy contribution of steric effects to the cis/trans equilibrium at the X-Pro motifs is found to be nonvariant (0.54 +/- 0.02 kcal/mol) with increase in steric bulk on the X group. Third, the current studies provide direct evidence for the weak intramolecular interactions namely the n(i-1i)*, the N-Pro center dot center dot center dot Hi+1 (C(5)a), and the C-7 hydrogen bond that operate and influence the structures, stabilities, and dynamics between different conformational states of X-Pro tertiary amide motifs. NMR and IR spectral data suggest that the cis conformers of X-Pro motifs are ensembles of short-lived rotamers about the C-X-N-Pro bond. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 66-77, 2014.