Manju Bansal

A novel method for prokaryotic promoter prediction based on DNA stability

BackgroundIn the post-genomic era, correct gene prediction has become one of the biggest challenges in genome annotation. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. This work presents a novel prokaryotic promoter prediction method based on DNA stability.ResultsThe promoter region is less stable and hence more prone to melting as compared to other genomic regions. Our analysis shows that a method of promoter prediction based on the differences in the stability of DNA sequences in the promoter and non-promoter region works much better compared to existing prokaryotic promoter prediction programs, which are based on sequence motif searches. At present the method works optimally for genomes such as that of Escherichia coli, which have near 50 % G+C composition and also performs satisfactorily in case of other prokaryotic promoters.ConclusionsOur analysis clearly shows that the change in stability of DNA seems to provide a much better clue than usual sequence motifs, such as Pribnow box and -35 sequence, for differentiating promoter region from non-promoter regions. To a certain extent, it is more general and is likely to be applicable across organisms. Hence incorporation of such features in addition to the signature motifs can greatly improve the presently available promoter prediction programs.

A hypothesis on the role of hydroxyproline in stabilizing collagen structure.

The possibility of hydroxyproline residues stabilizing the collagen triple-helical structure by the formation of additional hydrogen bonds through their γ-hydroxyl group has been studied from structural considerations. It is not possible for this hydroxyl group to form a direct hydrogen bond with a suitable group in a neighbouring chain of the triple-helical protofibril. However, in the modified one-bonded structure, which is stabilized by additional hydrogen bonds being formed through water molecules as intermediaries (put forward in 1968 by Ramachandran, G. N. and Chandrasekharan, R.), it is found that the γ-hydroxyl group of hydroxyproline can form a good hydrogen bond with the water oxygen as acceptor, the hydrogen bond length being 2.82 A. It is proposed that, in addition to stabilizing the collagen triple-helical structure due to the stereochemical properties of the pyrrolidine ring, hydroxyproline gives added stability by the formation of an extra hydrogen bond. Experimental studies on the determination of shrinkage and denaturation temperatures of native collagen and its synthetic analogues, as a function of their hydroxyproline content, are being undertaken to test this hypothesis.

HELANAL: A Program to Characterize Helix Geometry in Proteins

Abstract A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their Cα atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Dissecting α-helices: Position-specific analysis of α-helices in globular proteins

An analysis of the amino acid distributions at 15 positions, viz., N“, N′, Ncap, N1, N2, N3, N4, Mid, C4, C3, C2, C1, Ccap, C′, and C” in 1,131 α‐helices reveals that each position has its own unique characteristics. In general, natural helix sequences optimize by identifying the residues to be avoided at a given position and minimizing the occurrence of these avoided residues rather than by maximizing the preferred residues at various positions. Ncap is most selective in its choice of residues, with six amino acids (S, D, T, N, G, and P) being preferred at this position and another 11 (V, I, F, A, K, L, Y, R, E, M, and Q) being strongly avoided. Ser, Asp, and Thr are all more preferred at Ncap position than Asn, whose role at helix N‐terminus has been highlighted by earlier analyses. Furthermore, Asn is also found to be almost equally preferred at helix C‐terminus and a novel structural motif is identified, involving a hydrogen bond formed by Nδ2 of Asn at Ccap or C1 position, with the backbone carbonyl oxygen four residues inside the helix. His also forms a similar motif at the C‐terminus. Pro is the most avoided residue in the main body (N4 to C4 positions) and at C‐ter‐minus, including Ccap of an α‐helix. In 1,131 α‐helices, no helix contains Pro at C3 or C2 positions. However, Pro is highly favoured at N1 and C′. The doublet X‐Pro, with Pro at C′ position and extended backbone conformation for the X residue at Ccap, appears to be a common structural motif for termination of α‐helices, in addition to the Schellman motif. Main body of the helix shows a high preference for aliphatic residues Ala, Leu, Val, and Ile, while these are avoided at helix termini. A propensity scale for amino acids to occur in the middle of helices has been obtained. Comparison of this scale with several previously reported scales shows that this scale correlates best with the experimentally determined values. Proteins 31:460–476, 1998.

Definitions and nomenclature of nucleic acid structure parameters

At an EMBO Workshop on DNA Curvature and Bending, held at Churchill College, Cambridge, on 10-15 September 1988, two sessions were scheduled on definitions of parameters used to describe the geometry of nucleic acid chains and helices, and a common nomenclature for these parameters. The most widely used library of helix analysis programs, HELIB (Fratini et al., 1982; Dickerson, 1985) suffers from the fact that the translations and rotations as defined are not fully independent and depend to a certain extent upon the choice of overall helix axis. Several research groups have been engaged independently in developing alternative programs for the geometrical analysis of polynucleotide chains, but with different definitions of quantities calculated and with widely different nomenclature even when the same parameter was involved.

Collagen Structure: The Madras Triple Helix and the Current Scenario

This year marks the 50th anniversary of the coiled?‐?coil triple helical structure of collagen, first proposed by Ramachandrans group from Madras. The structure is unique among the protein secondary structures in that it requires a very specific tripeptide sequence repeat, with glycine being mandatory at every third position and readily accommodates the imino acids proline/hydroxyproline, at the other two positions. The original structure was postulated to be stabilized by two interchain hydrogen bonds, per tripeptide. Subsequent modeling studies suggested that the triple helix is stabilized by one direct inter chain hydrogen bond as well as water mediated hydrogen bonds. The hydroxyproline residues were also implicated to play an important role in stabilizing the collagen fibres. Several high resolution crystal structures of oligopeptides related to collagen have been determined in the last ten years. Stability of synthetic mimics of collagen has also been extensively studied. These have confirmed the essential correctness of the coiled‐coil triple helical structure of collagen, as well as the role of water and hydroxyproline residues, but also indicated additional sequence‐dependent features. This review discusses some of these recent results and their implications for collagen fiber formation.IUBMB Life, 57: 161‐172, 2005

Geometrical and sequence characteristics of α-helices in globular proteins

Understanding the sequence-structure relationships in globular proteins is important for reliable protein structure prediction and de novo design. Using a database of 1131

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

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Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes

-helices with nonidentical sequences from 205 nonhomologous globular protein chains, we have analyzed structural and sequence characteristics of

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

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