Secondary structures at polypeptide-chain termini and their features

An analysis of secondary structures (α-helices and β-strands) in the two terminal regions of polypeptide chains reveals features different from those observed over the whole protein structure. Compared with the overall distribution, the helices in the N-terminal region tend to be smaller and have higher propensities to contain Gln and Leu, while the C-terminal helices are longer and have a greater proportion of Lys and Glu. As a strand, the C-terminal region is never found in the interior of parallel β-sheets and has a higher propensity to be at the edge of antiparallel β-sheets. In contrast, compared with the whole structure the N-terminal region has a higher propensity to be in the interior of parallel β-sheets. Compared with the overall distributions, terminal helices and strands show distinct periodicities in length. The Schellman motif, which is a prevalent C-capping motif in helices, is not common in C-terminal helices. There are other observations that can be used in the design of helical peptides: more residues beyond the C-terminus of helices are used for capping interactions than residues before the N-terminus. Consideration of the distribution of terminal strands in the interior and at the edge of β-sheets suggests a sequential folding mechanism beginning at the N-terminus of the polypeptide chain

Disulfide bonds, their stereospecific environment and conservation in protein structures

We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms is along the back of the two covalent bonds at the sulfur atom of half cystine. With aromatic residues the geometries that direct one of the sulfur lone pair of electrons into the aromatic Π-system are avoided; an orientation in which the sulfide plane is normal or inclined to the aromatic plane and on top of its edge is normally preferred. The importance of the S···aromatic interaction is manifested in the high degree of its conservation across members in homologous protein families. These interactions, while providing extra overall stability to the native fold and reducing the accessibility of the disulfide bond and thereby preventing exchange reactions, also set the orientation of the conserved aromatic rings for further interactions and binding to another molecule. The conformational features and the mode of interactions of disulfide bridges should be useful for molecular design and protein engineering experiments

IntGeom: a server for the calculation of the interaction geometry between planar groups in proteins

IntGeom is a server for the calculation of the relative orientation between any two planar groups in protein side chains. IntGeom1 considers ten planar groups, while IntGeom2 is meant for studying the contact between a S-containing group and an aromatic residue. When the interaction is between two aromatic residues or involving an aromatic ring with Pro or Arg or an amide side chain, the occurrence of any C-H···π (N-H···π) interaction is also studied. All contacts between any two of the above types of residues juxtaposed on the protein structure can be displayed. The software is available at: http://www.boseinst.ernet.in/resources/bioinfo/stag.html

High frequency <i>in vitro </i>propagation of <i>Phyllanthus amarus </i>Schum. &Thom. <span style="font-size:14.0pt;line-height:115%;font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";color:black;mso-ansi-language:EN-IN; mso-fareast-language:EN-IN;mso-bidi-language:HI" lang="EN-IN">by shoot tip culture</span>

1184-1187With the aim of micropropagation of Phyllanthus amarus , an important medicinal herb, shoot tips were cultured in Murashige and Skoog's medium supplemented with kinetin/ BAP singly or in combination with IAA. Growth regulators at lower range (0.1- 1.0 mg L-1) stimulated direct regeneration of shoots. Kinetin was superior to BAP and kinetin-IAA combination was more suitable than kinetin alone. About 15 shoots were yielded per explant after 30 days of culture in the medium containing kinetin and IAA both at 0.1 mg L-1 &nbsp;The cluster of proliferated shoots elongated and rooted simultaneously under the same treatment following another subculture, thus shortening the total time schedule of micropropagation. Shoot tips of regenerated shoots were continuously used to regenerate new shoots with periodic transfer to fresh medium resulting in a steady supply of normal, healthy plants without any deviation in the production rate during a continuous one year culture. Micropropagated plants were successfully established in soil with high survivality (80%).</span

Geometry of nonbonded interactions involving planar groups in proteins

Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...Π, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as α-helices and β-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties

1-Naphthyl acetate as an alternative substrate of hemolysate cholinesterase: Direct visualization of enzyme activity within 10 minutes on polyacrylamide gels

662-671Hemolysate cholinesterase is currently recognized as the most preferred biomarker to detect acute organophosphorus poisoning. Direct visualization of cholinesterase activity on polyacrylamide gels is routinely practiced using acetylthiocholine as a substrate. Overnight incubation with the staining solution is required to understand the enzyme activity bands on gels. Therefore, the need arises to explore rapid detection methods, which can specifically detect hemolysate cholinesterase on polyacrylamide gels. Here, we have explored alternative substrates, such as 1-NA and 2-NA which might have the potential to behave as specific substrates for the detection of hemolysate cholinesterase activity on the gels. It is observed by the in silico studies that 1-NA bind at the active site of acetylcholinesterase akin to acetylcholine (ACh) with a better fitness score. Secondly, the hemolysate cholinesterase activity, as well as its inhibition by organophosphorus pesticides is understandable within 10 min using Fast Blue RR dye for the detection of 1-NA. The organophosphorus inhibited activity is regained in the presence of cholinesterase reactivator. Moreover, the enzyme activity bands formed using 1-NA proves the specificity of the substrate for hemolysate cholinesterase as in the presence of specific acetylcholinesterase inhibitors the band formation disappears. On the other hand, ATCh requires minimum 8-12 h staining time for detection of enzyme activity band following Karnovsky and Roots protocol. Our results prove that 1-NA is an alternative substrate of hemolysate cholinesterase which specifically detects the enzyme activity on gel rapidly. We recommend 1-NA for rapid detection of hemolysate cholinesterase activity on the gels

Aromatic-aromatic interactions in and around α-helices

To understand the role of aromatic-aromatic interactions in imparting specificity to the folding process, the geometries of four aromatic residues with different sequence spacing, located in &#945;-helices or five residues from helical ends, interacting with each other have been elucidated. The geometry is found to depend on the sequence difference. Specific interactions (C-H...&#928; and N-H...&#928; which result from this geometry may cause a given pair of residues (such as Phe-His) with a particular sequence difference to occur more than expected. The most conspicuous residue in an aromatic pair in the context of helix stability is His, which is found at the last (C1) position or the two positions (Ncap and Ccap) immediately flanking the helix. An &#945;-helix and a contiguous 310-helix or two helices separated by a non-helical residue can have interacting aromatic pairs, the geometry of interaction and the relative orientation between the helices being rather fixed. Short helices can also have interacting residues from either side

Retinoic Acid and Iron Metabolism: A Step Towards Design of a Novel Antitubercular Drug

The scenario of tuberculosis has gone deadly due to its high prevalence and emergence of widespread drug resistance. It is now high time to develop novel antimycobacterial strategies and to understand novel mechanisms of existing antimycobacterial compounds so that we are equipped with newer tuberculosis controlling molecules in the days to come. Iron has proven to be essential for pathogenesis of tuberculosis and retinoic acid is known to influence the iron metabolism pathway. Retenoic acid is also known to exhibit antitubercular effect in in vivo system. Therefore there is every possibility that retinoic acid by affecting the iron metabolism pathway exhibits its antimycobacterial effect. These aspects are reviewed in the present manuscript for understanding the antimycobacterial role of retinoic acid in the context of iron metabolism and other immunological aspects