Habitat distribution modelling and reinforcement of Elaeocarpus serratus L. - A threatened tree species of Assam,India for improvement of its conservation status

Elaeocarpus serratus L., commonly known as ‘rudraksh’ referred in the Ayurveda as a wonderful plant for strengthening body constitutions, has been recognized as a threatened plant of Assam, India. Traditionally, rudraksh beads, its bark and leaves are used to cure various ailments like stress, anxiety, depression, nerve pain, epilepsy, migraine, lack of concentration, asthma, hypertension, arthritis and liver diseases. The population stock of the species has been depleting very fast in its natural habitat due to rapid habitat fragmentation and changing climate altering the structural and functional integrity of the plant. Hence, conservation of E. serratus L. with proper scientific investigation to prevent from extinction in its wild habitat is urgently needed. The present study was emphasized with the specific objectives to study the distribution and population status, predication of suitable sites through ENM, standardization of macropropagation methods and reinforcement/reintroduction into the suitable wild habitat to improve conservation status. In the present investigation E. serratus L. was reported in few locations of Assam and Arunachal Pradesh with population sizes of mean density, frequency of occurrence and abundance in relation to other associated species as 0.333, 13.922 and 2.215 respectively. For improving the conservation status, potential area and habitat for reinforcement was predicted using Maximum Entropy (MaxEnt) distribution modelling algorithm. Subsequently, macropropagation protocol was standardized through seed germination and air-layering; saplings were raised and 1050 saplings were reintroduced to the wild habitats selected on the basis of ecological niche modelling. Survival rate was found significantly high as 68%, suggesting that our approach is effective for changing population status and to conserve the plant.     

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding

Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify alpha-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi,psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding.     

Evaluation of desialylation during 2-amino benzamide labeling of asparagine-linked oligosaccharides

Labeling of released asparagine-linked (N-linked) oligosaccharides from glycoproteins is commonly performed to aid in the separation and detection of the oligosaccharide. Of the many available oligosaccharide labels, 2-amino benzamide (2-AB) is a popular choice for providing a fluorescent product. The derivatization conditions can potentially lead to oligosaccharide desialylation. This work evaluated the extent of sialic acid loss during 2-AB labeling of N-linked oligosaccharides released from bovine fetuin, polyclonal human serum immunoglobulin G (IgG), and human α₁-acid glycoprotein (AGP) as well as of sialylated oligosaccharide reference standards and found that for more highly sialylated oligosaccharides the loss is greater than the <2% value commonly cited. Manufacturers of glycoprotein biotherapeutics need to produce products with a consistent state of sialylation and, therefore, require an accurate assessment of glycoprotein sialylation.     

Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation

The shortest helices (three-length 3(10) and four-length alpha), most abundant among helices of different lengths, have been analyzed from a database of protein structures. A characteristic feature of three-length 3(10)-helices is the shifted backbone conformation for the C-terminal residue (phi,psi angles: -95 degrees,0 degrees ), compared to the rest of the helix (-62 degrees,-24 degrees ). The deviation can be attributed to the release of electrostatic repulsion between the carbonyl oxygen atoms at the two C-terminal residues and further stabilization (due to a more linear geometry) of an intrahelical hydrogen bond. A consequence of this non-canonical C-terminal backbone conformation can be a potential origin of helix kinks when a 3(10)-helix is sequence-contiguous at the alpha-helix N-terminal. An analysis of hydrogen bonding, as well as hydrophobic interactions in the shortest helices shows that capping interactions, some of them not observed for longer helices, dominate at the N termini. Further, consideration of the distribution of amino acid residues indicates that the shortest helices resemble the N-terminal end of alpha-helices rather than the C terminus, implying that the folding of helices may be initiated at the N-terminal end, which does not get propagated in the case of the shortest helices. Finally, pairwise comparison of beta-turns and the shortest helices, based on correlation matrices of site-specific amino acid composition, and the relative abundance of these short secondary structural elements, leads to a helix nucleation scheme that considers the formation of an isolated beta-turn (and not an alpha-turn) as the helix nucleation step, with shortest 3(10)-helices as intermediates between the shortest alpha-helix and the beta-turn. Our results ascribe an important role played by shortest 3(10)-helices in proteins with important structural and folding implications.     

Role of terminal dipole charges in aggregation of α-helix pair in the voltage gated K+ channel

The voltage sensor domain (VSD) of the potassium ion channel KvAP is comprised of four (S1–S4) α-helix proteins, which are encompassed by several charged residues. Apart from these charges, each peptide α-helix having two inherent equal and opposite terminal dipolar charges behave like a macrodipole. The activity of voltage gated ion channel is electrostatic, where all the charges (charged residues and dipolar terminal charges) interact with each other and with the transmembrane potential. There are evidences that the role of the charged residues dominate the stabilization of the conformation and the gating process of the ion channel, but the role of the terminal dipolar charges are never considered in such analysis. Here, using electrostatic theory, we have studied the role of the dipolar terminal charges in aggregation of the S3b–S4 helix pair of KvAP in the absence of any external field (V = 0). A system attains stability, when its potential energy reaches minimum values. We have shown that the presence of terminal dipole charges (1) change the total potential energy of the charges on S3b–S4, affecting the stabilization of the α-helix pair within the bilayer lipid membrane and (2) the C- and the N-termini of the α-helices favor a different dielectric medium for enhanced stability. Thus, the dipolar terminal charges play a significant role in the aggregation of the two neighboring α-helices.     

Isolation of ACC deaminase producing PGPR from rice rhizosphere and evaluating their plant growth promoting activity under salt stress

Aims

Bacteria possessing ACC deaminase activity reduce the level of stress ethylene conferring resistance and stimulating growth of plants under various biotic and abiotic stresses. The present study aims at isolating efficient ACC deaminase producing PGPR strains from the rhizosphere of rice plants grown in coastal saline soils and quantifying the effect of potent PGPR isolates on rice seed germination and seedling growth under salinity stress and ethylene production from rice seedlings inoculated with ACC deaminase containing PGPR.

Methods

Soils from root region of rice growing in coastal soils of varying salinity were used for isolating ACC deaminase producing bacteria and three bacterial isolates were identified following polyphasic taxonomy. Seed germination, root growth and stress ethylene production in rice seedlings following inoculation with selected PGPR under salt stress were quantified.

Results

Inoculation with selected PGPR isolates had considerable positive impacts on different growth parameters of rice including germination percentage, shoot and root growth and chlorophyll content as compared to uninoculated control. Inoculation with the ACC deaminase producing strains reduced ethylene production under salinity stress.

Conclusions

This study demonstrates the effectiveness of rhizobacteria containing ACC deaminase for enhancing salt tolerance and consequently improving the growth of rice plants under salt-stress conditions.     

3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation

Does the amino acid use at the terminal positions of an α‐helix become altered depending on the context—more specifically, when there is an adjoining 3₁₀‐helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3₁₀–α and α–3₁₀ composite helices, respectively, found in known protein structures indicate that the secondary structural element occurring first imposes its characteristics on the sequence of the structural element coming next. Thus, when preceded by a 3₁₀‐helix, the preference of proline to occur at the N1 position of an α‐helix is shifted to the N2 position, a typical characteristic of the C‐terminal capping of the 3₁₀‐helix. When an α‐ or a 3₁₀‐helix leads into a helix of the other type, there is a bend at the junction, especially for the 3₁₀–α composite, with the two junction residues facing inward and buried within the structure. Thus a single helical cylinder may not properly represent a composite helix, the bend providing a means for the tertiary structure to assume a globular shape, very much akin to what a proline‐induced kink does to an α‐helix. The tertiary structural context in which β–3₁₀ and 3₁₀–β composites occurs can be different, causing the angle between the secondary structural elements in the two cases to be different. Composites of 3₁₀‐helices and β‐strands are much more conserved among members in families of homologous structures than those between two types of helices; in many of the former instances, the 3₁₀‐helix constitutes the loops in β‐hairpin or β–β‐corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary structure elements in a composite. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 147–162, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com