Pooja Rani

Diffusion of Hydration Water around Intrinsically Disordered Proteins

Hydration water dynamics around globular proteins have attracted considerable attention in the past decades. This work investigates the hydration water dynamics around partially/fully intrinsically disordered proteins and compares it to that of the globular proteins via molecular dynamics simulations. The translational diffusion of the hydration water is examined by evaluating the mean-square displacement and the velocity autocorrelation function, while the rotational diffusion is probed through the dipole-dipole time correlation function. The results reveal that the translational and rotational motions of water molecules at the surface of intrinsically disordered proteins/regions are less restricted as compared to those around globular proteins/ordered regions, which is reflected in their higher diffusion coefficient and lower orientational relaxation time. The restricted mobility of hydration water in the vicinity of the protein leads to a sublinear diffusion in a heterogeneous interface. A positive correlation between the mean number of hydrogen bonds and the diffusion coefficient of hydration water implies higher mobility of water molecules at the surface of disordered proteins, which is due to their higher number of hydrogen bonds. Enhanced hydration water mobility around disordered proteins/regions is also related to their higher hydration capacity, low hydrophobicity, and increased internal protein motions. Thus, we generalize that the intrinsically disordered proteins/regions are associated with higher hydration water mobility as compared to globular protein/ordered regions, which may help to elucidate their varied functional specificity.

Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

Strain RK1(T), a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1(T) belongs to the family Sphingobacteriaceae and showed highest sequence similarity to Parapedobacter koreensis Jip14(T) (95.63%). The major cellular fatty acids of strain RK1(T) were iso-C15:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C17:0 3-OH, summed feature 9 (10-methyl C16:0 and/or iso-C17:1ω9c), iso-C15:0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1(T) were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1(T) represents a novel species of the genus Parapedobacter, for which the name Parapedobacter indicus sp. nov. is proposed. The type strain is RK1(T) ( = DSM 28470(T) =MCC 2546(T)).

Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads

This work quantitatively characterizes intrinsic disorder in proteins in terms of sequence composition and backbone conformational entropy. Analysis of the normalized relative composition of the amino acid triads highlights a distinct boundary between globular and disordered proteins. The conformational entropy is calculated from the dihedral angles of the middle amino acid in the amino acid triad for the conformational ensemble of the globular, partially and completely disordered proteins relative to the non-redundant database. Both Monte Carlo (MC) and Molecular Dynamics (MD) simulations are used to characterize the conformational ensemble of the representative proteins of each group. The results show that the globular proteins span approximately half of the allowed conformational states in the Ramachandran space, while the amino acid triads in disordered proteins sample the entire range of the allowed dihedral angle space following Flory’s isolated-pair hypothesis. Therefore, only the sequence information in terms of the relative amino acid triad composition may be sufficient to predict protein disorder and the backbone conformational entropy, even in the absence of well-defined structure. The predicted entropies are found to agree with those calculated using mutual information expansion and the histogram method.

Local Structure and Dynamics of Hydration Water in Intrinsically Disordered Proteins.

Hydration water around protein surface plays a key role in structure, folding and dynamics of proteins. Intrinsically disordered proteins lack secondary and/or tertiary structure in their native state. Thus, characterizing the local structure and dynamics of hydration water around disordered proteins is challenging for both experimentalists and theoreticians. The local structure, orientation and dynamics of hydration water in the vicinity of intrinsically disordered proteins is investigated through molecular dynamics simulations. The analysis of the hydration capacity reveals that the disordered proteins have much larger binding capacity for hydration water than globular proteins. The surface and radial distribution of water molecules around the disordered proteins depict a similar trend. The local structure of the hydration water evaluated in terms of the tetrahedral order parameter, shows a higher order among the water molecules surrounding disordered proteins/regions. The residence time of water molecules clearly exhibits slow dynamics of hydration water around the surface of disordered proteins/regions as compared to globular proteins. The orientation of water molecules is found to be distinctly different for ordered and disordered proteins/regions. This analysis provides a better insight into the structure and dynamics of hydration water around disordered proteins.

Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil

A Gram-negative-staining, aerobic, non-motile, non-spore-forming, rod-shaped and yellow-pigmented bacterium, designated R11HT, was isolated from a soil sample collected from a hexachlorocyclohexane dumpsite located at Ummari village, Lucknow, Uttar Pradesh, India. The 16S rRNA gene sequence similarity between strain R11HT and the type strains of species of genus Sphingopyxis with validly published names ranged from 93.75 to 97.85 %. Strain R11HT showed the highest 16S rRNA gene sequence similarity to Sphingopyxis indica DS15T (97.85 %), followed by Sphingopyxis soli JCM15910T (97.79 %), Sphingopyxis ginsengisoli KCTC 12582T (97.77 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.34 %). The DNA G+C content of strain R11HT was 63.5 mol%. DNA-DNA relatedness between strain R11HT and its closest phylogenetic neighbours was well below the threshold value of 70 %, which suggested that strain R11HT represents a novel species of the genus Sphingopyxis. The major polar lipids of strain R11HT were sphingoglycolipid and other lipids commonly reported in this genus, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylmonomethylethanolamine. Spermidine was detected as the major polyamine. The chemotaxonomic markers in strain R11HT confirmed its classification in the genus Sphingopyxis, i.e. Q-10 as the major ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 2-OH as the predominant fatty acids. Results obtained from DNA-DNA hybridization and chemotaxonomic and phenotypic analyses clearly distinguished strain R11HT from its closest phylogenetic neighbours. Thus, strain R11HT represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis flava sp. nov. is proposed. The type strain is R11HT ( = DSM 28472T = MCC 2778T).

Capturing molten globule state of α-lactalbumin through constant pH molecular dynamics simulations.

The recently developed methods of constant pH molecular dynamics directly captures the correlation between protonation and conformation to probe protein structure, function, and dynamics. In this work, we investigate the effect of pH on the conformational properties of the protein human α-lactalbumin. Constant pH simulations at both acidic and alkaline medium indicate the formation of the molten globule state, which is in accordance with the previous experimental observations (especially, in acidic medium). The size of the protein measured by its radius of gyration (RG) exhibits a marked increase in both acidic and alkaline medium, which matches with the corresponding experimentally observed value of RG found in the molten globule. The probability of native contacts is also considerably reduced at acidic and basic pH as compared to that of native structure crystallized at neutral pH. The mean fractal dimension D2 of the protein records a sharp increase in basic medium as compared to those in neutral and acidic solutions implying a significant pH induced conformational change. The mean square fluctuations of all residues of the entire protein are found to increase by several folds in both acidic and basic medium, which may be correlated with the normalized solvent accessibility of the residues indicating role of solvent accessible surface area on protein internal dynamics. The helices comprising the α-domain of the protein are moderately preserved in the acidic and alkaline pH. However, the β-sheet structures present in the β-domain are completely disrupted in both acidic as well as basic pH.

Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil.

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming, yellow pigmented bacterial strain (UM1T) was isolated from the hexachlorocyclohexane (HCH)-contaminated dumpsite located at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain UM1T belongs to the genus Luteimonas with Luteimonas aestuarii B9T as the closest neighbour (97.2% 16S rRNA gene sequence similarity). The DNA G+C content of strain UM1T was 64.3 mol%. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Main fatty acids were iso-C15:0, iso-C11:0, iso-C11:0 3-OH, iso-C17:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Ubiquinone (Q-8) was the only respiratory quinone. Spermidine was detected as the major polyamine. The DNA-DNA relatedness value of strain UM1T with respect to its closest neighbour Luteimonas aestuarii B9T was well below 70 % (∼49%). Thus, data obtained from phylogenetic analysis, DNA-DNA hybridization, and chemotaxonomical and biochemical analyses supports classification of strain UM1T as representative of a novel species of the genus Luteimonas, for which the name Luteimonas tolerans sp. nov. is proposed. The type strain is UM1T (=DSM 28473T=MCC 2572T=KCTC 42936T).

Does lack of secondary structure imply intrinsic disorder in proteins? A sequence analysis.

Intrinsically disordered proteins (IDPs)/protein regions (IDPRs) lack unique three-dimensional structure at the level of secondary and/or tertiary structure and are represented as an ensemble of interchanging conformations. To investigate the role of presence/absence of secondary structures in promoting intrinsic disorder in proteins, a comparative sequence analysis of IDPs, IDPRs and proteins with minimal secondary structures (less than 5%) is required. A sequence analysis reveals proteins with minimal secondary structure content have high mean net positive charge, low mean net hydrophobicity and low sequence complexity. Interestingly, analysis of the relative local electrostatic interactions reveal that an increase in the relative repulsive interactions between amino acids separated by three or four residues lead to either loss of secondary structure or intrinsic disorder. IDPRs show increase in both local negative-negative and positive-positive repulsive interactions. While IDPs show a marked increase in the local negative-negative interactions, proteins with minimal secondary structure depict an increase in the local positive-positive interactions. IDPs and IDPRs are enriched in D, E and Q residues, while proteins with minimal secondary structure are depleted of these residues. Proteins with minimal secondary structures have higher content of G and C, while IDPs and IDPRs are depleted of these residues. These results confirm that proteins with minimal secondary structure have a distinctly different propensity for charge, hydrophobicity, specific amino acids and local electrostatic interactions as compared to IDPs/IDPRs. Thus we conclude that lack of secondary structure may be a necessary but not a sufficient condition for intrinsic disorder in proteins.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Erratum: Shape dependence of the radial distribution function of hydration water around proteins (2014 J. Phys.: Condensed Matter 26 335102)

The characterization of hydration water in proteins is important to understand their structure, function and folding properties. A calculation of the shape parameters reveals considerable asymmetry in the shapes of globular proteins. The present study suggests a generalized approach for the calculation of radial distribution of hydration water by accounting for the shape asymmetry in proteins. The surface and radial distribution function is analyzed for three groups of high resolution globular proteins and nonglobular proteins. This generalized approach depicts a considerable difference in the hydration water distribution pattern around aspherical proteins as compared to the earlier method and this difference is more pronounced for nonglobular proteins. The peaks for normalized RDF are found to be sharper compared to those of bulk water. The normalized RDF of hydration water exactly coincides with that of the bulk beyond 8.0 Å. The radial distribution of hydration water as a function of the water– protein distance matches with the experimentally observed distribution of hydration water around myoglobin. The results reveal that the distribution of hydration water is dependent on the shapes of proteins and hence a generalized approach should be used for the calculation of hydration water distribution around proteins, especially for nonglobular proteins.