Classification of 207 HPs into various groups by utilizing the functional annotation results of various bioinformatics tools.

<p>The chart shows that there are 83 enzymes, 28 proteins involve in transportation, 58 binding proteins, 21 proteins involved in cellular processes like transcription, translation, replication etc. and 17 showing miscellaneous functions among 207 HPs from <i>T</i>. <i>pallidum ssp</i>. <i>pallidum</i>.</p

List of HPs with virulence factors in <i>T</i>. <i>pallidum ssp</i>. <i>pallidum</i>.

<p>List of HPs with virulence factors in <i>T</i>. <i>pallidum ssp</i>. <i>pallidum</i>.</p

Sequence Analysis of Hypothetical Proteins from 26695 to Identify Potential Virulence Factors

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein

Measuring Structural Changes in Cytochrome c under Crowded Conditions Using In Vitro and In Silico Approaches

It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome c (cyt c) were determined using various spectroscopic and bioinformatics tools. The main conclusions of our study are (i) the monomer EG has a kosmotropic effect on the protein (stabilizes the protein), and has no significant effect on the tertiary structure; (ii) PEG 400 destabilizes the structure as well as the stability of the protein; and (iii) EG counteracts the destabilizing effect of PEG 400. From this investigation, it seems evident that proteins may fold or unfold in the crowded environment of the cell where various interactions assist them to maintain their structure for their functions. Bioinformatics approaches were also used to support all of the in vitro observations. Cyt c is functional protein; if the structure of the protein is modulated due to change in the environment its nature of function will also change. Our research addresses the question by modulating the environment around the protein, and the macromolecule (protein) conformation dynamics and interaction study via in vitro and in silico approaches which indirectly compares with that of the environment in-cellular milieu, which is highly crowded

Identification of Functional Candidates amongst Hypothetical Proteins of <i>Treponema pallidum ssp</i>. <i>pallidum</i>

<div><p>Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, <i>Treponema pallidum ssp</i>. <i>pallidum</i>, a Gram-negative sphirochaete, is an obligate human parasite. Genome of <i>T</i>. <i>pallidum ssp</i>. <i>pallidum</i> SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of <i>T</i>. <i>pallidum ssp</i>. <i>pallidum</i> using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of <i>T</i>. <i>pallidum ssp</i>. <i>pallidum</i> and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.</p></div