Using data from contact maps of the DNA-polymer of E. Coli (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. By suitable Monte Carlo Simulations, we show that the presence of these cross-links leads to a particular architecture and organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of E. Coli bacteria which has around 4.6 million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used 4642 monomer beads and observed that around 80 cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain of an even simple bacterial cell such as E. Coli is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify large scale structure of a polymer chain with a few cross-links.

In-vivo DNA organization at large length scales (∼ 100nm) is highly debated and polymer modelshave proved useful to understand the principle of DNA-organization. Here, we show that < 2% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA.We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the beadspring polymer with cross-links at these special positions. Simulations with cross-links at random positions along the chain show that the organization of the polymer is different in nature from the previous case.PACS numbers: 87.15.ak,82.35.Lr,82.35.Pq,87.16.Sr,61.25.hp It is established that DNA-polymer is not a random coil in either bacterial cells [1][2][3] or in eukaryotic cells [4][5][6][7]. Experimental methods such as CCC (chromosomal conformation capture) which was then further developed as 5C and then Hi-C have consistently shown the presence of topologically associated domains (TADs) in the contact maps (C-maps) of DNA-chains [8][9][10]. The Hi-C technique gives us the C-map which is the map of frequencies that a segment of the DNA chain (say i) is found in spatial proximity to another segment (say j) for all combinations i, j of segments along the contour length of the DNA-polymer. TADs are patches in Cmaps which indicate that some segments of the chain (at 1 mega-base pair(BP) to 1 kilo-BP resolution), are found spatially close to other particular segments with higher frequencies compared to the rest of the segments.The ds-DNA is stiff at length scales of 1nm but can be considered to be a flexible chain at length scales beyond 100nm [11] . The persistence length ℓ p of a naked DNA is 150 Base Pairs (BP) ≡ 50 nm [12] and the value of ℓ p in vivo is debated [13]. Since, the resolution of Hi-C experiments are well above this length scale [1,4], there has a focussed attempts in the last few years trying to understand the DNA organization and in particular origin of formation of TADs from the principles of polymer physics [14][15][16][17][18]. A series of studies indicate that TADs in eukaryotic cells are indicative of fractal globule organization of the polymer (as opposed to equilibrium globule) [4,19]. Recently, more detailed polymer models with either different lengths of loops or with many distinct (coarse-grained) diffusing binder molecules which cross-link different segments of the chain have reproduced TADs of sections of a particular eukaryotic DNA by performing optimizations in multi-parameter space. Distinct kinds of binder molecules link correspondingly distinct monomers (DNA-segments) along the chain, and the optimization parameters include the number of distinct kind of binders/monomers as well as the position and number of distinct monomers as well as diffusing cross-links along the contour [16,[20][21][22].We propose a much simpler model for shorter bacterial DNAs and ask a more general question: Does fixed cross-links...

The structure of Mycobacterium smegmatis single-stranded DNA-binding protein (SSB) has been determined using three data sets collected from related crystals. The structure is similar to that of its homologue from Mycobacterium tuberculosis, indicating that the clamp arrangement that stabilizes the dimer and the ellipsoidal shape of the tetramer are characteristic features of mycobacterial SSBs. The central OB fold is conserved in mycobacterial SSBs as well as those from Escherichia coli, Deinococcus radiodurans and human mitochondria. However, the quaternary structure exhibits considerable variability. The observed plasticity of the subunit is related to this variability. The crystal structures and modelling provide a rationale for the variability. The strand involved in the clamp mechanism, which leads to higher stability of the tetramer, appears to occur in all high-G+C Gram-positive bacteria. The higher stability is perhaps required by these organisms. The mode of DNA binding of mycobacterial SSBs is different from that of E. coli SSB partly on account of the difference in the shape of the tetramers. Another difference between the two modes is that the former contains additional ionic interactions and is more susceptible to salt concentration.

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Protein scaffolds as essential backbones for organization of supramolecular signalling complexes are a recurrent theme in several model systems. Scaffold proteins preferentially employ linear peptide binding motifs for recruiting their interaction partners. PDZ domains are one of the more commonly encountered peptide binding domains in several proteins including those involved in scaffolding functions. This domain is known for its promiscuity both in terms of ligand selection, mode of interaction with its ligands as well as its association with other protein interaction domains. PDZ domains are subject to several means of regulations by virtue of their functional diversity. Additionally, the PDZ domains are refractive to the effect of mutations and maintain their three-dimensional architecture under extreme mutational load. The biochemical and biophysical basis for this selectivity as well as promiscuity has been investigated and reviewed extensively. The present review focuses on the plasticity inherent in PDZ domains and its implications for modular organization as well as evolution of cellular signalling pathways in higher eukaryotes.

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PURPOSE To evaluate the sensitivity and specificity of Thermalytix, an artificial intelligence–based computer-aided diagnostics (CADx) engine, to detect breast malignancy by comparing the CADx output with the final diagnosis derived using standard screening modalities. METHODS This multisite observational study included 470 symptomatic and asymptomatic women who presented for a breast health checkup in two centers. Among them, 238 women had symptoms such as breast lump, nipple discharge, or breast pain, and the rest were asymptomatic. All participants underwent a Thermalytix test and one or more standard-of-care tests for breast cancer screening, as recommended by the radiologists. Results from Thermalytix and standard modalities were obtained independently in a blinded fashion for comparison. The ground truth used for analysis (normal or malignant) was the final impression of an expert clinician based on the symptoms and the available reports of standard modalities (mammography, ultrasonography, elastography, biopsy, fine-needle aspiration cytology, and so on). RESULTS For the 470 women, Thermalytix resulted in a sensitivity of 91.02% (symptomatic, 89.85%; asymptomatic, 100%) and specificity of 82.39% (symptomatic, 69.04%; asymptomatic, 92.41%) in detection of breast malignancy. Thermalytix showed an overall area under the curve (AUC) of 0.90, with an AUC of 0.82 for symptomatic and 0.98 for asymptomatic women. CONCLUSION High sensitivity and high AUC of Thermalytix in women of all age groups demonstrates the efficacy of the tool for breast cancer screening. Thermalytix, with its automated scoring and image annotations of potential malignancies and vascularity, can assist the clinician in better decision making and improve quality of care in an affordable and radiation-free manner. Thus, we believe Thermalytix is poised to be a promising modality for breast cancer screening.

The crystal structures of mutants of Mycobacterium smegmatis RecA (MsRecA) involving changes of Gln196 from glutamine to alanine, asparagine and glutamic acid, wild-type MsRecA and several of their nucleotide complexes have been determined using mostly low-temperature and partly room-temperature X-ray data. At both temperatures, nucleotide binding results in a movement of Gln196 towards the bound nucleotide in the wild-type protein. This movement is abolished in the mutants, thus establishing the structural basis for the triggering action of the residue in terms of the size, shape and the chemical nature of the side chain. The 19 crystal structures reported here, together with 11 previously reported MsRecA structures, provide further elaboration of the relation between the pitch of the ;inactive' RecA filament, the orientation of the C-terminal domain with respect to the main domain and the location of the switch residue. The low-temperature structures define one extreme of the range of positions the C-terminal domain can occupy. The movement of the C-terminal domain is correlated with those of the LexA-binding loop and the loop that connects the main and the N-terminal domains. These elements of molecular plasticity are made use of in the transition to the ;active' filament, as evidenced by the recently reported structures of RecA-DNA complexes. The available structures of RecA resulting from X-ray and electron-microscopic studies appear to represent different stages in the trajectory of the allosteric transformations of the RecA filament. The work reported here contributes to the description of the early stages of this trajectory and provides insight into structures relevant to the later stages.