Abstract

One of the most efficient chemical transformations in the natural product synthesis of steroid like molecules is the synthetic methodology that combines the pericyclic and intramolecular reactions termed as transannular Diels-Alder reaction (TADA). TADA reactions occur in (x+y+2)-membered triene macrocycles, which contain both the diene and the dienophile, to form A.B.C [x.6.y] type tricyclic compounds. Initially, a validation study was carried out to identify an appropriate method for studying this reaction pathway. Several methods including HF, post-HF methods such as Mpx and CC, and density functional B3LYP level were considered, and we found that B3LYP method used along with a reasonably smaller basis set (6-31G(d)) is adequate enough. We have extensively studied the TADA reactions of six possible cis/trans-isomers of 14-membered macrocycles, and correlated their reactivities with experimental data wherever applicable. We also have studied the effect of ring size on the TADA reactivity by performing calculations on 552, 562, 572, 652, 672, 752, 762 and 772 systems using the B3LYP level employing the 6-31G(d) and the cc-pVTZ basis sets. We have shown that the activation energy and the reaction energy decrease with respect to the increase in the ring size. In addition to the activation energies, the conformational preferences of the reactants were suggestd to be crucial for the reaction to take place, and on its stereochemical outcome. We have studied their conformational properties using replica exchange molecular dynamics simulations. Initially, we obtained force field parameters for the macrocyclic trienes based on MP2 calculations on six model systems. The analysis concentrated on the dihedral angle corresponding to the central bond of the diene moiety, and the distance between the reaction centers. The extent of conformational sampling of each of the macrocycles is compared with the reactivities. The presentation will discuss the TADA reactivity in terms of activation energies corresponding to the transition states of the reactions, and also based on the conformational properties of the reactants.

Abstract

Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.

Abstract

Riboswitches are RNA-based genetic control elements that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket. To facilitate an atomic detail interpretation of experimental investigations on the role of the adenine ligand on the conformational properties and kinetics of folding of the add adenine riboswitch, we performed molecular dynamics simulations in both the presence and the absence of the ligand. In the absence of ligand, structural deviations were observed in the J23 junction and the P1 stem. Destabilization of the P1 stem in the absence of ligand involves the loss of direct stabilizing interactions with the ligand, with additional contributions from the J23 junction region. The J23 junction of the riboswitch is found to be more flexible, and the tertiary contacts among the junction regions are altered in the absence of the adenine ligand; results suggest that the adenine ligand associates and dissociates from the riboswitch in the vicinity of J23. Good agreement was obtained with the experimental data with the results indicating dynamic behavior of the adenine ligand on the nanosecond time scale to be associated with the dynamic behavior of hydrogen bonding with the riboswitch. Results also predict that direct interactions of the adenine ligand with U74 of the riboswitch are not essential for stable binding although it is crucial for its recognition. The possibility of methodological artifacts and force-field inaccuracies impacting the present observations was checked by additional molecular dynamics simulations in the presence of 2,6-diaminopurine and in the crystal environment. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Abstract

DNA-RNA hybrids are heterogeneous nucleic acid duplexes that contain a DNA strand and a RNA strand. They are identified as key intermediates in transcription, and in other biological processes. These novel molecules have also been recognized as potential candidates in antisense therapy. While DNA exists in B-form, and RNA in A-form, the process of hybridization between these two distinct conformations, and the resultant structural features of the hybrid duplexes are interesting in their own right. It has been suggested that hybrids have unique conformational properties that form the basis of Ribonuclease H (RNase H) activity only on these molecules, and not on pure DNA or RNA. Quantitative examination of the conformational properties of hybrids is very important for understanding the RNase H activity. Several nanosecond long molecular dynamics (MD) simulations were performed on all the available structures in presence of explicit solvent environment. All the MD simulations were performed using the CHARMM27 all atom nucleic acid force field. In addition to the MD simulations on hybrids, control simulations were also performed on pure DNA and RNA duplexes with identical sequences. Several structural, dynamic and energetic properties including deviations, flexibility, intramolecular entropy, helical properties, and backbone conformational preferences were computed. The conformational properties of the sugar puckering angles revealed interesting trends that depend on the sequence of the duplex. RNA strands in all the duplexes sample conformational regions corresponding to a pure-A form nucleic acid. However, the DNA strands adopt mixing of A- and B- type conformations resulting in intermediate structures for the hybrids. The extent of this mixing depends primarily on the relative purine to pyrimidine composition ratio in the DNA strands, and sequence effects. The presentation will focus on the structural and dynamic properties of hybrid duplexes in comparison with those of pure-RNA and DNA duplexes.

Abstract

SAM-III riboswitch, involved in regulating sulfur metabolic pathways in lactic acid bacteria, is capable of differentiating S-adenosyl-L-methionine (SAM) from its structurally similar analog S-adenosyl-L-homocysteine (SAH). Atomic level understanding of the ligand recognition mechanism of riboswitches is essential for understanding their structure-function relationships in general. In the present study, we have employed molecular dynamics (MD) simulations on five model systems to elucidate the discrimination mechanism adopted by the SAM-III riboswitch that enables differential binding of SAM with respect to SAH. The structures of the binding pocket of the riboswitch, and the modes of binding of the adenine moiety of SAM obtained from the MD simulations are similar to the experimental structure. However, MD simulations of the riboswitch-SAH complexes lead to partial unbinding of the ligand and structural changes in the RNA binding pocket. Detailed analyses were performed to examine the structural and energetic factors involved in such a differentiation. The calculations reveal a novel mechanism by which the aptamer domain specifically recognizes the adenine moiety of SAM/SAH, but SAM is better stabilized in the binding pocket due to nonspecific electrostatic interactions involving the sulfonium group. Additionally, the results support less dependence of the ligand conformation in the bound form on the effective binding of SAM to the riboswitch.

Abstract

Identification of the structural and energetic determinants responsible for enhancing the stability of proteins is crucial. Hyperthermophilic proteins are naturally occurring proteins that exhibit high thermal stability and are good candidates for the investigation and understanding of structure-stability relationships. Sac7d from Sulfolobus acidocaldarius and Sso7d from Sulfolobus solfactaricus are two homologous hyperthermophilic proteins that were shown to be quite stable at high temperatures. Molecular dynamics simulations at the nanosecond time scale at different temperatures were performed to examine the factors affecting their stability. The three-dimensional structures of these proteins were observed to be similar to the experimental structure at 300 and 360 K but were found to undergo denaturation at 500 K. Both proteins exhibit similar unfolding pathways that correlates well with the calculated intermolecular interaction energies. The differential dynamic behaviors of these molecules at different temperatures were examined. Structural and energetic analysis of the contributions of salt bridges indicates a stabilizing effect at higher temperatures. However, the lifetimes of the salt bridges were found to be quite short, and several new salt bridges formed at 500 K supporting previous studies that the desolvation penalty due to the formation of salt bridges decreases at elevated temperatures. Hydrophobic interactions, which decrease with increase in temperature, were also found to be crucial in the stability of these proteins. Overall, the study shows that a balance among the salt bridge interactions, hydrophobic interactions, and solvent properties is primarily responsible for the high thermal stability of this class of proteins.

Abstract

Motion blur is one of the most common causes of image degradation. It is of increasing interest due to the deep penetration of digital cameras into consumer applications. In this paper, we start with a hypothesis that there is sufficient information within a blurred image and approach the deblurring problem as an optimisation process where the deblurring is to be done by satisfying a set of conditions. These conditions are derived from first principles underlying the degradation process assuming noise-free environments. We propose a novel but effective method for removing motion blur from a single blurred image via an iterative algorithm. The strength of this method is that it enables deblurring without resorting to estimation of the blur kernel or blur depth. The proposed iterative method has been tested on several images with different degrees of blur. The obtained results have been compared with state of the art techniques including those that require more than one input image. The results are consistently of high quality and comparable or superior to the existing methods which demonstrates the effectiveness of the proposed technique.

Abstract

We present a novel segmentation method to better capture the boundary of a non-homogeneous object such as the optic disk(OD), defined locally by two similar characteristic regions. Existing active contour models which utilise gradient information [12] or global region intensity [2] fail to localise aforementioned boundaries. We propose a region-based active contour model that uses local image information around each point of interest in multi-dimensional feature space. This model uses a local energy functional and level-set representation to achieve desired OD segmentation. The local energy functional defined on each image point provides sufficient information to determine a desired OD segmentation which is robust to the variations found in and around the OD region. This method has been evaluated against the segmentation provided by three medical experts on 138 retinal images. Both region and boundary-based assessment performed against two well established active contour models show strengths of the proposed method.

Abstract

The aim of a local descriptor or a feature descriptor is to efficiently represent the region detected by an interest point operator in a compact format for use in various applications related to matching. The common design principle behind most of the mainstream descriptors like SIFT, GLOH, Shape context etc is to capture the spatial distribution of features using histograms computed over a grid around interest points. Histograms provide compact representation but typically loose the spatial distribution information. In this paper, we propose to use projection-based representation to improve a descriptor’s capacity to capture spatial distribution information while retaining the invariance required. Based on this proposal, two descriptors based on the CS-LBP are introduced. The descriptors have been evaluated against known descriptors on a standard dataset and found to outperform, in most cases, the existing descriptors. The obtained results demonstrate that proposed approach has the advantages of both the statistical robustness of histogram and the capability of the projection based representation to capture spatial information.

Abstract

The presence of microaneurysms (MAs) is usually an early sign of diabetic retinopathy(DR) and their automatic detection from color retinal images is of clinical interest. In this paper, we present a new approach for automatic MA detection from digital colour fundus images. We formulate MA detection as a problem of target detection from clutter, where the probability of occurrence of target is considerably smaller compared to the clutter. A successive rejection-based strategy is proposed to progressively lower the number of clutter responses. The processing stages are designed to reject specific classes of clutter while passing majority of true MAs, using a set of specialized features. The true positives that remain after the final rejector are assigned a score which is based on its similarity to a true MA. Results of extensive evaluation of the proposed approach on three different retinal image datasets is reported, and are used to highlight the promise in the presented strategy.