| Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input RNA sequences. Starting from simplified linear-chain conformations, RNA molecules (<50 nt) fold to native-like structures within half an hour of simulation, facilitating rapid RNA structure prediction. All-atom reconstruction of energetically stable conformations generates iFoldRNA predicted RNA structures. The predicted RNA structures are within 2-5 A root mean squre deviations (RMSDs) from corresponding experimentally derived structures. RNA folding parameters including specific heat, contact maps, simulation trajectories, gyration radii, RMSDs from native state, fraction of native-like contacts are accessible from iFoldRNA. We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses. AVAILABILITY: http://iFoldRNA.dokhlab.org. |
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| Understanding the role of biomolecular dynamics in cellular processes leading to human diseases and the ability to rationally manipulate these processes is of fundamental importance in scientific research. The last decade has witnessed significant progress in probing biophysical behavior of proteins. However, we are still limited in understanding how changes in protein dynamics and inter-protein interactions occurring in short length- and time-scales lead to aberrations in their biological function. Bridging this gap in biology probed using computer simulations marks a challenging frontier in computational biology. Here we examine hypothesis-driven simplified protein models in conjunction with discrete molecular dynamics in the study of protein aggregation, implicated in series of neurodegenerative diseases, such as Alzheimer's and Huntington's diseases. Discrete molecular dynamics simulations of simplified protein models have emerged as a powerful methodology with its ability to bridge the gap in time and length scales from protein dynamics to aggregation, and provide an indispensable tool for probing protein aggregation. |
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| RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 A deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNA(Phe), pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. |
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| Nucleosomes form the fundamental repeating unit of eukaryotic chromatin. Subtle modifications in nucleosome structure and histone tails regulate chromatin states. Hence a comprehensive understanding of alterations in nucleosome structure is of fundamental importance in chromatin biophysics. The nature of core histone organization and nucleosome dynamics have been extensively studied using biophysical experiments, multiscale computational models and simulations. However, the precise mechanisms of how DNA sequence mediates nucleosome structure and stability remains to be completely understood. The eviction of H2A/H2B core histones from the histone octamer is known to expose nucleosomal DNA for transcription. In this issue of Biophysical Journal, Kelbauskas et al. have investigated the sequence dependence of H2A/H2B eviction mediated by histone chaperone yNAP-1 using single-molecule Forster Resonance Energy Transfer (FRET) and Fluorescence Correlation Spectroscopy (FCS) experiments. |
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| Mismatch repair proteins, DNA damage-recognition proteins and translesion DNA polymerases discriminate between Pt-GG adducts containing cis-diammine ligands (formed by cisplatin (CP) and carboplatin) and trans-RR-diaminocyclohexane ligands (formed by oxaliplatin (OX)) and this discrimination is thought to be important in determining differences in the efficacy, toxicity and mutagenicity of these platinum anticancer agents. We have postulated that these proteins recognize differences in conformation and/or conformational dynamics of the DNA containing the adducts. We have previously determined the NMR solution structure of OX-DNA, CP-DNA and undamaged duplex DNA in the 5-d(CCTCAGGCCTCC)-3 sequence context and have shown the existence of several conformational differences in the vicinity of the Pt-GG adduct. In this study we have used molecular dynamics simulations to explore differences in the conformational dynamics between OX-DNA, CP-DNA and undamaged DNA in the same sequence context. Twenty-five 10 ns unrestrained fully solvated molecular dynamics simulations were performed starting from two different DNA conformations using AMBER v8.0. All twenty-five simulations reached equilibrium within 4 ns, were independent of the starting structure and were in close agreement with the NMR solution structures. Our data show that the cis-diammine (CP) ligand preferentially forms hydrogen bonds on the 5 side of the Pt-GG adduct, while the trans-RR-diaminocyclohexane (OX) ligand preferentially forms hydrogen bonds on the 3 side of the adduct. In addition, our data show that these differences in hydrogen bond formation are strongly correlated with differences in conformational dynamics, specifically the fraction of time spent in different DNA conformations in the vicinity of the adduct, for CP- and OX-DNA adducts. We postulate that differential recognition of CP- and OX-GG adducts by mismatch repair proteins, DNA damage-recognition proteins and DNA polymerases may be due, in part, to differences in the fraction of time that the adducts spend in a conformation favorable for protein binding. |
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| Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases. |
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| Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histones tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosome at atomic levels. We report a novel multi-scale model of the fundamental chromatin unit - nucleosome, having a simplified model for rapid discrete molecular dynamics (DMD) simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperature, suggesting a mechanism of chromatin structural organization, whereby histone tails regulate inter- and intra-nucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed cold sites, which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A inter-histone interfaces indicating necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows bending across the H3-H3 is a prominent mode of intra-nucleosomal dynamics. We postulate that effects of salts on mono-nucleosomes can be modeled in DMD by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mono-nucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher order chromatin structure, mediated by salt bridge interactions with adjacent DNA. |
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| We built iFold to be a novel web-based platform for performing discrete molecular dynamics simulations of proteins. In silico protein folding involves searching for minimal frustration in the vast conformational landscape. Conventional approaches for simulating protein folding insufficiently address the problem of simulations in relevant time and length scales necessary for a mechanistic understanding of underlying biomolecular phenomena. Discrete molecular dynamics (DMD) offers an opportunity to bridge to the size and timescale gaps and uncover the structural and biological properties of experimentally undetectable protein dynamics. The iFold server supports large-scale simulations of protein folding, thermal denaturation, thermodynamic scan, simulated annealing and pfold analysis using DMD and coarse-grained protein model with structure-based Go-interactions between amino acids. Availability: http://ifold.dokhlab.org. Supplementary Information: Supplementary data are available at Bioinformatics online. |
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| Replicated sister centromeres become maximally separated by 600-800 nm in metaphase. Separation progressively decreases along chromosome arms such that sister chromatids are tightly juxtaposed at approximately 10 kb from the centromere. The molecular glue linking sister chromatids, cohesin, is recruited to a 20-50 kb region surrounding the centromere at 3- to 5-fold higher levels than centromere-distal locations. A major paradox is the accumulation of cohesin at regions of separated sister DNA strands. A second problem is the nature of the mechanical linkage coupling DNA to a dynamic microtubule plus-end. This linkage must resist detachment by mitotic forces while sliding along the polymerizing and depolymerizing microtubule lattice. We propose that pericentric chromatin is held together via intramolecular cohesion, similar to a foldback structure proposed for the fission yeast centromere. In contrast to fission yeast, the budding yeast core centromere (120 bp DNA wrapped around a specialized nucleosome containing two molecules of the centromere-specific histone H3 variant, Cse4) and flanking chromatin may adopt a cruciform configuration in metaphase. |
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| A novel protein structure alignment technique has been developed reducing much of the secondary and tertiary structure to a sequential representation greatly accelerating many structural computations, including alignment. Constructed from incidence relations in the Delaunay tetrahedralization, alignments of the sequential representation describe structural similarities that cannot be expressed with rigid-body superposition and complement existing techniques minimizing root-mean-squared distance through superposition. Restricting to the largest substructure superimposable by a single rigid-body transformation determines an alignment suitable for root-mean-squared distance comparisons and visualization. Restricted alignments of a test set of histones and histone-like proteins determined superpositions nearly identical to those produced by the established structure alignment routines of DaliLite and ProSup. Alignment of three, increasingly complex proteins: ferredoxin, cytidine deaminase, and carbamoyl phosphate synthetase, to themselves, demonstrated previously identified regions of self-similarity. All-against-all similarity index comparisons performed on a test set of 45 class I and class II aminoacyl-tRNA synthetases closely reproduced the results of established distance matrix methods while requiring 1/16 the time. Principal component analysis of pairwise tetrahedral decomposition similarity of 2300 molecular dynamics snapshots of tryptophanyl-tRNA synthetase revealed discrete microstates within the trajectory consistent with experimental results. The method produces results with sufficient efficiency for large-scale multiple structure alignment and is well suited to genomic and evolutionary investigations where no geometric model of similarity is known a priori. |
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| Some DNA damage-recognition proteins, transcription factors, mismatch repair proteins and DNA polymerases discriminate between cisplatin (CP)- and oxaliplatin (OX)-GG DNA adducts, and this is thought to help explain differences in efficacy, toxicity and mutagenicity of CP and OX. In addition, differential recognition of CP- and OX-GG adducts by some proteins has been shown to be highly dependent on the sequence context of the Pt-GG adduct. We have postulated that CP- and OX-GG adducts cause differences in the conformation and/or conformational dynamics of the DNA that provide the basis for differential protein recognition of the adducts. We have determined the NMR solution structure of CP-GG adducts, OX-GG adducts and undamaged DNA in the AGGC sequence context, and of OX-GG adducts and undamaged DNA in the TGGT sequence context. We have also employed molecular dynamics (MD) simulations to investigate the conformational dynamics of CP-GG adducts, OX-GG adducts and undamaged DNA in the AGGC and TGGA sequence contexts. These studies showed clear differences in the conformation dynamics between CP- and OX-GG adducts which correlated with the average conformational differences observed in the NMR solution structures and with conformations previously reported for the CP-GG DNA.HMG1a complex. When the conformational dynamics in both sequence contexts were compared it became evident that: (a) the patterns of hydrogen bond formation between Pt-amine-hydrogens and surrounding bases of the DNA were different for CP- and OX-GG adducts; (b) patterns of hydrogen bond formation were also influenced by the DNA sequence context of the Pt-GG adducts, and (c) differences in patterns of hydrogen bond formation were highly correlated with differences in the conformational dynamics of the adduct. Thus, we postulate that patterns of hydrogen bond formation between Pt-amine hydrogens and surrounding DNA bases are different for CP- and OX-GG adducts, and that those differences in hydrogen bond patterns result in DNA conformational differences that allow selective recognition of CP- and OX-GG adducts by a number of proteins that determine the relative cytotoxicity and mutagenicity of those adducts. |
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| Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histones tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosome at atomic levels. We report a novel multi-scale model of the fundamental chromatin unit - nucleosome, having a simplified model for rapid discrete molecular dynamics (DMD) simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperature, suggesting a mechanism of chromatin structural organization, whereby histone tails regulate inter- and intra-nucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core, termed cold sites, which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A inter-histone interfaces indicating necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows bending across the H3-H3 is a prominent mode of intra-nucleosomal dynamics. We postulate that effects of salts on mono-nucleosomes can be modeled in DMD by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating nucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher order chromatin structure, mediated by salt bridge interactions with adjacent DNA. |
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| The structural basis for differential protein recognition of cisplatin (CP)-DNA and oxaliplatin (OX)-DNA adducts has not been determined and could be important for the design of more effective platinum anticancer agents. We have recently reported high resolution solution NMR structures of OX-GG, CP-GG adducts and undamaged DNA dodecamers in the AG*G*C (G* = G coordinated to platinum) sequence context. A comparison of the structures of these platinated-DNA adducts revealed that the conformation of CP and OX in the AG*G*C sequence is significantly different than that observed previously in other sequence contexts, which may relate to the increased mutagenicity of CP adducts in the AG*G*C sequence context. However, the experimental conditions were not identical in our structural study compared to previous studies. Thus, to confirm the effect of the sequence context in the conformation of platinated adducts, structural studies using multidimensional NMR spectroscopy of the OX-adducted dodecamer in the sequence context d(CCTCTG*G*TCTCC) d(GGAGACCAGAGG) were performed. A comparison between the solution NMR structures of OX-TG*G*T and the OX-AG*G*C adducts solved in our laboratory also resulted in significant differences. The 1H NMR study of the temperature dependence of the exchangeable protons of the OX-DNA adducts revealed an unprecedented dynamic motion for the 5-flanking residue to the platinated adduct site in the T G*G*T sequence context. Compared to the OX-AG*G*C adduct, the OX-TG*G*T adduct exhibited less buckle, greater propeller twist, and less opening for the 5- and 3-G C base pairs. In addition, compared to the OX-AG*G*C adduct, the OX-TG*G*T adduct exhibited a greater roll, slide, and twist for the 5-flanking base pair step and greater tilt and less twist for the 3-flanking base-pair steps. In addition to the helical parameters, a greater chi angle value for the C4 and T20 residues of OX-TG*G*T adduct compared to those of the OX-AG*G*C adduct indicated a higher anti-character for the C4 and T20 residues of OX-TG*G*T adduct. The differences observed in the NMR structural features of OX-TG*G*T and OX-AG*G*C adducts highlight the importance of sequence context of DNA in explaining the discrimination shown for the translesion synthesis past the DNA-platinum adduct sites. We have also postulated that some of the differences in damage recognition protein binding and translesion synthesis past CP and OX adducts may be due to differences in the conformational flexibility of DNA containing those adducts. To test this postulate, we are currently performing a ten nanosecond unrestrained, fully solvated MD simulation of the OX-TG*G*T adduct along with those for the CP-DNA adduct and undamaged DNA in the same TG*G*T sequence context. These differences in the conformation and dynamic motion may help explain the effect of sequence context on the ability of damage recognition proteins to bind to Pt-DNA adducts. |
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| Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histones tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosome at atomic levels. We report a novel multi-scale model of the fundamental chromatin unit - nucleosome, having a simplified model for rapid discrete molecular dynamics (DMD) simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperature, suggesting a mechanism of chromatin structural organization, whereby histone tails regulate inter- and intra-nucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core, termed cold sites, which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A inter-histone interfaces indicating necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows bending across the H3-H3 is a prominent mode of intra-nucleosomal dynamics. We postulate that effects of salts on mono-nucleosomes can be modeled in DMD by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating nucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher order chromatin structure, mediated by salt bridge interactions with adjacent DNA. |
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| Nucleosomes are the fundamental repeating unit of eukaryotic chromatin. Experimental evidence suggests a direct role of histone tails and core histone variants in mediating chromatin stability, thereby modulating gene expression. However, how dynamics of histone tails and variant histones influences chromatin organization is not clearly understood. We have constructed a high-resolution model of the nucleosome core particle using simplified interaction potentials and performed Discrete Molecular Dynamics simulations of the model nucleosome core. We identify key histone-DNA interactions, termed cold sites, essential for nucleosome stability. We observe histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of simulated temperatures. This suggests a mechanism of chromatin structural organization, whereby histone tails regulate inter- and intra-nucleosomal assemblies via binding with nucleosomal DNA. Simulations at multiple effective salt concentrations show that histone tails have a direct functional role in stabilizing higher order chromatin structure, mediated by salt bridge interactions with adjacent DNA. To investigate the role of histone variants in chromatin organization, we constructed a homology model of centromere-specific nucleosome. A major paradox in centromere biology is accumulation of cohesin rings at regions of separated sister DNA strands. We propose that pericentric chromatin is held together via intramolecular cohesion. Equillibrium between intra- vs. inter-molecular cohesion results in oscillations in the position of the centromere relative to the chromosome axis, resulting in a C-loop cruciform topology of the kinetochore junction. |
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| Discrete Molecular Dynamics (DMD) simulations of the nucleosome core particle were performed to investigate dynamics of constituent DNA and histones. We observe histone tails binding to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperature, suggesting a structural mechanism of chromatin organization, whereby histone tails regulate inter- and intra-nucleosomal assemblies via binding with nucleosomal DNA. We characterize residues in H3-H3, H2A-H4 and H4-H2A inter-histone interfaces mediating nucleosome stability. We observe a fraction of histone-DNA contacts making strong interactions and dominate nucleosomal dynamics. Our findings suggest a direct functional role of histone tails in stabilizing higher order chromatin structure. |
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| During metaphase sister centromeres are segregated by 600-800 nm. Separation progressively decreases along chromosome arms such that sister chromatids are tightly juxtaposed at ~10 kb from the centromere. The molecular glue linking sister chromatids, cohesin, is recruited to a 20-50 kb region surrounding the centromere at 3-to 5-fold higher levels than centromere-distal locations. A major paradox is the accumulation of cohesin at regions of separated sister DNA strands. Bloom Lab has found that cohesin (SMC3) is organized in a cylindrical structure surrounding interpolar microtubules in metaphase. We propose that pericentric chromatin is held together via intramolecular cohesion, resulting in a Holliday-type junction at the centromere. Changes in intra-or inter-molecular cohesion results in oscillations in the position of the centromere relative to the chromosome axis. The range of force generated by the microtubule is on the order of that required to alter the transition zone position and hence the spatial position of the centromere. The structure predicted by this model may represent the fundamental unit of the kinetochore across phylogeny. |
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| We tested folding dynamics of three representative proteins: Eglin C (1CSE), SH3 (1NLO), and Chymotrypsin Inhibitor 2 (1YPC) investigating their thermodynamic pathways for unfolding and folding. We posit that a significant correlation in the frequencies of contact maps will depict similarities in folding and unfolding pathways. Using discrete molecular dynamics (DMD), we performed molecular dynamics simulations of the unfolding and folding pathways at complementary temperature ranges. We have collated data for 10 simulations for folding and unfolding trajectories of the three proteins and have generated the corresponding contact maps. Using this data, we design a cross-correlation metric for analyzing the frequencies of contact maps and compare the unfolding and folding pathways. |
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| Mechanistic analysis of the TrpRS mechanism has raised important questions concerning how binding interactions at the active site are coupled to the anticodon-binding site. Answers to these questions may be sought from correlated changes observed in multiple sequence alignments of the TrpRS family and, more generally, the class I aaRS superfamily. Cluster analysis of statistical D(DG) values associated with the multiple sequence alignment (Kim) reveal novel interactions between the signature catalytic peptides and other locations within class I aaRS. While pursuing multiple sequence alignments, we recognized that the sequence alignments were markedly improved by carefully aligning the known class I aaRS tertiary structures. Multiple structure alignments are currently a cumbersome process. To expedite multiple structure alignment, we have developed an algorithm that preserves considerable tertiary structure information in a simplified form (Roach, Sharma). The algorithm, based on consistent reduction of the edge structure of the Delaunay tessellation to a one-dimensional string, facilitates the use of existing software used for sequence alignment to compare 3D structures, speeding up such calculations by an order of magnitude. Principle Component Analysis (PCA) of aligned aaRS structures affords a method for approximating maximum parsimony structural trees. The resulting trees largely confirm the subclass organization derived from multiple sequence alignments for class I and class II aaRS. Notable exceptions, however, suggest that structural similarity does not parallel apparent genetic kinship. |
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| Pairwise and multiple sequence alignments have become fundamental methods in bioinformatic analysis. Although these techniques provide evidence of evolutionary development, protein structure expresses more explicitly evolutionary relationships between individual proteins and protein families. To this end, a novel structural comparison and alignment solution has been developed. The Delaunay tetrahedralization has shown to be a fairly robust representation of the geometric information inherent in the protein structure. Encoding the tetrahedralization in a one-dimensional representation that preserves much of the secondary structure, the problem of structural alignment is reduced to a problem of sequence alignment (mutates mutandis). The program, Tetrahedral Decomposition Alignment (TetraDA), implementing this technique has been applied to pairwise analysis of the Class I and Class II aminoacyl-tRNA synthetase families. Extensions constraining RMSD and developing multiple structural alignment are discussed. |
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| The project aims at building a high-level language and provides a Graphical User Interface for coding animation of Data Structures and algorithms. The software inputs commands from the applications console and stores it in its database. The interpreter then interprets the input commands and creates objects needed to for animation. These objects are utilized by the application and the code for animation (a Java applet code) is made based on the input commands of the user. The software allows for demonstration of sorting and searching algorithms, graph theory algorithms and data structures like arrays, stacks, queues, lists, trees and graphs. |
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| Subtle modifications of histone tails lead to complex changes in chromatin organization. Understanding these orchestrated modifications has lead us to the histone code hypothesis, which controls the expression of genes and thereby protein proliferation. Evolutionarily conseved histone variants also strongly influence the higher order chromatin organization by modifying the biophysical properties of constituent nucleosomes. We present here a computational study of dynamics of histone tails and histone variants and how they influence chromatin organization. We report that in simulations of mononucleosome dynamics, histone tails bind nucleosomal DNA. We also present a homology model of centromere-specific nucleosome containing Cse4 H3-variant protein. Simulations of centromeric nucleosome with flanking DNA demonstrates conformational rigidity is established at the kinetochore locus,in part due to the presence of essential N-terminal domain (END-domain) of Cse4. |
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| Despite significant advances in high performance computing resources, the complexity of simulating protein dynamics limits the problems that can be investigated in silico. The crux of the problem lies in rapid exploration of protein conformational ensemble. The iFold server (http://ifold.dokhlab.org) presents an efficient alternative approach: coupling the fast discrete molecular dynamics (DMD) conformational sampling algorithm with multiscale modeling. DMD is among of the fastest techniques for conformational sampling; accessing biologically relevant length and time scales by utilizing a multiscale protein modeling approach using simplified models for probing conformational dynamics, followed by high-resolution reconstruction of trajectories for detailed analyses. The iFold server provides a premier web-based resource for high-throughout analyses of protein dynamics using DMD, utilizing local Linux cluster computing resources. This approach is highly scalable and global cyber-infrastructure resources can be added for supporting massive simulation requirements. Customizable complex simulation modes such as protein folding, unfolding, thermodynamic scan, Pfold scan and simulated annealing are possible using iFold. In summary, amalgamating multiscale modeling and simulation tools at the iFold server with high performance computing resources has allowed probing protein dynamics at unprecedented scales. |
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| During metaphase sister centromeres are segregated by 600-800 nm. Separation progressively decreases along chromosome arms such that sister chromatids are tightly juxtaposed at ~10 kb from the centromere. The molecular glue linking sister chromatids, cohesin, is recruited to a 20-50 kb region surrounding the centromere at 3- to 5-fold higher levels than centromere-distal locations. A major paradox is the accumulation of cohesin at regions of separated sister DNA strands. Bloom Lab has found that cohesin (SMC3) is organized in a cylindrical structure surrounding interpolar microtubules in metaphase. We propose that pericentric chromatin is held together via intramolecular cohesion, resulting in a Holliday-type junction at the centromere. Changes in intra- or inter-molecular cohesion results in oscillations in the position of the centromere relative to the chromosome axis. The range of force generated by the microtubule is on the order of that required to alter the transition zone position and hence the spatial position of the centromere. The structure predicted by this model may represent the fundamental unit of the kinetochore across phylogeny. |
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| Discrete Molecular Dynamics (DMD) simulations of the nucleosome core particle were performed to investigate dynamics of constituent DNA and histones. We observe histone tails binding to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperature, suggesting a structural mechanism of chromatin organization, whereby histone tails regulate inter- and intra-nucleosomal assemblies via binding with nucleosomal DNA. We characterize residues in H3-H3', H2A-H4' and H4-H2A' inter-histone interfaces mediating nucleosome stability. We observe a fraction of histone-DNA contacts making strong interactions and dominate nucleosomal dynamics. Our findings suggest a direct functional role of histone tails in stabilizing higher order chromatin structure. |
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| Mechanistic analysis of the TrpRS mechanism has raised important questions concerning how binding interactions at the active site are coupled to the anticodon-binding site. Answers to these questions may be sought from correlated changes observed in multiple sequence alignments of the TrpRS family and, more generally, the class I aaRS superfamily. Cluster analysis of statistical (del)(del)G values associated with the multiple sequence alignment reveal novel interactions between the signature catalytic peptides and other locations within class I aaRS. While pursuing multiple sequence alignments, we recognized that the sequence alignments were markedly improved by carefully aligning the known class I aaRS tertiary structures. Multiple structure alignments are currently a cumbersome process. To expedite multiple structure alignment, we have developed an algorithm that preserves considerable tertiary structure information in a simplified form (Roach, Sharma). The algorithm, based on consistent reduction of the edge structure of the Delaunay tessellation to a one-dimensional string, facilitates the use of existing software used for sequence alignment to compare 3D structures, speeding up such calculations by an order of magnitude. Principle Component Analysis (PCA) of aligned aaRS structures affords a method for approximating maximum parsimony structural trees. The resulting trees largely confirm the subclass organization derived from multiple sequence alignments for class I and class II aaRS. Notable exceptions, however, suggest that structural similarity does not parallel apparent genetic kinship. |
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| With the rapid discovery of protein structures, structural comparison of proteins has become a central task in bioinformatics research. Identifying structural similarities can provide significant insights into the relation between structure and function of proteins. Reliable and efficient structural matching plays a key role in computer-aided rational drug design and in assessing the quality of structure prediction methods. However no single structural comparison technique has proven to be efficient and robust over a range of application. In this pro ject, we design and implement an efficient mechanism for structural comparison of proteins: utilizing as much bio-physical information of proteins as possible. |
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| Complex ICA is a recent advance in Blind Source Signal Separation techniques tailored for use in separating convoluted temporal signals. Thus, the use of ICA in the time domain is highly limited to such applications, where the mixtures are assumed to instantaneous mixture of the sources. An approach for blind source separation of convolved mixtures is proposed in the frequency domain. The problem in Frequency Domain then naturally demands a complex space analysis of the problem because of the complex components of the Fourier Series. In this project, we develop a Complex ICA framework for analyzing Videos and their Independent Components in the Fourier Domain. |
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| We present an implementation of interpreting facial-images and image sequences based on Active Appearance Model (AAM). We used the Intel OpenCV Library for graphics input of the image. The implementation is also a part of a Video Summarization Project build on Microsoft Visual Studio platform, in which this module recognizes the faces detected from a video and finds the identity of the person. An AAM contains a statistical, photo-realistic model of the shape and grey-level appearance of the object of interest which can generalize to almost any valid example. AAM employs an efficient iterative matching scheme for image interpretation. During a training phase we learn the relationship between model parameter displacements and the residual errors induced between a training image and a synthesized model example. To match to an image we measure the current residuals and use the model to predict changes to the current parameters, leading to a better fit. The software's source-code is built in Standard C++ with an extensive usage of the Standard Template Library. The code is documented using Doxygen and is available as Open-source for further development. It can also be used as a library-module for face-recognition whose interface is specified in the documentation. |
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| Wireless Sensor Networks have emerged as a new information-gathering paradigm based on the collaborative effort of a large number of sensing nodes. This paper describes the application of neural network technology in the problem domain of sensor data fusion. The first section of this paper introduces and reviews the problem presented by sensor fusion. The second section provides the background on neural-network and sensor data fusion. The subsequent section discusses the domains where neural-network is applied for sensor data fusion varying as wide as intelligent waste-water management to military surveillance. We provide a model for wide-area surveillance using Neural Network based Sensor Data Fusion. We also discuss how fuzzy modifications to artificial neural networks can improve the confidence level of sensor fusion. |
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