scholarly journals MOHCA-seq: RNA 3D models from single multiplexed proximity-mapping experiments

2014 ◽  
Author(s):  
Clarence Cheng ◽  
Fang-Chieh Chou ◽  
Wipapat Kladwang ◽  
Siqi Tian ◽  
Pablo Cordero ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Deep Sequencing ◽  
Structure Determination ◽  
Rna Structure ◽  
Tertiary Structure ◽  
3D Models ◽  
Biological Processes ◽  
3D Information ◽  
Nucleotide Resolution

Large RNAs control myriad biological processes but challenge tertiary structure determination. We report that integrating Multiplexed •OH Cleavage Analysis with tabletop deep sequencing (MOHCA-seq) gives nucleotide-resolution proximity maps of RNA structure from single straightforward experiments. After achieving 1-nm resolution models for RNAs of known structure, MOHCA-seq reveals previously unattainable 3D information for ligand-induced conformational changes in a double glycine riboswitch and the sixth community-wide RNA puzzle, an adenosylcobalamin riboswitch.

scholarly journals RNA 3D structure prediction guided by independent folding of homologous sequences

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Marcin Magnus ◽  
Kalli Kappel ◽  
Rhiju Das ◽  
Janusz M. Bujnicki
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
3D Structure ◽  
3D Models ◽  
Target Sequence ◽  
Rna Sequences ◽  
Homologous Sequences ◽  
3D Structure Prediction ◽  
Folding Simulations

Abstract Background The understanding of the importance of RNA has dramatically changed over recent years. As in the case of proteins, the function of an RNA molecule is encoded in its tertiary structure, which in turn is determined by the molecule’s sequence. The prediction of tertiary structures of complex RNAs is still a challenging task. Results Using the observation that RNA sequences from the same RNA family fold into conserved structure, we test herein whether parallel modeling of RNA homologs can improve ab initio RNA structure prediction. EvoClustRNA is a multi-step modeling process, in which homologous sequences for the target sequence are selected using the Rfam database. Subsequently, independent folding simulations using Rosetta FARFAR and SimRNA are carried out. The model of the target sequence is selected based on the most common structural arrangement of the common helical fragments. As a test, on two blind RNA-Puzzles challenges, EvoClustRNA predictions ranked as the first of all submissions for the L-glutamine riboswitch and as the second for the ZMP riboswitch. Moreover, through a benchmark of known structures, we discovered several cases in which particular homologs were unusually amenable to structure recovery in folding simulations compared to the single original target sequence. Conclusion This work, for the first time to our knowledge, demonstrates the importance of the selection of the target sequence from an alignment of an RNA family for the success of RNA 3D structure prediction. These observations prompt investigations into a new direction of research for checking 3D structure “foldability” or “predictability” of related RNA sequences to obtain accurate predictions. To support new research in this area, we provide all relevant scripts in a documented and ready-to-use form. By exploring new ideas and identifying limitations of the current RNA 3D structure prediction methods, this work is bringing us closer to the near-native computational RNA 3D models.

scholarly journals SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells

2016 ◽  
Vol 113 (37) ◽  
pp. 10322-10327 ◽  
Author(s):  
Matthew J. Smola ◽  
Thomas W. Christy ◽  
Kaoru Inoue ◽  
Cindo O. Nicholson ◽  
Matthew Friedersdorf ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Rna Structure ◽  
Noncoding Rna ◽  
Ex Vivo ◽  
Living Cells ◽  
Mammalian Development ◽  
Cellular Environment ◽  
Nucleotide Resolution ◽  
In Cells

The 18-kb Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation during female eutherian mammalian development. Global structural architecture, cell-induced conformational changes, and protein–RNA interactions within Xist are poorly understood. We used selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to examine these features of Xist at single-nucleotide resolution both in living cells and ex vivo. The Xist RNA forms complex well-defined secondary structure domains and the cellular environment strongly modulates the RNA structure, via motifs spanning one-half of all Xist nucleotides. The Xist RNA structure modulates protein interactions in cells via multiple mechanisms. For example, repeat-containing elements adopt accessible and dynamic structures that function as landing pads for protein cofactors. Structured RNA motifs create interaction domains for specific proteins and also sequester other motifs, such that only a subset of potential binding sites forms stable interactions. This work creates a broad quantitative framework for understanding structure–function interrelationships for Xist and other lncRNAs in cells.

scholarly journals An Anatomical Thermal 3D Model in Preclinical Research: Combining CT and Thermal Images

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1200
Author(s):  
Franziska Schollemann ◽  
Carina Barbosa Pereira ◽  
Stefanie Rosenhain ◽  
Andreas Follmann ◽  
Felix Gremse ◽  
...  
Keyword(s):  
Image Processing ◽  
Temperature Profile ◽  
3D Models ◽  
Animal Suffering ◽  
Preclinical Research ◽  
Thermal Images ◽  
Animal Trials ◽  
Superficial Skin ◽  
Ct Data ◽  
3D Information

Even though animal trials are a controversial topic, they provide knowledge about diseases and the course of infections in a medical context. To refine the detection of abnormalities that can cause pain and stress to the animal as early as possible, new processes must be developed. Due to its noninvasive nature, thermal imaging is increasingly used for severity assessment in animal-based research. Within a multimodal approach, thermal images combined with anatomical information could be used to simulate the inner temperature profile, thereby allowing the detection of deep-seated infections. This paper presents the generation of anatomical thermal 3D models, forming the underlying multimodal model in this simulation. These models combine anatomical 3D information based on computed tomography (CT) data with a registered thermal shell measured with infrared thermography. The process of generating these models consists of data acquisition (both thermal images and CT), camera calibration, image processing methods, and structure from motion (SfM), among others. Anatomical thermal 3D models were successfully generated using three anesthetized mice. Due to the image processing improvement, the process was also realized for areas with few features, which increases the transferability of the process. The result of this multimodal registration in 3D space can be viewed and analyzed within a visualization tool. Individual CT slices can be analyzed axially, sagittally, and coronally with the corresponding superficial skin temperature distribution. This is an important and successfully implemented milestone on the way to simulating the internal temperature profile. Using this temperature profile, deep-seated infections and inflammation can be detected in order to reduce animal suffering.

scholarly journals Virtual Archaeology of Death and Burial: A Procedure for Integrating 3D Visualization and Analysis in Archaeothanatology

2021 ◽  
Vol 7 (1) ◽  
pp. 540-555
Author(s):  
Hayley L. Mickleburgh ◽  
Liv Nilsson Stutz ◽  
Harry Fokkens
Keyword(s):  
Spatial Information ◽  
3D Visualization ◽  
Rapid Development ◽  
Three Dimensional ◽  
3D Models ◽  
The Body ◽  
Test Case ◽  
Archaeology Of Death ◽  
Human Burials ◽  
3D Information

Abstract The reconstruction of past mortuary rituals and practices increasingly incorporates analysis of the taphonomic history of the grave and buried body, using the framework provided by archaeothanatology. Archaeothanatological analysis relies on interpretation of the three-dimensional (3D) relationship of bones within the grave and traditionally depends on elaborate written descriptions and two-dimensional (2D) images of the remains during excavation to capture this spatial information. With the rapid development of inexpensive 3D tools, digital replicas (3D models) are now commonly available to preserve 3D information on human burials during excavation. A procedure developed using a test case to enhance archaeothanatological analysis and improve post-excavation analysis of human burials is described. Beyond preservation of static spatial information, 3D visualization techniques can be used in archaeothanatology to reconstruct the spatial displacement of bones over time, from deposition of the body to excavation of the skeletonized remains. The purpose of the procedure is to produce 3D simulations to visualize and test archaeothanatological hypotheses, thereby augmenting traditional archaeothanatological analysis. We illustrate our approach with the reconstruction of mortuary practices and burial taphonomy of a Bell Beaker burial from the site of Oostwoud-Tuithoorn, West-Frisia, the Netherlands. This case study was selected as the test case because of its relatively complete context information. The test case shows the potential for application of the procedure to older 2D field documentation, even when the amount and detail of documentation is less than ideal.

scholarly journals Crystal structure of Pistol, a class of self-cleaving ribozyme

2017 ◽  
Vol 114 (5) ◽  
pp. 1021-1026 ◽  
Author(s):  
Laura A. Nguyen ◽  
Jimin Wang ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Nonbridging Oxygen ◽  
Close Proximity ◽  
Domains Of Life ◽  
Guanine Base ◽  
A Minor

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2′-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5′ leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

scholarly journals The effects of Ca2+ and Cd2+ on the secondary and tertiary structure of bovine testis calmodulin. A circular-dichroism study

1986 ◽  
Vol 238 (2) ◽  
pp. 485-490 ◽  
Author(s):  
S R Martin ◽  
P M Bayley
Keyword(s):  
Circular Dichroism ◽  
Conformational Changes ◽  
Metal Ion ◽  
Tertiary Structure ◽  
Thermal Unfolding ◽  
Apparent Effect ◽  
Thermally Induced ◽  
Circular Dichroïsm ◽  
Secondary And Tertiary Structure

Near-u.v. and far-u.v. c.d. spectra of bovine testis calmodulin and its tryptic fragments (TR1C, N-terminal half, residues 1-77, and TR2C, C-terminal half, residues 78-148) were recorded in metal-ion-free buffer and in the presence of saturating concentrations of Ca2+ or Cd2+ under a range of different solvent conditions. The results show the following: if there is any interaction between the N-terminal and C-terminal halves of calmodulin, it has not apparent effect on the secondary or tertiary structure of either half; the conformational changes induced by Ca2+ or Cd2+ are substantially greater in TR2C than they are in TR1C; the presence of Ca2+ or Cd2+ confers considerable stability with respect to urea-induced denaturation, both for the whole molecule and for either of the tryptic fragments; a thermally induced transition occurs in whole calmodulin at temperatures substantially below the temperature of major thermal unfolding, both in the presence and in the absence of added metal ion; the effects of Cd2+ are identical with those of Ca2+ under all conditions studied.

Kinetic and structural analysis of the ultrasensitive behaviour of cyanobacterial ADP-glucose pyrophosphorylase

2000 ◽  
Vol 350 (1) ◽  
pp. 139-147 ◽  
Author(s):  
Diego F. GÓMEZ CASATI ◽  
Miguel A. AON ◽  
Alberto A. IGLESIAS
Keyword(s):  
Conformational Changes ◽  
Tertiary Structure ◽  
Fluorescence Emission ◽  
Maximal Activity ◽  
Size Exclusion ◽  
Exclusion Chromatography ◽  
Adp Glucose Pyrophosphorylase ◽  
Kinetics Of ◽  
Allosteric Regulators

The kinetic and (supra)molecular properties of the ultrasensitive behaviour of ADP-glucose pyrophosphorylase (AGPase) from Anabaena PCC 7120 (a cyanobacterium) were exhaustively studied. The response of the enzyme toward the allosteric activator 3-phosphoglycerate (3PGA) occurs with ultrasensitivity as a consequence of the cross-talk with the inhibitor Pi. Molecular ‘crowding’renders AGPase more sensitive to the interplay between the allosteric regulators and, consequently, enhances the ultrasensitive response. In crowded media, and when orthophosphate is present, the activation kinetics of the enzyme with 3PGA proceed with increased co-operativity and reduced affinity toward the activator. Under conditions of ultrasensitivity, the enzyme's maximal activation takes place in a narrow range of 3PGA concentrations. Moreover, saturation kinetics of the enzyme with respect to its substrates, glucose 1-phosphate and ATP, were different at low or high 3PGA levels in crowded media. Only under the latter conditions did AGPase exhibit discrimination between low or high levels of the activator, which increased the affinity toward the substrates and the maximal activity reached by the enzyme. Studies of fluorescence emission of tryptophan residues, fourth-derivative spectroscopy and size-exclusion chromatography indicated that the ultrasensitive behaviour is correlated with intramolecular conformational changes induced in the tertiary structure of the homotetrameric enzyme. The results suggest a physiological relevance of the ultrasensitive response of AGPase in vivo, since the enzyme could be subtly sensing changes in the levels of allosteric regulators and substrates, and thus determining the flux of metabolites toward synthesis of storage polysaccharides.

scholarly journals A method for RNA structure prediction shows evidence for structure in lncRNAs

2018 ◽  
Author(s):  
Riccardo Delli ponti ◽  
Alexandros Armaos ◽  
Stefanie Marti ◽  
Gian Gaetano Tartaglia
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Structure Prediction ◽  
Sequence Information ◽  
Time Warping ◽  
Single Nucleotide ◽  
Rna Molecules ◽  
Rna Structure Prediction ◽  
Dynamic Time ◽  
Nucleotide Resolution

AbstractTo compare the secondary structures of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure at single-nucleotide resolution using sequence information, and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modelling. CROSSalign can be applied to perform pair-wise comparisons and is able to find homologues between thousands of matches identifying the exact regions of similarity between profiles of different lengths. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/CROSSalign.

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