scholarly journals Chemical Reversible Crosslinking Enables Measurement of RNA 3D Distances and Alternative Conformations in Cells

2021 ◽  
Author(s):  
Ryan Van Damme ◽  
Kongpan Li ◽  
Minjie Zhang ◽  
Jianhui Bai ◽  
Wilson Lee ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Tertiary Structure ◽  
3D Structure ◽  
Three Dimensional ◽  
Direct Determination ◽  
Transcriptional Elongation ◽  
3D Structures ◽  
Rna Molecules ◽  
Cellular Context

Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety of biological processes. However, direct determination of RNA 3D structures in vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present a new method, Spatial 2'-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation, and high throughput sequencing, SHARC enables transcriptome-wide tertiary structure contact maps at high accuracy and precision, revealing heterogeneous RNA structures and interactions. SHARC data provide constraints that improves Rosetta-based RNA 3D structure modeling at near-nanometer resolution. Integrating SHARC-exo with other crosslinking-based methods, we discover compact folding of the 7SK RNA, a critical regulator of transcriptional elongation. These results establish a new strategy for measuring RNA 3D distances and alternative conformations in their native cellular context.

scholarly journals RNA 3D Structure Prediction Using Coarse-Grained Models

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Li ◽  
Shi-Jie Chen
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Biological Functions ◽  
3D Structures ◽  
Rna Molecules ◽  
Atomic Structures ◽  
Long Time

The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined structures enables the thriving development of computational approaches to modeling RNAs. However, computational methods based on all-atom simulations are intractable for large RNA systems, which demand long time simulations. Facing such a challenge, many coarse-grained (CG) models have been developed. Here, we provide a review of CG models for modeling RNA 3D structures, compare the performance of the different models, and offer insights into potential future developments.

scholarly journals Protein Folding: Search for Basic Physical Models

2003 ◽  
Vol 3 ◽  
pp. 623-635 ◽  
Author(s):  
Ivan Y. Torshin ◽  
Robert W. Harrison
Keyword(s):  
Protein Folding ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Physical Models ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Linear Sequence ◽  
Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

RNA Structure Analysis: A Multifaceted Approach

1999 ◽  
Author(s):  
Bruce A. Shapiro ◽  
Wojciech Kasprzak
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Tertiary Structure ◽  
Hammerhead Ribozyme ◽  
3D Structure ◽  
Computer Prediction ◽  
Rna Molecules ◽  
Tertiary Interactions ◽  
The One ◽  
Secondary And Tertiary Structure

Genomic information (nucleic acid and amino acid sequences) completely determines the characteristics of the nucleic acid and protein molecules that express a living organism’s function. One of the greatest challenges in which computation is playing a role is the prediction of higher order structure from the one-dimensional sequence of genes. Rules for determining macromolecule folding have been continually evolving. Specifically in the case of RNA (ribonucleic acid) there are rules and computer algorithms/systems (see below) that partially predict and can help analyze the secondary and tertiary interactions of distant parts of the polymer chain. These successes are very important for determining the structural and functional characteristics of RNA in disease processes and hi the cell life cycle. It has been shown that molecules with the same function have the potential to fold into similar structures though they might differ in their primary sequences. This fact also illustrates the importance of secondary and tertiary structure in relation to function. Examples of such constancy in secondary structure exist in transfer RNAs (tRNAs), 5s RNAs, 16s RNAs, viroid RNAs, and portions of retroviruses such as HIV. The secondary and tertiary structure of tRNA Phe (Kim et al., 1974), of a hammerhead ribozyme (Pley et al., 1994), and of Tetrahymena (Cate et al., 1996a, 1996b) have been shown by their crystal structure. Currently little is known of tertiary interactions, but studies on tRNA indicate these are weaker than secondary structure interactions (Riesner and Romer, 1973; Crothers and Cole, 1978; Jaeger et al., 1989b). It is very difficult to crystallize and/or get nuclear magnetic resonance spectrum data for large RNA molecules. Therefore, a logical place to start in determining the 3D structure of RNA is computer prediction of the secondary structure. The sequence (primary structure) of an RNA molecule is relatively easy to produce. Because experimental methods for determining RNA secondary and tertiary structure (when the primary sequence folds back on itself and forms base pairs) have not kept pace with the rapid discovery of RNA molecules and their function, use of and methods for computer prediction of secondary and tertiary structures have increasingly been developed.

scholarly journals Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions

2020 ◽  
Vol 48 (12) ◽  
pp. e71-e71 ◽  
Author(s):  
Christian Twittenhoff ◽  
Vivian B Brandenburg ◽  
Francesco Righetti ◽  
Aaron M Nuss ◽  
Axel Mosig ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Yersinia Pseudotuberculosis ◽  
Structural Information ◽  
Dimethyl Sulfate ◽  
Bacterial Pathogen ◽  
Structural Features ◽  
Global Scale ◽  
Rna Molecules ◽  
Different Temperatures

Abstract The dynamic conformation of RNA molecules within living cells is key to their function. Recent advances in probing the RNA structurome in vivo, including the use of SHAPE (Selective 2′-Hydroxyl Acylation analyzed by Primer Extension) or kethoxal reagents or DMS (dimethyl sulfate), provided unprecedented insights into the architecture of RNA molecules in the living cell. Here, we report the establishment of lead probing in a global RNA structuromics approach. In order to elucidate the transcriptome-wide RNA landscape in the enteric pathogen Yersinia pseudotuberculosis, we combined lead(II) acetate-mediated cleavage of single-stranded RNA regions with high-throughput sequencing. This new approach, termed ‘Lead-seq’, provides structural information independent of base identity. We show that the method recapitulates secondary structures of tRNAs, RNase P RNA, tmRNA, 16S rRNA and the rpsT 5′-untranslated region, and that it reveals global structural features of mRNAs. The application of Lead-seq to Y. pseudotuberculosis cells grown at two different temperatures unveiled the first temperature-responsive in vivo RNA structurome of a bacterial pathogen. The translation of candidate genes derived from this approach was confirmed to be temperature regulated. Overall, this study establishes Lead-seq as complementary approach to interrogate intracellular RNA structures on a global scale.

scholarly journals Computational Design and Analysis of a Magic Snake

2020 ◽  
Vol 12 (5) ◽  
Author(s):  
Zilong Li ◽  
Songming Hou ◽  
Thomas C. Bishop
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Computational Design ◽  
Space Curve ◽  
One Dimensional ◽  
3D Structures ◽  
Multi Scale ◽  
3D Space ◽  
Slender Bodies ◽  
Self Similar

Abstract The Magic Snake (Rubik’s Snake) is a toy that was invented decades ago. It draws much less attention than Rubik’s Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of “embedding” to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.

scholarly journals Tapered elasticæ as a route for axisymmetric morphing structures

Soft Matter ◽  
2020 ◽  
Vol 16 (33) ◽  
pp. 7739-7750
Author(s):  
Mingchao Liu ◽  
Lucie Domino ◽  
Dominic Vella
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Two Dimensional ◽  
3D Structures

Transforming flat two-dimensional (2D) sheets into three-dimensional (3D) structures by a combination of careful cutting and applied loads is an emerging manufacturing paradigm; we study how to design the cut pattern to obtain a desired 3D structure.

scholarly journals Natural hybrid silica/protein superstructure at atomic resolution

2020 ◽  
Vol 117 (49) ◽  
pp. 31088-31093
Author(s):  
Stefan Görlich ◽  
Abisheik John Samuel ◽  
Richard Johannes Best ◽  
Ronald Seidel ◽  
Jean Vacelet ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Three Dimensional ◽  
Inorganic Materials ◽  
Atomic Resolution ◽  
Axial Filament ◽  
X Ray Crystallography ◽  
Organic Hybrid ◽  
Hybrid Silica ◽  
Transmission Electron

Formation of highly symmetric skeletal elements in demosponges, called spicules, follows a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by a highly ordered proteinaceous scaffold, the axial filament. The enzymatically active proteins, silicateins, are assembled into a slender hybrid silica/protein crystalline superstructure that directs the morphogenesis of the spicules. Furthermore, silicateins are known to catalyze the formation of a large variety of other technologically relevant organic and inorganic materials. However, despite the biological and biotechnological importance of this macromolecule, its tertiary structure was never determined. Here we report the atomic structure of silicatein and the entire mineral/organic hybrid assembly with a resolution of 2.4 Å. In this work, the serial X-ray crystallography method was successfully adopted to probe the 2-µm-thick filaments in situ, being embedded inside the skeletal elements. In combination with imaging and chemical analysis using high-resolution transmission electron microscopy, we provide detailed information on the enzymatic activity of silicatein, its crystallization, and the emergence of a functional three-dimensional silica/protein superstructure in vivo. Ultimately, we describe a naturally occurring mineral/protein crystalline assembly at atomic resolution.

Protein Structure Prediction using Homology Modeling

2016 ◽  
pp. 339-359 ◽  
Author(s):  
Akanksha Gupta ◽  
Pallavi Mohanty ◽  
Sonika Bhatnagar
Keyword(s):  
Homology Modeling ◽  
Structure Prediction ◽  
High Throughput Sequencing ◽  
Tertiary Structure ◽  
Structural Information ◽  
Sequence Similarity ◽  
3D Structure ◽  
Comparative Modeling ◽  
Spatial Arrangement ◽  
Good Sequence

Sequence-structure deficit marks one of the critical problems in today's scenario where high-throughput sequencing has resulted in large datasets of protein sequences but their corresponding 3D structures still needs to be determined. Homology modeling, also termed as Comparative modeling refers to modeling of 3D structure of a protein by exploiting structural information from other known protein structures with good sequence similarity. Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. This chapter provides a brief description about protein tertiary structure prediction and Homology modeling. The authors provide a description of the steps involved in homology modeling protocols and provide information on the various resources available for the same.

scholarly journals RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA

2019 ◽  
Vol 35 (21) ◽  
pp. 4459-4461 ◽  
Author(s):  
Sha Gong ◽  
Chengxin Zhang ◽  
Yang Zhang
Keyword(s):  
Rna Structure ◽  
Large Scale ◽  
3D Structure ◽  
Structure Alignment ◽  
Coarse Grained ◽  
Supplementary Information ◽  
Art Programs ◽  
3D Structures ◽  
Rna Molecules ◽  
Functional Relations

Abstract Motivation Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. Results We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. Availability and implementation https://zhanglab.ccmb.med.umich.edu/RNA-align/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Novel Three-Dimensional Culture Device Favors a Myelinating Morphology of Neural Stem Cell-Derived Oligodendrocytes

2021 ◽  
Vol 9 ◽  
Author(s):  
Alessandra Flagelli ◽  
Olivia Candini ◽  
Stella Frabetti ◽  
Massimo Dominici ◽  
Luciana Giardino ◽  
...  
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
3D Culture ◽  
Precursor Cell ◽  
Research Report ◽  
Mrna Levels ◽  
Differentiation Markers ◽  
Functional Components

The complexity of the central nervous system (CNS) requires researchers to consider all the variables linked to the interaction between the different cell inhabitants. On this basis, any in vitro study of the physiological and pathological processes regarding the CNS should consider the balance between the standardization of the assay and the complexity of the cellular system which mimics the in vivo microenvironment. One of the main structural and functional components of the CNS is the oligodendrocyte precursor cell (OPC), responsible for developmental myelination and myelin turnover and repair during adulthood following differentiation into mature oligodendrocytes. In the present brief research report, we describe a 3D culture tool (VITVO) based on an inert and biocompatible synthetic polymer material scaffold, functionalized with laminin coating, and tested as a new culture microenvironment for neural stem/precursor cell (NSPC) differentiation compared to standard 2D cultures. NSPCs spontaneously differentiate in the three neural lineages (neurons, astrocytes and OPCs), identified by specific markers, along the fibers in the 3D structure. Analysis of the mRNA levels for lineage differentiation markers reveals a higher expression compared to those seeded on a 2D surface, suggesting an acceleration of the differentiation process. We then focused on the oligodendroglial lineage, showing that in VITVO, mature oligodendrocytes exhibit a myelinating morphology, proven by 3D image elaboration, linked to a higher expression of mature oligodendrocyte markers. This preliminary study on an innovative 3D culture system is the first robust step in producing new microenvironment-based strategies to investigate in vitro OPC and oligodendrocyte biology.

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