scholarly journals RNA structural motifs: building blocks of a modular biomolecule

2005 ◽  
Vol 38 (3) ◽  
pp. 221-243 ◽  
Author(s):  
Donna K. Hendrix ◽  
Steven E. Brenner ◽  
Stephen R. Holbrook
Keyword(s):  
Metal Binding ◽  
Tertiary Structure ◽  
Building Blocks ◽  
Dimensional Structure ◽  
Structural Elements ◽  
Structural Motifs ◽  
Binding Motifs ◽  
Internal Loops ◽  
Tertiary Interactions ◽  
Rna Structural Motifs

1. Introduction 2222. What is an RNA motif? 2222.1 Sequence vs. structural motifs 2222.2 RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition motifs 2242.5 Tools for identifying and classifying elements and motifs 2263. Types of RNA structural motifs 2283.1 Helices 2283.2 Hairpin loops 2283.3 Internal loops 2303.4 Junction loops/multiloops 2303.5 Binding motifs 2323.5.1 Metal binding 2323.5.2 Natural and selected aptamers 2343.6 Tertiary interactions 2344. Future directions 2365. Acknowledgments 2396. References 239RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common ‘structural elements’. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.

A new three-dimensional anionic cadmium(II) dicyanamide network

2014 ◽  
Vol 70 (11) ◽  
pp. 1054-1056 ◽  
Author(s):  
Qiang Li ◽  
Hui-Ting Wang
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Building Blocks ◽  
The Other ◽  
Dimensional Structure ◽  
Cadmium Nitrate ◽  
Nitrate Tetrahydrate ◽  
Anionic Framework

A new cadmium dicyanamide complex, poly[tetramethylphosphonium [μ-chlorido-di-μ-dicyanamido-κ4N1:N5-cadmium(II)]], [(CH3)4P][Cd(NCNCN)2Cl], was synthesized by the reaction of tetramethylphosphonium chloride, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution. In the crystal structure, each CdIIatom is octahedrally coordinated by four terminal N atoms from four anionic dicyanamide (dca) ligands and by two chloride ligands. The dicyanamide ligands play two different roles in the building up of the structure; one role results in the formation of [Cd(dca)Cl]2building blocks, while the other links the building blocks into a three-dimensional structure. The anionic framework exhibits a solvent-accessible void of 673.8 Å3, amounting to 47.44% of the total unit-cell volume. The cavities in the network are occupied by pairs of tetramethylphosphonium cations.

128 The “physiological” behaviour of DNA/RNA structural motifs in gas phase

2015 ◽  
Vol 33 (sup1) ◽  
pp. 82-83 ◽  
Author(s):  
Massimiliano Porrini ◽  
Valentina D’Atri ◽  
Josephine Abi-Ghanem ◽  
Frédéric Rosu ◽  
Valérie Gabelica
Keyword(s):  
Gas Phase ◽  
Structural Motifs ◽  
Rna Structural Motifs

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.

scholarly journals Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey

2020 ◽  
Vol 31 (3) ◽  
pp. 47-61
Author(s):  
Uus Saepuloh ◽  
Diah Iskandriati ◽  
Joko Pamungkas ◽  
Dedy Duryadi Solihin ◽  
Sela Septima Mariya ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Cynomolgus Monkey ◽  
Tertiary Structure ◽  
Vaccine Development ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Nucleotide Position ◽  
Structure Model ◽  
Three Dimensional Structure ◽  
Hiv 1

Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in Asian macaques. It is a potential confounding variable in biomedical research. SRV-2 also provides a valuable viral model compared to other retroviruses which can be used for understanding many aspects of retroviral-host interactions and immunosuppression, infection mechanism, retroviral structure, antiretroviral and vaccine development. In this study, we isolated the gene encoding reverse transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf ET1006) and predicted the three dimensional structure model using the iterative threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT Mf ET1006 consisted of 547 amino acids at nucleotide position 3284–4925 of whole genome SRV-2. The polymerase active site located in the finger/palm subdomain characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template modelling score (TM-score 0.90 ± 0.06) and root mean square deviation (RMSD) 4.7 ± 3.1Å, indicating that this model can be trusted and the accuracy can be seen from the appearance of protein folding in tertiary structure. The superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 (HIV-1) RT were performed to predict the structural in details and to optimise the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 0.911, RMSD 1.85 Å, and coverage of 0.953. This preliminary study of SRV-2 RT Mf ET1006 structure modelling is intriguing and provide some information to explore the molecular characteristic and biochemical mechanism of this enzyme.

scholarly journals WAVE ANALYSIS OF A L-BEAM STRUCTURE WITH A BLOCKING MASS

2020 ◽  
Author(s):  
Johnny Tiu ◽  
Richard Bachoo
Keyword(s):  
Systematic Approach ◽  
Building Blocks ◽  
Element Model ◽  
Structural Systems ◽  
Structural Elements ◽  
Wave Analysis ◽  
Beam Structure ◽  
Reflection Matrix ◽  
Geometric Changes ◽  
Transmission And Reflection

The wave vibration approach regards the vibrations present within a structure as waves, whereby each wave flows along a structural member and upon meeting a discontinuity; portions of the incident wave are reflected and transmitted across the discontinuity. The reflected, transmitted and propagating wave transformations are represented mathematically by matrices, which are used to develop a set of wave relation equations at each discontinuity that can be used to describe the frequency response of the system holistically. This method creates a systematic approach of analysing structures by utilizing common cases as building blocks for a specific structure. The L-joint, described as two beams meeting at right angles; is a ubiquitous case for spatial portal and structural frames, which may become geometrically complex. Such structures are well suited to a wave vibration approach due to the large number of geometric changes and the prevalence as well as recurrence of specific cases. In this paper, the L-joint expanded to include a blocking mass, typically employed in structural systems and allows for the isolation and reflection of vibration away from contiguous structural elements. Included are; variance of transmission and reflection matrix components as the size of the blocking mass increases, numerical examples and comparison to a Finite Element Model developed in ANSYS.

Electrocatalytic Difunctionalization of Olefins as a General Approach to the Synthesis of Vicinal Diamines

Synlett ◽  
2018 ◽  
Vol 29 (03) ◽  
pp. 257-265 ◽  
Author(s):  
Song Lin ◽  
Joseph Parry ◽  
Niankai Fu
Keyword(s):  
Natural Products ◽  
Building Blocks ◽  
Therapeutic Agents ◽  
Recent Contribution ◽  
Structural Motifs ◽  
Bioactive Natural Products ◽  
Methodological Approaches ◽  
Molecular Catalysts ◽  
Vicinal Diamines

Vicinal diamines are highly prevalent structural motifs in therapeutic agents, bioactive natural products, and molecular catalysts. However, there are currently few unified methodological approaches for making these pertinent synthetic building blocks. This Synpacts article provides an overview of selected landmark developments in the area of olefin diamination. In particular, we highlight our recent contribution on the electrocatalytic diazidation of olefins as a general, selective, and sustainable method for the synthesis of vicinal diamines.1 Introduction2 Background: Intermolecular Diamination of Olefins3 Background: Intermolecular Diazidation of Olefins4 Electrocatalytic Diazidation of Olefins

Prediction of Structural and Functional Aspects of Protein

2014 ◽  
pp. 317-333
Author(s):  
Arun G. Ingale
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Predict Protein Structure ◽  
Basic Ideas

To predict the structure of protein from a primary amino acid sequence is computationally difficult. An investigation of the methods and algorithms used to predict protein structure and a thorough knowledge of the function and structure of proteins are critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this chapter sheds light on the methods used for protein structure prediction. This chapter covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, it presents an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction, giving unique insight into the future applications of the modeled protein structures. In this chapter, current protein structure prediction methods are reviewed for a milieu on structure prediction, the prediction of structural fundamentals, tertiary structure prediction, and functional imminent. The basic ideas and advances of these directions are discussed in detail.

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