A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish

2010 ◽  
Vol 433 (2) ◽  
pp. 345-355 ◽  
Author(s):  
Elio Pizzo ◽  
Antonello Merlino ◽  
Mimmo Turano ◽  
Irene Russo Krauss ◽  
Francesca Coscia ◽  
...  
Keyword(s):  
Functional Properties ◽  
Danio Rerio ◽  
Three Dimensional ◽  
Biological Properties ◽  
Rnase A ◽  
Dimensional Structure ◽  
Structural And Functional Properties ◽  
Sequence Signature ◽  
Bactericidal Activities ◽  
Rnase A Superfamily

Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

scholarly journals Xanthan Gum–Konjac Glucomannan Blend Hydrogel for Wound Healing

Polymers ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 99 ◽  
Author(s):  
Andreia Alves ◽  
Sónia P. Miguel ◽  
André R.T.S. Araujo ◽  
María José de Jesús Valle ◽  
Amparo Sánchez Navarro ◽  
...  
Keyword(s):  
Xanthan Gum ◽  
Biomedical Application ◽  
Three Dimensional ◽  
High Water ◽  
Biological Properties ◽  
Konjac Glucomannan ◽  
Wound Dressings ◽  
Dimensional Structure ◽  
Future Application ◽  
High Water Content

Hydrogels are considered to be the most ideal materials for the production of wound dressings since they display a three-dimensional structure that mimics the native extracellular matrix of skin as well as a high-water content, which confers a moist environment at the wound site. Until now, different polymers have been used, alone or blended, for the production of hydrogels aimed for this biomedical application. From the best of our knowledge, the application of a xanthan gum–konjac glucomannan blend has not been used for the production of wound dressings. Herein, a thermo-reversible hydrogel composed of xanthan gum–konjac glucomannan (at different concentrations (1% and 2% w/v) and ratios (50/50 and 60/40)) was produced and characterized. The obtained data emphasize the excellent physicochemical and biological properties of the produced hydrogels, which are suitable for their future application as wound dressings.

Zona Pellucida Proteins, Fibrils, and Matrix

2020 ◽  
Vol 89 (1) ◽  
pp. 695-715
Author(s):  
Eveline S. Litscher ◽  
Paul M. Wassarman
Keyword(s):  
Extracellular Matrix ◽  
Zona Pellucida ◽  
Three Dimensional ◽  
Structural Features ◽  
Biological Properties ◽  
Preimplantation Development ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Early Embryos ◽  
N Terminus

The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1–4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2–ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.

scholarly journals Hydrogels for the Delivery of Plant-Derived (Poly)Phenols

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3254
Author(s):  
Nicola Micale ◽  
Andrea Citarella ◽  
Maria Sofia Molonia ◽  
Antonio Speciale ◽  
Francesco Cimino ◽  
...  
Keyword(s):  
Water Solubility ◽  
Biological Fluids ◽  
Three Dimensional ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Polymeric Networks ◽  
Wide Range ◽  
Swelling Capacity ◽  
Polymeric Component ◽  
External Stimuli

This review deals with hydrogels as soft and biocompatible vehicles for the delivery of plant-derived (poly)phenols, compounds with low general toxicity and an extraordinary and partially unexplored wide range of biological properties, whose use presents some major issues due to their poor bioavailability and water solubility. Hydrogels are composed of polymeric networks which are able to absorb large amounts of water or biological fluids while retaining their three-dimensional structure. Apart from this primary swelling capacity, hydrogels may be easily tailored in their properties according to the chemical structure of the polymeric component in order to obtain smart delivery systems that can be responsive to various internal/external stimuli. The functionalization of the polymeric component of hydrogels may also be widely exploited to facilitate the incorporation of bioactive compounds with different physicochemical properties into the system. Several prototype hydrogel systems have been designed for effective polyphenol delivery and potential employment in the treatment of human diseases. Therefore, the inherent features of hydrogels have been the focus of considerable research efforts over the past few decades. Herein, we review the most recent advances in (poly)phenol-loaded hydrogels by analyzing them primarily from the therapeutic perspective and highlighting the innovative aspects in terms of design and chemistry.

scholarly journals PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Adeel Malik ◽  
Ahmad Firoz ◽  
Vivekanand Jha ◽  
Shandar Ahmad
Keyword(s):  
Binding Sites ◽  
De Novo ◽  
Solvent Accessibility ◽  
Protein Structures ◽  
Three Dimensional ◽  
Data Bank ◽  
Dimensional Structure ◽  
Carbohydrate Binding ◽  
Structural And Functional Properties ◽  
Three Dimensional Models

Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins) as well as noncovalently (protein-carbohydrate complexes) is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i) Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB), (ii) Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii) CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth.

scholarly journals Temperature Induced Protein Unfolding and Folding of RNase a Studied by Time-Resolved Infrared Spectroscopy

1999 ◽  
Vol 19 (1-4) ◽  
pp. 233-235 ◽  
Author(s):  
H. Georg ◽  
C. W. Wharton ◽  
F. Siebert
Keyword(s):  
Time Course ◽  
Protein Unfolding ◽  
Structural Changes ◽  
Three Dimensional ◽  
Rnase A ◽  
Dimensional Structure ◽  
Time Range ◽  
Lag Phase ◽  
Structural Level ◽  
Time Resolved Infrared Spectroscopy

When a protein finds its native three-dimensional structure from the unstructured amino-acid chain various processes spanning a large time range are relevant. To understand the mechanism of protein folding one needs to cover the entire folding/ refolding (U↔N) reaction on a structural level. In the case of RNase A, the main structural changes occur in the ms time range, that can be monitored with rapid-scan- FTIR spectroscopy combined with rapid mixing techniques. To induce unfolding we inject aqueous protein solution into a hot IR cuvette and record the time course of the spectral changes. A lag phase is found when the unfolding conditions are relatively weak, suggesting an unfolding intermediate.

scholarly journals Capturing the complexity of topologically associating domains through multi-feature optimization

2021 ◽  
Author(s):  
Natalie Sauerwald ◽  
Carl Kingsford
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
Replication Timing ◽  
Biological Properties ◽  
Ctcf Binding ◽  
Dimensional Structure ◽  
Biological Targets ◽  
Topologically Associating Domains ◽  
Contact Frequency ◽  
Algorithmic Framework

AbstractThe three-dimensional structure of human chromosomes is tied to gene regulation and replication timing, but there is still a lack of consensus on the computational and biological definitions for chromosomal substructures such as topologically associating domains (TADs). TADs are described and identified by various computational properties leading to different TAD sets with varying compatibility with biological properties such as boundary occupancy of structural proteins. We unify many of these computational and biological targets into one algorithmic framework that jointly maximizes several computational TAD definitions and optimizes TAD selection for a quantifiable biological property. Using this framework, we explore the variability of TAD sets optimized for six different desirable properties of TAD sets: high occupancy of CTCF, RAD21, and H3K36me3 at boundaries, reproducibility between replicates, high intra- vs inter-TAD difference in contact frequencies, and many CTCF binding sites at boundaries. The compatibility of these biological targets varies by cell type, and our results suggest that these properties are better reflected as subpopulations or families of TADs rather than a singular TAD set fitting all TAD definitions and properties. We explore the properties that produce similar TAD sets (reproducibility and inter- vs intra-TAD difference, for example) and those that lead to very different TADs (such as CTCF binding sites and inter- vs intra-TAD contact frequency difference).

scholarly journals The Effects of a Short Self-Assembling Peptide on the Physical and Biological Properties of Biopolymer Hydrogels

Pharmaceutics ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1602
Author(s):  
Sumit Chowdhuri ◽  
Moumita Ghosh ◽  
Lihi Adler-Abramovich ◽  
Debapratim Das
Keyword(s):  
Tissue Engineering ◽  
Cartilage Tissue Engineering ◽  
Three Dimensional ◽  
Biological Properties ◽  
Cartilage Tissue ◽  
Dimensional Structure ◽  
Short Peptide ◽  
Hydrogel Scaffolds ◽  
Composite Hydrogels ◽  
Thixotropic Behavior

Hydrogel scaffolds have attracted much interest in the last few years for applications in the field of bone and cartilage tissue engineering. These scaffolds serve as a convenient three-dimensional structure on which cells can grow while sensing the native environment. Natural polymer-based hydrogels are an interesting choice for such purposes, but they lack the required mechanical properties. In contrast, composite hydrogels formed by biopolymers and short peptide hydrogelators possess mechanical characteristics suitable for osteogenesis. Here, we describe how combining the short peptide hydrogelator, Pyrene-Lysine-Cysteine (PyKC), with other biopolymers, can produce materials that are suitable for tissue engineering purposes. The presence of PyKC considerably enhances the strength and water content of the composite hydrogels, and confers thixotropic behavior. The hyaluronic acid-PyKC composite hydrogels were shown to be biocompatible, with the ability to support osteogenesis, since MC3 T3-E1 osteoblast progenitor cells grown on the materials displayed matrix calcification and osteogenic differentiation. The osteogenesis results and the injectability of these composite hydrogels hold promise for their future utilization in tissue engineering.

scholarly journals Structural and biophysical characterization of human RNase 6

2014 ◽  
Vol 70 (a1) ◽  
pp. C1643-C1643
Author(s):  
Donald Gagné ◽  
Jean-François Couture ◽  
Miljan Simonović ◽  
Nicolas Doucet
Keyword(s):  
Structural Integrity ◽  
Biological Function ◽  
Biological Activities ◽  
Structural Features ◽  
Catalytic Triad ◽  
Rnase A ◽  
Dimensional Structure ◽  
Biophysical Characterization ◽  
Human Rnase ◽  
Rnase A Superfamily

Human members of the RNase A superfamily include eight rapidly evolving homologous enzymes with varying ribonucleolytic activity. All eight canonical members are characterized by the presence of two histidines and a lysine forming the catalytic triad, in addition to strictly conserved cysteines involved in the formation of 3 or 4 disulfide bridges essential for structural integrity. Despite these architectural and catalytic similarities, human RNases are functionally diverse and their biological activities remain elusive. Apart from degrading RNA with varying degrees of efficiency, these structural homologues have acquired a variety of distinct biological functions, including anti-bactericidal, cytotoxic, angiogenic, immunosuppressive, anti-tumoral and/or anti-viral activities. Among human members of this vertebrate-specific family, RNase 6 and RNase 8 have never been structurally resolved. To better understand its biological function and to characterize its molecular interactions with RNA and/or potential unknown ligands, we present the three-dimensional structure of human RNase 6 in its apo form. While the enzyme shares similar structural features with other members of the RNase A superfamily, we emphasize interesting differences unique to RNase 6 that may be pertaining to its unique biological function. Additional NMR, CD and ITC biophysical characterization in presence of RNA ligands will also be presented.

Structure calculation of biological macromolecules from NMR data

1998 ◽  
Vol 31 (2) ◽  
pp. 145-237 ◽  
Author(s):  
PETER GÜNTERT
Keyword(s):  
Single Crystals ◽  
Structural Information ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
Three Dimensional Structure ◽  
Comparable Accuracy

The relationship between amino acid sequence, three-dimensional structure and biological function of proteins is one of the most intensely pursued areas of molecular biology and biochemistry. In this context, the three-dimensional structure has a pivotal role, its knowledge being essential to understand the physical, chemical and biological properties of a protein (Branden & Tooze, 1991; Creighton, 1993). Until 1984 structural information at atomic resolution could only be determined by X-ray diffraction techniques with protein single crystals (Drenth, 1994). The introduction of nuclear magnetic resonance (NMR) spectroscopy (Abragam, 1961) as a technique for protein structure determination (Wüthrich, 1986) has made it possible to obtain structures with comparable accuracy also in a solution environment that is much closer to the natural situation in a living being than the single crystals required for protein crystallography.

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