scholarly journals Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

2020 ◽  
Vol 21 (4) ◽  
pp. 1352 ◽  
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
József Tőzsér
Keyword(s):  
Structural Characteristics ◽  
Limited Proteolysis ◽  
Structural Data ◽  
Data Bank ◽  
Life Cycles ◽  
Evolutionary Relationships ◽  
Multiple Sequence ◽  
Dimer Interface ◽  
Viral Proteases ◽  
Eukaryotic Organisms

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

scholarly journals Structural Phylogenetics with Confidence

2020 ◽  
Vol 37 (9) ◽  
pp. 2711-2726
Author(s):  
Ashar J Malik ◽  
Anthony M Poole ◽  
Jane R Allison
Keyword(s):  
Molecular Dynamics ◽  
Sequence Similarity ◽  
Protein Structures ◽  
Structural Data ◽  
Data Bank ◽  
Homology Search ◽  
Hierarchical Level ◽  
Evolutionary Relationships ◽  
Major Protein ◽  
Alternative Means

Abstract For evaluating the deepest evolutionary relationships among proteins, sequence similarity is too low for application of sequence-based homology search or phylogenetic methods. In such cases, comparison of protein structures, which are often better conserved than sequences, may provide an alternative means of uncovering deep evolutionary signal. Although major protein structure databases such as SCOP and CATH hierarchically group protein structures, they do not describe the specific evolutionary relationships within a hierarchical level. Structural phylogenies have the potential to fill this gap. However, it is difficult to assess evolutionary relationships derived from structural phylogenies without some means of assessing confidence in such trees. We therefore address two shortcomings in the application of structural data to deep phylogeny. First, we examine whether phylogenies derived from pairwise structural comparisons are sensitive to differences in protein length and shape. We find that structural phylogenetics is best employed where structures have very similar lengths, and that shape fluctuations generated during molecular dynamics simulations impact pairwise comparisons, but not so drastically as to eliminate evolutionary signal. Second, we address the absence of statistical support for structural phylogeny. We present a method for assessing confidence in a structural phylogeny using shape fluctuations generated via molecular dynamics or Monte Carlo simulations of proteins. Our approach will aid the evolutionary reconstruction of relationships across structurally defined protein superfamilies. With the Protein Data Bank now containing in excess of 158,000 entries (December 2019), we predict that structural phylogenetics will become a useful tool for ordering the protein universe.

scholarly journals Variation and diversity of the breakpoint sequences on 4AL for the 4AL/5AL translocation in Triticum

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 635-641
Author(s):  
Wei Luo ◽  
Nana Qin ◽  
Yang Mu ◽  
Huaping Tang ◽  
Mei Deng ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Chromosomal Rearrangement ◽  
Evolutionary Relationships ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Single Nucleotide ◽  
Insertion And Deletion ◽  
Blast Analysis ◽  
Length Polymorphisms ◽  
Chromosomal Breakpoints

The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on their lengths, which ranged from 2009 to 2552 bp. Cluster analysis showed that they were further divided into three groups. Interesting evolutionary relationships among a few of the species were observed and discussed. Multiple sequence alignment of the 52 sequences made it possible to detect 13 insertion and deletion length polymorphisms (InDels) and 101 single nucleotide polymorphisms (SNPs). Furthermore, several species- or accession-specific SNPs or InDels were also identified. Based on BLAST analysis of the conserved sequences, the breakpoint was narrowed down to a 125 bp fragment. Taken together, the results obtained in this study enrich our understanding of chromosomal breakpoints and will be useful for the identification of other breakpoints in wheat.

Analyzing Motion Properties of Proteins Affected by Localized Structures From a Robot Kinematics Perspective

2015 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Data Bank ◽  
Complex Shape ◽  
Structural Data ◽  
Data Bank ◽  
Robot Kinematics ◽  
Motion Prediction ◽  
Serial Manipulators ◽  
Localized Structures ◽  
Motion Modes ◽  
Structural Compliance

On the basis of robot kinematics, we have thus far developed a method for predicting the motion of proteins from their 3D structural data given in the Protein Data Bank (PDB data). In this method, proteins are modeled as serial manipulators constrained by springs and the structural compliance properties of the models are evaluated. We focus on localized instead of whole structures of proteins. Employing the same model used in our method of motion prediction, the motion properties of the localized structures and the relation between the motion properties of localized and whole structures are analyzed. First, we present a method for graphically expressing the deformation of objects with a complex shape, such as proteins, by approximating the shape as a rectangular prism with a mesh on its surface. We then formulate a method for comparing the motion properties of localized structures cleaved from the whole structure and those remaining in it by expressing the motion of the latter using the decomposed motion modes of the former according to the structural compliance. Finally, we show a method for evaluating the effect of a localized structure on the motion properties of proteins by applying forces to localized structures. In the formulations, we demonstrate applications as illustrative examples using the PDB data of a real protein.

scholarly journals Understanding Structural Features of Microbial Lipases–-An Overview

2008 ◽  
Vol 3 ◽  
pp. ACI.S551 ◽  
Author(s):  
John Geraldine Sandana Mala ◽  
Satoru Takeuchi
Keyword(s):  
Structural Analysis ◽  
Candida Rugosa ◽  
Structural Data ◽  
Data Bank ◽  
Candida Rugosa Lipase ◽  
Structural Features ◽  
X Ray Crystallography ◽  
Versatile Tool ◽  
Microbial Lipases

The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) returns only 93 hits (as of September 2007) and, the NCBI database ( http://www.ncbi.nlm.nih.gov ) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

Computerized geological mapping in the Grenville Province, Quebec

1970 ◽  
Vol 7 (6) ◽  
pp. 1357-1373 ◽  
Author(s):  
H. R. Wynne-Edwards ◽  
A. Nandi ◽  
M. M. Kehlenbeck ◽  
A. F. Laurin ◽  
K. N. M. Sharma ◽  
...  
Keyword(s):  
Processing System ◽  
Structural Data ◽  
Data Bank ◽  
Geological Mapping ◽  
Grenville Province ◽  
Geological Interpretation ◽  
Rock Types ◽  
Potential Map ◽  
Computer Based ◽  
Project Data

Since 1965, the Quebec Department of Natural Resources has conducted reconnaissance mapping in the Grenville Province, completing to date over 70 000 square miles (181 000 km2). In 1968 a computer-based data processing system was designed at Queen's University, and applied to this Grenville Project. Data are recorded in the field on input documents designed to recover a complete description of the structure and lithology of an outcrop in a standard and reproducible form. From these records a data bank, now with descriptions of over 5000 outcrops, has been constructed for the field seasons of 1968 and 1969. Lthological sorting programs based on the textural and mineralogical qualities used to define rock types have been written to provide listings of some 40 potential map-units. Outcrop maps identifying lithologies have been drawn on a computer-driven drum plotter to provide the geologist with a basic document from which to make geological interpretation. Structural data have been extracted and plotted in equal-area projections, and also plotted on maps directly by machine, using standard structural symbols for layering, foliation, and lineation. The system has upgraded the standard of data collection in the field, and provides a rapid and versatile means of handling data and of interpreting the geology. The data bank, when made publicly available, will enable users of government geological maps and reports to reinterpret the area in their own manner, or freely to add any proprietary data in the preparation of revisions.

Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses

2016 ◽  
Vol 72 (3) ◽  
pp. 324-337 ◽  
Author(s):  
A. Janner
Keyword(s):  
Lattice Point ◽  
Three Dimensional ◽  
Structural Data ◽  
Data Bank ◽  
Coarse Grained ◽  
Large Set ◽  
Fine Grained ◽  
Coarse Grained Model ◽  
Digital Modeling ◽  
Icosahedral Viruses

Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article.

scholarly journals Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

2011 ◽  
Vol 40 (D1) ◽  
pp. D453-D460 ◽  
Author(s):  
A. R. Kinjo ◽  
H. Suzuki ◽  
R. Yamashita ◽  
Y. Ikegawa ◽  
T. Kudou ◽  
...  
Keyword(s):  
Protein Data Bank ◽  
Resource Description Framework ◽  
Structural Data ◽  
Data Bank ◽  
Data Archive ◽  
Description Framework ◽  
Resource Description

scholarly journals A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Dalgaard Mikkelsen ◽  
Hang Thi Thuy Cao ◽  
Thomas Roret ◽  
Nanna Rhein-Knudsen ◽  
Jesper Holck ◽  
...  
Keyword(s):  
Cell Walls ◽  
Sea Cucumber ◽  
Functional Characterization ◽  
Structural Data ◽  
Ring Structure ◽  
Optimal Temperature ◽  
Brown Seaweeds ◽  
Dimer Interface ◽  
The Common ◽  
Novel Protein

AbstractFucoidans are sulfated, fucose-rich marine polysaccharides primarily found in cell walls of brown seaweeds (macroalgae). Fucoidans are known to possess beneficial bioactivities depending on their structure and sulfation degree. Here, we report the first functional characterization and the first crystal structure of a prokaryotic sulfatase, PsFucS1, belonging to sulfatase subfamily S1_13, able to release sulfate from fucoidan oligosaccharides. PsFucS1 was identified in the genome of a Pseudoalteromonas sp. isolated from sea cucumber gut. PsFucS1 (57 kDa) is Ca2+ dependent and has an unusually high optimal temperature (68 °C) and thermostability. Further, the PsFucS1 displays a unique quaternary hexameric structure comprising a tight trimeric dimer complex. The structural data imply that this hexamer formation results from an uncommon interaction of each PsFucS1 monomer that is oriented perpendicular to the common dimer interface (~ 1500 Å2) that can be found in analogous sulfatases. The uncommon interaction involves interfacing (1246 Å2) through a bundle of α-helices in the N-terminal domain to form a trimeric ring structure. The high thermostability may be related to this unusual quaternary hexameric structure formation that is suggested to represent a novel protein thermostabilization mechanism.

scholarly journals Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult?

IUCrJ ◽  
2019 ◽  
Vol 6 (5) ◽  
pp. 788-793 ◽  
Author(s):  
Alice Brink ◽  
John R. Helliwell
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Design Research ◽  
Structural Data ◽  
Data Bank ◽  
Combine Data ◽  
Chemical Crystallography ◽  
File Formats ◽  
Structural Database ◽  
Circuitous Route

The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.

Sign in / Sign up

Export Citation Format

Share Document