scholarly journals Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Aparna Laskar ◽  
Aniruddha Chatterjee ◽  
Somnath Chatterjee ◽  
Euan J. Rodger
Keyword(s):  
Molecular Modeling ◽  
Structure Prediction ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
Evolutionary Divergence ◽  
Catalytic Core ◽  
Diverse Range ◽  
Wide Range ◽  
Surface Electrostatic Potential

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases.

scholarly journals Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

2019 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Geoffrey Hutchison
Keyword(s):  
Molecular Modeling ◽  
Structure Prediction ◽  
Distance Geometry ◽  
Three Dimensional ◽  
Property Prediction ◽  
Crystallographic Databases ◽  
Fragment Library ◽  
Wide Range ◽  
Computational Property ◽  
Improving Accuracy

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>

scholarly journals Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

2019 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Geoffrey Hutchison
Keyword(s):  
Molecular Modeling ◽  
Structure Prediction ◽  
Distance Geometry ◽  
Three Dimensional ◽  
Property Prediction ◽  
Crystallographic Databases ◽  
Fragment Library ◽  
Wide Range ◽  
Computational Property ◽  
Improving Accuracy

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>

scholarly journals Fast, Efficient Fragment-Based Coordinate Generation for Open Babel

2019 ◽  
Author(s):  
Naruki Yoshikawa ◽  
Geoffrey Hutchison
Keyword(s):  
Molecular Modeling ◽  
Structure Prediction ◽  
Distance Geometry ◽  
Three Dimensional ◽  
Property Prediction ◽  
Crystallographic Databases ◽  
Fragment Library ◽  
Wide Range ◽  
Computational Property ◽  
Improving Accuracy

<div>Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.</div>

Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?

1980 ◽  
Vol 13 (3) ◽  
pp. 339-386 ◽  
Author(s):  
O. B. Ptitsyn ◽  
A. V. Finkelstein
Keyword(s):  
Serine Proteases ◽  
Protein Structures ◽  
Three Dimensional ◽  
Sperm Whale ◽  
Globular Protein ◽  
Dimensional Structure ◽  
Evolutionary Divergence ◽  
Functional Convergence ◽  
Primary Structures ◽  
Sperm Whale Myoglobin

(A) Evolutionary similarities of protein structures Two decades have passed from the time that the three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded (Kendrew et al. 1960). Its structure, which now looks so simple and habitual, then seemed to be unusually complicated. The decoding of the subsequent proteins, lysozyme (Blake et al. 1965), ribonuclease (Kartha, Bello & Harker, 1967), chymotrypsin (Matthews et al. 1967), carboxypeptidase (Lipscomb et al. 1969) redoubled the feeling of amazement and even of some confusion before the extremely complicated, intricate and, above all, absolutely unlike protein structures. Some consolation against this background was the evident and far-reaching similarity between the three-dimensional structures of myoglobin and hemoglobin subunits (Perutz, Kendrew & Watson, 1965) and an analogous similarity between the structures of chymotrypsin and other serine proteases, elastase (Shotton & Watson, 1970) and trypsin (Stroud, Kay & Dickerson, 1972). However this similarity was easily explained by the far-reaching homology between the primary structures of myoglobin and hemoglobin and between the primary structures of serine proteases.

scholarly journals RNA secondary structure prediction with Convolutional Neural Networks

2021 ◽  
Author(s):  
Mehdi Saman Booy ◽  
Alexander Ilin ◽  
Pekka Orponen
Keyword(s):  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Optimal Solution ◽  
Rna Structures ◽  
Rna Sequences ◽  
Perfect Model ◽  
Wide Range ◽  
Data Driven Approach ◽  
Algorithmic Approaches

Predicting the secondary, i.e. base-pairing structure of a folded RNA strand is an important problem in synthetic and computational biology. First-principle algorithmic approaches to this task are challenging because existing models of the folding process are inaccurate, and even if a perfect model existed, finding an optimal solution would be in general NP-complete. In this paper, we propose a simple, yet extremely effective data-driven approach. We represent RNA sequences in the form of three-dimensional tensors in which we encode possible relations between all pairs of bases in a given sequence. We then use a convolutional neural network to predict a two-dimensional map which represents the correct pairings between the bases. Our model achieves significant accuracy improvements over existing methods on two standard datasets. Our experiments show excellent performance of the model across a wide range of sequence lengths and RNA families. We also observe considerable improvements in predicting complex pseudoknotted RNA structures, as compared to previous approaches.

scholarly journals Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody

2006 ◽  
Vol 395 (3) ◽  
pp. 473-481 ◽  
Author(s):  
Paul A. Ramsland ◽  
Simon S. Terzyan ◽  
Gwendolyn Cloud ◽  
Christina R. Bourne ◽  
William Farrugia ◽  
...  
Keyword(s):  
Serine Proteases ◽  
Three Dimensional ◽  
Catalytic Triad ◽  
Dimensional Structure ◽  
Gel Point ◽  
Antigen Binding ◽  
Antigen Binding Site ◽  
Fab Fragment ◽  
Peripheral Tissues ◽  
Fragment Antigen Binding

The 2.6 Å (1 Å=0.1 nm) resolution structure has been determined for the glycosylated Fab (fragment antigen binding) of an IgM (Yvo) obtained from a subject with Waldenström's macroglobulinaemia. Dynamic light scattering was used to estimate the gel point and monitor the formation of an ordered hydroscopic gel of Yvo IgM upon cooling. If a cryoglobulin forms gels in peripheral tissues and organs, the associated swelling and damage to microvasculature can result in considerable morbidity and mortality. The three-dimensional structure of the branched N-linked oligosaccharide associated with the CH1 domain (first constant domain of heavy chain) is reported. The carbohydrate may act to shield part of the lateral surface of the CH1 domain and crowd the junction between the CH1 and CH2 domains, thereby limiting the segmental flexibility of the Fab arms in intact Yvo IgM, especially at low temperatures. Recently, Yvo IgM was shown to have the properties of a naturally occurring proteolytic antibody [Paul, Karle, Planque, Taguchi, Salas, Nishiyama, Handy, Hunter, Edmundson and Hanson (2004) J. Biol. Chem. 279, 39611–39619; Planque, Bangale, Song, Karle, Taguchi, Poindexter, Bick, Edmundson, Nishiyama and Paul (2004) J. Biol Chem. 279, 14024–14032]. The Yvo protein displayed the ability to cleave, by a nucleophilic mechanism, the amide bonds of a variety of serine protease substrates and the gp120 coat protein of HIV. An atypical serine, arginine and glutamate motif is located in the middle of the Yvo antigen-binding site and displays an overall geometry that mimics the classical serine, histidine and aspartate catalytic triad of serine proteases. Our present findings indicate that pre-existing or natural antibodies can utilize at least one novel strategy for the cleavage of peptide bonds.

3D printing: an emerging technology for sensor fabrication

Sensor Review ◽  
2016 ◽  
Vol 36 (4) ◽  
pp. 333-338 ◽  
Author(s):  
Robert Bogue
Keyword(s):  
3D Printing ◽  
Three Dimensional ◽  
Diverse Range ◽  
Content Type ◽  
Sensor Fabrication ◽  
Wide Range ◽  
Complex Shapes ◽  
Printed Sensors ◽  
3D Printed ◽  
Manufacturing Techniques

Purpose This study aims to provide a technical insight into sensors fabricated by three-dimensional (3D) printing methods. Design/methodology/approach Following an introduction to 3D printing, this article first discusses printed sensors for strain and allied variables, based on a diverse range of principles and materials. It then considers ultrasonic and acoustic sensor developments and provides details of a sensor based on 3D printed electronic components for monitoring food quality in real-time. Finally, brief concluding comments are drawn. Findings Several variants of the 3D printing technique have been used in the fabrication of a range of sensors based on many different operating principles. These exhibit good performance and sometimes unique characteristics. A key benefit is the ability to overcome the limitations of conventional manufacturing techniques by creating complex shapes from a wide range of sensing materials. Originality/value 3D printing is a new and potentially important sensor fabrication technology, and this article provides details of a range of recently reported developments.

Nine Centuries of Man

2017 ◽  
Keyword(s):  
Twentieth Century ◽  
Diverse Range ◽  
Gender Expectations ◽  
Court Records ◽  
The Past ◽  
Wide Range ◽  
Police Reports ◽  
Late Twentieth ◽  
Scottish History ◽  
Late Twentieth Century

What did it mean to be a man in Scotland over the past nine centuries? Scotland, with its stereotypes of the kilted warrior and the industrial ‘hard man’, has long been characterised in masculine terms, but there has been little historical exploration of masculinity in a wider context. This interdisciplinary collection examines a diverse range of the multiple and changing forms of masculinities from the late eleventh to the late twentieth century, exploring the ways in which Scottish society through the ages defined expectations for men and their behaviour. How men reacted to those expectations is examined through sources such as documentary materials, medieval seals, romances, poetry, begging letters, police reports and court records, charity records, oral histories and personal correspondence. Focusing upon the wide range of activities and roles undertaken by men – work, fatherhood and play, violence and war, sex and commerce – the book also illustrates the range of masculinities that affected or were internalised by men. Together, the chapters illustrate some of the ways Scotland’s gender expectations have changed over the centuries and how, more generally, masculinities have informed the path of Scottish history

Diversity and Integration in Private International Law

2019 ◽  
Keyword(s):  
South America ◽  
International Law ◽  
Value Systems ◽  
Private International Law ◽  
Diverse Range ◽  
Cross Border ◽  
Wide Range ◽  
Depth Analysis ◽  
And Shifts ◽  
Substantive Law

This book opens a cross-regional dialogue and shifts the Eurocentric discussion on diversity and integration to a more inclusive engagement with South America in private international law issues. It promotes a contemporary vision of private international law as a discipline enabling legal interconnectivity, with the potential to transcend its disciplinary boundaries to further promote the reality of cross-border integration, with its focus on the ever-increasing cross-border mobility of individuals. Private international law embraces legal diversity and pluralism. Different legal traditions continue to meet, interact and integrate in different forms, at the national, regional and international levels. Different systems of substantive law couple with divergent systems of private international law (designed to accommodate the former in cross-border situations). This complex legal landscape impacts individuals and families in cross-border scenarios, and international commerce broadly conceived. Private international law methodologies and techniques offer means for the coordination of this constellation of legal orders and value systems in cross-border situations. Bringing together world-renowned academics and experienced private international lawyers from a wide range of jurisdictions in Europe and South America, this edited collection focuses on the connective capabilities of private international law in bridging and balancing legal diversity as a corollary for the development of integration. The book provides in-depth analysis of the role of private international law in dealing with legal diversity across a diverse range of topics and jurisdictions.

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