scholarly journals The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

2021 ◽  
Author(s):  
Akanksha Pandey ◽  
Edward L. Braun
Keyword(s):  
Protein Structure ◽  
Protein Structures ◽  
Tree Of Life ◽  
Model Complexity ◽  
Gene Trees ◽  
Accurate Picture ◽  
History Of ◽  
Optimal Tree ◽  
Standard Tree

Despite the long history of using protein sequences to infer the tree of life the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure; we test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1,500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology (ctenophores sister to other animals) regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments; buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies whereas solvent exposed and helix sites had unequal numbers of sites supporting the minority topologies. Given the plausible trees equal support for minority topologies is consistent with discordance among gene trees, making it possible the relatively slowly evolving buried (and sheet and coil) sites are giving an accurate picture of the true species tree as well as the amount of conflict among gene trees. Alternatively, the apparent support could reflect currently uncharacterized processes of molecular evolution. Regardless, it is clear that analyses of the deepest branches in the animal tree of life using sites in different structural environments are associated with a subtle data type effect that results in distinct phylogenetic signals.

scholarly journals The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences

Biophysica ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 87-105
Author(s):  
Akanksha Pandey ◽  
Edward L. Braun
Keyword(s):  
Protein Structure ◽  
Phylogenetic Analyses ◽  
Protein Structures ◽  
Tree Of Life ◽  
Model Complexity ◽  
Gene Trees ◽  
Accurate Picture ◽  
History Of ◽  
Phylogenomic Analyses ◽  
Standard Tree

Despite the long history of using protein sequences to infer the tree of life, the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure. We test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments: buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies, whereas solvent-exposed and helix sites had unequal numbers of sites, supporting the minority topologies. This suggests that the relatively slowly evolving buried, sheet, and coil sites are giving an accurate picture of the true species tree and the amount of conflict among gene trees. Taken as a whole, this study indicates that phylogenetic analyses using sites in different structural environments can yield different topologies for the deepest branches in the animal tree of life and that analyzing larger numbers of taxa eliminates this conflict. More broadly, our results highlight the desirability of incorporating information about protein structure into phylogenomic analyses.

scholarly journals DeepPSC (protein structure camera): computer vision-based protein backbone structure reconstruction from alpha carbon trace as a case study

2020 ◽  
Author(s):  
Xing Zhang ◽  
Junwen Luo ◽  
Yi Cai ◽  
Wei Zhu ◽  
Xiaofeng Yang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Protein Backbone ◽  
Protein Tertiary Structure ◽  
Structure Information ◽  
Alpha Carbon

AbstractDeep learning has been increasingly used in protein tertiary structure prediction, a major goal in life science. However, all the algorithms developed so far mostly use protein sequences as input, whereas the vast amount of protein tertiary structure information available in the Protein Data Bank (PDB) database remains largely unused, because of the inherent complexity of 3D data computation. In this study, we propose Protein Structure Camera (PSC) as an approach to convert protein structures into images. As a case study, we developed a deep learning method incorporating PSC (DeepPSC) to reconstruct protein backbone structures from alpha carbon traces. DeepPSC outperformed all the methods currently available for this task. This PSC approach provides a useful tool for protein structure representation, and for the application of deep learning in protein structure prediction and protein engineering.

scholarly journals Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

2021 ◽  
Vol 8 ◽  
Author(s):  
Nicola Bordin ◽  
Ian Sillitoe ◽  
Jonathan G. Lees ◽  
Christine Orengo
Keyword(s):  
Protein Structure ◽  
Function Space ◽  
Sequence Data ◽  
Protein Structures ◽  
Structure And Function ◽  
Structure Evolution ◽  
Structural Classification ◽  
Protein Sequence Data ◽  
History Of ◽  
And Function

This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.

Sequence Specific Dihedral Angle Distribution: Application in Protein Structure Prediction and Evaluation

1970 ◽  
Vol 19 (2) ◽  
pp. 217-226
Author(s):  
S. M. Minhaz Ud-Dean ◽  
Mahdi Muhammad Moosa
Keyword(s):  
Protein Structure ◽  
Dihedral Angle ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Protein Structures ◽  
Angle Distribution ◽  
Ramachandran Plot ◽  
Specific Data ◽  
Specific Distribution ◽  
Structure Evaluation

Protein structure prediction and evaluation is one of the major fields of computational biology. Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. Additionally, it will allow retrieval of the most probable Ramachandran angles for a given sequence along with the sequence specific data. Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. & Biotech. 19(2): 217-226, 2009 (December)

Press Propaganda and Subaltern Agents of Pan-Islamic Networks in the Muslim Mediterranean World prior to World War I

2018 ◽  
Author(s):  
Odile Moreau
Keyword(s):  
Middle East ◽  
World War I ◽  
North Africa ◽  
World War ◽  
Subaltern Studies ◽  
Resistance Movements ◽  
The Press ◽  
Mediterranean World ◽  
History Of

This chapter explores movement and circulation across the Mediterranean and seeks to contribute to a history of proto-nationalism in the Maghrib and the Middle East at a particular moment prior to World War I. The discussion is particularly concerned with the interface of two Mediterranean spaces: the Middle East (Egypt, Ottoman Empire) and North Africa (Morocco), where the latter is viewed as a case study where resistance movements sought external allies as a way of compensating for their internal weakness. Applying methods developed by Subaltern Studies, and linking macro-historical approaches, namely of a translocal movement in the Muslim Mediterranean, it explores how the Egypt-based society, al-Ittihad al-Maghribi, through its agent, Aref Taher, used the press as an instrument for political propaganda, promoting its Pan-Islamic programme and its goal of uniting North Africa.

Turning Aliens into Socialists

2010 ◽  
Vol 1 (1) ◽  
pp. 75-93
Author(s):  
Jessica Moberg
Keyword(s):  
Outer Space ◽  
The United States ◽  
Second World War ◽  
World War ◽  
History Of ◽  
Swedish History ◽  
Second World ◽  
The Universe ◽  
Highly Evolved

Immediately after the Second World War Sweden was struck by a wave of sightings of strange flying objects. In some cases these mass sightings resulted in panic, particularly after authorities failed to identify them. Decades later, these phenomena were interpreted by two members of the Swedish UFO movement, Erland Sandqvist and Gösta Rehn, as alien spaceships, or UFOs. Rehn argued that ‘[t]here is nothing so dramatic in the Swedish history of UFOs as this invasion of alien fly-things’ (Rehn 1969: 50). In this article the interpretation of such sightings proposed by these authors, namely that we are visited by extraterrestrials from outer space, is approached from the perspective of myth theory. According to this mythical theme, not only are we are not alone in the universe, but also the history of humankind has been shaped by encounters with more highly-evolved alien beings. In their modern day form, these kinds of ideas about aliens and UFOs originated in the United States. The reasoning of Sandqvist and Rehn exemplifies the localization process that took place as members of the Swedish UFO movement began to produce their own narratives about aliens and UFOs. The question I will address is: in what ways do these stories change in new contexts? Texts produced by the Swedish UFO movement are analyzed as a case study of this process.

A Case Study on the Process of Creating Interests in History of History-Deokhu

2019 ◽  
Vol 58 (1) ◽  
pp. 147-159
Author(s):  
Young-Seok Seo ◽  
Bong-Seok Kim
Keyword(s):  
History Of

Analysis of Oncogene Protein Structure Using Small World Network Concept

2020 ◽  
Vol 15 (7) ◽  
pp. 732-740
Author(s):  
Neetu Kumari ◽  
Anshul Verma
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
Degree Distribution ◽  
Protein Structures ◽  
Small World ◽  
Extreme Condition ◽  
Centrality Measures ◽  
Small World Network ◽  
Network Concept ◽  
Oncogene Protein

Background: The basic building block of a body is protein which is a complex system whose structure plays a key role in activation, catalysis, messaging and disease states. Therefore, careful investigation of protein structure is necessary for the diagnosis of diseases and for the drug designing. Protein structures are described at their different levels of complexity: primary (chain), secondary (helical), tertiary (3D), and quaternary structure. Analyzing complex 3D structure of protein is a difficult task but it can be analyzed as a network of interconnection between its component, where amino acids are considered as nodes and interconnection between them are edges. Objective: Many literature works have proven that the small world network concept provides many new opportunities to investigate network of biological systems. The objective of this paper is analyzing the protein structure using small world concept. Methods: Protein is analyzed using small world network concept, specifically where extreme condition is having a degree distribution which follows power law. For the correct verification of the proposed approach, dataset of the Oncogene protein structure is analyzed using Python programming. Results: Protein structure is plotted as network of amino acids (Residue Interaction Graph (RIG)) using distance matrix of nodes with given threshold, then various centrality measures (i.e., degree distribution, Degree-Betweenness correlation, and Betweenness-Closeness correlation) are calculated for 1323 nodes and graphs are plotted. Conclusion: Ultimately, it is concluded that there exist hubs with higher centrality degree but less in number, and they are expected to be robust toward harmful effects of mutations with new functions.

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