scholarly journals PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins

Database ◽  
2020 ◽  
Author(s):  
Hiroko X Kondo ◽  
Yusuke Kanematsu ◽  
Gen Masumoto ◽  
Yu Takano
Keyword(s):  
Protein Function ◽  
Heme Proteins ◽  
Structural Data ◽  
Data Bank ◽  
Protein Fold ◽  
Axial Ligands ◽  
Analysis Tools ◽  
Wide Range ◽  
Id Protein ◽  
Analytical Tools

Abstract Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure–function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/

scholarly journals AlphaFold2 transmembrane protein structure prediction shines

2021 ◽  
Author(s):  
Tamas Hegedus ◽  
Markus Geisler ◽  
Gergely Lukacs ◽  
Bianka Farkas
Keyword(s):  
Prescription Drugs ◽  
Protein Function ◽  
Structure Prediction ◽  
Drug Targets ◽  
Transmembrane Protein ◽  
Structural Data ◽  
Data Bank ◽  
Rational Drug Design ◽  
Abc Protein ◽  
Dynamics Simulations

Transmembrane (TM) proteins are major drug targets, indicated by the high percentage of prescription drugs acting on them. For a rational drug design and an understanding of mutational effects on protein function, structural data at atomic resolution are required. However, hydrophobic TM proteins often resist experimental structure determination and in spite of the increasing number of cryo-EM structures, the available TM folds are still limited in the Protein Data Bank. Recently, the DeepMind's AlphaFold2 machine learning method greatly expanded the structural coverage of sequences, with high accuracy. Since the employed algorithm did not take specific properties of TM proteins into account, the validity of the generated TM structures should be assessed. Therefore, we investigated the quality of structures at genome scales, at the level of ABC protein superfamily folds, and also in specific individual cases. We tested template-free structure prediction also with a new TM fold, dimer modeling, and stability in molecular dynamics simulations. Our results strongly suggest that AlphaFold2 performs astoundingly well in the case of TM proteins and that its neural network is not overfitted. We conclude that a careful application of its structural models will advance TM protein associated studies at an unexpected level.

scholarly journals Glycosaminoglycan-Protein Interactions and Their Roles in Human Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Deling Shi ◽  
Anran Sheng ◽  
Lianli Chi
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Human Disease ◽  
Cellular Adhesion ◽  
Human Diseases ◽  
Binding Motif ◽  
Gag Protein ◽  
Characterization Methods ◽  
Wide Range ◽  
Analytical Tools

Glycosaminoglycans (GAGs) are a family of linear and negatively charged polysaccharides that exist ubiquitously on the human cell surface as well as in the extracellular matrix. GAGs interact with a wide range of proteins, including proteases, growth factors, cytokines, chemokines and adhesion molecules, enabling them to mediate many physiological processes, such as protein function, cellular adhesion and signaling. GAG-protein interactions participate in and intervene in a variety of human diseases, including cardiovascular disease, infectious disease, neurodegenerative diseases and tumors. The breakthrough in analytical tools and approaches during the last two decades has facilitated a greater understanding of the importance of GAG-protein interactions and their roles in human diseases. This review focuses on aspects of the molecular basis and mechanisms of GAG-protein interactions involved in human disease. The most recent advances in analytical tools, especially mass spectrometry-based GAG sequencing and binding motif characterization methods, are introduced. An update of selected families of GAG binding proteins is presented. Perspectives on development of novel therapeutics targeting specific GAG-protein interactions are also covered in this review.

scholarly journals Growth Promotion or Osmotic Stress Response: How SNF1-Related Protein Kinase 2 (SnRK2) Kinases Are Activated and Manage Intracellular Signaling in Plants

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1443
Author(s):  
Yoshiaki Kamiyama ◽  
Sotaro Katagiri ◽  
Taishi Umezawa
Keyword(s):  
Protein Kinase ◽  
Plant Growth ◽  
Osmotic Stress ◽  
Protein Function ◽  
Intracellular Signaling ◽  
Growth Promotion ◽  
Research Field ◽  
Dependent Manner ◽  
Related Protein ◽  
Wide Range

Reversible phosphorylation is a major mechanism for regulating protein function and controls a wide range of cellular functions including responses to external stimuli. The plant-specific SNF1-related protein kinase 2s (SnRK2s) function as central regulators of plant growth and development, as well as tolerance to multiple abiotic stresses. Although the activity of SnRK2s is tightly regulated in a phytohormone abscisic acid (ABA)-dependent manner, recent investigations have revealed that SnRK2s can be activated by group B Raf-like protein kinases independently of ABA. Furthermore, evidence is accumulating that SnRK2s modulate plant growth through regulation of target of rapamycin (TOR) signaling. Here, we summarize recent advances in knowledge of how SnRK2s mediate plant growth and osmotic stress signaling and discuss future challenges in this research field.

scholarly journals Gold–Carbon Nanocomposites for Environmental Contaminant Sensing

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 719
Author(s):  
Shahrooz Rahmati ◽  
William Doherty ◽  
Arman Amani Babadi ◽  
Muhamad Syamim Akmal Che Mansor ◽  
Nurhidayatullaili Muhd Julkapli ◽  
...  
Keyword(s):  
Environmental Pollutants ◽  
High Sensitivity ◽  
Environmental Crisis ◽  
World Population ◽  
Chemical Contaminants ◽  
Carbon Nanocomposites ◽  
Minimal Sample ◽  
Wide Range ◽  
And Control ◽  
Analytical Tools

The environmental crisis, due to the rapid growth of the world population and globalisation, is a serious concern of this century. Nanoscience and nanotechnology play an important role in addressing a wide range of environmental issues with innovative and successful solutions. Identification and control of emerging chemical contaminants have received substantial interest in recent years. As a result, there is a need for reliable and rapid analytical tools capable of performing sample analysis with high sensitivity, broad selectivity, desired stability, and minimal sample handling for the detection, degradation, and removal of hazardous contaminants. In this review, various gold–carbon nanocomposites-based sensors/biosensors that have been developed thus far are explored. The electrochemical platforms, synthesis, diverse applications, and effective monitoring of environmental pollutants are investigated comparatively.

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 Open Plot Project: an open-source toolkit for 3-D structural data analysis

Solid Earth ◽  
2011 ◽  
Vol 2 (1) ◽  
pp. 53-63 ◽  
Author(s):  
S. Tavani ◽  
P. Arbues ◽  
M. Snidero ◽  
N. Carrera ◽  
J. A. Muñoz
Keyword(s):  
Spatial Distribution ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Structural Data ◽  
Geological Modelling ◽  
Analysis Tools ◽  
Transect Analysis ◽  
Selection Of

Abstract. In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis. The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software. The software (for both Windows and Linux O.S.), the User Manual, a set of example movies (complementary to the User Manual), and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

scholarly journals Software Tools for Energy Storage Valuation and Design

2021 ◽  
Author(s):  
Tu A. Nguyen ◽  
Raymond H. Byrne
Keyword(s):  
Energy Storage ◽  
Storage Systems ◽  
System Simulation ◽  
Energy Systems ◽  
Software Tools ◽  
Economic Benefits ◽  
Design Tools ◽  
Power System Simulation ◽  
Analysis Tools ◽  
Analytical Tools

Abstract Purpose of Review As the application space for energy storage systems (ESS) grows, it is crucial to valuate the technical and economic benefits of ESS deployments. Since there are many analytical tools in this space, this paper provides a review of these tools to help the audience find the proper tools for their energy storage analyses. Recent Findings There are many software tools for valuating ESS. These tools can be classified into two groups: (1) power system simulation and planning tools for analyzing the technical contributions of ESSs, and (2) techno-economic analysis tools for valuating the economic benefits of ESS deployment and specifying the optimal design of energy systems that include ESSs. While many of the tools, developed by the national laboratories, are free to use, the commercial tools are also of great importance in meeting the customers’ specific needs. Summary This paper provides a review of software tools for ESS valuation and design. A review of analysis tools for evaluating the technical impacts of energy storage deployments is also provided, as well as a discussion of development trends for valuation and design tools.

scholarly journals Protein dynamics revealed by NMR relaxation methods

2018 ◽  
Vol 2 (1) ◽  
pp. 93-105 ◽  
Author(s):  
Fa-An Chao ◽  
R. Andrew Byrd
Keyword(s):  
Protein Dynamics ◽  
Structural Biology ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Relaxation Methods ◽  
Genomic Databases ◽  
Wide Range

Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the worldwide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional co-ordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insights into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.

scholarly journals Towards the Development of Language Analysis Tools for the Written Latgalian Language

2020 ◽  
Author(s):  
Daiga Deksne ◽  
Anna Vulāne
Keyword(s):  
Web Service ◽  
Morphological Analysis ◽  
Written Language ◽  
Analysis Tool ◽  
Tool Development ◽  
Joint Effort ◽  
Analysis Tools ◽  
Language Analysis ◽  
Wide Range ◽  
Development Of Language

This paper reports on the development of spell checking and morphological analysis tools for Latgalian. The Latgalian written language is a historic variant of the Latvian language. There is a wide range of language analysis tools available for Latvian, whereas the Latgalian language lacks such tools. The work is done by the joint effort of linguists who work on morphologically marked lexicon creation and IT specialists who work on language tool development. For the creation of a morphological analysis tool, we reuse the FST technology used for the Latvian morphological analyzer. We create a spelling dictionary that can be used with the Hunspell engine. All tools are accessible via Web Service. For now, the Latgalian lexicon contains 13,139 lemmas marked by 105 inflection groups. The work of lexicon replenishment still continues.

scholarly journals The solution structure of pGolemi, a high affinity Mena EVH1 binding miniature protein, suggests explanations for paralog-specific binding to Ena/VASP homology (EVH) 1 domains

2009 ◽  
Vol 390 (5/6) ◽  
Author(s):  
Nina M. Link ◽  
Cornelia Hunke ◽  
Jonathan W. Mueller ◽  
Jutta Eichler ◽  
Peter Bayer
Keyword(s):  
Solution Structure ◽  
Specific Binding ◽  
Transmembrane Protein ◽  
Structural Data ◽  
Adaptor Proteins ◽  
Axonal Guidance ◽  
High Affinity ◽  
Binding Domains ◽  
Wide Range ◽  
Pancreatic Peptide

Abstract Ena/VASP homology 1 (EVH1) domains are polyproline binding domains that are present in a wide range of adaptor proteins, among them Ena/VASP proteins involved in actin remodeling and axonal guidance. The interaction of ActA, a transmembrane protein from the food-borne pathogen Listeria monocytogenes, with EVH1 domains has been shown to be crucial for recruitment of the host's actin skeleton and, as a consequence, for the infectivity of this bacterium. We present the structure of a synthetic high-affinity Mena EVH1 ligand, pGolemi, capable of paralog-specific binding, solved by NMR spectroscopy. This peptide shares the common pancreatic peptide fold with its scaffold, avian pancreatic peptide, but shows pivotal differences in the amino-terminus. The interplay of spatial fixation and flexibility appears to be the reason for its high affinity towards Mena EVH1. Combined with earlier investigations, our structural data shed light on the specificity determinants of pGolemi and the importance of additional binding epitopes around the residues Thr74 and Phe32 on EVH1 domains regulating paralog specificity. Our results are expected to facilitate the design of other high-affinity, paralog-specific EVH1 domain ligands, and serve as a fundament for the investigation of the molecular mode of action of EVH1 domains.

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