Learning Protein Functions from Bi-relational Graph of Proteins and Function Annotations

2011 ◽  
pp. 128-138 ◽  
Author(s):  
Jonathan Qiang Jiang
Keyword(s):  
Protein Functions ◽  
And Function

Chaperonin as the normal controls and pathological anti-stress response in the human reproductive system

2016 ◽  
pp. 126-129
Author(s):  
M. Makarenko ◽  
◽  
D. Hovsyeyev ◽  
L. Sydoryk ◽  
◽  
...  
Keyword(s):  
Reproductive System ◽  
Stress Proteins ◽  
Physiological Stress ◽  
Protein Complexes ◽  
Reproductive Function ◽  
Intercellular Signaling ◽  
Toll Like Receptors ◽  
Wide Range ◽  
Protein Functions ◽  
And Function

Different kinds of physiological stress cause mass changes in the cells, including the changes in the structure and function of the protein complexes and in separate molecules. The protein functions is determined by its folding (the spatial conclusion), which depends on the functioning of proteins of thermal shock- molecular chaperons (HSPs) or depends on the stress proteins, that are high-conservative; specialized proteins that are responsible for the correct proteinaceous folding. The family of the molecular chaperones/ chaperonins/ Hsp60 has a special place due to the its unique properties of activating the signaling cascades through the system of Toll-like receptors; it also stimulates the cells to produce anti- inflammatory cytokines, defensins, molecules of cell adhesion and the molecules of MHC; it functions as the intercellular signaling molecule. The pathological role of Hsp60 is established in a wide range of illnesses, from diabetes to atherosclerosis, where Hsp60 takes part in the regulation of both apoptosis and the autoimmune processes. The presence of the HSPs was found in different tissues that are related to the reproductive system. Key words: molecular chaperons (HSPs), Toll-like receptors, reproductive function, natural auto antibody.

A class act: conservation of homeodomain protein functions

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 61-77 ◽  
Author(s):  
J. Robert Manak ◽  
Matthew P. Scott
Keyword(s):  
Gene Function ◽  
Target Genes ◽  
Hox Genes ◽  
Homeobox Gene ◽  
Homeodomain Protein ◽  
Animal Development ◽  
Protein Functions ◽  
Unified View ◽  
Protein Classes ◽  
And Function

Dramatic successes in identifying vertebrate homeobox genes closely related to their insect relatives have led to the recognition of classes within the homeodomain superfamily. To what extent are the homeodomain protein classes dedicated to specific functions during development? Although information on vertebrate gene functions is limited, existing evidence from mice and nematodes clearly supports conservation of function for the Hox genes. Less compelling, but still remarkable, is the conservation of other homeobox gene classes and of regulators of homeotic gene expression and function. It is too soon to say whether the cases of conservation are unique and exceptional, or the beginning of a profoundly unified view of gene regulation in animal development. In any case, new questions are raised by the data: how can the differences between mammals and insects be compatible with conservation of homeobox gene function? Did the evolution of animal form involve a proliferation of new homeodomain proteins, new modes of regulation of existing gene types, or new relationships with target genes, or is evolutionary change largely the province of other classes of genes? In this review, we summarize what is known about conservation of homeobox gene function.

Determinants of Drosophila zw10 protein localization and function

1994 ◽  
Vol 107 (4) ◽  
pp. 785-798 ◽  
Author(s):  
B.C. Williams ◽  
M.L. Goldberg
Keyword(s):  
Chromosome Segregation ◽  
Sister Chromatid ◽  
Protein Localization ◽  
Metaphase Plate ◽  
Obvious Effect ◽  
Anaphase Onset ◽  
Protein Functions ◽  
Kinetochore Region ◽  
And Function ◽  
Feedback Pathway

We have examined several issues concerning how the Drosophila l(1)zw10 gene product functions to ensure proper chromosome segregation. (a) We have found that in zw10 mutant embryos and larval neuroblasts, absence of the zw10 protein has no obvious effect on either the congression of chromosomes to the metaphase plate or the morphology of the metaphase spindle, although many aberrations are observed subsequently in anaphase. This suggests that activity of the zw10 protein becomes essential at anaphase onset, a time at which the zw10 protein is redistributed to the kinetochore region of the chromosomes. (b) The zw10 protein appears to bind to kinetochores in mitotically arrested cells, eventually accumulating to high levels within the chromosome mass. Our results imply that zw10 may act as part of a novel feedback pathway that normally renders sister chromatid separation dependent upon spindle integrity. (c) The localization of zw10 protein is altered by two mitotic mutations, rough deal and abnormal anaphase resolution, that specifically disrupt anaphase. These findings indicate that the zw10 protein functions as part of a multicomponent mechanism ensuring proper chromosome segregation at the beginning of anaphase.

scholarly journals Posttranslational modifications in proteins: resources, tools and prediction methods

Database ◽  
2021 ◽  
Author(s):  
Shahin Ramazi ◽  
Javad Zahiri
Keyword(s):  
Computational Methods ◽  
Posttranslational Modifications ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Cellular Processes ◽  
Online Databases ◽  
Different Types ◽  
Protein Functions ◽  
And Function ◽  
Molecular Regulatory Mechanisms

Abstract Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.

scholarly journals Luminidependens (LD) is an Arabidopsis protein with prion behavior

2016 ◽  
Vol 113 (21) ◽  
pp. 6065-6070 ◽  
Author(s):  
Sohini Chakrabortee ◽  
Can Kayatekin ◽  
Greg A. Newby ◽  
Marc L. Mendillo ◽  
Alex Lancaster ◽  
...  
Keyword(s):  
Protein Conformation ◽  
Prion Proteins ◽  
Higher Order ◽  
Biological Processes ◽  
Yeast Prion ◽  
Yeast Prions ◽  
Arabidopsis Protein ◽  
Evolutionarily Conserved ◽  
Protein Functions ◽  
And Function

Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified candidate prion domains (PrDs) in nearly 500 plant proteins. Plant flowering is of particular interest with respect to biological memory, because its regulation involves remembering and integrating previously experienced environmental conditions. We investigated the prion-forming capacity of three prion candidates involved in flowering using a yeast model, where prion attributes are well defined and readily tested. In yeast, prions heritably change protein functions by templating monomers into higher-order assemblies. For most yeast prions, the capacity to convert into a prion resides in a distinct prion domain. Thus, new prion-forming domains can be identified by functional complementation of a known prion domain. The prion-like domains (PrDs) of all three of the tested proteins formed higher-order oligomers. Uniquely, the Luminidependens PrD (LDPrD) fully replaced the prion-domain functions of a well-characterized yeast prion, Sup35. Our results suggest that prion-like conformational switches are evolutionarily conserved and might function in a wide variety of normal biological processes.

scholarly journals Kinesin and Dynein Mechanics: Measurement Methods and Research Applications

2018 ◽  
Vol 140 (2) ◽  
Author(s):  
Zachary Abraham ◽  
Emma Hawley ◽  
Daniel Hayosh ◽  
Victoria A. Webster-Wood ◽  
Ozan Akkus
Keyword(s):  
Protein Function ◽  
Motor Proteins ◽  
Motor Protein ◽  
Clinical Importance ◽  
Magnetic Tweezers ◽  
Normal Function ◽  
Proper Function ◽  
Protein Functions ◽  
And Function ◽  
Shed Light

Motor proteins play critical roles in the normal function of cells and proper development of organisms. Among motor proteins, failings in the normal function of two types of proteins, kinesin and dynein, have been shown to lead many pathologies, including neurodegenerative diseases and cancers. As such, it is critical to researchers to understand the underlying mechanics and behaviors of these proteins, not only to shed light on how failures may lead to disease, but also to guide research toward novel treatment and nano-engineering solutions. To this end, many experimental techniques have been developed to measure the force and motility capabilities of these proteins. This review will (a) discuss such techniques, specifically microscopy, atomic force microscopy (AFM), optical trapping, and magnetic tweezers, and (b) the resulting nanomechanical properties of motor protein functions such as stalling force, velocity, and dependence on adenosine triphosophate (ATP) concentrations will be comparatively discussed. Additionally, this review will highlight the clinical importance of these proteins. Furthermore, as the understanding of the structure and function of motor proteins improves, novel applications are emerging in the field. Specifically, researchers have begun to modify the structure of existing proteins, thereby engineering novel elements to alter and improve native motor protein function, or even allow the motor proteins to perform entirely new tasks as parts of nanomachines. Kinesin and dynein are vital elements for the proper function of cells. While many exciting experiments have shed light on their function, mechanics, and applications, additional research is needed to completely understand their behavior.

scholarly journals SAXS, WAXS, MD, Protein fluctuations and function

2014 ◽  
Vol 70 (a1) ◽  
pp. C406-C406
Author(s):  
Lee Makowski ◽  
Hao Zhou ◽  
Yu Jing Wang
Keyword(s):  
Deep Understanding ◽  
Single Amino Acid ◽  
Small Molecule Ligands ◽  
Protein Functions ◽  
Functional Consequences ◽  
Structural Fluctuations ◽  
And Function ◽  
Intramolecular Motions ◽  
Flexibility Parameters ◽  
Protein Fluctuations

Conformational mobility is essential to many protein functions and design of therapies for a broad spectrum of human diseases depends on a deep understanding the linkage between protein structure, intramolecular motions and function. Methods for screening small molecules and mutations that alter fluctuations are essential for improved understanding of this linkage. To what extent do changes in intramolecular motions lead to changes in function? To address this question, we are using a combination of wide-angle x-ray solution scattering (WAXS) and molecular dynamics (MD) to generate novel insights into the magnitude, form and functional consequences of intramolecular motions of proteins in solution. WAXS has proven unexpectedly sensitive to the intramolecular motions of proteins in solution and can detect changes in flexibility generated by single amino acid replacements or binding of small molecule ligands. Here we formulate the effect of structural fluctuations on WAXS data in such a way as to make possible direct experimental assessment of the range of motion that proteins explore in solution. The approach differs from other strategies by treating it as an inverse source problem, deriving flexibility parameters directly from data rather than from an ensemble of structures generated to predict the data.

scholarly journals MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics

2019 ◽  
Author(s):  
Kai Cheng ◽  
Zhibin Ning ◽  
Xu Zhang ◽  
Leyuan Li ◽  
Bo Liao ◽  
...  
Keyword(s):  
Data Analysis ◽  
Microbial Communities ◽  
Search Strategy ◽  
Structure And Function ◽  
Research Field ◽  
Human Gut ◽  
Post Translational Modifications ◽  
Protein Functions ◽  
And Function

AbstractStudying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.

scholarly journals Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Differences in Protein Structure and Function among Stylophora Lineages from Contrasting Environments

2019 ◽  
Author(s):  
Eulalia Banguera-Hinestroza ◽  
Yvonne Sawall ◽  
Jean-François Flot
Keyword(s):  
Stress Response ◽  
Transmembrane Protein ◽  
Thermal Adaptation ◽  
Cell Surface Receptor ◽  
Reading Frame ◽  
Intrinsically Disordered ◽  
Protein Functions ◽  
Surface Receptor ◽  
Environmental Variations ◽  
And Function

More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae, which turn out to be an effective barcode gene for these corals. However, its function remains unknown. Recently, this gene revealed the existence of a hybrid Stylophora lineage (RS_LinA) inhabiting in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C) with its parental species (RS_LinB). Furthermore, in RS_LinB, the mtORF uncovered phylogeographic patterns that were strongly correlated with environmental variations. This was similar to the patterns unraveled by hsp70, suggesting that mtORF too might be involved in thermal adaptation. Here we used computational approaches to characterize the mtORF and to identify its potential role. Results showed that this gene encodes a transmembrane protein (0.97<P< 1.00) involved in transport (0.80<P< 0.87), regulation of metabolic processes (0.70<P<0.85), and likely in the cell-surface receptor signaling pathway (0.56<P<0.80). Predicted protein functions differed among Stylophora lineages and interestingly, in RS_LinB only, the protein was intrinsically disordered and displayed domains involved in cellular complexes and stress response (0.0001< P <0.001). These characteristics, exclusive of an endemic lineage adapted to extreme environmental fluctuations, support a role of the mtORF in stress response, speciation and adaptation.

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