scholarly journals A pan-plant protein complex map reveals deep conservation and novel assemblies

2019 ◽  
Author(s):  
Claire D. McWhite ◽  
Ophelia Papoulas ◽  
Kevin Drew ◽  
Rachael M. Cox ◽  
Viviana June ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Green Plant ◽  
Plant Evolution ◽  
Economic Systems ◽  
Plant Proteins ◽  
Protein Assemblies ◽  
Uncharacterized Protein ◽  
Protein Functions ◽  
Novel Interactions ◽  
Mutant Phenotypes

SUMMARYPlants are foundational to global ecological and economic systems, yet most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. Using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified novel interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical to agriculture. We also uncovered plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers the first cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.

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.

Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging

Science ◽  
2013 ◽  
Vol 341 (6146) ◽  
pp. 655-658 ◽  
Author(s):  
Anna Szymborska ◽  
Alex de Marco ◽  
Nathalie Daigle ◽  
Volker C. Cordes ◽  
John A. G. Briggs ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Super Resolution ◽  
Molecular Organization ◽  
Nuclear Pore ◽  
Protein Assemblies ◽  
Large Protein ◽  
Whole Cells ◽  
Molecular Machinery ◽  
Scaffold Structure ◽  
Super Resolution Microscopy

Much of life’s essential molecular machinery consists of large protein assemblies that currently pose challenges for structure determination. A prominent example is the nuclear pore complex (NPC), for which the organization of its individual components remains unknown. By combining stochastic super-resolution microscopy, to directly resolve the ringlike structure of the NPC, with single particle averaging, to use information from thousands of pores, we determined the average positions of fluorescent molecular labels in the NPC with a precision well below 1 nanometer. Applying this approach systematically to the largest building block of the NPC, the Nup107-160 subcomplex, we assessed the structure of the NPC scaffold. Thus, light microscopy can be used to study the molecular organization of large protein complexes in situ in whole cells.

scholarly journals Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution

Nature ◽  
2000 ◽  
Vol 403 (6770) ◽  
pp. 649-652 ◽  
Author(s):  
Claude Lemieux ◽  
Christian Otis ◽  
Monique Turmel
Keyword(s):  
Chloroplast Genome ◽  
Green Plant ◽  
Plant Evolution

scholarly journals Expression of Polarity Genes in Human Cancer

2015 ◽  
Vol 14s3 ◽  
pp. CIN.S18964 ◽  
Author(s):  
Wan-Hsin Lin ◽  
Yan W. Asmann ◽  
Panos Z. Anastasiadis
Keyword(s):  
Protein Complexes ◽  
Human Cancer ◽  
Expression Profiles ◽  
Tumor Formation ◽  
Model Systems ◽  
Epithelial Homeostasis ◽  
Directed Cell Migration ◽  
Protein Functions ◽  
Cancer Types ◽  
Polarity Proteins

Polarity protein complexes are crucial for epithelial apical-basal polarity and directed cell migration. Since alterations of these processes are common in cancer, polarity proteins have been proposed to function as tumor suppressors or oncogenic promoters. Here, we review the current understanding of polarity protein functions in epithelial homeostasis, as well as tumor formation and progression. As most previous studies focused on the function of single polarity proteins in simplified model systems, we used a genomics approach to systematically examine and identify the expression profiles of polarity genes in human cancer. The expression profiles of polarity genes were distinct in different human tissues and classified cancer types. Additionally, polarity expression profiles correlated with disease progression and aggressiveness, as well as with identified cancer types, where specific polarity genes were commonly altered. In the case of Scribble, gene expression analysis indicated its common amplification and upregulation in human cancer, suggesting a tumor promoting function.

scholarly journals A Protein Interaction Map of the Mitotic Spindle

2007 ◽  
Vol 18 (10) ◽  
pp. 3800-3809 ◽  
Author(s):  
Jonathan Wong ◽  
Yuko Nakajima ◽  
Stefan Westermann ◽  
Ching Shang ◽  
Jung-seog Kang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Interactions ◽  
Mitotic Spindle ◽  
Phosphorylation Site ◽  
Protein Functions ◽  
Regulation Mechanisms ◽  
Novel Interactions ◽  
Interaction Map ◽  
Spindle Function ◽  
Two Hybrid

The mitotic spindle consists of a complex network of proteins that segregates chromosomes in eukaryotes. To strengthen our understanding of the molecular composition, organization, and regulation of the mitotic spindle, we performed a system-wide two-hybrid screen on 94 proteins implicated in spindle function in Saccharomyces cerevisiae. We report 604 predominantly novel interactions that were detected in multiple screens, involving 303 distinct prey proteins. We uncovered a pattern of extensive interactions between spindle proteins reflecting the intricate organization of the spindle. Furthermore, we observed novel connections between kinetochore complexes and chromatin-modifying proteins and used phosphorylation site mutants of NDC80/TID3 to gain insights into possible phospho-regulation mechanisms. We also present analyses of She1p, a novel spindle protein that interacts with the Dam1 kinetochore/spindle complex. The wealth of protein interactions presented here highlights the extent to which mitotic spindle protein functions and regulation are integrated with each other and with other cellular activities.

scholarly journals Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

2016 ◽  
Author(s):  
Morgan N. Price ◽  
Kelly M. Wetmore ◽  
R. Jordan Waters ◽  
Mark Callaghan ◽  
Jayashree Ray ◽  
...  
Keyword(s):  
Protein Function ◽  
Large Scale ◽  
Hypothetical Proteins ◽  
Data Set ◽  
Protein Coding ◽  
Bacterial Proteins ◽  
Genome Wide ◽  
Protein Functions ◽  
Mutant Phenotypes ◽  
Related Proteins

SummaryThe function of nearly half of all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions of these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and we assayed mutant phenotypes across hundreds of distinct conditions. From 3,903 genome-wide mutant fitness assays, we obtained 14.9 million gene phenotype measurements and we identified a mutant phenotype for 8,487 proteins with previously unknown functions. The majority of these hypothetical proteins (57%) had phenotypes that were either specific to a few conditions or were similar to that of another gene, thus enabling us to make informed predictions of protein function. For 1,914 of these hypothetical proteins, the functional associations are conserved across related proteins from different bacteria, which confirms that these associations are genuine. This comprehensive catalogue of experimentally-annotated protein functions also enables the targeted exploration of specific biological processes. For example, sensitivity to a DNA-damaging agent revealed 28 known families of DNA repair proteins and 11 putative novel families. Across all sequenced bacteria, 14% of proteins that lack detailed annotations have an ortholog with a functional association in our data set. Our study demonstrates the utility and scalability of high-throughput genetics for large-scale annotation of bacterial proteins and provides a vast compendium of experimentally-determined protein functions across diverse bacteria.

scholarly journals Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

2021 ◽  
Author(s):  
Tim Neijenhuis ◽  
Siri C. van Keulen ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Protein Complexes ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Protein Interfaces ◽  
Density Maps ◽  
Medium Resolution ◽  
Wide Range ◽  
Multimeric Protein

A wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.

scholarly journals Complex+: Aided Decision-Making for the Study of Protein Complexes

2019 ◽  
Author(s):  
Mehrnoosh Oghbaie ◽  
Petr Šulc ◽  
David Fenyö ◽  
Michael Pennock ◽  
John LaCava
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Cell Biology ◽  
Protein Complexes ◽  
Conclusive Evidence ◽  
Computational Techniques ◽  
Protein Assemblies ◽  
Data Types ◽  
Research Strategies ◽  
Protein Interactome

AbstractProteins are the chief effectors of cell biology and their functions are typically carried out in the context of multi-protein assemblies; large collections of such interacting protein assemblies are often referred to as interactomes. Knowing the constituents of protein complexes is therefore important for investigating their molecular biology. Many experimental methods are capable of producing data of use for detecting and inferring the existence of physiological protein complexes. Each method has associated pros and cons, affecting the potential quality and utility of the data. Numerous informatic resources exist for the curation, integration, retrieval, and processing of protein interactions data. While each resource may possess different merits, none are definitive and few are wieldy, potentially limiting their effective use by non-experts. In addition, contemporary analyses suggest that we may still be decades away from a comprehensive map of a human protein interactome. Taken together, we are currently unable to maximally impact and improve biomedicine from a protein interactome perspective – motivating the development of experimental and computational techniques that help investigators to address these limitations. Here, we present a resource intended to assist investigators in (i) navigating the cumulative knowledge concerning protein complexes and (ii) forming hypotheses concerning protein interactions that may yet lack conclusive evidence, thus (iii) directing future experiments to address knowledge gaps. To achieve this, we integrated multiple data-types/different properties of protein interactions from multiple sources and after applying various methods of regularization, compared the protein interaction networks computed to those available in the EMBL-EBI Complex Portal, a manually curated, gold-standard catalog of macromolecular complexes. As a result, our resource provides investigators with reliable curation of bona fide and candidate physical interactors of their protein or complex of interest, prompting due scrutiny and further validation when needed. We believe this information will empower a wider range of experimentalists to conduct focused protein interaction studies and to better select research strategies that explicitly target missing information.

scholarly journals Annotating precision for integrative structural models using deep learning

2021 ◽  
Author(s):  
Nikhil Kasukurthi ◽  
Shruthi Viswanath
Keyword(s):  
Deep Learning ◽  
High Precision ◽  
Protein Complexes ◽  
Source Code ◽  
Structural Models ◽  
Protein Assemblies ◽  
Large Protein ◽  
Single Precision ◽  
Input Information ◽  
Gradient Based

Motivation: Integrative modeling of macromolecular structures usually results in an ensemble of models that satisfy the input information. The model precision, or variability among these models is estimated globally, i.e., a single precision value is reported for the model. However, it would be useful to identify regions of high and low precision. For instance, low-precision regions can suggest where the next experiments could be performed and high-precision regions can be used for further analysis, e.g., suggesting mutations. Results: We develop PrISM (Precision for Integrative Structural Models), using autoencoders to efficiently and accurately annotate precision for integrative models. The method is benchmarked and tested on five examples of binary protein complexes and five examples of large protein assemblies. The annotated precision is shown to be consistent with, and more informative than localization densities. The generated networks are also interpreted by gradient-based attention analysis. Availability: Source code is at https://github.com/isblab/prism.

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