scholarly journals NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains

2020 ◽  
Vol 21 (15) ◽  
pp. 5351
Author(s):  
Methanee Hiranyakorn ◽  
Saeko Yanaka ◽  
Tadashi Satoh ◽  
Thunchanok Wilasri ◽  
Benchawan Jityuti ◽  
...  
Keyword(s):  
Isotope Labeling ◽  
Hydrophobic Surface ◽  
Enzymatic Reactions ◽  
Multidomain Proteins ◽  
Solvent Exposure ◽  
Hydrophobic Surfaces ◽  
Cellular Processes ◽  
Nmr Characterization

Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins.

scholarly journals A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1

2021 ◽  
Vol 22 (14) ◽  
pp. 7390
Author(s):  
Nicole Wesch ◽  
Frank Löhr ◽  
Natalia Rogova ◽  
Volker Dötsch ◽  
Vladimir V. Rogov
Keyword(s):  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Biochemical Characterization ◽  
Effective Interaction ◽  
Regulatory Region ◽  
Titration Calorimetry ◽  
Enzymatic Reactions ◽  
Cellular Processes ◽  
Mechanism Of Interaction

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.

scholarly journals Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control

2014 ◽  
Vol 207 (4) ◽  
pp. 463-480 ◽  
Author(s):  
Jonathan Bizarro ◽  
Christophe Charron ◽  
Séverine Boulon ◽  
Belinda Westman ◽  
Bérengère Pradet-Balade ◽  
...  
Keyword(s):  
Isotope Labeling ◽  
Core Protein ◽  
3D Structure ◽  
Assembly Mechanism ◽  
Core Proteins ◽  
Assembly Factors ◽  
Assembly Factor

In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90–R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA+ adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs.

Characterization of secretomes from a human blood brain barrier endothelial cells in-vitro model after ischemia by stable isotope labeling with aminoacids in cell culture (SILAC)

2016 ◽  
Vol 133 ◽  
pp. 100-112 ◽  
Author(s):  
Victor Llombart ◽  
Teresa García-Berrocoso ◽  
Joan Josep Bech-Serra ◽  
Alba Simats ◽  
Alejandro Bustamante ◽  
...  
Keyword(s):  
Cell Culture ◽  
Endothelial Cells ◽  
Stable Isotope ◽  
Blood Brain Barrier ◽  
Human Blood ◽  
In Vitro Model ◽  
Isotope Labeling ◽  
Vitro Model

scholarly journals Adsorption of unfolded Cu/Zn superoxide dismutase onto hydrophobic surfaces catalyzes its formation of amyloid fibrils

2019 ◽  
Vol 32 (2) ◽  
pp. 77-85
Author(s):  
Mohammad Ashhar I Khan ◽  
Ulrich Weininger ◽  
Sven Kjellström ◽  
Shashank Deep ◽  
Mikael Akke
Keyword(s):  
Superoxide Dismutase ◽  
Surface Area ◽  
Amyloid Fibrils ◽  
Hydrophobic Surface ◽  
Fibril Formation ◽  
Hydrophobic Surfaces ◽  
Molecular Features ◽  
Denaturant Concentration

Abstract Intracellular aggregates of superoxide dismutase 1 (SOD1) are associated with amyotrophic lateral sclerosis. In vivo, aggregation occurs in a complex and dense molecular environment with chemically heterogeneous surfaces. To investigate how SOD1 fibril formation is affected by surfaces, we used an in vitro model system enabling us to vary the molecular features of both SOD1 and the surfaces, as well as the surface area. We compared fibril formation in hydrophilic and hydrophobic sample wells, as a function of denaturant concentration and extraneous hydrophobic surface area. In the presence of hydrophobic surfaces, SOD1 unfolding promotes fibril nucleation. By contrast, in the presence of hydrophilic surfaces, increasing denaturant concentration retards the onset of fibril formation. We conclude that the mechanism of fibril formation depends on the surrounding surfaces and that the nucleating species might correspond to different conformational states of SOD1 depending on the nature of these surfaces.

scholarly journals Watching cellular machinery in action, one molecule at a time

2016 ◽  
Vol 216 (1) ◽  
pp. 41-51 ◽  
Author(s):  
Enrico Monachino ◽  
Lisanne M. Spenkelink ◽  
Antoine M. van Oijen
Keyword(s):  
Dynamic Behavior ◽  
Single Molecule ◽  
Protein Complexes ◽  
Imaging Techniques ◽  
Ensemble Averaging ◽  
Cellular Processes ◽  
Cellular Machinery

Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.

scholarly journals Identification and characterization of novel filament-forming proteins in cyanobacteria

2019 ◽  
Author(s):  
Benjamin L. Springstein ◽  
Christian Woehle ◽  
Julia Weissenbach ◽  
Andreas O. Helbig ◽  
Tal Dagan ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Cytoskeletal Proteins ◽  
Tetratricopeptide Repeat ◽  
Cellular Processes ◽  
Tetratricopeptide Repeat Protein ◽  
Pcc 7120 ◽  
Pcc 7942

AbstractFilament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament-forming proteins in cyanobacteria. Surveying cyanobacterial genomes for coiled-coil-rich proteins (CCRPs) that are predicted as putative filament-forming proteins, we observed a higher proportion of CCRPs in filamentous cyanobacteria in comparison to unicellular cyanobacteria. Using our predictions, we identified nine protein families with putative intermediate filament (IF) properties. Polymerization assays revealed four proteins that formed polymers in vitro and three proteins that formed polymers in vivo. Fm7001 from Fischerella muscicola PCC 7414 polymerized in vitro and formed filaments in vivo in several organisms. Additionally, we identified a tetratricopeptide repeat protein - All4981 - in Anabaena sp. PCC 7120 that polymerized into filaments in vitro and in vivo. All4981 interacts with known cytoskeletal proteins and is indispensable for Anabaena viability. Although it did not form filaments in vitro, Syc2039 from Synechococcus elongatus PCC 7942 assembled into filaments in vivo and a Δsyc2039 mutant was characterized by an impaired cytokinesis. Our results expand the repertoire of known prokaryotic filament-forming CCRPs and demonstrate that cyanobacterial CCRPs are involved in cell morphology, motility, cytokinesis and colony integrity.

scholarly journals Label-free methods for optical in vitro characterization of protein–protein interactions

2021 ◽  
Author(s):  
Fabian Soltermann ◽  
Weston B. Struwe ◽  
Philipp Kukura
Keyword(s):  
Protein Interactions ◽  
Label Free ◽  
Protein Protein Interactions ◽  
Cellular Processes ◽  
P Protein ◽  
In Vitro Characterization ◽  
And Function

Protein–protein interactions are involved in the regulation and function of the majority of cellular processes.

scholarly journals A Proteomics Signature of Mild Hypospadias: A Pilot Study

2020 ◽  
Vol 8 ◽  
Author(s):  
Coriness Piñeyro-Ruiz ◽  
Horacio Serrano ◽  
Inmaculada Jorge ◽  
Eric Miranda-Valentin ◽  
Marcos R. Pérez-Brayfield ◽  
...  
Keyword(s):  
High Throughput ◽  
Energy Production ◽  
Isotope Labeling ◽  
Cellular Processes ◽  
Proteomics Approach ◽  
Liquid Chromatography Tandem Mass ◽  
Congenital Condition ◽  
Group A ◽  
Control Samples

Background and Objective: Mild hypospadias is a birth congenital condition characterized by the relocation of the male urethral meatus from its typical anatomical position near the tip of the glans penis, to a lower ventral position up to the brim of the glans corona, which can also be accompanied by foreskin ventral deficiency. For the most part, a limited number of cases have known etiology. We have followed a high-throughput proteomics approach to study the proteome in mild hypospadias patients.Methods: Foreskin samples from patients with mild hypospadias were collected during urethroplasty, while control samples were collected during elective circumcision (n = 5/group). A high-throughput, quantitative proteomics approach based on multiplexed peptide stable isotope labeling (SIL) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to ascertain protein abundance changes in hypospadias patients when compared to control samples.Results: A total of 4,815 proteins were quantitated (2,522 with at least two unique peptides). One hundred and thirty-three proteins from patients with mild hypospadias showed significant abundance changes with respect to control samples, where 38 proteins were increased, and 95 proteins were decreased. Unbiased functional biological analysis revealed that both mitochondrial energy production and apoptotic signaling pathways were enriched in mild hypospadias.Conclusions: This first comprehensive proteomics characterization of mild hypospadias shows molecular changes associated with essential cellular processes related to energy production and apoptosis. Further evaluation of the proteome may expand the search of novel candidates in the etiology of mild hypospadias and could also lead to the identification of biomarkers for this congenital urogenital condition.

scholarly journals Rapid Rubber Extraction and NMR Spectroscopy of Rubber, Extracted from the Endemic Species Scorzonera Tau-Saghyz

2020 ◽  
Vol 22 (1) ◽  
pp. 59
Author(s):  
K.K. Boguspaev ◽  
S.K. Turasheva ◽  
T.M. Seilkhanov ◽  
D.G. Faleev ◽  
M.S. Mutalkhanov ◽  
...  
Keyword(s):  
Adventitious Shoots ◽  
Physiological Age ◽  
Root Extract ◽  
Nmr Characterization ◽  
First Time ◽  
Rubber Good ◽  
Isoprene Rubber

Scorzonera tau-saghyz Lipsch. et G.G. Bosse is an endemic rubber producing plant, growing in mountain regions in South Kazakhstan. The rubber content in plants and the quality of biopolymer has an important impact on industrial rubber production. The results of this study showed that the amount of rubber in S. tau-saghyz roots fluctuates between 7.74% and 38.75%. The amount of synthesized and deposited rubber biopolymer particles depends on various factors such as physiological age of plant, origin, temperature, moisture and environmental conditions. We optimized the extraction method of natural rubber by using n-hexane as a solvent for direct extraction. This method allows extracting the maximum amount of rubber from 3‒4-year-old plants. NMR results show structural links of natural isoprene rubber in the root extract sample. There is a clear relationship between methyl, methine and methylene protons which corresponds to isoprene rubber structure. The samples having strongly marked singlets that are inherent for rubber functional groups confirms the stereospecific structure of rubber. Good solubility of the root extract in deuterated chloroform can characterize the low molecular weight of the polymer. NMR characterization of rubber, extracted from S. tau-saghyz roots, is reported for the first time. Regeneration in vitro provides an important opportunity for endemic preservation by rapidly increasing the number of plants. The best regeneration of adventitious shoots was obtained on MS medium containing 5.5 μM kinetin and 0.5 μM NAA. The plants were successfully acclimatized in a glasshouse with 75% of S. tau-saghyz plantlets, respectively surviving after transfer to ex vitro conditions.

scholarly journals Transcriptional Profile and Structural Conservation of SUMO-Specific Proteases inSchistosoma mansoni

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Roberta Verciano Pereira ◽  
Fernanda Janku Cabral ◽  
Matheus de Souza Gomes ◽  
Liana Konovaloff Jannotti-Passos ◽  
William Castro-Borges ◽  
...  
Keyword(s):  
Protein Localization ◽  
Cell Cycle Control ◽  
Developmentally Regulated ◽  
Cellular Processes ◽  
Significant Difference ◽  
Endopeptidase Activity ◽  
Regulated Expression ◽  
Differential Gene

Small ubiquitin-related modifier (SUMO) is involved in numerous cellular processes including protein localization, transcription, and cell cycle control. SUMOylation is a dynamic process, catalyzed by three SUMO-specific enzymes and reversed by Sentrin/SUMO-specific proteases (SENPs). Here we report the characterization of these proteases inSchistosoma mansoni. Usingin silicoanalysis, we identified two SENPs sequences, orthologs of mammalian SENP1 and SENP7, confirming their identities and conservation through phylogenetic analysis. In addition, the transcript levels ofSmsenp1/7in cercariae, adult worms, andin vitrocultivated schistosomula were measured by qRT-PCR. Our data revealed upregulation of theSmsenp1/7transcripts in cercariae and early schistosomula, followed by a marked differential gene expression in the other analyzed stages. However, no significant difference in expression profile between the paralogs was observed for the analyzed stages. Furthermore, in order to detect deSUMOylating capabilities in crude parasite extracts,SmSENP1 enzymatic activity was evaluated using SUMO-1-AMC substrate. The endopeptidase activity related to SUMO-1 precursor processing did not differ significantly between cercariae and adult worms. Taken together, these results support the developmentally regulated expression of SUMO-specific proteases inS. mansoni.

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