The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock.

The circadian clock times cellular processes to the day/night cycle via a Transcription-Translation negative Feedback Loop (TTFL). However, a mechanistic understanding of the negative arm in both the timing of the TTFL and its control of output is lacking. We posited that the formation of negative-arm protein complexes was fundamental to clock regulation stemming from the negative arm. Using a modified peptide microarray approach termed Linear motif discovery using rational design (LOCATE), we characterized the interaction of the disordered negative-arm clock protein FREQUENCY to its partner protein FREQUENCY-Interacting RNA helicase. LOCATE identified a specific Short Linear Motif (SLiM) and interaction hotspot as well as positively charged islands that mediate electrostatic interactions, suggesting a model where negative arm proteins form a fuzzy complex essential for clock timing and robustness. Further analysis revealed that the positively charged islands were an evolutionarily conserved feature in higher eukaryotes and contributed to proper clock function.

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Using Tandem Affinity Purification to Identify Circadian Clock Protein Complexes from Arabidopsis

10.1007/978-1-0716-1912-4_15 ◽

2021 ◽

pp. 189-203

Author(s):

Maria L. Sorkin ◽

Dmitri A. Nusinow

Keyword(s):

Circadian Clock ◽

Protein Complexes ◽

Affinity Purification ◽

Tandem Affinity Purification ◽

Clock Protein

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NuA4 and SWR1-C: two chromatin-modifying complexes with overlapping functions and componentsThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal's usual peer review process.

Biochemistry and Cell Biology ◽

10.1139/o09-062 ◽

2009 ◽

Vol 87 (5) ◽

pp. 799-815 ◽

Cited By ~ 60

Author(s):

Phoebe Y.T. Lu ◽

Nancy Lévesque ◽

Michael S. Kobor

Keyword(s):

Chromatin Structure ◽

Protein Complexes ◽

Peer Review Process ◽

Histone Variant ◽

Chromatin Remodelling ◽

Cellular Processes ◽

Evolutionarily Conserved ◽

And Function ◽

Histone Deposition ◽

Chemical Groups

Chromatin structure is important for the compaction of eukaryotic genomes, thus chromatin modifications play a fundamental role in regulating many cellular processes. The coordinated activities of various chromatin-remodelling and -modifying complexes are crucial in maintaining distinct chromatin neighbourhoods, which in turn ensure appropriate gene expression, as well as DNA replication, repair, and recombination. SWR1-C is an ATP-dependent histone deposition complex for the histone variant H2A.Z, whereas NuA4 is a histone acetyltransferase for histones H4, H2A, and H2A.Z. Together the NuA4 and SWR1-C chromatin-modifying complexes alter the chromatin structure through 3 distinct modifications in yeast: post-translational addition of chemical groups, ATP-dependent chromatin remodelling, and histone variant incorporation. These 2 multi-protein complexes share 4 subunits and function together to regulate the circuitry of H2A.Z biology. The components and functions of both multi-protein complexes are evolutionarily conserved and play important roles in multi-cellular development and cellular differentiation in higher eukaryotes. This review will summarize recent findings about NuA4 and SWR1-C and will focus on the connection between these complexes by investigating their physical and functional interactions through eukaryotic evolution.

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Post-translational modifications of Hsp90 and translating the chaperone code

Journal of Biological Chemistry ◽

10.1074/jbc.rev120.011833 ◽

2020 ◽

Vol 295 (32) ◽

pp. 11099-11117 ◽

Cited By ~ 2

Author(s):

Sarah J. Backe ◽

Rebecca A. Sager ◽

Mark R. Woodford ◽

Alan M. Makedon ◽

Mehdi Mollapour

Keyword(s):

Protein Complexes ◽

Cell Cycle Control ◽

Heat Shock Protein 90 ◽

Post Translational Modifications ◽

Cellular Processes ◽

Chaperone Function ◽

Short Period ◽

Evolutionarily Conserved ◽

Hsp90 Chaperone ◽

The Stability

Cells have a remarkable ability to synthesize large amounts of protein in a very short period of time. Under these conditions, many hydrophobic surfaces on proteins may be transiently exposed, and the likelihood of deleterious interactions is quite high. To counter this threat to cell viability, molecular chaperones have evolved to help nascent polypeptides fold correctly and multimeric protein complexes assemble productively, while minimizing the danger of protein aggregation. Heat shock protein 90 (Hsp90) is an evolutionarily conserved molecular chaperone that is involved in the stability and activation of at least 300 proteins, also known as clients, under normal cellular conditions. The Hsp90 clients participate in the full breadth of cellular processes, including cell growth and cell cycle control, signal transduction, DNA repair, transcription, and many others. Hsp90 chaperone function is coupled to its ability to bind and hydrolyze ATP, which is tightly regulated both by co-chaperone proteins and post-translational modifications (PTMs). Many reported PTMs of Hsp90 alter chaperone function and consequently affect myriad cellular processes. Here, we review the contributions of PTMs, such as phosphorylation, acetylation, SUMOylation, methylation, O-GlcNAcylation, ubiquitination, and others, toward regulation of Hsp90 function. We also discuss how the Hsp90 modification state affects cellular sensitivity to Hsp90-targeted therapeutics that specifically bind and inhibit its chaperone activity. The ultimate challenge is to decipher the comprehensive and combinatorial array of PTMs that modulate Hsp90 chaperone function, a phenomenon termed the “chaperone code.”

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E3 ubiquitin ligases

Essays in Biochemistry ◽

10.1042/bse0410015 ◽

2005 ◽

Vol 41 ◽

pp. 15-30 ◽

Cited By ~ 123

Author(s):

Helen C. Ardley ◽

Philip A. Robinson

Keyword(s):

Protein Complexes ◽

Loss Of Function ◽

Direct Role ◽

Cellular Processes ◽

Substrate Protein ◽

Protein Ubiquitination ◽

C Terminus ◽

Full Complement ◽

Spatio Temporal ◽

Eukaryotic Organisms

The selectivity of the ubiquitin–26 S proteasome system (UPS) for a particular substrate protein relies on the interaction between a ubiquitin-conjugating enzyme (E2, of which a cell contains relatively few) and a ubiquitin–protein ligase (E3, of which there are possibly hundreds). Post-translational modifications of the protein substrate, such as phosphorylation or hydroxylation, are often required prior to its selection. In this way, the precise spatio-temporal targeting and degradation of a given substrate can be achieved. The E3s are a large, diverse group of proteins, characterized by one of several defining motifs. These include a HECT (homologous to E6-associated protein C-terminus), RING (really interesting new gene) or U-box (a modified RING motif without the full complement of Zn2+-binding ligands) domain. Whereas HECT E3s have a direct role in catalysis during ubiquitination, RING and U-box E3s facilitate protein ubiquitination. These latter two E3 types act as adaptor-like molecules. They bring an E2 and a substrate into sufficiently close proximity to promote the substrate's ubiquitination. Although many RING-type E3s, such as MDM2 (murine double minute clone 2 oncoprotein) and c-Cbl, can apparently act alone, others are found as components of much larger multi-protein complexes, such as the anaphase-promoting complex. Taken together, these multifaceted properties and interactions enable E3s to provide a powerful, and specific, mechanism for protein clearance within all cells of eukaryotic organisms. The importance of E3s is highlighted by the number of normal cellular processes they regulate, and the number of diseases associated with their loss of function or inappropriate targeting.

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Characteristics of the Interaction between Thrombin Exosite1 and the Sequence 269-297 of Platelet Glycoprotein Ibα

Thrombosis and Haemostasis ◽

10.1055/s-0037-1615193 ◽

1998 ◽

Vol 80 (08) ◽

pp. 310-315 ◽

Cited By ~ 8

Author(s):

Marie-Christine Bouton ◽

Christophe Thurieau ◽

Marie-Claude Guillin ◽

Martine Jandrot-Perrus

Keyword(s):

Platelet Activation ◽

Electrostatic Interactions ◽

Platelet Glycoprotein ◽

Thrombin Receptor ◽

Central Position ◽

Amidolytic Activity ◽

N Terminus ◽

Hydrolysis Of ◽

Chemical Cross Linking ◽

Positively Charged

SummaryThe interaction between GPIb and thrombin promotes platelet activation elicited via the hydrolysis of the thrombin receptor and involves structures located on the segment 238-290 within the N-terminal domain of GPIbα and the positively charged exosite 1 on thrombin. We have investigated the ability of peptides derived from the 269-287 sequence of GPIbα to interact with thrombin. Three peptides were synthesized, including Ibα 269-287 and two scrambled peptides R1 and R2 which are comparable to Ibα 269-287 with regards to their content and distribution of anionic residues. However, R2 differs from both Ibα 269-287 and R1 by the shifting of one proline from a central position to the N-terminus. By chemical cross-linking, we observed the formation of a complex between 125I-Ibα 269-287 and α-thrombin that was inhibited by hirudin, the C-terminal peptide of hirudin, sodium pyrophosphate but not by heparin. The complex did not form when γ-thrombin was substituted for α-thrombin. Ibα 269-287 produced only slight changes in thrombin amidolytic activity and inhibited thrombin binding to fibrin. R1 and R2 also formed complexes with α-thrombin, modified slightly its catalytic activity and inhibited its binding to fibrin. Peptides Ibα 269-287 and R1 inhibited platelet aggregation and secretion induced by low thrombin concentrations whereas R2 was without effect. Our results indicate that Ibα 269-287 interacts with thrombin exosite 1 via mainly electrostatic interactions, which explains why the scrambled peptides also interact with exosite 1. Nevertheless, the lack of effect of R2 on thrombin-induced platelet activation suggests that proline 280 is important for thrombin interaction with GPIb.

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Faculty Opinions recommendation of Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1011212.178411 ◽

2003 ◽

Author(s):

Edward Egelman

Keyword(s):

Circadian Clock ◽

Clock Protein

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Rhythmic ATP release from the cyanobacterial circadian clock protein KaiC revealed by real‐time monitoring of bioluminescence using firefly luciferase

Genes to Cells ◽

10.1111/gtc.12825 ◽

2020 ◽

Author(s):

Risa Mutoh ◽

Keita Iwata ◽

Takahiro Iida ◽

Masahiro Ishiura ◽

Kiyoshi Onai

Keyword(s):

Circadian Clock ◽

Real Time ◽

Atp Release ◽

Firefly Luciferase ◽

Real Time Monitoring ◽

Clock Protein

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Identifying Evolutionarily Conserved Protein Complexes

Computational Prediction of Protein Complexes from Protein Interaction Networks ◽

10.1145/3064650.3064658 ◽

2017 ◽

pp. 165

Keyword(s):

Protein Complexes ◽

Evolutionarily Conserved

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Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Genetics ◽

10.1534/genetics.119.302254 ◽

2019 ◽

Vol 212 (3) ◽

pp. 729-742 ◽

Cited By ~ 2

Author(s):

Lena Annika Street ◽

Ana Karina Morao ◽

Lara Heermans Winterkorn ◽

Chen-Yu Jiao ◽

Sarah Elizabeth Albritton ◽

...

Keyword(s):

Gene Expression ◽

Histone Modifications ◽

Chromatin Immunoprecipitation ◽

Protein Complexes ◽

Regulatory Elements ◽

Evolutionarily Conserved ◽

Chromatin Immunoprecipitation Sequencing ◽

Gene Regulatory Elements ◽

Gene Regulatory ◽

Regulatory Sites

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

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