scholarly journals Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258315
Author(s):  
A. Katherine Hatstat ◽  
Michael D. Pupi ◽  
Dewey G. McCafferty
Keyword(s):  
Protein Interactions ◽  
Ubiquitin Ligases ◽  
Family Interactions ◽  
Structural Factors ◽  
Protein Protein Interactions ◽  
Biomolecular Interaction ◽  
Ww Domains ◽  
Consensus Sequences ◽  
Bioinformatic Tool ◽  
Py Motif

The Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand protein interactor recognition mechanisms across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we find that, on average, half of Nedd4 family interactions are likely PY-motif mediated. Further, we find that PPxY motifs are more prevalent than LPxY motifs and are more likely to occur in proline-rich regions and that PPxY regions are more disordered on average relative to LPxY-containing regions. Informed by consensus sequences for PY motifs across the Nedd4 interactome, we rationally designed a focused peptide library and employed a computational screen, revealing sequence- and biomolecular interaction-dependent determinants of WW-domain/PY-motif interactions. Cumulatively, our efforts provide a new bioinformatic tool and expand our understanding of sequence and structural factors that contribute to PY-motif mediated interactor recognition across the Nedd4 family.

scholarly journals Bioinformatic and computational analysis reveals the prevalence and nature of PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases

2020 ◽  
Author(s):  
A. Katherine Hatstat ◽  
Michael D. Pupi ◽  
Dewey G. McCafferty
Keyword(s):  
Protein Interactions ◽  
Ubiquitin Ligases ◽  
Family Interactions ◽  
Structural Factors ◽  
Protein Protein Interactions ◽  
Biomolecular Interaction ◽  
Ww Domains ◽  
Consensus Sequences ◽  
Bioinformatic Tool ◽  
Py Motif

AbstractThe Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand substrate specificity across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we find that, on average, half of Nedd4 family interactions are PY-motif mediated. Further, we find that PPxY motifs are more prevalent than LPxY motifs and are more likely to occur in proline-rich regions. Further, PPxY regions are more disordered on average relative to LPxY-containing regions. Informed by consensus sequences for PY motifs across the Nedd4 interactome, we rationally designed a peptide library and employed a computational screen, revealing sequence- and biomolecular interaction-dependent determinants of WW-domain/PY-motif interactions. Cumulatively, our efforts provide a new bioinformatic tool and expand our understanding of sequence and structural factors that contribute to PY-motif mediated substrate recognition across the Nedd4 family.

scholarly journals ATP and Tri-Polyphosphate (TPP) Suppress Protein Aggregate Growth by a Supercharging Mechanism

Biomedicines ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1646
Author(s):  
Jordan Bye ◽  
Kiah Murray ◽  
Robin Curtis
Keyword(s):  
Protein Interactions ◽  
Electrostatic Interactions ◽  
Colloidal Stability ◽  
Conformational Stability ◽  
Kinetic Studies ◽  
Structural Factors ◽  
Protein Protein Interactions ◽  
Protein Aggregate ◽  
Aggregate Growth

A common strategy to increase aggregation resistance is through rational mutagenesis to supercharge proteins, which leads to high colloidal stability, but often has the undesirable effect of lowering conformational stability. We show this trade-off can be overcome by using small multivalent polyphosphate ions, adenosine triphosphate (ATP) and tripolyphosphate (TPP) as excipients. These ions are equally effective at suppressing aggregation of ovalbumin and bovine serum albumin (BSA) upon thermal stress as monitored by dynamic and static light scattering. Monomer loss kinetic studies, combined with measurements of native state protein–protein interactions and ζ-potentials, indicate the ions reduce aggregate growth by increasing the protein colloidal stability through binding and overcharging the protein. Out of three additional proteins studied, ribonuclease A (RNaseA), α-chymotrypsinogen (α-Cgn), and lysozyme, we only observed a reduction in aggregate growth for RNaseA, although overcharging by the poly-phosphate ions still occurs for lysozyme and α-Cgn. Because the salts do not alter protein conformational stability, using them as excipients could be a promising strategy for stabilizing biopharmaceuticals once the protein structural factors that determine whether multivalent ion binding will increase colloidal stability are better elucidated. Our findings also have biological implications. Recently, it has been proposed that ATP also plays an important role in maintaining intracellular biological condensates and preventing protein aggregation in densely packed cellular environments. We expect electrostatic interactions are a significant factor in determining the stabilizing ability of ATP towards maintaining proteins in non-dispersed states in vivo.

scholarly journals Mammalian Hippo signalling: a kinase network regulated by protein–protein interactions

2012 ◽  
Vol 40 (1) ◽  
pp. 124-128 ◽  
Author(s):  
Alexander Hergovich
Keyword(s):  
Protein Interactions ◽  
Tumour Suppressor ◽  
Protein Protein Interactions ◽  
Large Tumour ◽  
Serine Threonine Kinase ◽  
Ww Domains ◽  
Threonine Kinase ◽  
Signalling Molecules ◽  
Kinase Cascade ◽  
Hippo Signalling

The Hippo signal transduction cascade controls cell growth, proliferation and death, all of which are frequently deregulated in tumour cells. Since initial studies in Drosophila melanogaster were instrumental in defining Hippo signalling, the machinery was named after the central Ste20-like kinase Hippo. Moreover, given that loss of Hippo signalling components Hippo, Warts, and Mats resulted in uncontrolled tissue overgrowth, Hippo signalling was defined as a tumour-suppressor cascade. Significantly, all of the core factors of Hippo signalling have mammalian orthologues that functionally compensate for loss of their counterparts in Drosophila. Furthermore, studies in Drosophila and mammalian cell systems showed that Hippo signalling represents a kinase cascade that is tightly regulated by PPIs (protein–protein interactions). Several Hippo signalling molecules contain SARAH (Salvador/RASSF1A/Hippo) domains that mediate specific PPIs, thereby influencing the activities of MST1/2 (mammalian Ste20-like serine/threonine kinase 1/2) kinases, the human Hippo orthologues. Moreover, WW domains are present in several Hippo factors, and these domains also serve as interaction surfaces for regulatory PPIs in Hippo signalling. Finally, the kinase activities of LATS1/2 (large tumour-suppressor kinase 1/2), the human counterparts of Warts, are controlled by binding to hMOB1 (human Mps one binder protein 1), the human Mats. Therefore Hippo signalling is regulated by PPIs on several levels. In the present paper, I review the current understanding of how these regulatory PPIs are regulated and contribute to the functionality of Hippo signalling.

scholarly journals Hormone signaling through protein destruction: a lesson from plants

2009 ◽  
Vol 296 (2) ◽  
pp. E223-E227 ◽  
Author(s):  
Xu Tan ◽  
Ning Zheng
Keyword(s):  
Protein Interactions ◽  
Hormone Receptors ◽  
Ubiquitin Ligases ◽  
Ubiquitin Proteasome System ◽  
Hormone Signaling ◽  
Protein Protein Interactions ◽  
Protein Subunit ◽  
Major Pathway ◽  
Signaling Mechanism ◽  
F Box Protein

Ubiquitin-dependent protein degradation has emerged as a major pathway regulating eukaryotic biology. By employing a variety of ubiquitin ligases to target specific cellular proteins, the ubiquitin-proteasome system controls physiological processes in a highly regulated fashion. Recent studies on a plant hormone auxin have unveiled a novel paradigm of signal transduction in which ubiquitin ligases function as hormone receptors. Perceived by the F-box protein subunit of the SCFTIR1 ubiquitin ligase, auxin directly promotes the recruitment of a family of transcriptional repressors for ubiquitination, thereby activating extensive transcriptional programs. Structural studies have revealed that auxin functions through a “molecular glue” mechanism to enhance protein-protein interactions with the assistance of another small molecule cofactor, inositol hexakisphosphate. Given the extensive repertoire of similar ubiquitin ligases in eukaryotic cells, this novel and widely adopted hormone-signaling mechanism in plants may also exist in other organisms.

scholarly journals Interactome Data and Databases: Different Types of Protein Interaction

2004 ◽  
Vol 5 (2) ◽  
pp. 173-178 ◽  
Author(s):  
Javier De Las Rivas ◽  
Alberto de Luis
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Interaction Network ◽  
Short Review ◽  
Experimental Methods ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Bioinformatic Tool ◽  
Different Types

In recent years, the biomolecular sciences have been driven forward by overwhelming advances in new biotechnological high-throughput experimental methods and bioinformatic genome-wide computational methods. Such breakthroughs are producing huge amounts of new data that need to be carefully analysed to obtain correct and useful scientific knowledge. One of the fields where this advance has become more intense is the study of the network of ‘protein–protein interactions’, i.e. the ‘interactome’. In this short review we comment on the main data and databases produced in this field in last 5 years. We also present a rationalized scheme of biological definitions that will be useful for a better understanding and interpretation of ‘what a protein–protein interaction is’ and ‘which types of protein–protein interactions are found in a living cell’. Finally, we comment on some assignments of interactome data to defined types of protein interaction and we present a new bioinformatic tool called APIN (Agile Protein Interaction Network browser), which is in development and will be applied to browsing protein interaction databases.

scholarly journals Target recognition in tandem WW domains: complex structures for parallel and antiparallel ligand orientation in h-FBP21 tandem WW

2021 ◽  
Author(s):  
Marius T. Wenz ◽  
Miriam Bertazzon ◽  
Jana Sticht ◽  
Stevan Aleksić ◽  
Daniela Gjorgjevikj ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tandem Repeats ◽  
Molecular Simulations ◽  
Peptide Sequence ◽  
Complex Structures ◽  
Protein Protein Interactions ◽  
Ww Domains ◽  
Binding Partner ◽  
Density Based Clustering ◽  
Ligand Orientation

Protein-protein interactions often rely on specialized recognition domains, such as WW domains, which bind to specific proline-rich sequences. The specificity of these protein-protein interactions can be increased by tandem repeats, i.e. two WW domains connected by a linker. With a flexible linker, the WW domains can move freely with respect to each other. Additionally, the tandem WW domains can bind in two different orientations to their target sequences. This makes the elucidation of complex structures of tandem WW domains extremely challenging. Here, we identify and characterize two complex structures of the tandem WW domain of human formin-binding protein 21 and a peptide sequence from its natural binding partner, the core-splicing protein SmB/B′. The two structures differ in the ligand orientation, and consequently also in the relative orientation of the two WW domains. We analyze and probe the interactions in the complexes by molecular simulations and NMR experiments. The workflow to identify the complex structures uses molecular simulations, density-based clustering and peptide docking. It is designed to systematically generate possible complex structures for repeats of recognition domains. These stuctures will help us to understand the synergistic and multivalency effects that generate the astonishing versatility and specificity of protein-protein interactions.

scholarly journals WW Domains of Rsp5p Define Different Functions: Determination of Roles in Fluid Phase and Uracil Permease Endocytosis in Saccharomyces cerevisiae

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 91-101 ◽  
Author(s):  
Beata Gajewska ◽  
Joanna Kamińska ◽  
Alicja Jesionowska ◽  
Nancy C Martin ◽  
Anita K Hopper ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Fluid Phase ◽  
Temperature Sensitive ◽  
Protein Protein Interactions ◽  
Ww Domains ◽  
Ubiquitin Protein Ligase ◽  
Cellular Processes ◽  
Fluid Phase Endocytosis ◽  
Ubiquitination Pathway ◽  
Punctate Pattern

Abstract Rsp5p, ubiquitin-protein ligase, an enzyme of the ubiquitination pathway, contains three WW domains that mediate protein-protein interactions. To determine if these domains adapt Rsp5p to a subset of substrates involved in numerous cellular processes, we generated mutations in individual or combinations of the WW domains. The rsp5-w1, rsp5-w2, and rsp5-w3 mutant alleles complement RSP5 deletions at 30°. Thus, individual WW domains are not essential. Each rsp5-w mutation caused temperature-sensitive growth. Among variants with mutations in multiple WW domains, only rsp5-w1w2 complemented the deletion. Thus, the WW3 domain is sufficient for Rsp5p essential functions. To determine whether rsp5-w mutations affect endocytosis, fluid phase and uracil permease (Fur4p) endocytosis was examined. The WW3 domain is important for both processes. WW2 appears not to be important for fluid phase endocytosis whereas it is important for Fur4p endocytosis. In contrast, the WW1 domain affects fluid phase endocytosis, but it does not appear to function in Fur4p endocytosis. Thus, various WW domains play different roles in the endocytosis of these two substrates. Rsp5p is located in the cytoplasm in a punctate pattern that does not change during the cell cycle. Altering WW domains does not change the location of Rsp5p.

scholarly journals WW Domains Provide a Platform for the Assembly of Multiprotein Networks

2005 ◽  
Vol 25 (16) ◽  
pp. 7092-7106 ◽  
Author(s):  
Robert J. Ingham ◽  
Karen Colwill ◽  
Caley Howard ◽  
Sabine Dettwiler ◽  
Caesar S. H. Lim ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Ww Domain ◽  
Ww Domains ◽  
Peptide Motifs ◽  
Cytoskeletal Regulation ◽  
Associated Proteins ◽  
Cleavage And Polyadenylation ◽  
Single Polypeptide ◽  
Proline Rich Peptide

ABSTRACT WW domains are protein modules that mediate protein-protein interactions through recognition of proline-rich peptide motifs and phosphorylated serine/threonine-proline sites. To pursue the functional properties of WW domains, we employed mass spectrometry to identify 148 proteins that associate with 10 human WW domains. Many of these proteins represent novel WW domain-binding partners and are components of multiprotein complexes involved in molecular processes, such as transcription, RNA processing, and cytoskeletal regulation. We validated one complex in detail, showing that WW domains of the AIP4 E3 protein-ubiquitin ligase bind directly to a PPXY motif in the p68 subunit of pre-mRNA cleavage and polyadenylation factor Im in a manner that promotes p68 ubiquitylation. The tested WW domains fall into three broad groups on the basis of hierarchical clustering with respect to their associated proteins; each such cluster of bound proteins displayed a distinct set of WW domain-binding motifs. We also found that separate WW domains from the same protein or closely related proteins can have different specificities for protein ligands and also demonstrated that a single polypeptide can bind multiple classes of WW domains through separate proline-rich motifs. These data suggest that WW domains provide a versatile platform to link individual proteins into physiologically important networks.

scholarly journals WW, PH and C-Terminal Domains Cooperate to Direct the Subcellular Localizations of PLEKHA5, PLEKHA6 and PLEKHA7

2021 ◽  
Vol 9 ◽  
Author(s):  
Sophie Sluysmans ◽  
Isabelle Méan ◽  
Lionel Jond ◽  
Sandra Citi
Keyword(s):  
Protein Interactions ◽  
Cultured Cells ◽  
Coiled Coil ◽  
Cell Junctions ◽  
Structural Basis ◽  
Chimeric Proteins ◽  
Ph Domain ◽  
Protein Protein Interactions ◽  
Ww Domains ◽  
Lateral Localization

PLEKHA5, PLEKHA6, and PLEKHA7 (WW-PLEKHAs) are members of the PLEKHA family of proteins that interact with PDZD11 through their tandem WW domains. WW-PLEKHAs contribute to the trafficking and retention of transmembrane proteins, including nectins, Tspan33, and the copper pump ATP7A, at cell-cell junctions and lateral membranes. However, the structural basis for the distinct subcellular localizations of PLEKHA5, PLEKHA6, and PLEKHA7 is not clear. Here we expressed mutant and chimeric proteins of WW-PLEKHAs in cultured cells to clarify the role of their structural domains in their localization. We found that the WW-mediated interaction between PLEKHA5 and PDZD11 is required for their respective association with cytoplasmic microtubules. The PH domain of PLEKHA5 is required for its localization along the lateral plasma membrane and promotes the lateral localization of PLEKHA7 in a chimeric molecule. Although the PH domain of PLEKHA7 is not required for its localization at the adherens junctions (AJ), it promotes a AJ localization of chimeric proteins. The C-terminal region of PLEKHA6 and PLEKHA7 and the coiled-coil region of PLEKHA7 promote their localization at AJ of epithelial cells. These observations indicate that the localizations of WW-PLEKHAs at specific subcellular sites, where they recruit PDZD11, are the result of multiple cooperative protein-lipid and protein-protein interactions and provide a rational basis for the identification of additional proteins involved in trafficking and sorting of WW-PLEKHAs.

scholarly journals Small-Molecule Approaches to Targeted Protein Degradation

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Tyler B. Faust ◽  
Katherine A. Donovan ◽  
Hong Yue ◽  
Philip P. Chamberlain ◽  
Eric S. Fischer
Keyword(s):  
Protein Degradation ◽  
Protein Interactions ◽  
Cancer Biology ◽  
Ubiquitin Ligases ◽  
Ubiquitin Proteasome System ◽  
Annual Review ◽  
Publication Date ◽  
Protein Protein Interactions ◽  
Rate Limiting Step ◽  
Ubiquitin Proteasome

Many essential biological processes are regulated through proximity, from membrane receptor signaling to transcriptional activity. The ubiquitin-proteasome system controls protein degradation, with ubiquitin ligases as the rate-limiting step. Ubiquitin ligases are commonly controlled at the level of substrate recruitment and, therefore, by proximity. There are natural and synthetic small molecules that also operate through induced proximity. For example, thalidomide is effective in treating multiple myeloma and functions as a molecular glue that stabilizes novel protein-protein interactions between a ubiquitin ligase and proteins not otherwise targeted by the ligase, leading to neo-substrate degradation. Emerging data on new degrader molecules have uncovered diverse mechanisms distinct from molecular glues, which often mirror the regulatory mechanisms that control substrate-ligase proximity in nature. In this review, we summarize our current understanding of biological and synthetic regulation of protein degradation and share our view on how these diverse mechanisms have inspired novel therapeutic directions. Expected final online publication date for the Annual Review of Cancer Biology, Volume 5 is March 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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