The molecular basis of plant cellulose synthase complex organisation and assembly

Protein Interfaces ◽

Cellulose Synthase Complex ◽

Cellulose Synthases

The material properties of cellulose are heavily influenced by the organisation of β-1,4-glucan chains into a microfibril. It is likely that the structure of this microfibril is determined by the spatial arrangement of catalytic cellulose synthase (CESA) proteins within the cellulose synthase complex (CSC). In land plants, CESA proteins form a large complex composed of a hexamer of trimeric lobes termed the rosette. Each rosette synthesises a single microfibril likely composed of 18 glucan chains. In this review, the biochemical events leading to plant CESA protein assembly into the rosette are explored. The protein interfaces responsible for CESA trimerization are formed by regions that define rosette-forming CESA proteins. As a consequence, these regions are absent from the ancestral bacterial cellulose synthases (BcsAs) that do not form rosettes. CSC assembly occurs within the context of the endomembrane system, however the site of CESA assembly into trimers and rosettes is not determined. Both the N-Terminal Domain and Class Specific Region of CESA proteins are intrinsically disordered and contain all of the identified phosphorylation sites, making both regions candidates as sites for protein–protein interactions and inter–lobe interface formation. We propose a sequential assembly model, whereby CESA proteins form stable trimers shortly after native folding, followed by sequential recruitment of lobes into a rosette, possibly assisted by Golgi-localised STELLO proteins. A comprehensive understanding of CESA assembly into the CSC will enable directed engineering of CESA protein spatial arrangements, allowing changes in cellulose crystal packing that alter its material properties.

Protein-protein docking using learned three-dimensional representations

10.1101/738690 ◽

2019 ◽

Cited By ~ 1

Author(s):

Georgy Derevyanko ◽

Guillaume Lamoureux

Keyword(s):

Protein Interactions ◽

Network Architecture ◽

Protein Complexes ◽

Three Dimensional ◽

Spatial Arrangement ◽

Protein Docking ◽

Translational Invariance ◽

Shape Complementarity ◽

Spatial Features

AbstractProtein-protein interactions are determined by a number of hard-to-capture features related to shape complementarity, electrostatics, and hydrophobicity. These features may be intrinsic to the protein or induced by the presence of a partner. A conventional approach to protein-protein docking consists in engineering a small number of spatial features for each protein, and in minimizing the sum of their correlations with respect to the spatial arrangement of the two proteins. To generalize this approach, we introduce a deep neural network architecture that transforms the raw atomic densities of each protein into complex three-dimensional representations. Each point in the volume containing the protein is described by 48 learned features, which are correlated and combined with the features of a second protein to produce a score dependent on the relative position and orientation of the two proteins. The architecture is based on multiple layers of SE(3)-equivariant convolutional neural networks, which provide built-in rotational and translational invariance of the score with respect to the structure of the complex. The model is trained end-to-end on a set of decoy conformations generated from 851 nonredundant protein-protein complexes and is tested on data from the Protein-Protein Docking Benchmark Version 4.0.

Amphipathic helical peptides hamper protein-protein interactions of the intrinsically disordered chromatin nuclear protein 1 (NUPR1)

Biochimica et Biophysica Acta (BBA) - General Subjects ◽

10.1016/j.bbagen.2018.03.009 ◽

2018 ◽

Vol 1862 (6) ◽

pp. 1283-1295 ◽

Cited By ~ 12

Author(s):

Patricia Santofimia-Castaño ◽

Bruno Rizzuti ◽

Olga Abián ◽

Adrián Velázquez-Campoy ◽

Juan L. Iovanna ◽

...

Keyword(s):

Protein Interactions ◽

Nuclear Protein ◽

Helical Peptides ◽

Intrinsically Disordered

Intrinsic Disorder in Tetratricopeptide Repeat Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms21103709 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3709 ◽

Cited By ~ 1

Author(s):

Nathan W. Van Bibber ◽

Cornelia Haerle ◽

Roy Khalife ◽

Bin Xue ◽

Vladimir N. Uversky

Keyword(s):

Protein Interactions ◽

Posttranslational Modifications ◽

Tandem Repeats ◽

Intrinsically Disordered Protein ◽

Intrinsic Disorder ◽

Systematic Analysis ◽

Tetratricopeptide Repeats ◽

Tetratricopeptide Repeat Proteins

Among the realm of repeat containing proteins that commonly serve as “scaffolds” promoting protein-protein interactions, there is a family of proteins containing between 2 and 20 tetratricopeptide repeats (TPRs), which are functional motifs consisting of 34 amino acids. The most distinguishing feature of TPR domains is their ability to stack continuously one upon the other, with these stacked repeats being able to affect interaction with binding partners either sequentially or in combination. It is known that many repeat-containing proteins are characterized by high levels of intrinsic disorder, and that many protein tandem repeats can be intrinsically disordered. Furthermore, it seems that TPR-containing proteins share many characteristics with hybrid proteins containing ordered domains and intrinsically disordered protein regions. However, there has not been a systematic analysis of the intrinsic disorder status of TPR proteins. To fill this gap, we analyzed 166 human TPR proteins to determine the degree to which proteins containing TPR motifs are affected by intrinsic disorder. Our analysis revealed that these proteins are characterized by different levels of intrinsic disorder and contain functional disordered regions that are utilized for protein-protein interactions and often serve as targets of various posttranslational modifications.

Chasing coevolutionary signals in intrinsically disordered proteins complexes

Scientific Reports ◽

10.1038/s41598-020-74791-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Javier A. Iserte ◽

Tamas Lazar ◽

Silvio C. E. Tosatto ◽

Peter Tompa ◽

Cristina Marino-Buslje

Keyword(s):

Protein Interactions ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Contact Prediction ◽

Regulatory Processes ◽

Wide Range ◽

Predict Protein Structure ◽

Biological Interpretation

Abstract Intrinsically disordered proteins/regions (IDPs/IDRs) are crucial components of the cell, they are highly abundant and participate ubiquitously in a wide range of biological functions, such as regulatory processes and cell signaling. Many of their important functions rely on protein interactions, by which they trigger or modulate different pathways. Sequence covariation, a powerful tool for protein contact prediction, has been applied successfully to predict protein structure and to identify protein–protein interactions mostly of globular proteins. IDPs/IDRs also mediate a plethora of protein–protein interactions, highlighting the importance of addressing sequence covariation-based inter-protein contact prediction of this class of proteins. Despite their importance, a systematic approach to analyze the covariation phenomena of intrinsically disordered proteins and their complexes is still missing. Here we carry out a comprehensive critical assessment of coevolution-based contact prediction in IDP/IDR complexes and detail the challenges and possible limitations that emerge from their analysis. We found that the coevolutionary signal is faint in most of the complexes of disordered proteins but positively correlates with the interface size and binding affinity between partners. In addition, we discuss the state-of-art methodology by biological interpretation of the results, formulate evaluation guidelines and suggest future directions of development to the field.

Peptide-based Interaction Proteomics

Molecular & Cellular Proteomics ◽

10.1074/mcp.r120.002034 ◽

2020 ◽

Vol 19 (7) ◽

pp. 1070-1075 ◽

Cited By ~ 3

Author(s):

Katrina Meyer ◽

Matthias Selbach

Keyword(s):

Protein Interactions ◽

Synthetic Peptides ◽

Intrinsically Disordered Regions ◽

Interaction Partners ◽

Linear Motifs ◽

Cellulose Membranes ◽

Interaction Proteomics ◽

Proteins Interactions

Protein-protein interactions are often mediated by short linear motifs (SLiMs) that are located in intrinsically disordered regions (IDRs) of proteins. Interactions mediated by SLiMs are notoriously difficult to study, and many functionally relevant interactions likely remain to be uncovered. Recently, pull-downs with synthetic peptides in combination with quantitative mass spectrometry emerged as a powerful screening approach to study protein-protein interactions mediated by SLiMs. Specifically, arrays of synthetic peptides immobilized on cellulose membranes provide a scalable means to identify the interaction partners of many peptides in parallel. In this minireview we briefly highlight the relevance of SLiMs for protein-protein interactions, outline existing screening technologies, discuss unique advantages of peptide-based interaction screens and provide practical suggestions for setting up such peptide-based screens.

The Disordered Cellular Multi-Tasker WIP and Its Protein–Protein Interactions: A Structural View

Biomolecules ◽

10.3390/biom10071084 ◽

2020 ◽

Vol 10 (7) ◽

pp. 1084 ◽

Cited By ~ 2

Author(s):

Chana G. Sokolik ◽

Nasrin Qassem ◽

Jordan H. Chill

Keyword(s):

Protein Interactions ◽

Cell Biology ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Actin Binding ◽

Structural Description ◽

Terminal Domain ◽

Binding Partners

WASp-interacting protein (WIP), a regulator of actin cytoskeleton assembly and remodeling, is a cellular multi-tasker and a key member of a network of protein–protein interactions, with significant impact on health and disease. Here, we attempt to complement the well-established understanding of WIP function from cell biology studies, summarized in several reviews, with a structural description of WIP interactions, highlighting works that present a molecular view of WIP’s protein–protein interactions. This provides a deeper understanding of the mechanisms by which WIP mediates its biological functions. The fully disordered WIP also serves as an intriguing example of how intrinsically disordered proteins (IDPs) exert their function. WIP consists of consecutive small functional domains and motifs that interact with a host of cellular partners, with a striking preponderance of proline-rich motif capable of interactions with several well-recognized binding partners; indeed, over 30% of the WIP primary structure are proline residues. We focus on the binding motifs and binding interfaces of three important WIP segments, the actin-binding N-terminal domain, the central domain that binds SH3 domains of various interaction partners, and the WASp-binding C-terminal domain. Beyond the obvious importance of a more fundamental understanding of the biology of this central cellular player, this approach carries an immediate and highly beneficial effect on drug-design efforts targeting WIP and its binding partners. These factors make the value of such structural studies, challenging as they are, readily apparent.

Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules

Nature Communications ◽

10.1038/s41467-019-12528-4 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 4

Author(s):

Charlotte Rimbault ◽

Kashyap Maruthi ◽

Christelle Breillat ◽

Camille Genuer ◽

Sara Crespillo ◽

...

Keyword(s):

Protein Interactions ◽

Pdz Domain ◽

Specific Inhibitor ◽

Rational Approach ◽

Protein Protein Interaction ◽

Domain Specific ◽

Postsynaptic Protein ◽

Protein Interfaces ◽

Direct Generation

Abstract Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved interaction surfaces. In this case, direct generation of selective and competitive inhibitors is hindered by high similarity within the evolutionary-related protein interfaces. We report here a strategy that uses a semi-rational approach to separate the modulator design into two functional parts. We first achieve specificity toward a region outside of the interface by using phage display selection coupled with molecular and cellular validation. Highly selective competition is then generated by appending the more degenerate interaction peptide to contact the target interface. We apply this approach to specifically bind a single PDZ domain within the postsynaptic protein PSD-95 over highly similar PDZ domains in PSD-93, SAP-97 and SAP-102. Our work provides a paralog-selective and domain specific inhibitor of PSD-95, and describes a method to efficiently target other conserved PPI modules.

Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation

Molecules ◽

10.3390/molecules25204705 ◽

2020 ◽

Vol 25 (20) ◽

pp. 4705

Author(s):

Adiran Garaizar ◽

Ignacio Sanchez-Burgos ◽

Rosana Collepardo-Guevara ◽

Jorge R. Espinosa

Keyword(s):

Phase Separation ◽

Liquid Phase ◽

Protein Interactions ◽

Conformational Dynamics ◽

Liquid Phase Separation ◽

Phase Behaviour ◽

Coarse Grained ◽

Liquid Liquid Phase Separation

Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid–liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, including conformational switching, where they transition between alternate conformational ensembles. Using Molecular Dynamics simulations of a minimal coarse-grained model for IDRs, we show that the role of protein conformation has a non-trivial effect in the liquid–liquid phase behaviour of IDRs. When an IDR transitions to a conformational ensemble enriched in disordered extended states, LLPS is enhanced. In contrast, IDRs that switch to ensembles that preferentially sample more compact and structured states show inhibited LLPS. This occurs because extended and disordered protein conformations facilitate LLPS-stabilising multivalent protein–protein interactions by reducing steric hindrance; thereby, such conformations maximize the molecular connectivity of the condensed liquid network. Extended protein configurations promote phase separation regardless of whether LLPS is driven by homotypic and/or heterotypic protein–protein interactions. This study sheds light on the link between the dynamic conformational plasticity of IDRs and their liquid–liquid phase behaviour.