InterPep2: Global Peptide-Protein Docking with Structural Templates

AbstractMotivationInteractions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming, and because of the disordered nature of the ligand, the interactions are especially difficult to predict through software, requiring specialized solutions. Although several prediction-methods exist, most are limited in performance or availability.ResultsInterPep2 is a freely available method for predicting the structure of peptide-protein interactions. We have previously shown that structural templates can be used to accurately predict peptide-protein binding sites, and that using templates from regular protein-protein interactions will increase the number of sites found. Here, we show that the same principle can be extended to dock the peptide to the binding surface using InterPep2. A key component of InterPep2 is the ability to score plausible interaction templates using a RandomForest trained to predict the DockQ-score using sequence and structural features. InterPep2 is tested on a difficult dataset of 251 peptide-protein complexes, where it correctly positions 136 (54%) at the correct site compared to 114 (45%) for the second best method. Analyzing the confidence score InterPep2 recalls more true positives across all specificity levels compared to the second best method, for example at 10% False Positive Rate it correctly identifies 59% of the complexes compared to 44% for the second best method.AvailabilityThe program is available from: http://wallnerlab.org/InterPepContactBjörn Wallner [email protected]

Download Full-text

InterPep2: global peptide–protein docking using interaction surface templates

Bioinformatics ◽

10.1093/bioinformatics/btaa005 ◽

2020 ◽

Vol 36 (8) ◽

pp. 2458-2465 ◽

Cited By ~ 2

Author(s):

Isak Johansson-Åkhe ◽

Claudio Mirabello ◽

Björn Wallner

Keyword(s):

Protein Interactions ◽

Protein Complexes ◽

Structural Features ◽

Protein Docking ◽

Supplementary Information ◽

Peptide Ligand ◽

Protein Protein Interactions ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Improved Performance

Abstract Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide–protein interactions. Improved performance is obtained by using templates from both peptide–protein and regular protein–protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide–protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0 Å LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide–protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0 Å LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18). Availability and implementation The program is available from: http://wallnerlab.org/InterPep2. Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids

10.1101/2021.02.08.430344 ◽

2021 ◽

Author(s):

Huaying Zhao ◽

Di Wu ◽

Ai Nguyen ◽

Yan Li ◽

Regina C. Adão ◽

...

Keyword(s):

Phase Separation ◽

Secondary Structure ◽

Protein Interactions ◽

Protein Secondary Structure ◽

Size Composition ◽

Structural Features ◽

N Protein ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Ribonucleoprotein Particles

SummaryNucleocapsid (N) protein of the SARS-CoV-2 virus packages the viral genome into well-defined ribonucleoprotein particles, but the molecular pathway is still unclear. N-protein is dimeric and consists of two folded domains with nucleic acid (NA) binding sites, surrounded by intrinsically disordered regions that promote liquid-liquid phase separation. Here we use biophysical tools to study N-protein interactions with oligonucleotides of different length, examining the size, composition, secondary structure, and energetics of the resulting states. We observe formation of supramolecular clusters or nuclei preceding growth into phase-separated droplets. Short hexanucleotide NA forms compact 2:2 N-protein/NA complexes with reduced disorder. Longer oligonucleotides expose additional N-protein interactions and multi-valent protein-NA interactions, which generate higher-order mixed oligomers and simultaneously promote growth of droplets. Phase separation is accompanied by a significant increase in protein secondary structure, different from that caused by initial NA binding, which may contribute to the assembly of ribonucleoprotein particles within molecular condensates.

Download Full-text

Structure determination of protein-peptide complexes from NMR chemical shift data using MELD.

10.1101/2021.12.31.474671 ◽

2022 ◽

Author(s):

Arup Mondal ◽

G.V.T. Swapna ◽

Jingzhou Hao ◽

LiChung Ma ◽

Monica J. Roth ◽

...

Keyword(s):

Chemical Shift ◽

Protein Interactions ◽

Protein Complexes ◽

Bound State ◽

Nmr Chemical Shift ◽

Modeling Tools ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Chemical Shift Data ◽

Shift Data

Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding upon binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine structures of peptide-protein complexes. Here, we demonstrate this approach for polypeptide com-plexes formed with the extraterminal (ET) domain of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can form different conformations (e.g., helices and hair-pins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding pos-es, using only backbone chemical shift data, in excellent agreement with experimentally-determined structures. The approach also predicts relative binding affinities of different peptides. This hybrid MELD-NMR approach provides a powerful new tool for structural analysis of protein-polypeptide complexes in the low NMR information content regime, which can be used successfully for flexible systems where one polypeptide binding partner folds upon complex formation.

Download Full-text

Evolutionary Study of Disorder in Protein Sequences

Biomolecules ◽

10.3390/biom10101413 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1413

Author(s):

Kristina Kastano ◽

Gábor Erdős ◽

Pablo Mier ◽

Gregorio Alanis-Lobato ◽

Vasilis J. Promponas ◽

...

Keyword(s):

Protein Interactions ◽

Intrinsically Disordered Proteins ◽

Protein Complexes ◽

Cell Types ◽

Disordered Proteins ◽

Protein Protein Interactions ◽

Globular Structure ◽

Large Variability ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions

Intrinsically disordered proteins (IDPs) contain regions lacking intrinsic globular structure (intrinsically disordered regions, IDRs). IDPs are present across the tree of life, with great variability of IDR type and frequency even between closely related taxa. To investigate the function of IDRs, we evaluated and compared the distribution of disorder content in 10,695 reference proteomes, confirming its high variability and finding certain correlation along the Euteleostomi (bony vertebrates) lineage to number of cell types. We used the comparison of orthologs to study the function of disorder related to increase in cell types, observing that multiple interacting subunits of protein complexes might gain IDRs in evolution, thus stressing the function of IDRs in modulating protein-protein interactions, particularly in the cell nucleus. Interestingly, the conservation of local compositional biases of IDPs follows residue-type specific patterns, with E- and K-rich regions being evolutionarily stable and Q- and A-rich regions being more dynamic. We provide a framework for targeted evolutionary studies of the emergence of IDRs. We believe that, given the large variability of IDR distributions in different species, studies using this evolutionary perspective are required.

Download Full-text

Computational investigation for modelling the protein-protein interaction of TasA(28-261) – TapA(33-253): a decisive process in biofilm formation by Bacillus subtilis

10.1101/2020.04.26.062109 ◽

2020 ◽

Author(s):

Nidhi Verma ◽

Shubham Srivastava ◽

Ruchi Malik ◽

Jay Kant Yadav ◽

Pankaj Goyal ◽

...

Keyword(s):

Bacillus Subtilis ◽

Protein Interaction ◽

Biofilm Formation ◽

Structural Features ◽

Protein Docking ◽

Structural Basis ◽

Chronic Infections ◽

Protein Protein Interaction ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions

AbstractBiofilms have significant role in microbial persistence, antibiotic resistance and chronic infections; consequently, there is a pressing need for development of novel “anti-biofilm strategies”. One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of ‘amyloid like proteins’ (ALPs) in extracellular matrix. Such interactions could be potential targets for development of novel anti-biofilm strategies; therefore, assessing the structural features of these interactions could be of great scientific value. Characterization of biomolecular interaction with conventional structure biology tools including X-Ray diffraction and Nuclear Magnetic Resonance is technically challenging, expensive and time-consuming. In contrast, modelling such interactions is time-efficient, economical and might provide deeper understanding of structural basis of interactions. Therefore, during the present study, protein-protein interaction of TasA(28-261)–TapA(33-253) (which is a decisive process for biofilm formation by Bacillus subtilis) was modeled using in silico approaches viz., molecular modelling, protein-protein docking and molecular dynamics simulations. Results identified amino-acid residues present within intrinsically disordered regions of both proteins to be critical for interaction. These results were further supported with PCA and FEL analyses. Results presented here represent novel finding and we hypothesize that aa identified during the present study could be targeted for inhibition of biofilm formation by B. subtilis.

Download Full-text

Cyclin binding Cy motifs have multiple activities in the initiation of DNA replication

10.1101/681668 ◽

2019 ◽

Cited By ~ 2

Author(s):

Manzar Hossain ◽

Kuhulika Bhalla ◽

Bruce Stillman

Keyword(s):

Cell Cycle ◽

Dna Replication ◽

Protein Interactions ◽

Origin Recognition Complex ◽

Protein Complexes ◽

Cycle Phase ◽

Protein Motifs ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Initiation Of Dna Replication

SummaryThe initiation of DNA replication involves the cell cycle-dependent assembly and disassembly of protein complexes, including the Origin Recognition Complex (ORC) and CDC6 AAA+ ATPases. We report that multiple short, linear protein motifs (SLiMs) within intrinsically disordered regions in ORC1 and CDC6, including Cyclin-binding (Cy) motifs, mediate Cyclin-CDK dependent and independent protein-protein interactions, conditional on cell cycle phase. The ORC1 Cy motif mediates an auto-regulatory self-interaction, and the same Cy motif prevents CDC6 binding to ORC1 in mitosis, but then facilitates the destruction of ORC1 in S phase. In contrast, in G1, the CDC6 Cy motif promotes ORC1-CDC6 interaction independent of Cyclin-CDK protein phosphorylation. CDC6 interaction with ORC also requires a basic region of ORC1 that in yeast mediates ORC-DNA interactions. We also demonstrate that protein phosphatase 1 binds directly to a SLiM in ORC1, causing de-phosphorylation upon mitotic exit. Thus, Cy-motifs have wider roles, functioning as a ligand and as a degron.

Download Full-text

Co-evolutionary analysis accurately predicts details of interactions between the Integrator complex subunits

10.1101/696583 ◽

2019 ◽

Author(s):

Bernard Fongang ◽

Yingjie Zhu ◽

Eric J. Wagner ◽

Andrzej Kudlicki ◽

Maga Rowicka

Keyword(s):

Protein Interactions ◽

False Positive ◽

Protein Complexes ◽

False Positive Rate ◽

Attractive Alternative ◽

Evolutionary Analysis ◽

Protein Protein Interactions ◽

Small Proteins ◽

Positive Rate ◽

Specificity Factor

ABSTRACTSolving the structure of large, multi-subunit complexes is difficult despite recent advances in cryoEM, due to remaining challenges to express and purify complex subunits. Computational approaches that predict protein-protein interactions, including Direct Coupling Analysis (DCA), represent an attractive alternative to dissect interactions within protein complexes. However, due to high computational complexity and high false positive rate they are applicable only to small proteins. Here, we present a modified DCA to predict residues and domains involved in interactions of large proteins. To reduce false positive levels and increase accuracy of prediction, we use local Gaussian averaging and predicted secondary structure elements. As a proof-of-concept, we apply our method to two Integrator subunits, INTS9 and INTS11, which form a heterodimeric structure previously solved by crystallography. We accurately predict the domains of INTS9/11 interaction. We then apply this approach to predict the interaction domains of two complexes whose structure is currently unknown: 1) The heterodimer formed by the Cleavage and Polyadenylation Specificity Factor 100-kD (CPSF100) and 73-kD (CPSF73); 2) The heterotrimer formed by INTS4/9/11. Our predictions of interactions within these two complexes are supported by experimental data, demonstrating that our modified DCA is a useful method for predicting interactions and can easily be applied to other complexes.

Download Full-text

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

Current Medicinal Chemistry ◽

10.2174/0929867326666190620101637 ◽

2020 ◽

Vol 27 (37) ◽

pp. 6306-6355 ◽

Cited By ~ 2

Author(s):

Marian Vincenzi ◽

Flavia Anna Mercurio ◽

Marilisa Leone

Keyword(s):

Drug Discovery ◽

Protein Interaction ◽

Protein Interactions ◽

Structural Information ◽

Protein Complexes ◽

Structural Features ◽

Protein Protein Interactions ◽

Modular Architecture ◽

Post Translational Modifications ◽

Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

Download Full-text

Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1620360114 ◽

2017 ◽

Vol 114 (9) ◽

pp. 2224-2229 ◽

Cited By ~ 18

Author(s):

Daniel A. Weisz ◽

Haijun Liu ◽

Hao Zhang ◽

Sundarapandian Thangapandian ◽

Emad Tajkhorshid ◽

...

Keyword(s):

Mass Spectrometry ◽

Photosystem Ii ◽

Protein Interactions ◽

Protein Complexes ◽

Protein Docking ◽

Cross Linking ◽

Protein Protein Interactions ◽

Cytochrome B559 ◽

Reaction Center Complex ◽

Assembly Intermediate

Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b559, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b559, in close proximity to the QB site. Protein–protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the “mass tags” selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein–protein interactions in membrane protein complexes.

Download Full-text

Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase Separation

10.1101/375071 ◽

2018 ◽

Cited By ~ 2

Author(s):

David T McSwiggen ◽

Anders S Hansen ◽

Hervé Marie-Nelly ◽

Sheila Teves ◽

Alec B Heckert ◽

...

Keyword(s):

Phase Separation ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Protein Interactions ◽

Viral Dna ◽

Herpes Simplex Virus 1 ◽

Pol Ii ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Simplex Virus

SummaryDuring lytic infection, Herpes Simplex Virus 1 generates replication compartments (RCs) in host nuclei that efficiently recruit protein factors, including host RNA Polymerase II (Pol II). Pol II and other cellular factors form hubs in uninfected cells that are proposed to phase separate via multivalent protein-protein interactions mediated by their intrinsically disordered regions. Using a battery of live cell microscopic techniques, we show that although RCs superficially exhibit many characteristics of phase separation, the recruitment of Pol II instead derives from nonspecific interactions with the viral DNA. We find that the viral genome remains nucleosome-free, profoundly affecting the way Pol II explores RCs by causing it to repetitively visit nearby binding sites, thereby creating local Pol II accumulations. This mechanism, distinct from phase separation, allows viral DNA to outcompete host DNA for cellular proteins. Our work provides new insights into the strategies used to create local molecular hubs in cells.

Download Full-text