scholarly journals Prediction of Protein–Protein Binding Interactions in Dimeric Coiled Coils by Information Contained in Folding Energy Landscapes

2021 ◽  
Vol 22 (3) ◽  
pp. 1368
Author(s):  
Panagiota S. Georgoulia ◽  
Sinisa Bjelic
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Coiled Coil ◽  
Extensive Study ◽  
Coiled Coils ◽  
Folding Energy ◽  
Energy Landscapes ◽  
Binding Interactions ◽  
Interacting Protein ◽  
Protein Partners

Coiled coils represent the simplest form of a complex formed between two interacting protein partners. Their extensive study has led to the development of various methods aimed towards the investigation and design of complex forming interactions. Despite the progress that has been made to predict the binding affinities for protein complexes, and specifically those tailored towards coiled coils, many challenges still remain. In this work, we explore whether the information contained in dimeric coiled coil folding energy landscapes can be used to predict binding interactions. Using the published SYNZIP dataset, we start from the amino acid sequence, to simultaneously fold and dock approximately 1000 coiled coil dimers. Assessment of the folding energy landscapes showed that a model based on the calculated number of clusters for the lowest energy structures displayed a signal that correlates with the experimentally determined protein interactions. Although the revealed correlation is weak, we show that such correlation exists; however, more work remains to establish whether further improvements can be made to the presented model.

scholarly journals Coiled-coil networking shapes cell molecular machinery

2012 ◽  
Vol 23 (19) ◽  
pp. 3911-3922 ◽  
Author(s):  
Yongqiang Wang ◽  
Xinlei Zhang ◽  
Hong Zhang ◽  
Yi Lu ◽  
Haolong Huang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Critical Role ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Protein Protein Interactions ◽  
Full Spectrum ◽  
Kinetochore Assembly ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Systematic Understanding

The highly abundant α-helical coiled-coil motif not only mediates crucial protein–protein interactions in the cell but is also an attractive scaffold in synthetic biology and material science and a potential target for disease intervention. Therefore a systematic understanding of the coiled-coil interactions (CCIs) at the organismal level would help unravel the full spectrum of the biological function of this interaction motif and facilitate its application in therapeutics. We report the first identified genome-wide CCI network in Saccharomyces cerevisiae, which consists of 3495 pair-wise interactions among 598 predicted coiled-coil regions. Computational analysis revealed that the CCI network is specifically and functionally organized and extensively involved in the organization of cell machinery. We further show that CCIs play a critical role in the assembly of the kinetochore, and disruption of the CCI network leads to defects in kinetochore assembly and cell division. The CCI network identified in this study is a valuable resource for systematic characterization of coiled coils in the shaping and regulation of a host of cellular machineries and provides a basis for the utilization of coiled coils as domain-based probes for network perturbation and pharmacological applications.

scholarly journals A Multiplexed Bacterial Two-Hybrid for Rapid Characterization of Protein-Protein Interactions and Iterative Protein Design

2020 ◽  
Author(s):  
W. Clifford Boldridge ◽  
Ajasja Ljubetič ◽  
Hwangbeom Kim ◽  
Nathan Lubock ◽  
Dániel Szilágyi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Coiled Coil ◽  
Building Blocks ◽  
Coiled Coils ◽  
Next Generation ◽  
Protein Protein Interactions ◽  
Library Size ◽  
Large Sets ◽  
Synthetic Cell ◽  
Two Hybrid

AbstractMyriad biological functions require protein-protein interactions (PPIs), and engineered PPIs are crucial for applications ranging from drug design to synthetic cell circuits. Understanding and engineering specificity in PPIs is particularly challenging as subtle sequence changes can drastically alter specificity. Coiled-coils are small protein domains that have long served as a simple model for studying the sequence-determinants of specificity and have been used as modular building blocks to build large protein nanostructures and synthetic circuits. Despite their simple rules and long-time use, building large sets of well-behaved orthogonal pairs that can be used together is still challenging because predictions are often inaccurate, and, as the library size increases, it becomes difficult to test predictions at scale. To address these problems, we first developed a method called the Next-Generation Bacterial Two-Hybrid (NGB2H), which combines gene synthesis, a bacterial two-hybrid assay, and a high-throughput next-generation sequencing readout, allowing rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way. After validating the NGB2H system on previously characterized libraries, we designed, built, and tested large sets of orthogonal synthetic coiled-coils. In an iterative set of experiments, we assayed more than 8,000 PPIs, used the dataset to train a novel linear model-based coiled-coil scoring algorithm, and then characterized nearly 18,000 interactions to identify the largest set of orthogonal PPIs to date with twenty-two on-target interactions.

scholarly journals Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions

2020 ◽  
Vol 6 (8) ◽  
pp. eaax5783 ◽  
Author(s):  
M. A. Gonzalez-Lozano ◽  
F. Koopmans ◽  
P. F. Sullivan ◽  
J. Protze ◽  
G. Krause ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Conformational Dynamics ◽  
Synaptic Proteins ◽  
Cross Linking ◽  
Synaptic Protein ◽  
Protein Partners ◽  
Associated Proteins ◽  
Model Protein

Synaptic transmission is the predominant form of communication in the brain. It requires functionally specialized molecular machineries constituted by thousands of interacting synaptic proteins. Here, we made use of recent advances in cross-linking mass spectrometry (XL-MS) in combination with biochemical and computational approaches to reveal the architecture and assembly of synaptic protein complexes from mouse brain hippocampus and cerebellum. We obtained 11,999 unique lysine-lysine cross-links, comprising connections within and between 2362 proteins. This extensive collection was the basis to identify novel protein partners, to model protein conformational dynamics, and to delineate within and between protein interactions of main synaptic constituents, such as Camk2, the AMPA-type glutamate receptor, and associated proteins. Using XL-MS, we generated a protein interaction resource that we made easily accessible via a web-based platform (http://xlink.cncr.nl) to provide new entries into exploration of all protein interactions identified.

scholarly journals High-resolution structures of a heterochiral coiled coil

2015 ◽  
Vol 112 (43) ◽  
pp. 13144-13149 ◽  
Author(s):  
David E. Mortenson ◽  
Jay D. Steinkruger ◽  
Dale F. Kreitler ◽  
Dominic V. Perroni ◽  
Gregory P. Sorenson ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Structural Information ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Protein Protein Interactions ◽  
Polypeptide Chains ◽  
Packing Interactions

Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein–protein interactions. Coiled–coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled–coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.

scholarly journals Improved prediction of protein-protein interactions using AlphaFold2

2021 ◽  
Author(s):  
Patrick Bryant ◽  
Gabriele Pozzati ◽  
Arne Elofsson
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Interacting Proteins ◽  
Bacterial Protein ◽  
Protein Protein Interactions ◽  
Multiple Sequence ◽  
Test Set ◽  
Interacting Protein ◽  
Identification Rate ◽  
Homologous Sequences

Abstract Predicting the structure of interacting protein chains is fundamental for understanding the function of proteins. Here, we examine the use of AlphaFold2 (AF2) for predicting the structure of heterodimeric protein complexes. We find that using the default AF2 protocol, 44% of the models in a test set can be predicted accurately. However, by optimising the multiple sequence alignment, we can increase the accuracy to 59%. In comparison, the alternative fold-and-dock method RoseTTAFold is only successful in 10% of the cases on this set, template-based docking 35% and traditional docking methods 22%. We can distinguish acceptable (DockQ>0.23) from incorrect models with an AUC of 0.85 on the test set by analysing the predicted interfaces. The success is higher for bacterial protein pairs, pairs with large interaction areas consisting of helices or sheets, and many homologous sequences. Further, we test the possibility to distinguish interacting from non-interacting proteins and find that by analysing the predicted interfaces, we can separate truly interacting from non-interacting proteins with an AUC of 0.82 in the ROC curve, compared to 0.76 with a recently published method. In addition, when using a more realistic negative set, including mammalian proteins, the identification rate remains (AUC=0.83), resulting in that 27% of interactions can be identified at a 1% FPR. All scripts and tools to run our protocol are freely available at: https://gitlab.com/ElofssonLab/FoldDock.

Guidelines for the assembly of novel coiled-coil structures: α-sheets and α-cylinders

2001 ◽  
Vol 68 ◽  
pp. 111-123 ◽  
Author(s):  
John Walshaw ◽  
Jennifer M. Shipway ◽  
Derek N. Woolfson
Keyword(s):  
Protein Design ◽  
Protein Interactions ◽  
Protein Structures ◽  
Coiled Coil ◽  
Data Bank ◽  
Coiled Coils ◽  
Heptad Repeat ◽  
Protein Protein Interactions ◽  
Helical Bundles ◽  
Heptad Repeats

The coiled coil is a ubiquitous motif that guides many different protein-protein interactions. The accepted hallmark of coiled coils is a seven-residue (heptad) sequence repeat. The positions of this repeat are labelled a-b-c-d-e-f-g, with residues at a and d tending to be hydrophobic. Such sequences form amphipathic α-helices, which assemble into helical bundles via knobs-into-holes interdigitation of residues from neighbouring helices. We wrote an algorithm, SOCKET, to identify this packing in protein structures, and used this to gather a database of coiled-coil structures from the Protein Data Bank. Surprisingly, in addition to commonly accepted structures with a single, contiguous heptad repeat, we identified sequences with multiple, offset heptad repeats. These 'new' sequence patterns help to explain oligomer-state specification in coiled coils. Here we focus on the structural consequences for sequences with two heptad repeats offset by two residues, i.e. a/f′-b/g′-c/a′-d/b′-e/c′-f/d′-g/e′. This sets up two hydrophobic seams on opposite sides of the helix formed. We describe how such helices may combine to bury these hydrophobic surfaces in two different ways and form two distinct structures: open 'α-sheets' and closed 'α-cylinders'. We highlight these with descriptions of natural structures and outline possibilities for protein design.

scholarly journals Condensin and cohesin display different arm conformations with characteristic hinge angles

2002 ◽  
Vol 156 (3) ◽  
pp. 419-424 ◽  
Author(s):  
David E. Anderson ◽  
Ana Losada ◽  
Harold P. Erickson ◽  
Tatsuya Hirano
Keyword(s):  
Catalytic Domain ◽  
Protein Complexes ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Structure Characteristic ◽  
Catalytic Domains ◽  
Open Conformation ◽  
Chromatid Cohesion ◽  
Structural Maintenance Of Chromosomes ◽  
Smc Proteins

Structural maintenance of chromosomes (SMC) proteins play central roles in higher-order chromosome dynamics from bacteria to humans. In eukaryotes, two different SMC protein complexes, condensin and cohesin, regulate chromosome condensation and sister chromatid cohesion, respectively. Each of the complexes consists of a heterodimeric pair of SMC subunits and two or three non-SMC subunits. Previous studies have shown that a bacterial SMC homodimer has a symmetrical structure in which two long coiled-coil arms are connected by a flexible hinge. A catalytic domain with DNA- and ATP-binding activities is located at the distal end of each arm. We report here the visualization of vertebrate condensin and cohesin by electron microscopy. Both complexes display the two-armed structure characteristic of SMC proteins, but their conformations are remarkably different. The hinge of condensin is closed and the coiled-coil arms are placed close together. In contrast, the hinge of cohesin is wide open and the coiled-coils are spread apart from each other. The non-SMC subunits of both condensin and cohesin form a globular complex bound to the catalytic domains of the SMC heterodimers. We propose that the “closed” conformation of condensin and the “open” conformation of cohesin are important structural properties that contribute to their specialized biochemical and physiological functions.

scholarly journals Titin N2A Domain and Its Interactions at the Sarcomere

2021 ◽  
Vol 22 (14) ◽  
pp. 7563
Author(s):  
Adeleye O. Adewale ◽  
Young-Hoon Ahn
Keyword(s):  
Protein Interactions ◽  
Biological Effects ◽  
Passive Force ◽  
Protein Protein Interactions ◽  
Interacting Protein ◽  
Large Size ◽  
Protein Partners ◽  
Myosin Filaments ◽  
Stress Sensing ◽  
Modular Structures

Titin is a giant protein in the sarcomere that plays an essential role in muscle contraction with actin and myosin filaments. However, its utility goes beyond mechanical functions, extending to versatile and complex roles in sarcomere organization and maintenance, passive force, mechanosensing, and signaling. Titin’s multiple functions are in part attributed to its large size and modular structures that interact with a myriad of protein partners. Among titin’s domains, the N2A element is one of titin’s unique segments that contributes to titin’s functions in compliance, contraction, structural stability, and signaling via protein–protein interactions with actin filament, chaperones, stress-sensing proteins, and proteases. Considering the significance of N2A, this review highlights structural conformations of N2A, its predisposition for protein–protein interactions, and its multiple interacting protein partners that allow the modulation of titin’s biological effects. Lastly, the nature of N2A for interactions with chaperones and proteases is included, presenting it as an important node that impacts titin’s structural and functional integrity.

scholarly journals Improved prediction of protein-protein interactions using AlphaFold2 and extended multiple-sequence alignments

2021 ◽  
Author(s):  
Patrick Bryant ◽  
Gabriele Pozzati ◽  
Arne Elofsson
Keyword(s):  
Protein Interactions ◽  
Error Rate ◽  
Protein Complexes ◽  
Sequence Information ◽  
Protein Protein Interactions ◽  
Single Chain ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Test Set ◽  
Interacting Protein

Predicting the structure of single-chain proteins is now close to being a solved problem due to the recent achievement of AlphaFold2 (AF2). However, predicting the structure of interacting protein chains is still a challenge. Here, we utilise AF2 to optimise a protocol for predicting the structure of heterodimeric protein complexes using only sequence information. We find that using the default AF2 protocol, 32% of the models in the Dockground test set can be modelled accurately. By tuning the input alignment and identifying the best model, we adjusted the performance to 43%. Our protocol uses MSAs generated by AF2 and MSAs paired on the organism level generated with HHblits. In a more extensive, more realistic, independent test set, the accuracy is 59%. In comparison, the alternative fold-and-dock method RoseTTAFold is only successful in 10% of the cases on this set and traditional docking methods 22%. However, for the traditional method, the performance would be lower if the bound form of both monomers was not known. The success is higher for bacterial protein pairs, pairs with large interaction areas consisting of helices or sheets, and many homologous sequences. We can distinguish acceptable (DockQ>0.23) from incorrect models with an AUC of 0.84 on the test set by analysing the predicted interfaces. At an error rate of 1%, 13% are acceptable (at a 10% error rate, 40% of the models are acceptable). All scripts and tools to run our protocol are freely available at: https://gitlab.com/ElofssonLab/FoldDock.

Automatedde novophasing and model building of coiled-coil proteins

2015 ◽  
Vol 71 (3) ◽  
pp. 606-614 ◽  
Author(s):  
Sebastian Rämisch ◽  
Robert Lizatović ◽  
Ingemar André
Keyword(s):  
Structure Prediction ◽  
Initial Phase ◽  
Model Building ◽  
De Novo ◽  
Protein Complexes ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Phase Estimation ◽  
Molecular Replacement ◽  
Experimental Phasing

Models generated byde novostructure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein–protein complexes andde novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential ofde novomodels of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71–103% of the residues present in the deposited structures, had the correct sequence and had freeRvalues that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, namedCCsolve, combines methods forde novostructure prediction, initial phase estimation and automated model building into one pipeline.CCsolveis robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility ofde novophasing of protein–protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

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