Template-based structure modeling of protein–protein interactions

Szilágyi, András; Zhang, Yang

doi:10.1016/j.sbi.2013.11.005

Cited by 160 publications

(144 citation statements)

References 82 publications

(159 reference statements)

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“…mutagenesis) on the binding interface [23,24]. In order to authenticate our CRMP2-Ubc9-SUMO model, we had to make two assumptions: ( i ) CRMP2 interacts with Ubc9 in a manner similar to that between Ubc9 and RanGAP1 and ( ii ) Lys374 of CRMP2 can act as an anchor to refine the complex.…”

Section: Resultsmentioning

confidence: 99%

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

et al. 2018

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Drug discovery campaigns directly targeting the voltage-gated sodium channel NaV1.7, a highly prized target in chronic pain, have not yet been clinically successful. In a differentiated approach, we demonstrated allosteric control of trafficking and activity of NaV1.7 by prevention of SUMOylation of collapsin response mediator protein 2 (CRMP2). Spinal administration of a SUMOylation incompetent CRMP2 (CRMP2 K374A) significantly attenuated pain behavior in the spared nerve injury (SNI) model of neuropathic pain, underscoring the importance of SUMOylation of CRMP2 as a pathologic event in chronic pain. Using a rational design strategy, we identified a heptamer peptide harboring CRMP2’s SUMO motif that disrupted the CRMP2-Ubc9 interaction, inhibited CRMP2 SUMOylation, inhibited NaV1.7 membrane trafficking, and specifically inhibited NaV1.7 sodium influx in sensory neurons. Importantly, this peptide reversed nerve injury-induced thermal and mechanical hypersensitivity in the SNI model, supporting the practicality of discovering pain drugs by indirectly targeting NaV1.7 via prevention of CRMP2 SUMOylation. Here, our goal was to map the unique interface between CRMP2 and Ubc9, the E2 SUMO conjugating enzyme. Using computational and biophysical approaches, we demonstrate the enzyme/substrate nature of Ubc9/CRMP2 binding and identify hot spots on CRMP2 that may form the basis of future drug discovery campaigns disrupting the CRMP2-Ubc9 interaction to recapitulate allosteric regulation of NaV1.7 for pain relief.

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Section: Resultsmentioning

confidence: 99%

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

et al. 2018

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“…The analysis protocol we propose relies on sequence data only. As a consequence, our strategy can provide useful information on a protein interface both in remote homology-based complex reconstruction and when no structural template is available, and it is inherently complementary to current methods based on the analysis of structural similarity (42) or sequence similarity (6,7,10,43) to a set of available templates.…”

Section: Discussionmentioning

confidence: 99%

“…When experimental structural data are absent or incomplete, template-based homology modeling of protein complexes represents the most reliable option (5,6). Similarly to modeling of tertiary structure for single-chain proteins, homology modeling of protein-protein interactions follows a conservation-based approach, in which the quaternary structure of one or more experimentally solved complexes with enough sequence similarity to a target complex (the templates) is projected onto the target.…”

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confidence: 99%

Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

Rodriguez-Rivas

Marsili

Juan

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Protein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein-protein interfaces. We show that sequencebased coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequencebased accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.coevolution | protein-protein interaction | protein complex | homology modeling | contact prediction C ells function as a remarkably synchronized orchestra of finely tuned molecular interactions, and establishing this molecular network has become a major goal of molecular biology. Important methodological and technical advances have led to the identification of a large number of novel protein-protein interactions and to major contributions to our understanding of the functioning of cells and organisms (1, 2). In contrast, and despite relevant advances in EM (3) and crystallography (4), the molecular details of a large number of interactions remain unknown.When experimental structural data are absent or incomplete, template-based homology modeling of protein complexes represents the most reliable option (5, 6). Similarly to modeling of tertiary structure for single-chain proteins, homology modeling of protein-protein interactions follows a conservation-based approach, in which the quaternary structure of one or more experimentally solved complexes with enough sequence similarity to a target complex (the templates) is projected onto the target. Templatebased techniques have provided models for a large number of protein complexes with structurally solved homologous complexes (7-10). Unfortunately, proteins involved in homologous protein dimers tend to systema...

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“…Experimental techniques, such as X-ray crystallography and NMR provide an accurate means to determine the structure of a protein [3]; and cryo-electron microscopy techniques have achieved atomic resolution [1]. The speed of these techniques however, falls far behind that of sequencing technologies, leaving a large gap between the known sequences of proteins and their structures [4].…”

Section: Introductionmentioning

confidence: 99%

PRIMO: An Interactive Homology Modeling Pipeline

et al. 2016

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The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

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Template-based structure modeling of protein–protein interactions

Cited by 160 publications

References 82 publications

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

PRIMO: An Interactive Homology Modeling Pipeline

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