Performance of human and server prediction in <scp>CAPRI</scp> rounds 38‐45

Duan, Rui; Qiu, Liming; Xu, Xianjin; Ma, Zhiwei; Merideth, Benjamin Ryan; Shyu, Chi‐Ren; Zou, Xiaoqin

doi:10.1002/prot.25956

Cited by 8 publications

(4 citation statements)

References 73 publications

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“…For a given protein-protein complex, the different clusters have distinct average properties, meaning that the substates differ in terms of interface size (∆ASA), interface shape complementarity (Gap index) and number of interface H bonds, as shown in Figure 6 . Interestingly, all the systems studied visit substates with iRMSD greater than 1 Å, which is the cutoff used to define high quality models in the CAPRI standards ( Duan et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Martin

Frezza

2022

Front. Mol. Biosci.

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Protein-protein interactions are at the basis of many protein functions, and the knowledge of 3D structures of protein-protein complexes provides structural, mechanical and dynamical pieces of information essential to understand these functions. Protein-protein interfaces can be seen as stable, organized regions where residues from different partners form non-covalent interactions that are responsible for interaction specificity and strength. They are commonly described as a peripheral region, whose role is to protect the core region that concentrates the most contributing interactions, from the solvent. To get insights into the dynamics of protein-protein complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on eight different protein-protein complexes of different functional class and interface size by taking into account the bound and unbound forms. On the one hand, we characterized structural changes upon binding of the proteins, and on the other hand we extensively analyzed the interfaces and the structural waters involved in the binding. Based on our analysis, in 6 cases out of 8, the interfaces rearranged during the simulation time, in stable and long-lived substates with alternative residue-residue contacts. These rearrangements are not restricted to side-chain fluctuations in the periphery but also affect the core interface. Finally, the analysis of the waters at the interface and involved in the binding pointed out the importance to take into account their role in the estimation of the interaction strength.

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Section: Resultsmentioning

confidence: 99%

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Martin

Frezza

2022

Front. Mol. Biosci.

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“…According to recent results from CAPRI (critical assessment of predicted interactions), a well-established community-wide experiment to benchmark docking methods, HADDOCK ranks among the best-performing docking methods. 61 Close contesters are ClusPro, 62 HDock, 63 MDOCKPP, 64 and LZerd. 65 Each of these docking methods expects a globular protein as the receptor protein.…”

Section: Discussionmentioning

confidence: 99%

Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW

Wenz

Bertazzon

Sticht

et al. 2022

J. Chem. Inf. Model.

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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 forminbinding 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 structures will help us to understand the synergistic and multivalency effects that generate the astonishing versatility and specificity of protein−protein interactions.

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“…According to recent results from CAPRI (Critical Assessment of Predicted Interactions), a well-established community-wide experiment to benchmark docking methods, HADDOCK ranks among the the best-performing docking methods. 61 Close contesters are ClusPro, 62 HDock, 63 MDOCKPP, 64 and LZerd. 65 Each of these docking methods expects a globular protein as the receptor protein.…”

Section: Discussionmentioning

confidence: 99%

Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW

Wenz

Bertazzon

Sticht

et al. 2021

Preprint

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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.

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Performance of human and server prediction in CAPRI rounds 38‐45

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as

Cited by 8 publications

References 73 publications

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW

Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW

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