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Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein–Protein Interfaces, How and Why? Molecules 2022; 27:molecules27061841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022] Open
Abstract
Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface.
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Affiliation(s)
- Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
- Correspondence:
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Juste-Dolz A, do Nascimento NM, Monzó I, Grau-García E, Román-Ivorra JA, Lopez-Paz JL, Escorihuela J, Puchades R, Morais S, Gimenez-Romero D, Maquieira Á. New structural insights into the role of TROVE2 complexes in the on-set and pathogenesis of systemic lupus erythematosus determined by a combination of QCM-D and DPI. Anal Bioanal Chem 2018; 411:4709-4720. [PMID: 30317445 DOI: 10.1007/s00216-018-1407-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of self-recognition of the autoantigen TROVE2, a common biomarker in autoimmune diseases, has been studied with a quartz crystal microbalance with dissipation monitoring (QCM-D) and dual polarization interferometry (DPI). The complementarity and remarkable analytical features of both techniques has allowed new insights into the onset of systemic lupus erythematosus (SLE) to be achieved at the molecular level. The in vitro study for SLE patients and healthy subjects suggests that anti-TROVE2 autoantibodies may undergo an antibody bipolar bridging. An epitope-paratope-specific binding initially occurs to activate a hidden Fc receptor in the TROVE2 tertiary structure. This bipolar mechanism may contribute to the pathogenic accumulation of anti-TROVE2 autoantibody immune complex in autoimmune disease. Furthermore, the specific calcium-dependent protein-protein bridges point out at how the TRIM21/TROVE2 association might occur, suggesting that the TROVE2 protein could stimulate the intracellular immune signaling via the TRIM21 PRY-SPRY domain. These findings may help to better understand the origins of the specificity and affinity of TROVE2 interactions, which might play a key role in the SLE pathogenesis. This manuscript gives one of the first practical applications of two novel functions (-df/dD and Δh/molec) for the analysis of the data provided by QCM-D and DPI. In addition, it is the first time that QCM-D has been used for mapping hidden Fc receptors as well as linear epitopes in a protein tertiary structure. Graphical abstract ᅟ.
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Affiliation(s)
- Augusto Juste-Dolz
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022, Valencia, Spain
| | - Noelle M do Nascimento
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022, Valencia, Spain
| | - Isidro Monzó
- Departamento de Química-Física, Universitat de València, C/ Dr. Moliner 50, 46100, Burjassot, Spain
| | - Elena Grau-García
- Departamento de Reumatología, Hospital Universitario y Politécnico La Fe, and Rheumatology Research Group, Instituto de Investigación Sanitaria La Fe, Avenida de Fernando Abril Martorell No 106, 46026, Valencia, Spain
| | - Jose A Román-Ivorra
- Departamento de Reumatología, Hospital Universitario y Politécnico La Fe, and Rheumatology Research Group, Instituto de Investigación Sanitaria La Fe, Avenida de Fernando Abril Martorell No 106, 46026, Valencia, Spain
| | - José Luis Lopez-Paz
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, C/ Dr. Moliner 50, 46100, Burjassot, Spain
| | - Rosa Puchades
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Sergi Morais
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain
| | - David Gimenez-Romero
- Departamento de Química-Física, Universitat de València, C/ Dr. Moliner 50, 46100, Burjassot, Spain.
| | - Ángel Maquieira
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain.
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