1
|
Mirchandani-Duque M, Choucri M, Hernández-Mondragón JC, Crespo-Ramírez M, Pérez-Olives C, Ferraro L, Franco R, Pérez de la Mora M, Fuxe K, Borroto-Escuela DO. Membrane Heteroreceptor Complexes as Second-Order Protein Modulators: A Novel Integrative Mechanism through Allosteric Receptor-Receptor Interactions. MEMBRANES 2024; 14:96. [PMID: 38786931 PMCID: PMC11122807 DOI: 10.3390/membranes14050096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Bioluminescence and fluorescence resonance energy transfer (BRET and FRET) together with the proximity ligation method revealed the existence of G-protein-coupled receptors, Ionotropic and Receptor tyrosine kinase heterocomplexes, e.g., A2AR-D2R, GABAA-D5R, and FGFR1-5-HT1AR heterocomplexes. Molecular integration takes place through allosteric receptor-receptor interactions in heteroreceptor complexes of synaptic and extra-synaptic regions. It involves the modulation of receptor protomer recognition, signaling and trafficking, as well as the modulation of behavioral responses. Allosteric receptor-receptor interactions in hetero-complexes give rise to concepts like meta-modulation and protein modulation. The introduction of receptor-receptor interactions was the origin of the concept of meta-modulation provided by Katz and Edwards in 1999, which stood for the fine-tuning or modulation of nerve cell transmission. In 2000-2010, Ribeiro and Sebastiao, based on a series of papers, provided strong support for their view that adenosine can meta-modulate (fine-tune) synaptic transmission through adenosine receptors. However, another term should also be considered: protein modulation, which is the key feature of allosteric receptor-receptor interactions leading to learning and consolidation by novel adapter proteins to memory. Finally, it must be underlined that allosteric receptor-receptor interactions and their involvement both in brain disease and its treatment are of high interest. Their pathophysiological relevance has been obtained, especially for major depressive disorder, cocaine use disorder, and Parkinson's disease.
Collapse
Affiliation(s)
- Marina Mirchandani-Duque
- Receptomics and Brain Disorders Lab, Department of Human Physiology Physical Education and Sport, Faculty of Medicine, University of Malaga, 29010 Málaga, Spain;
| | - Malak Choucri
- Department of Neuroscience, Karolinska Institutet, Biomedicum (B0852), Solnavägen 9, 17165 Solna, Sweden;
| | - Juan C. Hernández-Mondragón
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (J.C.H.-M.); (M.C.-R.); (M.P.d.l.M.)
| | - Minerva Crespo-Ramírez
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (J.C.H.-M.); (M.C.-R.); (M.P.d.l.M.)
| | - Catalina Pérez-Olives
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08007 Barcelona, Spain;
| | - Luca Ferraro
- Department of Life Sciences and Biotechnology, Section of Medicinal and Health Products University of Ferrara, 44121 Ferrara, Italy; (L.F.); (R.F.)
| | - Rafael Franco
- Department of Life Sciences and Biotechnology, Section of Medicinal and Health Products University of Ferrara, 44121 Ferrara, Italy; (L.F.); (R.F.)
| | - Miguel Pérez de la Mora
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (J.C.H.-M.); (M.C.-R.); (M.P.d.l.M.)
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet, Biomedicum (B0852), Solnavägen 9, 17165 Solna, Sweden;
| | - Dasiel O. Borroto-Escuela
- Receptomics and Brain Disorders Lab, Department of Human Physiology Physical Education and Sport, Faculty of Medicine, University of Malaga, 29010 Málaga, Spain;
- Department of Neuroscience, Karolinska Institutet, Biomedicum (B0852), Solnavägen 9, 17165 Solna, Sweden;
| |
Collapse
|
2
|
Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS. ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570727. [PMID: 38106144 PMCID: PMC10723403 DOI: 10.1101/2023.12.07.570727] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Ada Shaw
- Applied Mathematics, Harvard University
| | | | | | - Mafalda Dias
- Centre for Genomic Regulation, Universitat Pompeu Fabra
| | | | | | - Yarin Gal
- Computer Science, University of Oxford
| | | |
Collapse
|