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Lagunes L, Briggs K, Martin-Holder P, Xu Z, Maurer D, Ghabra K, Deeds EJ. Modeling reveals the strength of weak interactions in stacked-ring assembly. Biophys J 2024; 123:1763-1780. [PMID: 38762753 DOI: 10.1016/j.bpj.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Cells employ many large macromolecular machines for the execution and regulation of processes that are vital for cell and organismal viability. Interestingly, cells cannot synthesize these machines as functioning units. Instead, cells synthesize the molecular parts that must then assemble into the functional complex. Many important machines, including chaperones such as GroEL and proteases such as the proteasome, comprise protein rings that are stacked on top of one another. While there is some experimental data regarding how stacked-ring complexes such as the proteasome self-assemble, a comprehensive understanding of the dynamics of stacked-ring assembly is currently lacking. Here, we developed a mathematical model of stacked-trimer assembly and performed an analysis of the assembly of the stacked homomeric trimer, which is the simplest stacked-ring architecture. We found that stacked rings are particularly susceptible to a form of kinetic trapping that we term "deadlock," in which the system gets stuck in a state where there are many large intermediates that are not the fully assembled structure but that cannot productively react. When interaction affinities are uniformly strong, deadlock severely limits assembly yield. We thus predicted that stacked rings would avoid situations where all interfaces in the structure have high affinity. Analysis of available crystal structures indicated that indeed the majority-if not all-of stacked trimers do not contain uniformly strong interactions. Finally, to better understand the origins of deadlock, we developed a formal pathway analysis and showed that, when all the binding affinities are strong, many of the possible pathways are utilized. In contrast, optimal assembly strategies utilize only a small number of pathways. Our work suggests that deadlock is a critical factor influencing the evolution of macromolecular machines and provides general principles for understanding the self-assembly efficiency of existing machines.
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Affiliation(s)
- Leonila Lagunes
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California; Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, California
| | - Koan Briggs
- Department of Physics, University of Kansas, Lawrence, Kansas
| | - Paige Martin-Holder
- Department of Molecular Immunology, Microbiology and Genetics, UCLA, Los Angeles, California
| | - Zaikun Xu
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Dustin Maurer
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Karim Ghabra
- Computational and Systems Biology IDP, UCLA, Los Angeles, California
| | - Eric J Deeds
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, California; Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, California; Center for Computational Biology, University of Kansas, Lawrence, Kansas.
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Kamada Y, Umeda C, Mukai Y, Ohtsuka H, Otsubo Y, Yamashita A, Kosugi T. Structure-based engineering of Tor complexes reveals that two types of yeast TORC1 produce distinct phenotypes. J Cell Sci 2024; 137:jcs261625. [PMID: 38415789 PMCID: PMC10941655 DOI: 10.1242/jcs.261625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/18/2024] [Indexed: 02/29/2024] Open
Abstract
Certain proteins assemble into diverse complex states, each having a distinct and unique function in the cell. Target of rapamycin (Tor) complex 1 (TORC1) plays a central role in signalling pathways that allow cells to respond to the environment, including nutritional status signalling. TORC1 is widely recognised for its association with various diseases. The budding yeast Saccharomyces cerevisiae has two types of TORC1, Tor1-containing TORC1 and Tor2-containing TORC1, which comprise different constituent proteins but are considered to have the same function. Here, we computationally modelled the relevant complex structures and then, based on the structures, rationally engineered a Tor2 mutant that could form Tor complex 2 (TORC2) but not TORC1, resulting in a redesign of the complex states. Functional analysis of the Tor2 mutant revealed that the two types of TORC1 induce different phenotypes, with changes observed in rapamycin, caffeine and pH dependencies of cell growth, as well as in replicative and chronological lifespan. These findings uncovered by a general approach with huge potential - model structure-based engineering - are expected to provide further insights into various fields such as molecular evolution and lifespan.
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Affiliation(s)
- Yoshiaki Kamada
- Interdisciplinary Research Unit, National Institute for Basic Biology (NIBB), National Institutes of Natural Sciences (NINS), Okazaki, Aichi, 444-8585, Japan
- Basic Biology Program, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, 240-0193, Japan
| | - Chiharu Umeda
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Yukio Mukai
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology (NIBB), National Institutes of Natural Sciences (NINS), Okazaki, Aichi, 444-8585, Japan
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology (NIBB), National Institutes of Natural Sciences (NINS), Okazaki, Aichi, 444-8585, Japan
| | - Takahiro Kosugi
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi, 444-8585, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Aichi, 444-8585, Japan
- Molecular Science Program, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, 240-0193, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
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Lee JY, Gebauer E, Seeliger MA, Bahar I. Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments. Curr Opin Struct Biol 2024; 84:102770. [PMID: 38211377 PMCID: PMC11044982 DOI: 10.1016/j.sbi.2023.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024]
Abstract
The eukaryotic protein kinase domain has been a broadly explored target for drug discovery, despite limitations imposed by its high sequence conservation as a shared modular domain and the development of resistance to drugs. One way of addressing those limitations has been to target its potential allosteric sites, shortly called allo-targeting, in conjunction with, or separately from, its conserved catalytic/orthosteric site that has been widely exploited. Allosteric regulation has gained importance as an alternative to overcome the drawbacks associated with the indiscriminate effect of targeting the active site, and it turned out to be particularly useful for these highly promiscuous and broadly shared kinase domains. Yet, allo-targeting often faces challenges as the allosteric sites are not as clearly defined as its orthosteric sites, and the effect on the protein function may not be unambiguously assessed. A robust understanding of the consequence of site-specific allo-targeting on the conformational dynamics of the target protein is essential to design effective allo-targeting strategies. Recent years have seen important advances in in silico identification of druggable sites and distinguishing among them those sites expected to allosterically mediate conformational switches essential to signal transmission. The present opinion underscores the utility of such computational approaches applied to the kinase domain, with the help of comparison between computational predictions and experimental observations.
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Affiliation(s)
- Ji Young Lee
- Laufer Center for Physical & Quantitative Biology, Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, NY 11794, USA
| | - Emma Gebauer
- Laufer Center for Physical & Quantitative Biology, Department of Pharmacological Sciences, School of Medicine, Stony Brook University, NY 11794, USA
| | - Markus A Seeliger
- Laufer Center for Physical & Quantitative Biology, Department of Pharmacological Sciences, School of Medicine, Stony Brook University, NY 11794, USA.
| | - Ivet Bahar
- Laufer Center for Physical & Quantitative Biology, Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, NY 11794, USA.
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Tee WV, Berezovsky IN. Allosteric drugs: New principles and design approaches. Curr Opin Struct Biol 2024; 84:102758. [PMID: 38171188 DOI: 10.1016/j.sbi.2023.102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Focusing on an important biomedical implication of allostery - design of allosteric drugs, we describe characteristics of allosteric sites, effectors, and their modes of actions distinguishing them from the orthosteric counterparts and calling for new principles and protocols in the quests for allosteric drugs. We show the importance of considering both binding affinity and allosteric signaling in establishing the structure-activity relationships (SARs) toward design of allosteric effectors, arguing that pairs of allosteric sites and their effector ligands - the site-effector pairs - should be generated and adjusted simultaneously in the framework of what we call directed design protocol. Key ideas and approaches for designing allosteric effectors including reverse perturbation, targeted and agnostic analysis are also discussed here. Several promising computational approaches are highlighted, along with the need for and potential advantages of utilizing generative models to facilitate discovery/design of new allosteric drugs.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671.
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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