1
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Jin S, Ahn Y, Park J, Park M, Lee S, Lee WJ, Seo D. Temporal Patterns of Angular Displacement of Endosomes: Insights into Motor Protein Exchange Dynamics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306849. [PMID: 38828676 PMCID: PMC11304332 DOI: 10.1002/advs.202306849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/24/2024] [Indexed: 06/05/2024]
Abstract
The material transport system, facilitated by motor proteins, plays a vital role in maintaining a non-equilibrium cellular state. However, understanding the temporal coordination of motor protein activity requires an advanced imaging technique capable of measuring 3D angular displacement in real-time. In this study, a Fourier transform-based plasmonic dark-field microscope has been developed using anisotropic nanoparticles, enabling the prolonged and simultaneous observation of endosomal lateral and rotational motion. A sequence of discontinuous 3D angular displacements has been observed during the pause and run phases of transport. Notably, a serially correlated temporal pattern in the intermittent rotational events has been demonstrated during the tug-of-war mechanism, indicating Markovian switching between the exploitational and explorational modes of motor protein exchange prior to resuming movement. Alterations in transition frequency and the exploitation-to-exploration ratio upon dynein inhibitor treatment highlight the relationship between disrupted motor coordination and reduced endosomal transport efficiency. Collectively, these results suggest the importance of orchestrated temporal motor protein patterns for efficient cellular transport.
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Affiliation(s)
- Siwoo Jin
- Department of Physics and ChemistryDGISTDaegu42988Republic of Korea
| | - Yongdeok Ahn
- Department of Physics and ChemistryDGISTDaegu42988Republic of Korea
| | - Jiseong Park
- Department of Physics and ChemistryDGISTDaegu42988Republic of Korea
| | - Minsoo Park
- Department of Physics and ChemistryDGISTDaegu42988Republic of Korea
| | - Sang‐Chul Lee
- Division of Nanotechnology, and Department of DGISTDaegu42988Republic of Korea
| | - Wonhee J. Lee
- Department of Physics and ChemistryDGISTDaegu42988Republic of Korea
| | - Daeha Seo
- Department of Physics and ChemistryDGISTDaegu42988Republic of Korea
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2
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Michaelian K. The Pigment World: Life's Origins as Photon-Dissipating Pigments. Life (Basel) 2024; 14:912. [PMID: 39063667 PMCID: PMC11277707 DOI: 10.3390/life14070912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Many of the fundamental molecules of life share extraordinary pigment-like optical properties in the long-wavelength UV-C spectral region. These include strong photon absorption and rapid (sub-pico-second) dissipation of the induced electronic excitation energy into heat through peaked conical intersections. These properties have been attributed to a "natural selection" of molecules resistant to the dangerous UV-C light incident on Earth's surface during the Archean. In contrast, the "thermodynamic dissipation theory for the origin of life" argues that, far from being detrimental, UV-C light was, in fact, the thermodynamic potential driving the dissipative structuring of life at its origin. The optical properties were thus the thermodynamic "design goals" of microscopic dissipative structuring of organic UV-C pigments, today known as the "fundamental molecules of life", from common precursors under this light. This "UV-C Pigment World" evolved towards greater solar photon dissipation through more complex dissipative structuring pathways, eventually producing visible pigments to dissipate less energetic, but higher intensity, visible photons up to wavelengths of the "red edge". The propagation and dispersal of organic pigments, catalyzed by animals, and their coupling with abiotic dissipative processes, such as the water cycle, culminated in the apex photon dissipative structure, today's biosphere.
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Affiliation(s)
- Karo Michaelian
- Department of Nuclear Physics and Application of Radiation, Instituto de Física, Universidad Nacional Autónoma de México, Circuito Interior de la Investigación Científica, Cuidad Universitaria, Cuidad de México CP 04510, Mexico
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3
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Liu Y, Zhang SY, Kleijn IT, Stumpf MPH. Approximate Bayesian computation for inferring Waddington landscapes from single-cell data. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231697. [PMID: 39076359 PMCID: PMC11285904 DOI: 10.1098/rsos.231697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/01/2024] [Indexed: 07/31/2024]
Abstract
Single-cell technologies allow us to gain insights into cellular processes at unprecedented resolution. In stem cell and developmental biology snapshot data allow us to characterize how the transcriptional states of cells change between successive cell types. Here, we show how approximate Bayesian computation (ABC) can be employed to calibrate mathematical models against single-cell data. In our simulation study, we demonstrate the pivotal role of the adequate choice of distance measures appropriate for single-cell data. We show that for good distance measures, notably optimal transport with the Sinkhorn divergence, we can infer parameters for mathematical models from simulated single-cell data. We show that the ABC posteriors can be used (i) to characterize parameter sensitivity and identify dependencies between different parameters and (ii) to construct representations of the Waddington or epigenetic landscape, which forms a popular and interpretable representation of the developmental dynamics. In summary, these results pave the way for fitting mechanistic models of stem cell differentiation to single-cell data.
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Affiliation(s)
- Yujing Liu
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Stephen Y. Zhang
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | | | - Michael P. H. Stumpf
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- School of BioScience, University of Melbourne, Melbourne, Australia
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4
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Tangde VM, Bhalekar AA, Andresen B. Thermodynamic Stability Theories of Irreversible Processes and the Fourth Law of Thermodynamics. ENTROPY (BASEL, SWITZERLAND) 2024; 26:442. [PMID: 38920451 PMCID: PMC11202706 DOI: 10.3390/e26060442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024]
Abstract
Three approaches for determining the thermodynamic stability of irreversible processes are described in generalized formulations. The simplest is the Gibbs-Duhem theory, specialized to irreversible trajectories, which uses the concept of virtual displacement in the reverse direction. Its only drawback is that even a trajectory leading to an explosion is identified as a thermodynamically stable motion. In the second approach, we use a thermodynamic Lyapunov function and its time rate from the Lyapunov thermodynamic stability theory (LTS, previously known as CTTSIP). In doing so, we demonstrate that the second differential of entropy, a frequently used Lyapunov function, is useful only for investigating the stability of equilibrium states. Nonequilibrium steady states do not qualify. Without using explicit perturbation coordinates, we further identify asymptotic thermodynamic stability and thermodynamic stability under constantly acting disturbances of unperturbed trajectories as well as of nonequilibrium steady states. The third approach is also based on the Lyapunov function from LTS, but here we additionally use the rates of perturbation coordinates, based on the Gibbs relations and without using their explicit expressions, to identify not only asymptotic thermodynamic stability but also thermodynamic stability under constantly acting disturbances. Only those trajectories leading to an infinite rate of entropy production (unstable states) are excluded from this conclusion. Finally, we use these findings to formulate the Fourth Law of thermodynamics based on the thermodynamic stability. It is a comprehensive statement covering all nonequilibrium trajectories, close to as well as far from equilibrium. Unlike previous suggested "fourth laws", this one meets the same level of generality that is associated with the original zeroth to third laws. The above is illustrated using the Schlögl reaction with its multiple steady states in certain regions of operation.
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Affiliation(s)
- Vijay M. Tangde
- Department of Chemistry, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440 033, India; (V.M.T.); (A.A.B.)
| | - Anil A. Bhalekar
- Department of Chemistry, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440 033, India; (V.M.T.); (A.A.B.)
| | - Bjarne Andresen
- Niels Bohr Institute, University of Copenhagen, Jagtvej 155 A, DK-2200 Copenhagen N, Denmark
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5
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Zhu L, Wang J. Quantifying Landscape-Flux via Single-Cell Transcriptomics Uncovers the Underlying Mechanism of Cell Cycle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308879. [PMID: 38353329 DOI: 10.1002/advs.202308879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/23/2024] [Indexed: 04/25/2024]
Abstract
Recent developments in single-cell sequencing technology enable the acquisition of entire transcriptome data. Understanding the underlying mechanism and identifying the driving force of transcriptional regulation governing cell function directly from these data remains challenging. This study reconstructs a continuous vector field of the cell cycle based on discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium dynamic landscape-flux. It reveals that large fluctuations disrupt the global landscape and genetic perturbations alter landscape-flux, thus identifying key genes in maintaining cell cycle dynamics and predicting associated functional effects. Additionally, it quantifies the fundamental energy cost of the cell cycle initiation and unveils that sustaining the cell cycle requires curl flux and dissipation to maintain the oscillatory phase coherence. This study enables the inference of the cell cycle gene regulatory networks directly from the single-cell transcriptomic data, including the feedback mechanisms and interaction intensity. This provides a golden opportunity to experimentally verify the landscape-flux theory and also obtain its associated quantifications. It also offers a unique framework for combining the landscape-flux theory and single-cell high-through sequencing experiments for understanding the underlying mechanisms of the cell cycle and can be extended to other nonequilibrium biological processes, such as differentiation development and disease pathogenesis.
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Affiliation(s)
- Ligang Zhu
- College of Physics, Jilin University, Changchun, 130021, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Jin Wang
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China
- Department of Chemistry, Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA
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6
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Pham AT, Mani M, Wang X, Vafabakhsh R. Multiscale biophysical analysis of nucleolus disassembly during mitosis. Proc Natl Acad Sci U S A 2024; 121:e2312250121. [PMID: 38285946 PMCID: PMC10861868 DOI: 10.1073/pnas.2312250121] [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: 07/19/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024] Open
Abstract
During cell division, precise and regulated distribution of cellular material between daughter cells is a critical step and is governed by complex biochemical and biophysical mechanisms. To achieve this, membraneless organelles and condensates often require complete disassembly during mitosis. The biophysical principles governing the disassembly of condensates remain poorly understood. Here, we used a physical biology approach to study how physical and material properties of the nucleolus, a prominent nuclear membraneless organelle in eukaryotic cells, change during mitosis and across different scales. We found that nucleolus disassembly proceeds continuously through two distinct phases with a slow and reversible preparatory phase followed by a rapid irreversible phase that was concurrent with the nuclear envelope breakdown. We measured microscopic properties of nucleolar material including effective diffusion rates and binding affinities as well as key macroscopic properties of surface tension and bending rigidity. By incorporating these measurements into the framework of critical phenomena, we found evidence that near mitosis surface tension displays a power-law behavior as a function of biochemically modulated interaction strength. This two-step disassembly mechanism maintains structural and functional stability of nucleolus while enabling its rapid and efficient disassembly in response to cell cycle cues.
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Affiliation(s)
- An T. Pham
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL60208
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL60208
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
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7
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Duranti C, Iorio J, Bagni G, Chioccioli Altadonna G, Fillion T, Lulli M, D'Alessandro FN, Montalbano A, Lastraioli E, Fanelli D, Coppola S, Schmidt T, Piazza F, Becchetti A, Arcangeli A. Integrins regulate hERG1 dynamics by girdin-dependent Gαi3: signaling and modeling in cancer cells. Life Sci Alliance 2024; 7:e202302135. [PMID: 37923359 PMCID: PMC10624597 DOI: 10.26508/lsa.202302135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
The hERG1 potassium channel is aberrantly over expressed in tumors and regulates the cancer cell response to integrin-dependent adhesion. We unravel a novel signaling pathway by which integrin engagement by the ECM protein fibronectin promotes hERG1 translocation to the plasma membrane and its association with β1 integrins, by activating girdin-dependent Gαi3 proteins and protein kinase B (Akt). By sequestering hERG1, β1 integrins make it avoid Rab5-mediated endocytosis, where unbound channels are degraded. The cycle of hERG1 expression determines the resting potential (Vrest) oscillations and drives the cortical f-actin dynamics and thus cell motility. To interpret the slow biphasic kinetics of hERG1/β1 integrin interplay, we developed a mathematical model based on a generic balanced inactivation-like module. Integrin-mediated cell adhesion triggers two contrary responses: a rapid stimulation of hERG1/β1 complex formation, followed by a slow inhibition which restores the initial condition. The protracted hERG1/β1 integrin cycle determines the slow time course and cyclic behavior of cell migration in cancer cells.
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Affiliation(s)
- Claudia Duranti
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
| | - Jessica Iorio
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
| | - Giacomo Bagni
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
| | - Ginevra Chioccioli Altadonna
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Thibault Fillion
- https://ror.org/04jr1s763 Department of Physics, University of Florence, and Florence Section of INFN, Florence, Italy
- Université d'Orléans and Centre de Biophysique Moléculaire (CBM), CNRS UPR 4301, Orléans, France
| | - Matteo Lulli
- https://ror.org/04jr1s763 Department of Experimental and Clinical Biochemical Sciences, Section of General Pathology, University of Florence, Florence, Italy
| | - Franco Nicolas D'Alessandro
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alberto Montalbano
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
| | - Elena Lastraioli
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
- CSDC (Center for the Study of complex dynamics), University of Florence, Florence, Italy
| | - Duccio Fanelli
- https://ror.org/04jr1s763 Department of Physics, University of Florence, and Florence Section of INFN, Florence, Italy
- CSDC (Center for the Study of complex dynamics), University of Florence, Florence, Italy
| | - Stefano Coppola
- Department of Physics, University of Leiden, Leiden, Netherlands
| | - Thomas Schmidt
- Department of Physics, University of Leiden, Leiden, Netherlands
| | - Francesco Piazza
- https://ror.org/04jr1s763 Department of Physics, University of Florence, and Florence Section of INFN, Florence, Italy
- Université d'Orléans and Centre de Biophysique Moléculaire (CBM), CNRS UPR 4301, Orléans, France
- CSDC (Center for the Study of complex dynamics), University of Florence, Florence, Italy
| | - Andrea Becchetti
- https://ror.org/01ynf4891 Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Annarosa Arcangeli
- https://ror.org/04jr1s763 Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Florence, Italy
- CSDC (Center for the Study of complex dynamics), University of Florence, Florence, Italy
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8
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Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ. Mesoscale molecular assembly is favored by the active, crowded cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558334. [PMID: 37781612 PMCID: PMC10541124 DOI: 10.1101/2023.09.19.558334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The mesoscale organization of molecules into membraneless biomolecular condensates is emerging as a key mechanism of rapid spatiotemporal control in cells1. Principles of biomolecular condensation have been revealed through in vitro reconstitution2. However, intracellular environments are much more complex than test-tube environments: They are viscoelastic, highly crowded at the mesoscale, and are far from thermodynamic equilibrium due to the constant action of energy-consuming processes3. We developed synDrops, a synthetic phase separation system, to study how the cellular environment affects condensate formation. Three key features enable physical analysis: synDrops are inducible, bioorthogonal, and have well-defined geometry. This design allows kinetic analysis of synDrop assembly and facilitates computational simulation of the process. We compared experiments and simulations to determine that macromolecular crowding promotes condensate nucleation but inhibits droplet growth through coalescence. ATP-dependent cellular activities help overcome the frustration of growth. In particular, actomyosin dynamics potentiate droplet growth by reducing confinement and elasticity in the mammalian cytoplasm, thereby enabling synDrop coarsening. Our results demonstrate that mesoscale molecular assembly is favored by the combined effects of crowding and active matter in the cytoplasm. These results move toward a better predictive understanding of condensate formation in vivo.
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Affiliation(s)
- Tong Shu
- Institute for Systems Genetics, NYU Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Gaurav Mitra
- Department of Chemistry, New York University, New York, New York, USA
| | | | | | - Emmanuel D. Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Glen M. Hocky
- Department of Chemistry, New York University, New York, New York, USA
- Simons Center for Computational Physical Chemistry, New York University, New York, New York, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
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9
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Michaelian K. The Non-Equilibrium Thermodynamics of Natural Selection: From Molecules to the Biosphere. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1059. [PMID: 37510006 PMCID: PMC10378079 DOI: 10.3390/e25071059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
Evolutionary theory suggests that the origin, persistence, and evolution of biology is driven by the "natural selection" of characteristics improving the differential reproductive success of the organism in the given environment. The theory, however, lacks physical foundation, and, therefore, at best, can only be considered a heuristic narrative, of some utility for assimilating the biological and paleontological data at the level of the organism. On deeper analysis, it becomes apparent that this narrative is plagued with problems and paradoxes. Alternatively, non-equilibrium thermodynamic theory, derived from physical law, provides a physical foundation for describing material interaction with its environment at all scales. Here we describe a "natural thermodynamic selection" of characteristics of structures (or processes), based stochastically on increases in the global rate of dissipation of the prevailing solar spectrum. Different mechanisms of thermodynamic selection are delineated for the different biotic-abiotic levels, from the molecular level at the origin of life, up to the level of the present biosphere with non-linear coupling of biotic and abiotic processes. At the levels of the organism and the biosphere, the non-equilibrium thermodynamic description of evolution resembles, respectively, the Darwinian and Gaia descriptions, although the underlying mechanisms and the objective function of selection are fundamentally very different.
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Affiliation(s)
- Karo Michaelian
- Department of Nuclear Physics and Application of Radiation, Instituto de Física, Universidad Nacional Autónoma de México, Circuito Interior de la Investigación Científica, Ciudad Universitaria, Mexico City C.P. 04510, Mexico
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10
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Chu X, Wang J. Insights into the cell fate decision-making processes from chromosome structural reorganizations. BIOPHYSICS REVIEWS 2022; 3:041402. [PMID: 38505520 PMCID: PMC10914134 DOI: 10.1063/5.0107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/25/2022] [Indexed: 03/21/2024]
Abstract
The cell fate decision-making process, which provides the capability of a cell transition to a new cell type, involves the reorganizations of 3D genome structures. Currently, the high temporal resolution picture of how the chromosome structural rearrangements occur and further influence the gene activities during the cell-state transition is still challenging to acquire. Here, we study the chromosome structural reorganizations during the cell-state transitions among the pluripotent embryonic stem cell, the terminally differentiated normal cell, and the cancer cell using a nonequilibrium landscape-switching model implemented in the molecular dynamics simulation. We quantify the chromosome (de)compaction pathways during the cell-state transitions and find that the two pathways having the same destinations can merge prior to reaching the final states. The chromosomes at the merging states have similar structural geometries but can differ in long-range compartment segregation and spatial distribution of the chromosomal loci and genes, leading to cell-type-specific transition mechanisms. We identify the irreversible pathways of chromosome structural rearrangements during the forward and reverse transitions connecting the same pair of cell states, underscoring the critical roles of nonequilibrium dynamics in the cell-state transitions. Our results contribute to the understanding of the cell fate decision-making processes from the chromosome structural perspective.
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Affiliation(s)
- Xiakun Chu
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong 511400, China
| | - Jin Wang
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
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11
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Arceo XG, Koslover EF, Zid BM, Brown AI. Mitochondrial mRNA localization is governed by translation kinetics and spatial transport. PLoS Comput Biol 2022; 18:e1010413. [PMID: 35984860 PMCID: PMC9432724 DOI: 10.1371/journal.pcbi.1010413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/31/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
For many nuclear-encoded mitochondrial genes, mRNA localizes to the mitochondrial surface co-translationally, aided by the association of a mitochondrial targeting sequence (MTS) on the nascent peptide with the mitochondrial import complex. For a subset of these co-translationally localized mRNAs, their localization is dependent on the metabolic state of the cell, while others are constitutively localized. To explore the differences between these two mRNA types we developed a stochastic, quantitative model for MTS-mediated mRNA localization to mitochondria in yeast cells. This model includes translation, applying gene-specific kinetics derived from experimental data; and diffusion in the cytosol. Even though both mRNA types are co-translationally localized we found that the steady state number, or density, of ribosomes along an mRNA was insufficient to differentiate the two mRNA types. Instead, conditionally-localized mRNAs have faster translation kinetics which modulate localization in combination with changes to diffusive search kinetics across metabolic states. Our model also suggests that the MTS requires a maturation time to become competent to bind mitochondria. Our work indicates that yeast cells can regulate mRNA localization to mitochondria by controlling mitochondrial volume fraction (influencing diffusive search times) and gene translation kinetics (adjusting mRNA binding competence) without the need for mRNA-specific binding proteins. These results shed light on both global and gene-specific mechanisms that enable cells to alter mRNA localization in response to changing metabolic conditions.
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Affiliation(s)
- Ximena G. Arceo
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Elena F. Koslover
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Brian M. Zid
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Aidan I. Brown
- Department of Physics, Ryerson University, Toronto, Canada
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12
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Anglès F, Wang C, Balch WE. Spatial covariance analysis reveals the residue-by-residue thermodynamic contribution of variation to the CFTR fold. Commun Biol 2022; 5:356. [PMID: 35418593 PMCID: PMC9008016 DOI: 10.1038/s42003-022-03302-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although the impact of genome variation on the thermodynamic properties of function on the protein fold has been studied in vitro, it remains a challenge to assign these relationships across the entire polypeptide sequence in vivo. Using the Gaussian process regression based principle of Spatial CoVariance, we globally assign on a residue-by-residue basis the biological thermodynamic properties that contribute to the functional fold of CFTR in the cell. We demonstrate the existence of a thermodynamically sensitive region of the CFTR fold involving the interface between NBD1 and ICL4 that contributes to its export from endoplasmic reticulum. At the cell surface a new set of residues contribute uniquely to the management of channel function. These results support a general ‘quality assurance’ view of global protein fold management as an SCV principle describing the differential pre- and post-ER residue interactions contributing to compartmentalization of the energetics of the protein fold for function. Our results set the stage for future analyses of the quality systems managing protein sequence-to-function-to-structure broadly encompassing genome design leading to protein function in complex cellular relationships responsible for diversity and fitness in biology in response to the environment. Spatial covariance analysis shows how each residue in the critical fold region of chloride channel CFTR, defective in cystic fibrosis patients, contributes to CFTR’s export from the endoplasmic reticulum and function in the cell.
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Affiliation(s)
- Frédéric Anglès
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Chao Wang
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - William E Balch
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA.
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13
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Cook J, Pawar S, Endres RG. Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium. PLoS Comput Biol 2021; 17:e1009643. [PMID: 34860834 PMCID: PMC8673627 DOI: 10.1371/journal.pcbi.1009643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 12/15/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities. There is a growing interest in microbial communities due to their important role in biogeochemical cycling as well as plant and animal health. Although our understanding of thermodynamic constraints on individual cells is rapidly improving, the impact of these constraints on complex microbial communities remains largely unexplored theoretically and empirically. Here, we develop a new microbial community model which allows thermodynamic efficiency and entropy production to be calculated directly. We find that availability of substrates with greater free-energy allows for a faster rate of niche generation, leading to higher final species diversity. We also show that when the free-energy availability is low, species with reactions close to thermodynamic equilibrium are favoured, leading to more diverse and efficient communities. In addition to the conventional interaction types (competition and facilitation), our model reveals the existence of two novel interaction types mediated by products rather than substrates. Though the conventional interactions are generally the strongest, the novel interaction types are significant when free-energy availability is low. Our results suggest that non-equilibrium thermodynamics need to be considered when studying microbial community dynamics.
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Affiliation(s)
- Jacob Cook
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
- * E-mail: (JC); (RGE)
| | - Samraat Pawar
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Robert G. Endres
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
- * E-mail: (JC); (RGE)
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Chu X, Wang J. Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics. PLoS Comput Biol 2021; 17:e1009596. [PMID: 34752443 PMCID: PMC8631624 DOI: 10.1371/journal.pcbi.1009596] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/30/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer reflects the dysregulation of the underlying gene network, which is strongly related to the 3D genome organization. Numerous efforts have been spent on experimental characterizations of the structural alterations in cancer genomes. However, there is still a lack of genomic structural-level understanding of the temporal dynamics for cancer initiation and progression. Here, we use a landscape-switching model to investigate the chromosome structural transition during the cancerization and reversion processes. We find that the chromosome undergoes a non-monotonic structural shape-changing pathway with initial expansion followed by compaction during both of these processes. Furthermore, our analysis reveals that the chromosome with a more expanding structure than those at both the normal and cancer cell during cancerization exhibits a sparse contact pattern, which shows significant structural similarity to the one at the embryonic stem cell in many aspects, including the trend of contact probability declining with the genomic distance, the global structural shape geometry and the spatial distribution of loci on the chromosome. In light of the intimate structure-function relationship at the chromosomal level, we further describe the cell state transition processes by the chromosome structural changes, suggesting an elevated cell stemness during the formation of the cancer cells. We show that cell cancerization and reversion are highly irreversible processes in terms of the chromosome structural transition pathways, spatial repositioning of chromosomal loci and hysteresis loop of contact evolution analysis. Our model draws a molecular-scale picture of cell cancerization from the chromosome structural perspective. The process contains initial reprogramming towards the stem cell followed by the differentiation towards the cancer cell, accompanied by an initial increase and subsequent decrease of the cell stemness.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York, United States of America
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York, United States of America
- Department of Physics and Astronomy, State University of New York at Stony Brook, Stony Brook, New York, United States of America
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15
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Weng J, Wang A, Zhang D, Liao C, Li G. A double bilayer to study the nonequilibrium environmental response of GIRK2 in complex states. Phys Chem Chem Phys 2021; 23:15784-15795. [PMID: 34286758 DOI: 10.1039/d1cp01785c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G protein-gated inwardly rectifying potassium (GIRK) channels play essential roles in electrical signaling in neurons and muscle cells. Nonequilibrium environments provide crucial driving forces behind many cellular events. Here, we apply the antiparallel alignment double bilayer model to study GIRK2 in response to the time-dependent membrane potential. Using molecular dynamics and umbrella sampling, we examined the time-dependent environmental impact on the ion conduction, energy basis, and primary motions of GIRK2 in different complex states with phosphatidylinositol-4,5-bisphosphate (PIP2) and G-protein βγ subunits (Gβγ). The antiparallel alignment double bilayer model enables us to study the transport performance in inward and outward K+ and mixed K+ and Na+. We obtained the recoverable discharge process of GIRK2 complexed with both PIP2 and Gβγ, compared with occasional conduction under PIP2-only regulation. Calculations of potential of mean force suggest different regulation by the helix bundle crossing (HBC) gate and G-loop gate regarding different complex states and under a membrane potential. In a nonequilibrium environment, distinct functional rocking motions of GIRK2 were identified under strengthened correlations between the transmembrane helices and downstream cytoplasmic domains with binding of PIP2, cations, and Gβγ. The findings suggest the potential domain motions and dynamics associated with a nonequilibrium environment and highlight the application of the antiparallel alignment double bilayer model to investigate factors in an asymmetric environment.
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Affiliation(s)
- Junben Weng
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China. and University of Chinese Academy of Sciences, Beijing, China
| | - Anhui Wang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Dinglin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China. and University of Chinese Academy of Sciences, Beijing, China
| | - Chenyi Liao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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Dutta A, Chattopadhyay H. A Brief on Biological Thermodynamics for Human Physiology. J Biomech Eng 2021; 143:070802. [PMID: 33704420 DOI: 10.1115/1.4050458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 11/08/2022]
Abstract
Thermodynamics, the science of energy interactions, governs the direction of processes found in nature. While the subject finds wide applications in science and technology, its connection to biological sciences and in particular to bio-engineering is becoming increasingly important. In this work, after a brief introduction to the fundamental concepts in thermodynamics, we focus on its application in human physiology. A review of application of thermodynamics to the interaction between human body and environment is presented. Research works on biological systems such as the nervous system and the cardiovascular systems are summarized. The thermodynamics of metabolism is reviewed, and finally, the role of the subject in understanding and combating diseases is highlighted.
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Affiliation(s)
- Abhijit Dutta
- Department of Mechanical Engineering, MCKV Institute of Engineering, Howrah 711204, India; Department of Mechanical Engineering, Jadavpur University, Kolkata 700032, India
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17
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Physical bioenergetics: Energy fluxes, budgets, and constraints in cells. Proc Natl Acad Sci U S A 2021; 118:2026786118. [PMID: 34140336 DOI: 10.1073/pnas.2026786118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. Here we review recent advances and discuss open questions and challenges in physical bioenergetics.
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18
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Dutta M, Jana B. Computational modeling of dynein motor proteins at work. Chem Commun (Camb) 2021; 57:272-283. [PMID: 33332489 DOI: 10.1039/d0cc05857b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, we will summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. We implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes we employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here we explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.
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Affiliation(s)
- Mandira Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata - 700032, India.
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