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Song K, Makarov DE, Vouga E. Information-theoretical limit on the estimates of dissipation by molecular machines using single-molecule fluorescence resonance energy transfer experiments. J Chem Phys 2024; 161:044111. [PMID: 39046347 DOI: 10.1063/5.0218040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/05/2024] [Indexed: 07/25/2024] Open
Abstract
Single-molecule fluorescence resonance energy transfer (FRET) experiments are commonly used to study the dynamics of molecular machines. While in vivo molecular processes often break time-reversal symmetry, the temporal directionality of cyclically operating molecular machines is often not evident from single-molecule FRET trajectories, especially in the most common two-color FRET studies. Solving a more quantitative problem of estimating the energy dissipation/entropy production by a molecular machine from single-molecule data is even more challenging. Here, we present a critical assessment of several practical methods of doing so, including Markov-model-based methods and a model-free approach based on an information-theoretical measure of entropy production that quantifies how (statistically) dissimilar observed photon sequences are from their time reverses. The Markov model approach is computationally feasible and may outperform model free approaches, but its performance strongly depends on how well the assumed model approximates the true microscopic dynamics. Markov models are also not guaranteed to give a lower bound on dissipation. Meanwhile, model-free, information-theoretical methods systematically underestimate entropy production at low photoemission rates, and long memory effects in the photon sequences make these methods demanding computationally. There is no clear winner among the approaches studied here, and all methods deserve to belong to a comprehensive data analysis toolkit.
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Affiliation(s)
- Kevin Song
- Department of Computer Science, University of Texas at Austin, Austin, Texas 78712, USA
| | - Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Etienne Vouga
- Department of Computer Science, University of Texas at Austin, Austin, Texas 78712, USA
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Mayer MP, Blair L, Blatch GL, Borges TJ, Chadli A, Chiosis G, de Thonel A, Dinkova-Kostova A, Ecroyd H, Edkins AL, Eguchi T, Fleshner M, Foley KP, Fragkostefanakis S, Gestwicki J, Goloubinoff P, Heritz JA, Heske CM, Hibshman JD, Joutsen J, Li W, Lynes M, Mendillo ML, Mivechi N, Mokoena F, Okusha Y, Prahlad V, Repasky E, Sannino S, Scalia F, Shalgi R, Sistonen L, Sontag E, van Oosten-Hawle P, Vihervaara A, Wickramaratne A, Wang SXY, Zininga T. Stress biology: Complexity and multifariousness in health and disease. Cell Stress Chaperones 2024; 29:143-157. [PMID: 38311120 PMCID: PMC10939078 DOI: 10.1016/j.cstres.2024.01.006] [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] [Indexed: 02/06/2024] Open
Abstract
Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response, unfolded protein response, and integrated stress response, that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate the expression of most genes but increase the expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in the repair of stress-induced damage to macromolecules and cellular structures. Sixty-one years after the discovery of the heat shock response by Ferruccio Ritossa, many aspects of stress biology are still enigmatic. Recent progress in the understanding of stress responses and molecular chaperones was reported at the 12th International Symposium on Heat Shock Proteins in Biology, Medicine and the Environment in the Old Town Alexandria, VA, USA from 28th to 31st of October 2023.
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Affiliation(s)
- Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Laura Blair
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gregory L Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates; Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Thiago J Borges
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Ahmed Chadli
- Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Gabriela Chiosis
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aurélie de Thonel
- CNRS, UMR 7216, 75250 Paris Cedex 13, Paris, France; Univeristy of Paris Diderot, Sorbonne Paris Cité, Paris, France; Département Hospitalo-Universitaire DHU PROTECT, Paris, France
| | - Albena Dinkova-Kostova
- Division of Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Takanori Eguchi
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Monika Fleshner
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | | | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Jason Gestwicki
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jennifer A Heritz
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Christine M Heske
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenny Joutsen
- Department of Pathology, Lapland Central Hospital, Lapland Wellbeing Services County, Rovaniemi, Finland
| | - Wei Li
- Department of Dermatology and the Norris Comprehensive Cancer Center, University of Southern California Keck Medical Center, Los Angeles, CA 90033, USA
| | - Michael Lynes
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nahid Mivechi
- Molecular Chaperone Biology, Medical College of Georgia, Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Fortunate Mokoena
- Department of Biochemistry, North-West University, Mmabatho 2735, South Africa
| | - Yuka Okusha
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Veena Prahlad
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Elizabeth Repasky
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sara Sannino
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Federica Scalia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Emily Sontag
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | | | - Anniina Vihervaara
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Anushka Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn Xiang Yang Wang
- Developmental Therapeutics Program, VCU Comprehensive Massey Cancer Center, VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
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Mistry AC, Chowdhury D, Chakraborty S, Haldar S. Elucidating the novel mechanisms of molecular chaperones by single-molecule technologies. Trends Biochem Sci 2024; 49:38-51. [PMID: 37980187 DOI: 10.1016/j.tibs.2023.10.009] [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: 05/23/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/20/2023]
Abstract
Molecular chaperones play central roles in sustaining protein homeostasis and preventing protein aggregation. Most studies of these systems have been performed in bulk, providing averaged measurements, though recent single-molecule approaches have provided an in-depth understanding of the molecular mechanisms of their activities and structural rearrangements during substrate recognition. Chaperone activities have been observed to be substrate specific, with some associated with ATP-dependent structural dynamics and others via interactions with co-chaperones. This Review aims to describe the novel mechanisms of molecular chaperones as revealed by single-molecule approaches, and to provide insights into their functioning and its implications for protein homeostasis and human diseases.
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Affiliation(s)
- Ayush Chandrakant Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India; Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India; Department of Chemistry, Ashoka University, Sonepat, Haryana 131029, India.
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