[{"date_updated":"2025-09-30T12:33:33Z","page":"249-274","project":[{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid","day":"01","external_id":{"pmid":["39929539"],"isi":["001488641500013"]},"corr_author":"1","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"last_name":"Wolde","full_name":"Wolde, Pieter Rein Ten","first_name":"Pieter Rein Ten"}],"_id":"19701","ddc":["570"],"has_accepted_license":"1","publisher":"Annual Reviews","oa":1,"file_date_updated":"2025-05-19T07:55:51Z","scopus_import":"1","publication":"Annual review of biophysics","date_published":"2025-05-01T00:00:00Z","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","doi":"10.1146/annurev-biophys-060524-102720","title":"Information processing in biochemical networks","publication_identifier":{"eissn":["1936-1238"]},"pmid":1,"acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","year":"2025","intvolume":"        54","article_processing_charge":"Yes (in subscription journal)","volume":54,"abstract":[{"lang":"eng","text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components."}],"month":"05","isi":1,"department":[{"_id":"GaTk"}],"status":"public","oa_version":"Published Version","file":[{"file_id":"19710","creator":"dernst","date_created":"2025-05-19T07:55:51Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-05-19T07:55:51Z","file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","file_size":317925,"checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","success":1}],"OA_place":"publisher","citation":{"short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual review of biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>.","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>.","apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual review of biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025.","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual review of biophysics. 54, 249–274."},"date_created":"2025-05-18T22:02:50Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"page":"247-273","date_updated":"2025-09-09T12:06:24Z","day":"01","OA_type":"hybrid","external_id":{"pmid":["38346243"],"isi":["001278237500012"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"}],"publication_status":"published","quality_controlled":"1","corr_author":"1","oa":1,"file_date_updated":"2025-01-27T13:44:59Z","publisher":"Annual Reviews","_id":"18910","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"first_name":"Gilad","last_name":"Haran","full_name":"Haran, Gilad"}],"ddc":["570"],"has_accepted_license":"1","doi":"10.1146/annurev-biophys-070323-022428","type":"journal_article","scopus_import":"1","date_published":"2024-07-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Annual Review of Biophysics","year":"2024","intvolume":"        53","acknowledgement":"G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial Chair. He has been partially funded by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant 742637, SMALLOSTERY), by National Science Foundation–US-Israel Binational Science Foundation grant 2021700, and by an Israel Science Foundation Breakthrough grant (1924/22). P.S. acknowledges funding from the Austrian Science Fund (project “AlloSpace,” I05812) and intramural funding from the Institute of Science and Technology Austria.","pmid":1,"publication_identifier":{"eissn":["1936-1238"],"issn":["1936-122X"]},"title":"NMR and single-molecule FRET insights into fast protein motions and their relation to function","status":"public","department":[{"_id":"PaSc"}],"article_processing_charge":"No","month":"07","volume":53,"isi":1,"abstract":[{"text":"Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2025-01-27T13:40:34Z","article_type":"original","OA_place":"publisher","citation":{"short":"P. Schanda, G. Haran, Annual Review of Biophysics 53 (2024) 247–273.","ama":"Schanda P, Haran G. NMR and single-molecule FRET insights into fast protein motions and their relation to function. <i>Annual Review of Biophysics</i>. 2024;53:247-273. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">10.1146/annurev-biophys-070323-022428</a>","chicago":"Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2024. <a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">https://doi.org/10.1146/annurev-biophys-070323-022428</a>.","mla":"Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.” <i>Annual Review of Biophysics</i>, vol. 53, Annual Reviews, 2024, pp. 247–73, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">10.1146/annurev-biophys-070323-022428</a>.","apa":"Schanda, P., &#38; Haran, G. (2024). NMR and single-molecule FRET insights into fast protein motions and their relation to function. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">https://doi.org/10.1146/annurev-biophys-070323-022428</a>","ista":"Schanda P, Haran G. 2024. NMR and single-molecule FRET insights into fast protein motions and their relation to function. Annual Review of Biophysics. 53, 247–273.","ieee":"P. Schanda and G. Haran, “NMR and single-molecule FRET insights into fast protein motions and their relation to function,” <i>Annual Review of Biophysics</i>, vol. 53. Annual Reviews, pp. 247–273, 2024."},"oa_version":"Published Version","file":[{"success":1,"checksum":"c90861542ae3f9147939030d5bafed3c","content_type":"application/pdf","date_updated":"2025-01-27T13:44:59Z","file_size":3025589,"file_name":"2024_AnnualReviews_Schanda.pdf","access_level":"open_access","date_created":"2025-01-27T13:44:59Z","creator":"dernst","relation":"main_file","file_id":"18911"}]},{"acknowledgement":"We would like to thank all members of the Pilizota lab, as well as Calin Guet, Orkun Soyer, Munehiro Asally, Peter Swain, and in particular Matt Scott and Ariel Amir, for their support, comments, and useful discussions. T.P. and W.-C.L. were supported by the Leverhulme Trust, grant RPG-2019-187, and T.P. is supported by EPSRC Fellowship EP/V03264X/1. E.K. was supported by a European Molecular Biology Organization Long-Term Postdoctoral Fellowship, ALTF 44-2021.","year":"2024","intvolume":"        53","title":"Bacterial Electrophysiology","pmid":1,"publication_identifier":{"issn":["1936-122X"],"eissn":["1936-1238"]},"doi":"10.1146/annurev-biophys-030822-032215","scopus_import":"1","publication":"Annual Review of Biophysics","language":[{"iso":"eng"}],"date_published":"2024-07-01T00:00:00Z","type":"journal_article","article_type":"original","date_created":"2024-07-28T22:01:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","file":[{"checksum":"e0505553b3cee624fa865f0cc5a99ecc","success":1,"file_size":1276645,"date_updated":"2024-07-29T10:56:01Z","file_name":"2024_AnnualReviewBiophys_Lo.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"17339","relation":"main_file","creator":"dernst","date_created":"2024-07-29T10:56:01Z"}],"citation":{"short":"W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024) 487–510.","ama":"Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. <i>Annual Review of Biophysics</i>. 2024;53:487-510. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">10.1146/annurev-biophys-030822-032215</a>","chicago":"Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2024. <a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">https://doi.org/10.1146/annurev-biophys-030822-032215</a>.","apa":"Lo, W. C., Krasnopeeva, E., &#38; Pilizota, T. (2024). Bacterial Electrophysiology. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">https://doi.org/10.1146/annurev-biophys-030822-032215</a>","mla":"Lo, Wei Chang, et al. “Bacterial Electrophysiology.” <i>Annual Review of Biophysics</i>, vol. 53, Annual Reviews, 2024, pp. 487–510, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">10.1146/annurev-biophys-030822-032215</a>.","ieee":"W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,” <i>Annual Review of Biophysics</i>, vol. 53. Annual Reviews, pp. 487–510, 2024.","ista":"Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual Review of Biophysics. 53, 487–510."},"status":"public","article_processing_charge":"Yes (in subscription journal)","volume":53,"abstract":[{"lang":"eng","text":"Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology."}],"month":"07","isi":1,"department":[{"_id":"CaGu"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001278237500021"],"pmid":["38382113"]},"day":"01","project":[{"grant_number":"ALTF 44-2021","name":"Bacterial cytoplasm glass transition: passive physiological switch or active survival strategy","_id":"eb872896-77a9-11ec-83b8-f59a38ec17f8"}],"date_updated":"2025-09-08T08:34:43Z","page":"487-510","file_date_updated":"2024-07-29T10:56:01Z","oa":1,"_id":"17325","author":[{"last_name":"Lo","full_name":"Lo, Wei Chang","first_name":"Wei Chang"},{"first_name":"Ekaterina","id":"1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A","full_name":"Krasnopeeva, Ekaterina","last_name":"Krasnopeeva"},{"first_name":"Teuta","last_name":"Pilizota","full_name":"Pilizota, Teuta"}],"has_accepted_license":"1","ddc":["570"],"publisher":"Annual Reviews","publication_status":"published","quality_controlled":"1"}]