---
OA_place: publisher
OA_type: hybrid
_id: '19701'
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.'
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).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Pieter Rein Ten
full_name: Wolde, Pieter Rein Ten
last_name: Wolde
citation:
ama: Tkačik G, Wolde PRT. Information processing in biochemical networks. Annual
Review of Biophysics. 2025;54:249-274. doi:10.1146/annurev-biophys-060524-102720
apa: Tkačik, G., & Wolde, P. R. T. (2025). Information processing in biochemical
networks. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-060524-102720
chicago: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical
Networks.” Annual Review of Biophysics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-biophys-060524-102720.
ieee: G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,”
Annual Review of Biophysics, 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.
mla: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical
Networks.” Annual Review of Biophysics, vol. 54, Annual Reviews, 2025,
pp. 249–74, doi:10.1146/annurev-biophys-060524-102720.
short: G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.
corr_author: '1'
date_created: 2025-05-18T22:02:50Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-08-12T09:25:42Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1146/annurev-biophys-060524-102720
external_id:
isi:
- '001488641500013'
pmid:
- '39929539'
file:
- access_level: open_access
checksum: 9ab623b2bc45dcd5fdd2c9577ea8ae9f
content_type: application/pdf
creator: dernst
date_created: 2025-05-19T07:55:51Z
date_updated: 2025-05-19T07:55:51Z
file_id: '19710'
file_name: 2025_AnnualReviewBiophysics_Tkacik.pdf
file_size: 317925
relation: main_file
success: 1
file_date_updated: 2025-05-19T07:55:51Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 249-274
pmid: 1
project:
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Information processing in biochemical networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18910'
abstract:
- lang: eng
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.
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.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gilad
full_name: Haran, Gilad
last_name: Haran
citation:
ama: Schanda P, Haran G. NMR and single-molecule FRET insights into fast protein
motions and their relation to function. Annual Review of Biophysics. 2024;53:247-273.
doi:10.1146/annurev-biophys-070323-022428
apa: Schanda, P., & Haran, G. (2024). NMR and single-molecule FRET insights
into fast protein motions and their relation to function. Annual Review of
Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-070323-022428
chicago: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights
into Fast Protein Motions and Their Relation to Function.” Annual Review of
Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-070323-022428.
ieee: P. Schanda and G. Haran, “NMR and single-molecule FRET insights into fast
protein motions and their relation to function,” Annual Review of Biophysics,
vol. 53. Annual Reviews, pp. 247–273, 2024.
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.
mla: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into
Fast Protein Motions and Their Relation to Function.” Annual Review of Biophysics,
vol. 53, Annual Reviews, 2024, pp. 247–73, doi:10.1146/annurev-biophys-070323-022428.
short: P. Schanda, G. Haran, Annual Review of Biophysics 53 (2024) 247–273.
corr_author: '1'
date_created: 2025-01-27T13:40:34Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-09T12:06:24Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1146/annurev-biophys-070323-022428
external_id:
isi:
- '001278237500012'
pmid:
- '38346243'
file:
- access_level: open_access
checksum: c90861542ae3f9147939030d5bafed3c
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:44:59Z
date_updated: 2025-01-27T13:44:59Z
file_id: '18911'
file_name: 2024_AnnualReviews_Schanda.pdf
file_size: 3025589
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:44:59Z
has_accepted_license: '1'
intvolume: ' 53'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 247-273
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
issn:
- 1936-122X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: NMR and single-molecule FRET insights into fast protein motions and their relation
to function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 53
year: '2024'
...
---
_id: '17325'
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.
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.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Wei Chang
full_name: Lo, Wei Chang
last_name: Lo
- first_name: Ekaterina
full_name: Krasnopeeva, Ekaterina
id: 1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A
last_name: Krasnopeeva
- first_name: Teuta
full_name: Pilizota, Teuta
last_name: Pilizota
citation:
ama: Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annual Review
of Biophysics. 2024;53:487-510. doi:10.1146/annurev-biophys-030822-032215
apa: Lo, W. C., Krasnopeeva, E., & Pilizota, T. (2024). Bacterial Electrophysiology.
Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-030822-032215
chicago: Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.”
Annual Review of Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-030822-032215.
ieee: W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,”
Annual Review of Biophysics, 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.
mla: Lo, Wei Chang, et al. “Bacterial Electrophysiology.” Annual Review of Biophysics,
vol. 53, Annual Reviews, 2024, pp. 487–510, doi:10.1146/annurev-biophys-030822-032215.
short: W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024)
487–510.
date_created: 2024-07-28T22:01:09Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T08:34:43Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1146/annurev-biophys-030822-032215
external_id:
isi:
- '001278237500021'
pmid:
- '38382113'
file:
- access_level: open_access
checksum: e0505553b3cee624fa865f0cc5a99ecc
content_type: application/pdf
creator: dernst
date_created: 2024-07-29T10:56:01Z
date_updated: 2024-07-29T10:56:01Z
file_id: '17339'
file_name: 2024_AnnualReviewBiophys_Lo.pdf
file_size: 1276645
relation: main_file
success: 1
file_date_updated: 2024-07-29T10:56:01Z
has_accepted_license: '1'
intvolume: ' 53'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 487-510
pmid: 1
project:
- _id: eb872896-77a9-11ec-83b8-f59a38ec17f8
grant_number: ALTF 44-2021
name: 'Bacterial cytoplasm glass transition: passive physiological switch or active
survival strategy'
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
issn:
- 1936-122X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bacterial Electrophysiology
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 53
year: '2024'
...