Networks of Networks: An Essay on Multi-Level Biological Organization
Open accessAbstract
The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology.
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The cellular signaling is organized in a nesting doll-like organization, a complex network of networks, with even a single node in a protein-protein interaction network representing a multileveled network itself.
“The problem is further complicated by the nesting doll (Matryoshka)-like organization of the cellular signaling, which represents a complex network of networks, with even a single node in a protein–protein interaction network representing a multileveled network itself [54].”
From Intrinsically disordered proteins play diverse roles in cell signaling (2022) · cites this paper as [54]
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Self-citationShimizu, K., & Toh, H. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.088 · Cited by 62 · see citing works
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Zhang, L., Li, M., & Liu, Z. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006393 · Cited by 21 · see citing works
Kahali, B., & Ghosh, T. C. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2012.706071 · Cited by 15 · see citing works
Ordered Disorder of the Astrocytic Dystrophin-Associated Protein Complex in the Norm and Pathology
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Intrinsically disordered proteins play diverse roles in cell signaling
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Self-citation
- Authors
- Uversky, V. N., & Giuliani, A.
- Affiliations
- University of South Florida (US)
- Istituto Superiore di Sanità (IT)
- Corresponding author
- Uversky, Vladimir N.
- Giuliani, Alessandro
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2021-06-21
- Volume
- 12
- Pages
- 706260-706260
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC8255927
- OpenAlex
- W3175706715
- Cited by
- 28
- References
- 131
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 7 · 2023: 3 · 2022: 11 · 2021: 1
- FWCI
- 0.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › Complex Network Analysis Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- protein-protein interaction network, allosteric communication, complex systems dynamics, biological causation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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