Literature DB >> 35170314

Intrinsically Disordered Proteins: Critical Components of the Wetware.

Prakash Kulkarni1, Supriyo Bhattacharya2, Srisairam Achuthan3, Amita Behal1, Mohit Kumar Jolly4, Sourabh Kotnala1, Atish Mohanty1, Govindan Rangarajan5,6, Ravi Salgia1, Vladimir Uversky7,8.   

Abstract

Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.

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Year:  2022        PMID: 35170314      PMCID: PMC9250291          DOI: 10.1021/acs.chemrev.1c00848

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   72.087


  232 in total

Review 1.  Amyloidogenesis of natively unfolded proteins.

Authors:  Vladimir N Uversky
Journal:  Curr Alzheimer Res       Date:  2008-06       Impact factor: 3.498

Review 2.  Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins.

Authors:  Arvind Ramanathan; Heng Ma; Akash Parvatikar; S Chakra Chennubhotla
Journal:  Curr Opin Struct Biol       Date:  2021-01-06       Impact factor: 6.809

3.  Intrinsically disordered proteins and conformational noise: implications in cancer.

Authors:  Gita Mahmoudabadi; Krithika Rajagopalan; Robert H Getzenberg; Sridhar Hannenhalli; Govindan Rangarajan; Prakash Kulkarni
Journal:  Cell Cycle       Date:  2012-12-19       Impact factor: 4.534

Review 4.  Functional roles for noise in genetic circuits.

Authors:  Avigdor Eldar; Michael B Elowitz
Journal:  Nature       Date:  2010-09-09       Impact factor: 49.962

Review 5.  Intrinsically disordered proteins in human diseases: introducing the D2 concept.

Authors:  Vladimir N Uversky; Christopher J Oldfield; A Keith Dunker
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

6.  Phosphorylation-induced Conformational Ensemble Switching in an Intrinsically Disordered Cancer/Testis Antigen.

Authors:  Yanan He; Yihong Chen; Steven M Mooney; Krithika Rajagopalan; Ajay Bhargava; Elizabeth Sacho; Keith Weninger; Philip N Bryan; Prakash Kulkarni; John Orban
Journal:  J Biol Chem       Date:  2015-08-04       Impact factor: 5.157

7.  Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.

Authors:  Christopher J Oldfield; Jingwei Meng; Jack Y Yang; Mary Qu Yang; Vladimir N Uversky; A Keith Dunker
Journal:  BMC Genomics       Date:  2008       Impact factor: 3.969

Review 8.  Multicellularity in green algae: upsizing in a walled complex.

Authors:  David S Domozych; Catherine E Domozych
Journal:  Front Plant Sci       Date:  2014-11-18       Impact factor: 5.753

Review 9.  Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory.

Authors:  Dongya Jia; Mohit Kumar Jolly; Prakash Kulkarni; Herbert Levine
Journal:  Cancers (Basel)       Date:  2017-06-22       Impact factor: 6.639

Review 10.  Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.

Authors:  Marija Buljan; Guilhem Chalancon; A Keith Dunker; Alex Bateman; S Balaji; Monika Fuxreiter; M Madan Babu
Journal:  Curr Opin Struct Biol       Date:  2013-05-22       Impact factor: 6.809

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  1 in total

1.  IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.

Authors:  João M C Teixeira; Zi Hao Liu; Ashley Namini; Jie Li; Robert M Vernon; Mickaël Krzeminski; Alaa A Shamandy; Oufan Zhang; Mojtaba Haghighatlari; Lei Yu; Teresa Head-Gordon; Julie D Forman-Kay
Journal:  J Phys Chem A       Date:  2022-08-28       Impact factor: 2.944

  1 in total

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