Structural modules of the stress-induced protein HflX: an outlook on its evolution and biological role

Srinivasan, Krishnamoorthi; Dey, Sandip; Sengupta, Jayati

doi:10.1007/s00294-018-0905-x

Cited by 14 publications

(11 citation statements)

References 43 publications

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“…Again this suggests, as in the previously discussed examples, that the stress-sensing protein is in a 'tense' form but binds GTP in a reversible manner (Fischer et al, 2012), as requested for the first step of a Landauer's principle-based MxD action. The protein also features an ATP-binding domain that acts as a RNA helicase, unfolding regions of the large ribosomal RNA that are not properly folded (Srinivasan et al, 2018). Overall, the protein detects ribosomes that have been altered by heat stress and helps restore them into subunits with an active conformation.…”

Section: Accurate Template Recognition During Translation and Antibiomentioning

confidence: 99%

Omnipresent Maxwell's demons orchestrate information management in living cells

Boël

Danot

Lorenzo

et al. 2019

Microbial Biotechnology

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Summary The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information‐managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy‐efficient way that is vastly better than our contemporary computers.

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Section: Accurate Template Recognition During Translation and Antibiomentioning

confidence: 99%

Omnipresent Maxwell's demons orchestrate information management in living cells

Boël

Danot

Lorenzo

et al. 2019

Microbial Biotechnology

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“…Recently, Zea et al (2013) found a negative correlation between conformational diversity and protein evolutionary rate, suggesting that the structural constraints underlying protein dynamism, essential for protein function, could modulate protein divergence. Postsequencing functional analyses based on alignments of complete or partial sequences of several genomes is one powerful tool for interpreting the genomic information in the biological sciences by deducing similarities and differences in gene and its protein product in distinct species (Kittler and Oliver, 2006;Srinivasan et al, 2019). Thus, the findings described herein reveal important insights into differences in thee conservation degree and organizational pattern of the secondary structural domains between bacterial and human heat shock gene and protein.…”

Section: (With 2 Figures)mentioning

confidence: 89%

Clustering accentuated matches and highly conserved domains between bacterial and human heat shock gene and protein

Gabriel

2020

Braz. J. Biol.

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“…Some G proteins have the ability to bind and/or hydrolyse more than one nucleotide apart from GTP. This may be explained by the presence of additional domains (for example, the Hflx proteins, which have a G domain as well as an ATP binding ND1 domain (22). Alternately the nucleotide specificity may be altered by changes in the G4 box motif ("NKXD").…”

Section: Discussionmentioning

confidence: 99%

“…The Era family of proteins are speculated to be involved in translocation based on their association with 16s rRNA (19) and EngB proteins are involved in coordination of cell cycle events and assembly of 50S ribosome units in bacteria (20).The EngA/Der/YfgK/YphC class of proteins, which are yet to be structurally and functionally characterized, have the unique feature of two tandemly occurring GTPase domains separated by an acidic linker (20). Moreover, some G proteins like Septins, Dynamin, TrmE, IRG, AIG1/Toc are also known as GADs (GTPases activated by Dimerization) since their GTPase cycle is regulated by nucleotide binding and subsequent dimerization (21) while HflX class of proteins bind both ATP and GTP (22).…”

Section: Introductionmentioning

confidence: 99%

G-domain prediction across the diversity of G protein families

Sanghavi

Rashmi

Dasgupta

et al. 2019

Preprint

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Guanine nucleotide binding proteins are characterized by a structurally and mechanistically conserved GTP-binding domain, indispensable for binding GTP. The G domain comprises of five adjacent consensus motifs called G boxes, which are separated by amino acid spacers of different lengths. Several G proteins, discovered over time, are characterized by diverse function and sequence. This sequence diversity is also observed in the G box motifs (specifically the G5 box) as well as the inter-G box spacer length. The Spacers and Mismatch Algorithm (SMA) introduced in this study, can predict G-domains in a given G protein sequence, based on user-specified constraints for approximate G-box patterns and inter-box gaps in each G protein family. The SMA parameters can be customized as more G proteins are discovered and characterized structurally. Family-specific G box motifs including the less characterized G5 motif as well as G domain boundaries were predicted with higher precision. Overall, our analysis suggests the possible classification of G protein families based on family-specific G box sequences and lengths of inter-G box spacers. Significance StatementIt is difficult to define the boundaries of a G domain as well as predict G boxes and important GTP-binding residues of a G protein, if structural information is not available. Sequence alignment and phylogenetic methods are often unsuccessful, given the sequence diversity across G protein families. SMA is a unique method which uses approximate pattern matching as well as inter-motif separation constraints to predict the locations of G-boxes. It is able to predict all G boxes including the less characterized G5 motif which marks the carboxy-terminal boundary of a G domain. Thus, SMA can be used to predict G domain boundaries within a large multi-domain protein as long as the user-specified constraints are satisfied. Main Text

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Structural modules of the stress-induced protein HflX: an outlook on its evolution and biological role

Cited by 14 publications

References 43 publications

Omnipresent Maxwell's demons orchestrate information management in living cells

Omnipresent Maxwell's demons orchestrate information management in living cells

Clustering accentuated matches and highly conserved domains between bacterial and human heat shock gene and protein

G-domain prediction across the diversity of G protein families

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