ArticleGenome research2003
Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 46 citations in OpenAlex.
- Structural and evolutionary insights into understudied bacterial serine-threonine pseudokinase families.Biochemical Society transactions · 2025Review
- A complete allosteric map of a GTPase switch in its native cellular network.Cell systems · 2023Article
- A survey of TIR domain sequence and structure divergence.Immunogenetics · 2020Article
- Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments.Database : the journal of biological databases and curation · 2020Article
- The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region.The Journal of biological chemistry · 2019Article
- Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.PLoS computational biology · 2018Article
- Differential Disruption of Nucleocytoplasmic Trafficking Pathways by Rhinovirus 2A Proteases.Journal of virology · 2017Article
- Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.PLoS computational biology · 2016Article
- Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis.Molecular cell · 2015Article
- Co-conserved MAPK features couple D-domain docking groove to distal allosteric sites via the C-terminal flanking tail.PloS one · 2015Article
- Solution structures of Mengovirus Leader protein, its phosphorylated derivatives, and in complex with nuclear transport regulatory protein, RanGTPase.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- A Bayesian sampler for optimization of protein domain hierarchies.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.BMC bioinformatics · 2012Article
- Low-dose irradiation causes rapid alterations to the proteome of the human endothelial cell line EA.hy926.Radiation and environmental biophysics · 2011Article
- Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.Statistical applications in genetics and molecular biology · 2011Article
- Article
- Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.Biology direct · 2010Article
- A typhus group-specific protease defies reductive evolution in rickettsiae.Journal of bacteriology · 2009Article
- Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.Bioinformatics (Oxford, England) · 2009Article
- The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches.Journal of molecular biology · 2009Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Proteins comprising the core of the eukaryotic cellular machinery are often highly conserved, presumably due to selective constraints maintaining important structural features. We have developed statistical procedures to decompose these constraints into distinct categories and to pinpoint critical structural features within each category. When applied to P-loop GTPases, this revealed within Rab, Rho, Ras, and Ran a canonical network of molecular interactions centered on bound nucleotide. This network presumably performs a crucial structural and/or mechanistic role considering that it has persisted for more than a billion years after the divergence of these families. We call these 'FY-pivot' GTPases after their most distinguishing feature, a phenylalanine or tyrosine that functions as a pivot within this network. Specific families deviate somewhat from canonical features in interesting ways, presumably reflecting their functional specialization during evolution. We illustrate this here for Ran GTPases, within which two highly conserved histidines, His30 and His139, strikingly diverge from their canonical counterparts. These, along with other residues specifically conserved in Ran, such as Tyr98, Lys99, and Phe138, appear to work in conjunction with FY-pivot canonical residues to facilitate alternative conformations in which these histidines are strategically positioned to couple Ran's basic patch and C-terminal switch to nucleotide exchange and effector binding. Other core components of the cellular machinery are likewise amenable to this approach, which we term Contrast Hierarchical Alignment and Interaction Network (CHAIN) analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.