scholarly journals SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent

2006 ◽  
Vol 34 (12) ◽  
pp. 3546-3554 ◽  
Author(s):  
N. E. Davey
Keyword(s):  
Motif Discovery ◽  
Linear Motif ◽  
Evolutionary Descent

scholarly journals The SLiMDisc server: short, linear motif discovery in proteins

2007 ◽  
Vol 35 (suppl_2) ◽  
pp. W455-W459 ◽  
Author(s):  
Norman E. Davey ◽  
Richard J. Edwards ◽  
Denis C. Shields
Keyword(s):  
Motif Discovery ◽  
Linear Motif

scholarly journals The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock.

2022 ◽  
Author(s):  
Meaghan S. Jankowski ◽  
Daniel Griffith ◽  
Divya G. Shastry ◽  
Jacqueline F. Pelham ◽  
Garrett M. Ginell ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Electrostatic Interactions ◽  
Motif Discovery ◽  
Rational Design ◽  
Protein Complexes ◽  
Linear Motif ◽  
Cellular Processes ◽  
Evolutionarily Conserved ◽  
Positively Charged ◽  
Clock Protein

The circadian clock times cellular processes to the day/night cycle via a Transcription-Translation negative Feedback Loop (TTFL). However, a mechanistic understanding of the negative arm in both the timing of the TTFL and its control of output is lacking. We posited that the formation of negative-arm protein complexes was fundamental to clock regulation stemming from the negative arm. Using a modified peptide microarray approach termed Linear motif discovery using rational design (LOCATE), we characterized the interaction of the disordered negative-arm clock protein FREQUENCY to its partner protein FREQUENCY-Interacting RNA helicase. LOCATE identified a specific Short Linear Motif (SLiM) and interaction hotspot as well as positively charged islands that mediate electrostatic interactions, suggesting a model where negative arm proteins form a fuzzy complex essential for clock timing and robustness. Further analysis revealed that the positively charged islands were an evolutionarily conserved feature in higher eukaryotes and contributed to proper clock function.

Genetic Optimization for (l,d)-Motif Discovery

2012 ◽  
Vol 35 (7) ◽  
pp. 1429
Author(s):  
Hong-Wei HUO ◽  
Dan-Dan GUO ◽  
Qiang YU ◽  
Yi-Pu ZHANG ◽  
Wei NIU
Keyword(s):  
Motif Discovery ◽  
Genetic Optimization

scholarly journals The HGR motif is the antiangiogenic determinant of vasoinhibin: implications for a therapeutic orally active oligopeptide

Angiogenesis ◽  
2021 ◽  
Author(s):  
Juan Pablo Robles ◽  
Magdalena Zamora ◽  
Lourdes Siqueiros-Marquez ◽  
Elva Adan-Castro ◽  
Gabriela Ramirez-Hernandez ◽  
...  
Keyword(s):  
Therapeutic Agent ◽  
Clinical Evidence ◽  
Therapeutic Potential ◽  
Peripartum Cardiomyopathy ◽  
Loss Of Function ◽  
Functional Determinant ◽  
Melanoma Tumor ◽  
Linear Motif ◽  
Anti Cancer ◽  
Orally Active

AbstractThe hormone prolactin acquires antiangiogenic and antivasopermeability properties after undergoing proteolytic cleavage to vasoinhibin, an endogenous prolactin fragment of 123 or more amino acids that inhibits the action of multiple proangiogenic factors. Preclinical and clinical evidence supports the therapeutic potential of vasoinhibin against angiogenesis-related diseases including diabetic retinopathy, peripartum cardiomyopathy, rheumatoid arthritis, and cancer. However, the use of vasoinhibin in the clinic has been limited by difficulties in its production. Here, we removed this barrier to using vasoinhibin as a therapeutic agent by showing that a short linear motif of just three residues (His46-Gly47-Arg48) (HGR) is the functional determinant of vasoinhibin. The HGR motif is conserved throughout evolution, its mutation led to vasoinhibin loss of function, and oligopeptides containing this sequence inhibited angiogenesis and vasopermeability with the same potency as whole vasoinhibin. Furthermore, the oral administration of an optimized cyclic retro-inverse vasoinhibin heptapeptide containing HGR inhibited melanoma tumor growth and vascularization in mice and exhibited equal or higher antiangiogenic potency than other antiangiogenic molecules currently used as anti-cancer drugs in the clinic. Finally, by unveiling the mechanism that obscures the HGR motif in prolactin, we anticipate the development of vasoinhibin-specific antibodies to solve the on-going challenge of measuring endogenous vasoinhibin levels for diagnostic and interventional purposes, the design of vasoinhibin antagonists for managing insufficient angiogenesis, and the identification of putative therapeutic proteins containing HGR.

scholarly journals CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Scala ◽  
Antonio Federico ◽  
Dario Greco
Keyword(s):  
Dna Methylation ◽  
Motif Discovery ◽  
Cpg Methylation ◽  
Functional Interpretation ◽  
Dna Motifs ◽  
Molecular Alterations ◽  
Link Type ◽  
Dna Motif ◽  
Quantitative Manner ◽  
Dna Motif Discovery

Abstract Background The investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determinants of methylation stability, the DNA composition of the CpG surrounding regions has been shown to have a crucial role in the maintenance and establishment of methylation statuses. This aspect has been previously characterized in a quantitative manner by inspecting the nucleotidic composition in the region. Research in this field still lacks a qualitative perspective, linked to the identification of certain sequences (or DNA motifs) related to particular DNA methylation phenomena. Results Here we present a novel computational strategy based on short DNA motif discovery in order to characterize sequence patterns related to aberrant CpG methylation events. We provide our framework as a user-friendly, shiny-based application, CpGmotifs, to easily retrieve and characterize DNA patterns related to CpG methylation in the human genome. Our tool supports the functional interpretation of deregulated methylation events by predicting transcription factors binding sites (TFBS) encompassing the identified motifs. Conclusions CpGmotifs is an open source software. Its source code is available on GitHub https://github.com/Greco-Lab/CpGmotifs and a ready-to-use docker image is provided on DockerHub at https://hub.docker.com/r/grecolab/cpgmotifs.

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