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In Silico Elucidation of the Recognition Dynamics of Ubiquitin

Dong Long, Rafael Brüschweiler, Ruth Nussinov
2011 PLoS Computational Biology  
Elucidation of the mechanism of biomacromolecular recognition events has been a topic of intense interest over the past century.  ...  Here, we investigate the recognition dynamics of ubiquitin via microsecond all-atom molecular dynamics simulation providing both thermodynamic and kinetic information.  ...  Author Contributions Conceived and designed the experiments: DL RB. Performed the experiments: DL RB. Analyzed the data: DL RB. Wrote the paper: DL RB.  ... 
doi:10.1371/journal.pcbi.1002035 pmid:21533067 pmcid:PMC3080845 fatcat:36l2hb67uvavpld7xvvfggo2uu

Single Molecule Study of Rela During the Stringent Response in Live E. Coli Cells

Wenting Li, Heejun Choi, Emmanuelle Bouveret, Yan Zhang, James¯ Weisshaar
2014 Biophysical Journal  
We probed the secondary structural changes of apolipoprotein upon its binding to the AgNP, and we make direct quantitative comparisons of our simulations with experimentally measured CD spectra.  ...  Consistent with the CD spectra, we observed a decrease in a-helices coupled with an increase in b-sheets in apolipoprotein upon biocorona formation.  ...  The ASB family acts as the substrate recognition subunits of ElonginBC-Cullin-SOCS-box (ECS) type E3 ubiquitin ligase complexes.  ... 
doi:10.1016/j.bpj.2013.11.2621 fatcat:tk3cwl3tfngi7hzstvwhjrofwu

Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding

T. Hagai, Y. Levy
2010 Proceedings of the National Academy of Sciences of the United States of America  
Our study implies that, in addition to its known role as a recognition signal, the ubiquitin attachment may be directly involved in the cellular process it regulates by changing the biophysical properties  ...  In this study, we investigate the effects of ubiquitination on the folding thermodynamics and mechanism of various substrates using computational tools and find that ubiquitination changes the thermal  ...  We thank many people from the field of ubiquitination, and especially Tommer Ravid, for helpful discussions.  ... 
doi:10.1073/pnas.0912335107 pmid:20080694 pmcid:PMC2836630 fatcat:rcszwdptzzdavlh2du3cwiupxm

Regulation of nervous system development by F-box mediated ubiquitination

Banu Saritas-Yildirim, Elena S. Casey
2010 Developmental Biology  
Studies of cell cycle regulation show that a major mechanism of protein degradation is through F-box proteins, which function in the recognition and recruitment of specific targets for the ubiquitin/26S  ...  Elucidating the processes involved in the adoption of the glycinergic and GABAergic phenotypes is critical to understanding overall CNS development.  ... 
doi:10.1016/j.ydbio.2010.05.435 fatcat:xlbvtwlkwzexfgq5elocs46pb4

Bio-Guided Fractionation of Ethanol Extract of Leaves of Esenbeckia alata Kunt (Rutaceae) Led to the Isolation of Two Cytotoxic Quinoline Alkaloids: Evidence of Selectivity Against Leukemia Cells

Juan Manuel Álvarez-Caballero, Luis Enrique Cuca-Suárez, Ericsson Coy-Barrera
2019 Biomolecules  
Therefore, as a rationale to the observed cytotoxic selectivity, an in-silico evaluation by molecular docking and molecular dynamics was also explored.  ...  Bio-guided fractionation performed on the leaves-derived ethanol extract of Esenbeckia alata (Rutaceae), a plant used in traditional medicine, led to the isolation of two alkaloids, kokusaginine 1 and  ...  The in-silico study of the interaction between 1-2 and UBA5 was extended using molecular dynamics (MD) simulations as the next step to expand the information about the binding mode of these test alkaloids  ... 
doi:10.3390/biom9100585 pmid:31597257 pmcid:PMC6843300 fatcat:e23zshjyqzab7dy5bamq6janza

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Sutapa Dutta, Stefano Corni, Giorgia Brancolini
2022 International Journal of Molecular Sciences  
A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented.  ...  In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface  ...  A full set of in silico methods have been applied [94] , such as docking, molecular dynamics (MD), and statistical analysis.  ... 
doi:10.3390/ijms23031484 pmid:35163407 pmcid:PMC8835741 fatcat:rll4wtj5mrcspl4rb5seeykv4e

Transcriptional regulation of GlyT2 and GAD67 in X. laevis

Alexander V. Chalphin, Conor W. Sipe, Margaret S. Saha
2010 Developmental Biology  
Studies of cell cycle regulation show that a major mechanism of protein degradation is through F-box proteins, which function in the recognition and recruitment of specific targets for the ubiquitin/26S  ...  Elucidating the processes involved in the adoption of the glycinergic and GABAergic phenotypes is critical to understanding overall CNS development.  ... 
doi:10.1016/j.ydbio.2010.05.434 fatcat:3klezdrupzck3fosw64h4bjmse

Regulation of endoderm development by zebrafish Nipbl

Akihiko Muto, Thomas F. Schilling, Anne L. Calof, Arthur D. Lander
2010 Developmental Biology  
Studies of cell cycle regulation show that a major mechanism of protein degradation is through F-box proteins, which function in the recognition and recruitment of specific targets for the ubiquitin/26S  ...  Elucidating the processes involved in the adoption of the glycinergic and GABAergic phenotypes is critical to understanding overall CNS development.  ... 
doi:10.1016/j.ydbio.2010.05.433 fatcat:s7umcmpqxfhndbzov5kac6t4oa

HDAC6 as a target for neurodegenerative diseases: what makes it different from the other HDACs?

Claudia Simões-Pires, Vincent Zwick, Alessandra Nurisso, Esther Schenker, Pierre-Alain Carrupt, Muriel Cuendet
2013 Molecular Neurodegeneration  
This review describes the specific role of HDAC6 compared to the other HDACs in the context of neurodegeneration, by collecting in silico, in vitro and in vivo results regarding the inhibition and/or knockdown  ...  Such an example is HDAC6 for which the role in neurodegeneration has been partially elucidated so far. The strategy to be adopted in promising therapeutics targeting HDAC6 is still controversial.  ...  Table 1 summarizes the key amino acid residues in the second catalytic domain of HDAC6, which are responsible for recognition and binding of inhibitors and ubiquitin [44, 45] .  ... 
doi:10.1186/1750-1326-8-7 pmid:23356410 pmcid:PMC3615964 fatcat:kugxp4okmjf6pgecwo3vfyapsm

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

R. Bryn Fenwick, Santi Esteban-Martín, Xavier Salvatella
2011 European Biophysics Journal  
We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery.  ...  For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur.  ...  Taken from Zhang et al. (2007) Challenges in characterizing molecular recognition and allostery In the preceding sections, we have detailed the use of ensembles to elucidate mechanisms of binding and  ... 
doi:10.1007/s00249-011-0754-8 pmid:22089251 pmcid:PMC3222826 fatcat:uemkpg7nhfahthjo63t5znbrxa

Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane

Jan Knop, Tim Lienemann, Haifa El-Kilani, Sven Falke, Catharina Krings, Maria Sindalovskaya, Johannes Bergler, Christian Betzel, Stefan Hoth
2021 International Journal of Molecular Sciences  
Plant U-box armadillo repeat (PUB-ARM) ubiquitin (Ub) ligases have important functions in plant defense through the ubiquitination of target proteins.  ...  We uncovered the structure of a full-length plant ubiquitin ligase and the structural requirements of SAUL1, which are crucial for its function in patch formation.  ...  Subsequently, we applied in silico modeling for further elucidation of the structural organization of SAUL1.  ... 
doi:10.3390/ijms22179455 pmid:34502365 fatcat:reiufh26dnarbkmczsxudsihpe

Bacterial Effectors and Their Functions in the Ubiquitin-Proteasome System: Insight from the Modes of Substrate Recognition

Minsoo Kim, Ryota Otsubo, Hanako Morikawa, Akira Nishide, Kenji Takagi, Chihiro Sasakawa, Tsunehiro Mizushima
2014 Cells  
Protein ubiquitination plays indispensable roles in the regulation of cell homeostasis and pathogenesis of neoplastic, infectious, and neurodegenerative diseases.  ...  Other effectors bind and modify components of the host ubiquitin system, and some are themselves subject to ubiquitination.  ...  Acknowledgments This work was supported in part by the following grants from the Japan Society for the Promotion of Science (JSPS) and MEXT of Japan: a Grant-in-Aid for Specially Promoted Research (23000012  ... 
doi:10.3390/cells3030848 pmid:25257025 pmcid:PMC4197628 fatcat:qa5ixmxgnfa2vkulcckdqcrrze

Dengue Non-coding RNA: TRIMmed for Transmission

Giel P. Göertz, Gorben P. Pijlman
2015 Cell Host and Microbe  
ACKNOWLEDGMENTS The authors wish to apologize to all authors whose work could not be cited due to space restrictions. We acknowledge Just Vlak and Mia Hikke for comments and suggestions.  ...  Manokaran et al. (2015) now show in Science that sfRNA from DENV2 binds to the ubiquitin ligase TRIM25 and thereby inhibits vRNA recognition by the cytoplasmic non-self RNA sensor RIG-I.  ...  As a result, flavivirus epidemics can be highly dynamic, with different viral strains co-circulating and/or competing in the same area.  ... 
doi:10.1016/j.chom.2015.07.009 pmid:26269946 fatcat:atbh3frcwrdprmrzl6dnzdt3dm

Targeting ubiquitination for cancer therapies

John Kenneth Morrow, Hui-Kuan Lin, Shao-Cong Sun, Shuxing Zhang
2015 Future Medicinal Chemistry  
Ubiquitination involves covalent attachment of ubiquitin, a small 8-kDa protein, to a substrate and results in recognition and shuttling of the substrate to the 26S proteasome complex for degradation [  ...  In this review, we will discuss the current state of small molecules that target various elements of ubiquitination.  ...  E3 elements in the UPS are considered to be primarily responsible for the specific recognition of a large number of target proteins, acting as the substrate recognition component of the UPS pathway [2  ... 
doi:10.4155/fmc.15.148 pmid:26630263 pmcid:PMC4976843 fatcat:o7oqdk7ownhevkaxcmrv4xrxnm

Quantitative Theory for Protein-Protein Interactions in a Crowded Environment

Youngchan Kim, Jeetain Mittal
2012 Biophysical Journal  
FtsL and FtsB rapidly degrade in the absence of one another in vivo, so their interaction is a possible regulation point in division.  ...  Here, we present a detailed structural characterization done through the use of use of in vitro biophysical interaction assays, in vivo screening methods, and computational modeling.  ...  The process of ubiquitination is mediated by ubiquitin ligases, such as the MARCH ligases in this study.  ... 
doi:10.1016/j.bpj.2011.11.2597 fatcat:u3d53j5mcvgtffk56qn5dhbpoi
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