Zobrazeno 1 - 10
of 12
pro vyhledávání: '"Piya Patra"'
Publikováno v:
PLoS ONE, Vol 11, Iss 5, p e0155911 (2016)
A considerable proportion of protein-protein interactions (PPIs) in the cell are estimated to be mediated by very short peptide segments that approximately conform to specific sequence patterns known as linear motifs (LMs), often present in the disor
Externí odkaz:
https://doaj.org/article/1066bb678f234bcdb471a149b339c19b
Autor:
Piya Patra, Yi Qin Gao
Publikováno v:
The Journal of Physical Chemistry B. 126:9187-9206
Sequence-specific recognition of transcription factor (TF) binding motifs in the target site of DNA over the vast amount of non-target DNA is of primary importance for the transcriptional regulation of gene expression by the TFs. Binding of TFs to th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fa18c34b379fdbed1630148573860986
https://doi.org/10.1021/acs.jpcb.2c05749
https://doi.org/10.1021/acs.jpcb.2c05749
Publikováno v:
Current opinion in structural biology. 77
Gene expression is regulated by many factors, including transcription factors, chromatin three-dimensional topology, modifications of DNA and histone proteins, and non-coding RNAs. The execution of these complex mechanisms requires an effectively coo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f240c277b1d6e1aaf1a67fe4ceb30b9b
https://pubmed.ncbi.nlm.nih.gov/36274420
https://pubmed.ncbi.nlm.nih.gov/36274420
Publikováno v:
BiopolymersREFERENCES. 113(8)
Translocation of positively charged cell penetrating peptides (CPP) through cell membrane is important in drug delivery. Here we report all-atom molecular dynamics simulations to investigate how a biphosphate salt in a solvent affects the interaction
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::25168d800d4a9864783b99a20573fe20
https://pubmed.ncbi.nlm.nih.gov/35621373
https://pubmed.ncbi.nlm.nih.gov/35621373
Publikováno v:
Chemical Science
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8c00537dfcf7115b4dffc92c7d4f95bf
https://pubmed.ncbi.nlm.nih.gov/34168783
https://pubmed.ncbi.nlm.nih.gov/34168783
Publikováno v:
Journal of Computer-Aided Molecular Design. 32:929-936
Anion binding CαNN motif is found in functionally important regions of protein structures. This motif based only on backbone atoms from three adjacent residues, recognizes free sulphate or phosphate ion as well as phosphate groups in nucleotides and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::dccf8e421a82d2ef537331ba66e4a40f
https://doi.org/10.1007/s10822-018-0157-3
https://doi.org/10.1007/s10822-018-0157-3
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 85:2179-2190
Among different ligand binding motifs, anion binding CαNN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or bi-phosphate and participate in differen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f5eb5bb7e43c0246e415745a9fbe5256
https://doi.org/10.1002/prot.25382
https://doi.org/10.1002/prot.25382
Publikováno v:
Biopolymers. 110
Self-assembly by amphiphilic molecules with solvent exposed hydrophobic groups are relevant in biomolecular systems as well as in technological applications. Here we study such self-assembly in these systems using a model system of spherical particle
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f1700123a040a454dbd039a157d4d67e
https://doi.org/10.1002/bip.23330
https://doi.org/10.1002/bip.23330
Publikováno v:
Chemical Physics Letters. 750:137503
Here we study anionic biphosphate condensation around cationic HIV-1 Tat peptide to understand interaction between charged functional groups with counter-anion. Our all-atom molecular dynamics simulations show that the counter-anion condensation arou
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::98e3195af6b19326266f393e5cbdb19b
https://doi.org/10.1016/j.cplett.2020.137503
https://doi.org/10.1016/j.cplett.2020.137503
Publikováno v:
Journal of computer-aided molecular design. 32(9)
Anion binding C
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::8dafb95bff681ea66d92b9ecc9685b7f
https://pubmed.ncbi.nlm.nih.gov/30182143
https://pubmed.ncbi.nlm.nih.gov/30182143