Zobrazeno 1 - 10
of 25
pro vyhledávání: '"Ajeet K. Sharma"'
Autor:
Inayat Ullah Irshad, Ajeet K. Sharma
Publikováno v:
Biophysical Reports, Vol 3, Iss 4, Pp 100131- (2023)
E. coli is one of the most widely used organisms for understanding the principles of cellular and molecular genetics. However, we are yet to understand the origin of several experimental observations related to the regulation of gene expression in E.
Externí odkaz:
https://doaj.org/article/1ae16b43a8b441e0b777e137b29b753f
Publikováno v:
Frontiers in Molecular Biosciences, Vol 8 (2021)
Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to ex
Externí odkaz:
https://doaj.org/article/818a68eb137c4cff96558968a214e311
Autor:
Daniel A. Nissley, Ajeet K. Sharma, Nabeel Ahmed, Ulrike A. Friedrich, Günter Kramer, Bernd Bukau, Edward P. O’Brien
Publikováno v:
Nature Communications, Vol 7, Iss 1, Pp 1-13 (2016)
The folding of protein domains can occur concomitant with their synthesis, and the rates at which individual codons are translated by the ribosome can affect the folding process. Here the authors present a kinetic model that accurately predicts the p
Externí odkaz:
https://doaj.org/article/644393080ecd46ffb8ae9c3eca310651
Autor:
Ajeet K, Sharma, Johannes, Venezian, Ayala, Shiber, Günter, Kramer, Bernd, Bukau, Edward P, O'Brien
Publikováno v:
Proc Natl Acad Sci U S A
The presence of a single cluster of nonoptimal codons was found to decrease a transcript’s half-life through the interaction of the ribosome-associated quality control machinery with stalled ribosomes in Saccharomyces cerevisiae. The impact of mult
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::267fe86aa1019bea205a8bc147d46821
https://pubmed.ncbi.nlm.nih.gov/34911752
https://pubmed.ncbi.nlm.nih.gov/34911752
Autor:
Ajeet K. Sharma
Publikováno v:
Physical review. E. 103(6-1)
Various feedback mechanisms regulate the expression of different genes to ensure the required protein levels inside a cell. In this paper, we develop a kinetic model for one such mechanism that autoregulates RF2 protein synthesis in E. coli through p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e905a5539841c9faa412afac473af4b
https://pubmed.ncbi.nlm.nih.gov/34271674
https://pubmed.ncbi.nlm.nih.gov/34271674
Autor:
Joseph R. Persichetti, Ajeet K. Sharma, H. Lee Woodcock, Phillip S. Hudson, Edward P. O'Brien, David K. Wolfe
Publikováno v:
J Chem Theory Comput
Markov state models can describe ensembles of pathways via kinetic networks but are difficult to create when large free-energy barriers limit unbiased sampling. Chain-of-states simulations allow sampling over large free-energy barriers but are often
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0b0e5cb43026f655a2c585dc3b507c32
https://europepmc.org/articles/PMC7322723/
https://europepmc.org/articles/PMC7322723/
Autor:
Ajeet K. Sharma, Edward P. O'Brien
Publikováno v:
Current Opinion in Structural Biology. 49:94-103
Protein folding research has been dominated by the assumption that thermodynamics determines protein structure and function. And that when the folding process is compromised in vivo the proteostasis machinery-chaperones, deaggregases, the proteasome-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::78d94e27fe27378a153ccbcbf7076568
https://doi.org/10.1016/j.sbi.2018.01.005
https://doi.org/10.1016/j.sbi.2018.01.005
Autor:
Prajwal Ciryam, Günter Kramer, Pietro Sormanni, Nabeel Ahmed, Edward P. O'Brien, Ajeet K. Sharma, Ulrike A. Friedrich
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 15, Iss 5, p e1007070 (2019)
PLoS Computational Biology, Vol 15, Iss 5, p e1007070 (2019)
Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions, hence bioinformatics methods con
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::967462f4250d66c282f6a72f3b51f1c4
https://doi.org/10.1101/490730
https://doi.org/10.1101/490730
Autor:
Edward P. O'Brien, Ajeet K. Sharma
The introduction of a single, non-optimal codon cluster into a transcript was found to cause ribosomes to queue upstream of it and decrease the transcript’s half-life through the action of the dead box protein Dhh1p, which interacts with stalled ri
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9aafe6bd9f781a9822d416a9903ba126
https://doi.org/10.1101/490995
https://doi.org/10.1101/490995
Publikováno v:
Journal of the American Chemical Society. 138:1180-1195
An emerging paradigm in the field of in vivo protein biophysics is that nascent-protein behavior is a type of nonequilibrium phenomenon, where translation-elongation kinetics can be more important in determining nascent-protein behavior than the ther
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5673da70e8bd2c3ed0e6ef52ddaea89d
https://doi.org/10.1021/jacs.5b08145
https://doi.org/10.1021/jacs.5b08145