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pro vyhledávání: '"Robert I. Cukier"'
Autor:
Robert I. Cukier
Publikováno v:
ACS Omega, Vol 3, Iss 8, Pp 9907-9920 (2018)
Externí odkaz:
https://doaj.org/article/43673f2976734601a1fe962a7673de3b
Autor:
Chi Jin, Robert I. Cukier
Publikováno v:
The Journal of chemical physics. 151(17)
Proteins are classified into families based on evolutionary relationships and common structure-function characteristics. Availability of large data sets of gene-derived protein sequences drives this classification. Sequence space is exponentially lar
Publikováno v:
The Journal of Physical Chemistry B. 121:10242-10248
Oxazole yellow (YOPRO), a cyanine dye consisting of benzoxazole and quinoline rings connected by a linker, is almost nonfluorescent in water, but its fluorescence is greatly enhanced after intercalation in double-stranded DNA, forming the basis of DN
Autor:
Fadi Assaf, Yuri A. Nedialkov, Kristopher Opron, Amanda J. Anderson, Zachary F. Burton, Robert I. Cukier, Guo-Wei Wei, Hailey L. Caudill
Publikováno v:
Transcription
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to
Autor:
Robert I. Cukier, Hongfeng Lou
Publikováno v:
The Journal of chemical physics. 149(23)
Entropy maximization methods that update a probability distribution P0(x) to a new distribution P(x) with the use of externally known, averaged constraints find use in diverse areas. Jaynes developed a Maximum Entropy Procedure (MEP) that is an objec
Autor:
Hongfeng Lou, Robert I. Cukier
Publikováno v:
Chemical Physics. 538:110872
A Markov chain can be used to model a joint probability density of a sequence, p R 1 R 2 . . . R N x 1 , x 2 , . . x N , from neighbor pair probability data: p R n R n + 1 x n | x n + 1 n = 1 , 2 , . . . N - 1 , the R n ′ s specifying the type of r
Autor:
Robert I. Cukier
Publikováno v:
The Journal of chemical physics. 148(10)
Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a
Publikováno v:
The Journal of Physical Chemistry B. 119:6591-6602
Signal transduction is of vital importance to the growth and adaptation of living organisms. The key to understand mechanisms of biological signal transduction is elucidation of the conformational dynamics of its signaling proteins, as the activation
Publikováno v:
Nucleic Acids Research
Transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in RNA, is essential for life. Results from molecular dynamics (MD) simulations of eukaryotic RNA polymerase (RNAP) II and bacterial RNAP with experi
Autor:
Zachary F. Burton, Yuri A. Nedialkov, Irina Artsimovitch, Evgeny Nudler, Kristopher Opron, Maria L. Kireeva, Fadi Assaf, Robert I. Cukier, Mikhail Kashlev
Publikováno v:
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1829:187-198
The bridge α-helix in the β′ subunit of RNA polymerase (RNAP) borders the active site and may have roles in catalysis and translocation. In Escherichia coli RNAP, a bulky hydrophobic segment near the N-terminal end of the bridge helix is identifi