Zobrazeno 1 - 10
of 111
pro vyhledávání: '"Igor N Berezovsky"'
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 12, p e1006686 (2018)
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling p
Externí odkaz:
https://doaj.org/article/bc70ba955f9e48409c54544a03897131
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 6, p e1006228 (2018)
The omnipresence of allosteric regulation together with the fundamental role of structural dynamics in this phenomenon have initiated a great interest to the detection of regulatory exosites and design of corresponding effectors. However, despite a g
Externí odkaz:
https://doaj.org/article/48c65a1011f549a69d12a1aebf0abc0d
Autor:
Enrico Guarnera, Igor N Berezovsky
Publikováno v:
PLoS Computational Biology, Vol 12, Iss 3, p e1004678 (2016)
Allostery is one of the pervasive mechanisms through which proteins in living systems carry out enzymatic activity, cell signaling, and metabolism control. Effective modeling of the protein function regulation requires a synthesis of the thermodynami
Externí odkaz:
https://doaj.org/article/a9ef5be6ff804e7bb123e7dbf4de5792
Autor:
Simon Mitternacht, Igor N Berezovsky
Publikováno v:
PLoS Computational Biology, Vol 7, Iss 12, p e1002301 (2011)
Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited by the protein also in th
Externí odkaz:
https://doaj.org/article/31631116c2ab4ae48c74e2be68eb3acb
Autor:
Simon Mitternacht, Igor N Berezovsky
Publikováno v:
PLoS Computational Biology, Vol 7, Iss 9, p e1002148 (2011)
Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site t
Externí odkaz:
https://doaj.org/article/14584a69fa284588b6eeee6bb0df3baa
Publikováno v:
PLoS Computational Biology, Vol 3, Iss 3, p e52 (2007)
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design sequences with
Externí odkaz:
https://doaj.org/article/4401985a39044bd5b8c80e202dc8c106
Publikováno v:
PLoS Computational Biology, Vol 3, Iss 1, p e5 (2007)
There have been considerable attempts in the past to relate phenotypic trait--habitat temperature of organisms--to their genotypes, most importantly compositions of their genomes and proteomes. However, despite accumulation of anecdotal evidence, an
Externí odkaz:
https://doaj.org/article/5f0e1f8e960d4b079f416fcfd3453764
Publikováno v:
PLoS Computational Biology, Vol 1, Iss 4, p e47 (2005)
Evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. However, it is sometimes difficult to discern their causes without a clear understanding of underlyin
Externí odkaz:
https://doaj.org/article/dfa719380d874ddbb1aa6231a27f6013
Publikováno v:
Current Research in Structural Biology, Vol 7, Iss , Pp 100142- (2024)
Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands – phosphate
Externí odkaz:
https://doaj.org/article/6d225fb39eab47c59ab5526adbc3bd5d
Publikováno v:
Current Research in Structural Biology, Vol 7, Iss , Pp 100129- (2024)
Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them i
Externí odkaz:
https://doaj.org/article/f6b4dd65a97543b2b6ad6d8273b19add