Zobrazeno 1 - 10
of 185
pro vyhledávání: '"Dmitrii E Makarov"'
Autor:
Masoumeh Ozmaian, Dmitrii E Makarov
Publikováno v:
PLoS ONE, Vol 18, Iss 6, p e0287200 (2023)
Knots in proteins and DNA are known to have significant effect on their equilibrium and dynamic properties as well as on their function. While knot dynamics and thermodynamics in electrically neutral and uniformly charged polymer chains are relativel
Externí odkaz:
https://doaj.org/article/379333c2d1e64636b1bdae3e13ae24bd
Publikováno v:
Physical Review Research, Vol 5, Iss 1, p L012026 (2023)
A key challenge in single-molecule studies is deducing underlying molecular kinetics from low-dimensional data, as distinct physical scenarios can exhibit similar observable behaviors such as anomalous diffusion. We show that information-theoretic an
Externí odkaz:
https://doaj.org/article/305e802a89884e2ea622eb272fd6dfe1
Publikováno v:
Biophysical Reports, Vol 1, Iss 2, Pp 100029- (2021)
Single-molecule experiments that monitor time evolution of molecular observables in real time have expanded beyond measuring transition rates toward measuring distributions of times of various molecular events. Of particular interest is the first-pas
Externí odkaz:
https://doaj.org/article/77aaf8121e80432aa6663ee3c4d37e48
Autor:
Flurin Sturzenegger, Franziska Zosel, Erik D. Holmstrom, Karin J. Buholzer, Dmitrii E. Makarov, Daniel Nettels, Benjamin Schuler
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-11 (2018)
How interactions between binding partners form or break is hidden in the transition paths from the encounter to the formation of a stable complex. Here authors use single‐molecule spectroscopy to measure the transition path times for the associatio
Externí odkaz:
https://doaj.org/article/fb0baaec43a44cbeac635378d9bb4a00
Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins
Publikováno v:
Scientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
Abstract A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast,
Externí odkaz:
https://doaj.org/article/f3a3e22f75774b28b052c2e346b47321
Autor:
Ali Imran, Brandon S. Moyer, Aaron J. Wolfe, Michael S. Cosgrove, Dmitrii E. Makarov, Liviu Movileanu
Publikováno v:
The Journal of Physical Chemistry Letters. 13:4021-4028
Surface-tethered ligand-receptor complexes are key components in biological signaling and adhesion. They also find increasing utility in single-molecule assays and biotechnological applications. Here, we study the real-time binding kinetics between v
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::13606c05edadb5bf23e890b8374984db
https://doi.org/10.1021/acs.jpclett.2c00621
https://doi.org/10.1021/acs.jpclett.2c00621
Autor:
Aljaž Godec, Dmitrii E. Makarov
Publikováno v:
The journal of physical chemistry letters.
We discuss some of the practical challenges that one faces in using stochastic thermodynamics to infer directionality of molecular machines from experimental single-molecule trajectories. Because of the limited spatiotemporal resolution of single-mol
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c86465caef4e9c2ecbcd7e4661e1adc1
https://pubmed.ncbi.nlm.nih.gov/36566432
https://pubmed.ncbi.nlm.nih.gov/36566432
Publikováno v:
The journal of physical chemistry. B. 126(40)
Single-molecule experiments have now achieved a time resolution allowing observation of transition paths, the brief trajectory segments where the molecule undergoing an unfolding or folding transition enters the energetically or entropically unfavora
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::516fd96897644dc9c22beead42610b3e
https://pubmed.ncbi.nlm.nih.gov/36194758
https://pubmed.ncbi.nlm.nih.gov/36194758
Publikováno v:
The Journal of Chemical Physics. 158:111101
Single-molecule and single-particle tracking experiments are typically unable to resolve fine details of thermal motion at short timescales where trajectories are continuous. We show that, when a diffusive trajectory [Formula: see text] is sampled at
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6f6bd32b3a2fb5855e7ae2bfa4a84dc6
https://doi.org/10.1063/5.0142166
https://doi.org/10.1063/5.0142166
Publikováno v:
Proc Natl Acad Sci U S A
Recent single-molecule experiments have observed transition paths, i.e., brief events where molecules (particularly biomolecules) are caught in the act of surmounting activation barriers. Such measurements offer unprecedented mechanistic insights int
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::027d9824c8ceb9e84cb9283c39f3756b
https://doi.org/10.1073/pnas.2008307117
https://doi.org/10.1073/pnas.2008307117