Zobrazeno 1 - 10
of 219
pro vyhledávání: '"John J. Kozak"'
Autor:
John J. Kozak, Harry B. Gray
Publikováno v:
J Phys Chem B
In an important advance in our understanding of protein folding, Wolynes and Onuchic found that the frustration ratio, T(f) /T(s), for funneled energy Landscapes is T(f) /T(s) ~ 1.6. In recent work on four heme proteins, we showed that when a protein
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f5160aae0a160cd8ae11c5fc16f5a57b
https://resolver.caltech.edu/CaltechAUTHORS:20201124-122000714
https://resolver.caltech.edu/CaltechAUTHORS:20201124-122000714
Publikováno v:
Journal of Inorganic Biochemistry
We have investigated the structural stability of the SARS-CoV-2 main protease monomer (Mpro). We quantified the spatial and angular changes in the structure using two independent analyses, one based on a spatial metrics (δ, ratio), the second on ang
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::99737c40c3d6b0d65706fcb6d54d2744
https://resolver.caltech.edu/CaltechAUTHORS:20200716-094538897
https://resolver.caltech.edu/CaltechAUTHORS:20200716-094538897
Publikováno v:
J Inorg Biochem
We have analyzed the early stages of unfolding of cytochromes c-b562 (PDB ID: 2BC5) and Rd apo b562 (PDB ID: 1YYJ). Our geometrical approach proceeds from an analysis of the crystal structure reported for each protein. We quantify, residue-by-residue
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7bd820b1bbd35095680bc127e3dee2f5
https://europepmc.org/articles/PMC8111852/
https://europepmc.org/articles/PMC8111852/
Publikováno v:
ChemRxiv
article-version (number) 1
article-version (status) pre
article-version (number) 1
article-version (status) pre
In an analysis of the structural stability of the coronavirus main protease (Mpro), we identified regions of the protein that could be disabled by cobalt(III)-cation binding to histidines and cysteines [1]. Here we have extended our work to include c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::58d4ca662f3ad15273366e6060284ac9
https://doi.org/10.26434/chemrxiv.12673436
https://doi.org/10.26434/chemrxiv.12673436
Publikováno v:
J Inorg Biochem
We use crystallographic data for four helical iron proteins (cytochrome c-b(562), cytochrome c’, sperm whale myoglobin, human cytoglobin) to calculate radial and angular signatures as each unfolds from the native state stepwise though four unfolded
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::81ac19679debf991b91b0ad39038582c
https://europepmc.org/articles/PMC7453651/
https://europepmc.org/articles/PMC7453651/
Publikováno v:
The Journal of Physical Chemistry B. 122:11289-11294
We present a geometrical method that can identify secondary structural motifs in proteins via angular correlations. The method uses crystal structure coordinates to calculate angular and radial signatures of each residue relative to an external refer
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::349208a8c11ee323bc9374c033464f51
https://doi.org/10.1021/acs.jpcb.8b07130
https://doi.org/10.1021/acs.jpcb.8b07130
Autor:
Myung Hoon, Han, Won June, Kim, Eok Kyun, Lee, Hyungjun, Kim, Sébastien, Lebègue, John J, Kozak
Publikováno v:
Journal of physics. Condensed matter : an Institute of Physics journal. 32(3)
We study the magnetocrystalline anisotropy (MCA) energy of Fe
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::4c58f9cc3d9fec2cc73d80502bc0886e
https://pubmed.ncbi.nlm.nih.gov/31491781
https://pubmed.ncbi.nlm.nih.gov/31491781
We study the intrinsic nature of the finite system-size effect in estimating shear viscosity of dilute and dense fluids within the framework of the Green-Kubo approach. From extensive molecular dynamics simulations, we observe that the size effect on
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::044b51b37274d8b2f30d6a9f62bda931
http://arxiv.org/abs/1907.08773
http://arxiv.org/abs/1907.08773
Autor:
John J. Kozak, Harry B. Gray
Publikováno v:
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry. 24(6)
We have developed a geometrical approach to quantify differences in the stereochemistry of α-helical and turning regions in four iron proteins. Two spatial signatures are used to analyze residue coordinate data for each protein; and a third is emplo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eaac8945286dc02d5c26131254d0dbc1
https://pubmed.ncbi.nlm.nih.gov/31511993
https://pubmed.ncbi.nlm.nih.gov/31511993
Publikováno v:
The Journal of Physical Chemistry B. 120:11888-11896
We study the structural stability of helical and non-helical regions in chain A of human intelectin-1. Using a geometrical model introduced previously, a computational analysis based on the recently reported crystal structure of this protein by Kiess
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::662a770eca4da6a98e0b6721354a669e
https://doi.org/10.1021/acs.jpcb.6b08691
https://doi.org/10.1021/acs.jpcb.6b08691