Miroslav Hodak

Works (11)

Updated: July 7th, 2023 21:17

2017 journal article

Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione through the Formation of Metal–Sulfur Clusters

Biochemistry, 56(24), 3129–3141.

By: N. Dolgova *, C. Yu *, J. Cvitkovic*, M. Hodak n, K. Nienaber*, K. Summers *, J. Cotelesage*, J. Bernholc n  ...

MeSH headings : Binding Sites; Cisplatin / chemistry; Cisplatin / metabolism; Copper / chemistry; Copper / metabolism; Copper Transport Proteins; Glutathione / chemistry; Glutathione / metabolism; Metallochaperones / chemistry; Metallochaperones / isolation & purification; Metallochaperones / metabolism; Molecular Chaperones; Molecular Conformation; Molecular Dynamics Simulation; Monte Carlo Method; Oxidation-Reduction; Platinum / chemistry; Platinum / metabolism; Sulfur / chemistry; Sulfur / metabolism
TL;DR: Analysis of simultaneous binding of copper and cisplatin to Atox1 under physiological conditions shows that both metals are bound to the protein through copper-sulfur-platinum bridges. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018

2017 journal article

Selective sensing of ethylene and glucose using carbon-nanotube-based sensors: an ab initio investigation

Nanoscale, 9(4), 1687–1698.

By: Y. Li n, M. Hodak n, W. Lu n & J. Bernholc n 

TL;DR: A clear atomistic picture emerges about the mechanisms involved in glucose and ethylene sensing: semiconducting nanotubes exhibit good sensitivities in both cases, and the current through metallic nanot tubes is only weakly affected by analyte attachment. (via Semantic Scholar)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2016 journal article

Mechanisms of NH3 and NO2 detection in carbon-nanotube-based sensors: An ab initio investigation

Carbon, 101, 177–183.

By: Y. Li n, M. Hodak n, W. Lu n & J. Bernholc n 

Sources: NC State University Libraries, Crossref, NC State University Libraries
Added: August 6, 2018

2015 journal article

Enzymatic Mechanism of Copper-Containing Nitrite Reductase

Biochemistry, 54(5), 1233–1242.

By: Y. Li  n, M. Hodak n & J. Bernholc n 

MeSH headings : Achromobacter / enzymology; Achromobacter / genetics; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Copper / chemistry; Copper / metabolism; Nitric Oxide / chemistry; Nitric Oxide / genetics; Nitric Oxide / metabolism; Nitrite Reductases / chemistry; Nitrite Reductases / genetics; Nitrite Reductases / metabolism; Oxidation-Reduction
TL;DR: First-principles calculations are carried out and it is shown that the available structural data are consistent only with a single mechanism, and the origins of the two protons necessary for the enzymatic function are identified. (via Semantic Scholar)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2011 journal article

Mechanism of copper(II)-induced misfolding of Parkinson's disease protein

Scientific Reports, 1.

By: F. Rose, M. Hodak & J. Bernholc 

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

Insights into prion protein function from atomistic simulations

PRION, 4(1), 13–19.

By: M. Hodak n & J. Bernholc n 

author keywords: prion; PrP; copper; attachment; function; ab initio; DFT
MeSH headings : Animals; Binding Sites; Computer Simulation; Copper / metabolism; Humans; Models, Molecular; Prions / chemistry; Prions / metabolism
TL;DR: The results of recent ab initio calculations of copper-prion protein interactions focusing on the recently discovered concentration-dependent binding modes in the octarepeat region of this protein demonstrate the predictive power and applicability of abinitio simulations for studies of metal-biomolecular complexes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 journal article

Functional implications of multistage copper binding to the prion protein

Proceedings of the National Academy of Sciences, 106(28), 11576–11581.

By: M. Hodak n, R. Chisnell n, W. Lu n & J. Bernholc n 

author keywords: copper attachment; hybrid DFT; misfolding; neurodegenerative diseases; metalloprotein
TL;DR: The results show that copper attachment leads to rearrangement of the structure of the Cu-bonded octarepeat region and to development of turns in areas separating copper-bound residues that make the flexible N-terminal domain more rigid and thus more resistant to misfolding, suggesting that copper binding plays a beneficial role in the initial stages of prion diseases. (via Semantic Scholar)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2008 journal article

Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems

Journal of Chemical Physics, 128(1).

By: M. Hodak, W. Lu & J. Bernholc 

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Recent developments and applications of the real-space multigrid method

Journal of Physics. Condensed Matter, 20(29).

By: J. Bernholc , M. Hodak & W. Lu

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Implementation of ultrasoft pseudopotentials in large-scale grid-based electronic structure calculations

PHYSICAL REVIEW B, 76(8).

By: M. Hodak n, S. Wang n, W. Lu n & J. Bernholc n 

TL;DR: Algorithms and procedures used to achieve an effective implementation in the real-space multigrid code are described, and test results for first-row diatomics, bulk transition metals, and energy-conserving quantum molecular dynamics of water are provided. (via Semantic Scholar)
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Added: August 6, 2018

2003 journal article

Systems of C-60 molecules inside (10,10) and (15,15) nanotube: A Monte Carlo study

PHYSICAL REVIEW B, 68(8).

By: M. Hodak* & L. Girifalco*

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Source: Web Of Science
Added: August 6, 2018

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