Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect (Q42352954)

27 October 2017

Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect (English)

1 reference

Shina Caroline Lynn Kamerlin

27 October 2017

Birgit Strodel

3

0 references

object named as

Shina Caroline Lynn Kamerlin

series ordinal

2

0 references

author name string

Qinghua Liao

series ordinal

1

1 reference

27 October 2017

18 June 2015

1 reference

Journal of Physical Chemistry Letters

27 October 2017

1 reference

27 October 2017

6

1 reference

27 October 2017

2657-2662

1 reference

27 October 2017

13

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

27 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Force field independent metal parameters using a nonbonded dummy model

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Role of metal ions in the self-assembly of the Alzheimer's amyloid-β peptide.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Cu(2+) affects amyloid-β (1-42) aggregation by increasing peptide-peptide binding forces

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Bioinorganic chemistry of Alzheimer's disease

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

The heterogeneous nature of Cu2+ interactions with Alzheimer's amyloid-β peptide.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Substoichiometric levels of Cu2+ ions accelerate the kinetics of fiber formation and promote cell toxicity of amyloid-{beta} from Alzheimer disease

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF).

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Coordination dynamics of zinc in proteins

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Bioinorganic chemistry of copper and zinc ions coordinated to amyloid-beta peptide

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

The structure of the amyloid-beta peptide high-affinity copper II binding site in Alzheimer disease

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

The structure of holo and metal-deficient wild-type human Cu, Zn superoxide dismutase and its relevance to familial amyotrophic lateral sclerosis

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Conformational variability of the Cu site in one subunit of bovine CuZn superoxide dismutase: the importance of mobility in the Glu119-Leu142 loop region for catalytic function

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Crystallographic structures of bovine copper-zinc superoxide dismutase reveal asymmetry in two subunits: functionally important three and five coordinate copper sites captured in the same crystal

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Determination of new Cu+, Cu2+, and Zn2+ Lennard-Jones ion parameters in acetonitrile

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Three dimensional models of Cu(2+)-Aβ(1-16) complexes from computational approaches.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

NMR studies of zinc, copper, and iron binding to histidine, the principal metal ion complexing site of amyloid-beta peptide

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Alanine-2 carbonyl is an oxygen ligand in Cu2+ coordination of Alzheimer's disease amyloid-beta peptide--relevance to N-terminally truncated forms.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4493862

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

17 August 2018

1 reference

12 December 2020

Pulse EPR spectroscopy reveals the coordination sphere of copper(II) ions in the 1-16 amyloid-beta peptide: a key role of the first two N-terminus residues

1 reference

12 December 2020

Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures

1 reference

12 December 2020

Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems

1 reference

12 December 2020

Mechanisms Whereby Mononuclear Copper Proteins Functionalize Organic Substrates

1 reference

12 December 2020

10.1021/ACS.JPCLETT.5B01122

Identifiers

DOI

1 reference

27 October 2017

1 reference

27 October 2017

1 reference

PMCID

4493862