Dmitri Klimov: PUBLICATIONS

Kim, S., Chang, W., Kumar, R., & Klimov, D.K. (2011) Naproxen interferes with the assembly of Abeta oligomers implicated in Alzheimer's disease. Biophys. J. 100, 2024-2032.

Lockhart, C., Kim, S., Kumar, R., & Klimov, D.K. (2011) Does amino acid sequence determine the properties of Abeta dimer? J. Chem. Phys. 135, 035103.

Lockhart, C. & Klimov, D.K. (2012) Molecular interactions of Alzheimer's biomarker FDDNP with Abeta peptide. Biophys. J. 103, 2341-2351.

Lockhart, C., Kim, S., & Klimov, D.K. (2012) Explicit solvent molecular dynamics simulations of Abeta peptide interacting with ibuprofen ligands. J. Phys. Chem. B 116, 12922-12932.

Kim, S. & Klimov, D.K. (2013) Binding to the lipid monolayer induces conformational transition in Abeta monomer. J. Mol. Model. 19, 737-750.

Lockhart, C. & Klimov, D.K. (2013) Revealing hidden helix propensity in Abeta peptides by molecular dynamics simulations. J. Phys. Chem. B 117, 12030-12038.

Lockhart, C. & Klimov, D.K. (2014) Alzheimer's Abeta10-40 Peptide Binds and Penetrates DMPC Bilayer: An Isobaric-Isothermal Replica Exchange Molecular Dynamics Study. J. Phys. Chem. B 118, 2638-2648.

Lockhart, C. & Klimov, D.K. (2014) Binding of Abeta peptide creates lipid density depression in DMPC bilayer. BBA Biomembranes 1838, 2678-2688.

Lockhart, C. & Klimov, D.K. (2015) Calcium enhances binding of Abeta monomer to DMPC lipid bilayer. Biophys. J. 108, 1807-1818.

Lockhart, C., O'Connor, J., Armentrout, S.,& Klimov, D.K. (2015) Greedy replica exchange algorithm improves performance on heterogeneous computing grids. J. Mol. Model. , in press, doi 10.1007/s00894-015-2763-5

Parikh, N. D. & Klimov, D.K. (2015) Molecular mechanisms of Alzheimer's biomarker FDDNP binding to Abeta amyloid fibril. J. Phys. Chem. B (accepted, DOI: 10.1021/acs.jpcb.5b06112).

Lockhart, C. & Klimov, D.K. (2016) The Alzheimer's Disease Abeta Peptide Binds to the Anionic DMPS Lipid Bilayer. BBA Biomembranes, 1858, 1118–1128.

Smith, A., Lockhart, C. & Klimov, D.K. (2016) Does Replica Exchange with Solute Tempering efficiently sample Aβ peptide conformational ensembles?" J. Chem. Theor. Comput., 12, 5201–5214.

Parikh, N. and Klimov, D. K. (2017) Inclusion of lipopeptides into the DMPC lipid bilayer prevents Abeta peptide insertion. Phys. Chem. Chem. Phys. 19, 10087-10098 (2017).

M Siwy, C Lockhart, DK Klimov. Is the conformational ensemble of Alzheimer's Aβ10-40 peptide force field dependent? PLOS Computational Biology 13, e1005314 (2017).

C Lockhart, DK Klimov. Cholesterol changes the mechanism of Abeta peptide binding to the DMPC bilayer. J. Chem. Inform. Model. 57, 2554–2565 (2017).

AK Smith, DK Klimov, Binding of cytotoxic Abeta25-35 peptide to the DMPC lipid bilayer. J. Chem. Inform. Model. 58, 1053–1065 (2018).

AK Smith, DK Klimov. Molecular Dynamics Investigation of Ternary Bilayer Formed by Saturated Phosphotidylcholine, Sphingomyelin, and Cholesterol. J. Phys. Chem. B 122, 11311-11325 (2018).

C Lockhart, AK Smith, DK Klimov. Methionine Oxidation Changes the Mechanism of A Peptide Binding to the DMPC Bilayer. Scientific Reports (submitted, 2019).

Publications 2006-2011

[42] Barsegov, V., Klimov, D.K., & Thirumalai, D. (2006) Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: Theory and applications. Biophys. J. 90, 3827-3941.

[43] Dong, X., Klimov, D.K., & Blaisten-Barojas, E. (2007) Protein folding with the adaptive tempering Monte Carlo method. Mol. Sim. 33, 577-582.

[44} Raman, E. P., Barsegov, V. & Klimov, D. K. (2007) Folding of tandem-linked domains. Proteins: Struct. Funct. Bioinform. 67, 795-810.

[45] Takeda, T & Klimov, D. K. (2007) Dissociation of Abeta16-22 amyloid fibrils probed by molecular dynamics. J. Mol. Biol. 368, 1202-1213.

[46] Bura, E., Klimov, D.K., & Barsegov, V. (2007) Analyzing forced unfolding of protein tandems by ordered variates: 1. Independent unfolding times. Biophys. J. 93, 1100-1115.

[47] Bura, E., Klimov, D.K and Barsegov, V. (2008) Analyzing forced unfolding of protein tandems by ordered aariates: 2. Dependent unfolding times. Biophys. J. 94, 2516-2528.

[48] Raman, E. P., Takeda, T., Barsegov, V. & Klimov, D. K. (2007) Mechanical unbinding of Abeta peptides from amyloid fibrils. J. Mol. Biol. 373, 785-800.

[49] Wang, P. & Klimov, D. K. (2008) Lattice simulations of cotranslational folding of single domain proteins. Proteins: Struct. Funct. Bioinform. 70, 925-937.

[50] Li, M.S., Klimov, D.K., Straub, J.E., & Thirumalai, D. (2008) Probing the mechanisms of fibril formation using lattice models. J. Chem. Phys. (in press).

[51] Takeda, T. & Klimov, D. K. (2008) Temperature induced dissociation of Abeta monomers from amyloid fibrils. Biophysical J. 95, 1758-1772.

[52] Takeda, T. & Klimov, D. K. (2009) Replica exchange simulations of the thermodynamics of Abeta fibril growth. Biophysical J. 96, 442-452.

[53] Takeda, T. & Klimov, D.K. (2009) Interpeptide interactions induce helix to strand structural transition in Abeta peptides. Proteins Struct. Funct. Bioinform. (accepted, doi 10.1002/prot.22406).

[54} Takeda, T., & Klimov, D.K. (2009) Probing energetics of Abeta fibril elongation by molecular dynamics simulations. Biophys. J. doi:10.1016/j.bpj.2009.03.015.

[55] Takeda, T., & Klimov, D.K. (2009) Probing the effect of amino-terminal truncation for Abeta1-40 Peptides. J. Phys. Chem. B 113, 6692-6702.

[56} Takeda, T., & Klimov, D.K. (2009) Side chain interactions can impede amyloid fibril growth: Replica exchange simulations of Abeta peptide mutant. J. Phys. Chem. B 113, 11848-11857.

[57] Raman, E. P., Takeda, T., & Klimov, D.K. (2009) Molecular dynamics simulations of ibuprofen binding to Abeta peptides. Biophys. J. 97, 2070-2079.

[58] Takeda, T., & Klimov, D.K. (2010) Computational backbone mutagenesis of Abeta peptides: Probing the role of backbone hydrogen bonds in aggregation. J. Phys. Chem. B 114, 4755-4762.

[59] Chang, W. E., Takeda, T., Raman, E. P., & Klimov, D.K. (2010) Molecular dynamics simulations of anti-aggregation effect of ibuprofen. Biophys. J. 98, 2662-2670.

[60] Kim, S., Takeda, T., & Klimov, D.K. (2010) Globular state in the oligomers formed by Abeta peptides J. Chem. Phys. (in press).

[61] Takeda, T., Chang, W. E., Raman, E. P., & Klimov, D.K. (2010) Binding of non-steroidal anti-inflammatory drugs to Abeta fibril. Proteins Str. Funct. Bioinform. 78, 2849-2860.

[62] Kim, S., Takeda, T., & Klimov, D.K. (2010) Mapping conformational ensembles of Abeta oligomers in molecular dynamics simulations. Biophys. J.. 99, 1949-1958.

[63] Takeda, T., Kumar, R., Raman, E. P., & Klimov, D.K. (2010) Non-steroidal anti-inflammatory drug naproxen destabilizes Abeta amyloid fibrils: A molecular dynamics investigation J. Phys. Chem. B 114, 15394-15402.

[64] Kim, S., Chang, W., Kumar, R., & Klimov, D.K. (2011) Naproxen interferes with the assembly of Abeta oligomers implicated in Alzheimer's disease. Biophys. J. (accepted).


Created in March 2011 .  Last update: January, 2019.


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