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Dmitri Klimov - Publications

Affiliations: 
George Mason University, Washington, DC 
Area:
General Biophysics, Biochemistry, Computer Science
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Bowers SR, Lockhart C, Klimov DK. Replica Exchange with Hybrid Tempering Efficiently Samples PGLa Peptide Binding to Anionic Bilayer. Journal of Chemical Theory and Computation. PMID 37676235 DOI: 10.1021/acs.jctc.3c00787  0.429
2023 Delfing BM, Laracuente XE, Olson A, Foreman KW, Paige M, Kehn-Hall K, Lockhart C, Klimov DK. Binding of Viral Nuclear Localization Signal Peptides to Importin-α Nuclear Transport Protein. Biophysical Journal. PMID 37542371 DOI: 10.1016/j.bpj.2023.07.024  0.457
2023 Lockhart C, Luo X, Olson A, Delfing BM, Laracuente XE, Foreman KW, Paige M, Kehn-Hall K, Klimov DK. Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites? Journal of Chemical Information and Modeling. PMID 37531558 DOI: 10.1021/acs.jcim.3c00631  0.323
2023 Delfing BM, Olson A, Laracuente XE, Foreman KW, Paige M, Kehn-Hall K, Lockhart C, Klimov DK. Binding of Venezuelan Equine Encephalitis Virus Inhibitors to Importin-α Receptors Explored with All-Atom Replica Exchange Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 37001021 DOI: 10.1021/acs.jpcb.3c00429  0.338
2023 Khayat E, Delfing BM, Laracuente X, Olson A, Lockhart C, Klimov DK. Lysine Acetylation Changes the Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer. Acs Chemical Neuroscience. 14: 494-505. PMID 36656569 DOI: 10.1021/acschemneuro.2c00722  0.544
2022 Vergilio J, Lockhart C, Klimov DK. Transmembrane Aggregation of Aβ10-40 Peptides in an Anionic Lipid Bilayer. Journal of Chemical Information and Modeling. 62: 6228-6241. PMID 36455155 DOI: 10.1021/acs.jcim.2c01192  0.51
2022 Bowers SR, Klimov DK, Lockhart C. Mechanisms of Binding of Antimicrobial Peptide PGLa to DMPC/DMPG Membrane. Journal of Chemical Information and Modeling. PMID 35266698 DOI: 10.1021/acs.jcim.1c01518  0.396
2021 Gurunathan V, Hamre J, Klimov DK, Jafri MS. Data Mining of Molecular Simulations Suggest Key Amino Acid Residues for Aggregation, Signaling and Drug Action. Biomolecules. 11. PMID 34680174 DOI: 10.3390/biom11101541  0.39
2021 Khayat E, Lockhart C, Delfing BM, Smith AK, Klimov DK. Met35 Oxidation Hinders Aβ25-35 Peptide Aggregation within the Dimyristoylphosphatidylcholine Bilayer. Acs Chemical Neuroscience. PMID 34383481 DOI: 10.1021/acschemneuro.1c00407  0.436
2021 Siwy CM, Delfing BM, Lockhart C, Smith AK, Klimov DK. Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer. The Journal of Physical Chemistry. B. PMID 33656350 DOI: 10.1021/acs.jpcb.0c11253  0.362
2020 Khayat E, Klimov DK, Smith AK. Phosphorylation Promotes Aβ25-35 Peptide Aggregation within the DMPC Bilayer. Acs Chemical Neuroscience. 11: 3430-3441. PMID 33006281 DOI: 10.1021/acschemneuro.0c00541  0.474
2020 Lockhart C, Smith AK, Klimov DK. Three Popular Force Fields Predict Consensus Mechanism of Amyloid β Peptide Binding to the Dimyristoylgylcerophosphocholine Bilayer. Journal of Chemical Information and Modeling. PMID 32176493 DOI: 10.1021/acs.jcim.0c00096  0.438
2019 Smith AK, Khayat E, Lockhart C, Klimov DK. Do cholesterol and sphingomyelin change the mechanism of Aβ25-35 peptide binding to zwitterionic bilayer? Journal of Chemical Information and Modeling. PMID 31738555 DOI: 10.1021/acs.jcim.9b00763  0.503
2019 Smith AK, Klimov DK. De novo aggregation of Alzheimer's Aβ25-35 peptides in a lipid bilayer. Scientific Reports. 9: 7161. PMID 31073226 DOI: 10.1038/s41598-019-43685-7  0.53
2019 Lockhart C, Smith AK, Klimov DK. Methionine Oxidation Changes the Mechanism of Aβ Peptide Binding to the DMPC Bilayer. Scientific Reports. 9: 5947. PMID 30976055 DOI: 10.1038/s41598-019-42304-9  0.414
2018 Smith AK, Klimov DK. BINDING OF CYTOTOXIC Aβ25-35 PEPTIDE TO THE DMPC LIPID BILAYER. Journal of Chemical Information and Modeling. PMID 29727180 DOI: 10.1021/acs.jcim.8b00045  0.561
2017 Lockhart C, Klimov DK. Cholesterol changes the mechanism of Aβ peptide binding to the DMPC bilayer. Journal of Chemical Information and Modeling. PMID 28910085 DOI: 10.1021/acs.jcim.7b00431  0.472
2017 Parikh N, Klimov DK. Inclusion of lipopeptides into the DMPC lipid bilayers prevents Aβ peptide insertion. Physical Chemistry Chemical Physics : Pccp. PMID 28367578 DOI: 10.1039/c7cp01003f  0.482
2017 Siwy CM, Lockhart C, Klimov DK. Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent? Plos Computational Biology. 13: e1005314. PMID 28085875 DOI: 10.1371/journal.pcbi.1005314  0.427
2017 Lockhart C, Klimov DK. Probing the Binding of Aβ Peptides to Lipid Bilayers Biophysical Journal. 112: 364a. DOI: 10.1016/j.bpj.2016.11.1973  0.415
2016 Smith AK, Lockhart C, Klimov DK. Does Replica Exchange with Solute Tempering efficiently sample Aβ peptide conformational ensembles? Journal of Chemical Theory and Computation. PMID 27560127 DOI: 10.1021/acs.jctc.6b00660  0.454
2016 Lockhart C, Klimov DK. The Alzheimer's disease Aβ peptide binds to the anionic DMPS lipid bilayer. Biochimica Et Biophysica Acta. 1858: 1118-1128. PMID 26947182 DOI: 10.1016/j.bbamem.2016.03.001  0.492
2015 Parikh ND, Klimov DK. Molecular Mechanisms of Alzheimer's Biomarker FDDNP Binding to Aβ Amyloid Fibril. The Journal of Physical Chemistry. B. 119: 11568-80. PMID 26237080 DOI: 10.1021/acs.jpcb.5b06112  0.534
2015 Lockhart C, Klimov DK. Binding of Aβ Monomer to DMPC Bilayer using Isobaric-Isothermal Replica Exchange Molecular Dynamics Biophysical Journal. 108: 64a-65a. DOI: 10.1016/j.bpj.2014.11.386  0.387
2014 Lockhart C, Klimov DK. Binding of Aβ peptide creates lipid density depression in DMPC bilayer. Biochimica Et Biophysica Acta. 1838: 2678-88. PMID 25037005 DOI: 10.1016/j.bbamem.2014.07.010  0.352
2014 Lockhart C, Klimov DK. Alzheimer's Aβ10-40 peptide binds and penetrates DMPC bilayer: an isobaric-isothermal replica exchange molecular dynamics study. The Journal of Physical Chemistry. B. 118: 2638-48. PMID 24547901 DOI: 10.1021/jp412153s  0.467
2013 Lockhart C, Klimov DK. Revealing hidden helix propensity in Aβ peptides by molecular dynamics simulations. The Journal of Physical Chemistry. B. 117: 12030-8. PMID 24016319 DOI: 10.1021/jp407705j  0.489
2013 Kim S, Klimov DK. Binding to the lipid monolayer induces conformational transition in Aβ monomer. Journal of Molecular Modeling. 19: 737-50. PMID 23053007 DOI: 10.1007/s00894-012-1596-8  0.488
2013 Lockhart C, Klimov DK. Binding of FDDNP Biomarker to Alzheimer's Disease Aβ Peptide Biophysical Journal. 104: 360a. DOI: 10.1016/j.bpj.2012.11.2000  0.429
2012 Lockhart C, Klimov DK. Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide. Biophysical Journal. 103: 2341-51. PMID 23283233 DOI: 10.1016/j.bpj.2012.10.003  0.513
2012 Lockhart C, Kim S, Klimov DK. Explicit solvent molecular dynamics simulations of Aβ peptide interacting with ibuprofen ligands. The Journal of Physical Chemistry. B. 116: 12922-32. PMID 23051147 DOI: 10.1021/jp306208n  0.581
2011 Lockhart C, Kim S, Kumar R, Klimov DK. Does amino acid sequence determine the properties of Aβ dimer? The Journal of Chemical Physics. 135: 035103. PMID 21787025 DOI: 10.1063/1.3610427  0.398
2011 Kim S, Chang WE, Kumar R, Klimov DK. Naproxen interferes with the assembly of Aβ oligomers implicated in Alzheimer's disease. Biophysical Journal. 100: 2024-32. PMID 21504739 DOI: 10.1016/J.Bpj.2011.02.044  0.785
2010 Takeda T, Kumar R, Raman EP, Klimov DK. Nonsteroidal anti-inflammatory drug naproxen destabilizes Aβ amyloid fibrils: a molecular dynamics investigation. The Journal of Physical Chemistry. B. 114: 15394-402. PMID 20979356 DOI: 10.1021/Jp107955V  0.803
2010 Kim S, Takeda T, Klimov DK. Mapping conformational ensembles of aβ oligomers in molecular dynamics simulations. Biophysical Journal. 99: 1949-58. PMID 20858441 DOI: 10.1016/J.Bpj.2010.07.008  0.668
2010 Takeda T, Chang WE, Raman EP, Klimov DK. Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril. Proteins. 78: 2849-60. PMID 20635343 DOI: 10.1002/Prot.22804  0.721
2010 Kim S, Takeda T, Klimov DK. Globular state in the oligomers formed by Abeta peptides. The Journal of Chemical Physics. 132: 225101. PMID 20550420 DOI: 10.1063/1.3447894  0.686
2010 Chang WE, Takeda T, Raman EP, Klimov DK. Molecular dynamics simulations of anti-aggregation effect of ibuprofen. Biophysical Journal. 98: 2662-70. PMID 20513411 DOI: 10.1016/J.Bpj.2010.02.031  0.768
2010 Takeda T, Klimov DK. Computational backbone mutagenesis of Abeta peptides: probing the role of backbone hydrogen bonds in aggregation. The Journal of Physical Chemistry. B. 114: 4755-62. PMID 20302321 DOI: 10.1021/Jp911533Q  0.722
2009 Raman EP, Takeda T, Klimov DK. Molecular dynamics simulations of Ibuprofen binding to Abeta peptides. Biophysical Journal. 97: 2070-9. PMID 19804739 DOI: 10.1016/J.Bpj.2009.07.032  0.81
2009 Takeda T, Klimov DK. Side chain interactions can impede amyloid fibril growth: replica exchange simulations of Abeta peptide mutant. The Journal of Physical Chemistry. B. 113: 11848-57. PMID 19708712 DOI: 10.1016/J.Bpj.2009.12.3557  0.692
2009 Takeda T, Klimov DK. Probing energetics of Abeta fibril elongation by molecular dynamics simulations. Biophysical Journal. 96: 4428-37. PMID 19486667 DOI: 10.1016/J.Bpj.2009.03.015  0.746
2009 Takeda T, Klimov DK. Probing the effect of amino-terminal truncation for Abeta1-40 peptides. The Journal of Physical Chemistry. B. 113: 6692-702. PMID 19419218 DOI: 10.1021/Jp9016773  0.669
2009 Takeda T, Klimov DK. Interpeptide interactions induce helix to strand structural transition in Abeta peptides. Proteins. 77: 1-13. PMID 19350616 DOI: 10.1002/Prot.22406  0.72
2009 Takeda T, Klimov DK. Replica exchange simulations of the thermodynamics of Abeta fibril growth. Biophysical Journal. 96: 442-52. PMID 19167295 DOI: 10.1016/J.Bpj.2008.10.008  0.72
2008 Li MS, Klimov DK, Straub JE, Thirumalai D. Probing the mechanisms of fibril formation using lattice models. The Journal of Chemical Physics. 129: 175101. PMID 19045373 DOI: 10.1063/1.2989981  0.332
2008 Takeda T, Klimov DK. Temperature-induced dissociation of Abeta monomers from amyloid fibril. Biophysical Journal. 95: 1758-72. PMID 18502791 DOI: 10.1529/Biophysj.108.131698  0.704
2007 Raman EP, Takeda T, Barsegov V, Klimov DK. Mechanical unbinding of abeta peptides from amyloid fibrils. Journal of Molecular Biology. 373: 785-800. PMID 17868685 DOI: 10.1016/J.Jmb.2007.08.034  0.796
2007 Takeda T, Klimov DK. Dissociation of Abeta(16-22) amyloid fibrils probed by molecular dynamics. Journal of Molecular Biology. 368: 1202-13. PMID 17382346 DOI: 10.1016/J.Jmb.2007.02.066  0.73
2007 Raman EP, Barsegov V, Klimov DK. Folding of tandem-linked domains. Proteins. 67: 795-810. PMID 17380511 DOI: 10.1002/Prot.21339  0.668
2007 Dong X, Klimov D, Blaisten-Barojas E. Protein folding with the adaptive tempering Monte Carlo method Molecular Simulation. 33: 577-582. DOI: 10.1080/08927020600930532  0.316
2005 Dunlavy DM, O'Leary DP, Klimov D, Thirumalai D. HOPE: a homotopy optimization method for protein structure prediction. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 1275-88. PMID 16379534 DOI: 10.1089/Cmb.2005.12.1275  0.305
2004 Klimov DK, Straub JE, Thirumalai D. Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proceedings of the National Academy of Sciences of the United States of America. 101: 14760-5. PMID 15465917 DOI: 10.1073/Pnas.0404570101  0.414
2003 Thirumalai D, Klimov DK, Dima RI. Emerging ideas on the molecular basis of protein and peptide aggregation Current Opinion in Structural Biology. 13: 146-159. PMID 12727507 DOI: 10.1016/S0959-440X(03)00032-0  0.501
2003 Klimov DK, Thirumalai D. Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure (London, England : 1993). 11: 295-307. PMID 12623017 DOI: 10.1016/S0969-2126(03)00031-5  0.464
2002 Massi F, Klimov D, Thirumalai D, Straub JE. Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Science : a Publication of the Protein Society. 11: 1639-47. PMID 12070316 DOI: 10.1110/Ps.3150102  0.501
1997 Veitshans T, Klimov D, Thirumalai D. Protein folding kinetics: Timescales, pathways and energy landscapes in terms of sequence-dependent properties Folding and Design. 2: 1-22. PMID 9080195 DOI: 10.1016/S1359-0278(97)00002-3  0.358
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