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For: Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995. [DOI: 10.1063/1.470117] [Citation(s) in RCA: 15008] [Impact Index Per Article: 517.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
201
Hahn DF, Gapsys V, de Groot BL, Mobley DL, Tresadern G. Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J Chem Inf Model 2024;64:5063-5076. [PMID: 38895959 PMCID: PMC11234369 DOI: 10.1021/acs.jcim.4c00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/21/2024]
202
Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, Ponder JW, Shen J, Smith RJH, Yang W, Ren P, Schnieders MJ. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. J Chem Phys 2024;161:012501. [PMID: 38958156 PMCID: PMC11223778 DOI: 10.1063/5.0214652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]  Open
203
Xue M, Shen C, Zhang Z. Nontrivial effects of geometric and charge defects on one-dimensional confined water. J Chem Phys 2024;161:014704. [PMID: 38949586 DOI: 10.1063/5.0216298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024]  Open
204
Tóth Ugyonka H, Hantal G, Szilágyi I, Idrissi A, Jorge M, Jedlovszky P. Spatial organization of the ions at the free surface of imidazolium-based ionic liquids. J Colloid Interface Sci 2024;676:989-1000. [PMID: 39068842 DOI: 10.1016/j.jcis.2024.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
205
Rangaswamy R, Sneha S, Hemavathy N, Umashankar V, Jeyakanthan J. Computational discovery of AKT serine/threonine kinase 1 inhibitors through shape screening for rheumatoid arthritis intervention. Mol Divers 2024:10.1007/s11030-024-10910-z. [PMID: 38970640 DOI: 10.1007/s11030-024-10910-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/02/2024] [Indexed: 07/08/2024]
206
Seiferth D, Biggin PC. Exploring the influence of pore shape on conductance and permeation. Biophys J 2024:S0006-3495(24)00449-1. [PMID: 38973159 DOI: 10.1016/j.bpj.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/17/2024] [Accepted: 07/05/2024] [Indexed: 07/09/2024]  Open
207
Yuan Y, Chen L, Song K, Cheng M, Fang L, Kong L, Yu L, Wang R, Fu Z, Sun M, Wang Q, Cui C, Wang H, He J, Wang X, Liu Y, Jiang B, Jiang J, Wang C, Yan X, Zhang X, Gao L. Stable peptide-assembled nanozyme mimicking dual antifungal actions. Nat Commun 2024;15:5636. [PMID: 38965232 PMCID: PMC11224359 DOI: 10.1038/s41467-024-50094-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]  Open
208
Tabatabai ASD, Dehghanian E, Mansouri-Torshizi H. Comparative Linkage of Novel Anti-Tumor Pd(II) Complex with Bio-Macromulecules: Fluorescence, UV-Vis, DFT, Molecular Docking and Molecular Dynamics Simulation Studies. J Fluoresc 2024:10.1007/s10895-024-03820-8. [PMID: 38967860 DOI: 10.1007/s10895-024-03820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
209
Calcagno F, Maryasin B, Garavelli M, Avagliano D, Rivalta I. Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM. J Comput Chem 2024;45:1562-1575. [PMID: 38514234 DOI: 10.1002/jcc.27338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
210
Hossein A, Beaven AH, Sapp K, Sodt AJ. Softening in Two-Component Lipid Mixtures by Spontaneous Curvature Variance. J Phys Chem B 2024;128:6317-6326. [PMID: 38889363 DOI: 10.1021/acs.jpcb.3c08117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
211
Duan Q, Ye Z, Zhou K, Wang F, Lian C, Shang Y, Liu H. An Investigation into the Transdermal Behavior of Active Ingredients by Combination of Experiments and Multiscale Simulations. J Phys Chem B 2024;128:6327-6337. [PMID: 38913878 DOI: 10.1021/acs.jpcb.4c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
212
Moqadam M, Gartan P, Talandashti R, Chiapparino A, Titeca K, Gavin AC, Reuter N. A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain. J Phys Chem B 2024;128:6338-6351. [PMID: 38903016 PMCID: PMC11228987 DOI: 10.1021/acs.jpcb.4c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
213
Liebau J, Laatsch BF, Rusnak J, Gunderson K, Finke B, Bargender K, Narkiewicz-Jodko A, Weeks K, Williams MT, Shulgina I, Musier-Forsyth K, Bhattacharyya S, Hati S. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. Biochemistry 2024;63:1621-1635. [PMID: 38607680 PMCID: PMC11223479 DOI: 10.1021/acs.biochem.3c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
214
Nguyen HNA, Sharp L, Lyman E, Saenz JP. Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering. Biophys J 2024;123:1896-1902. [PMID: 38850024 PMCID: PMC11267422 DOI: 10.1016/j.bpj.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]  Open
215
Janke U, Geist N, Weilbeer E, Levin W, Delcea M. Impact of Protein Corona Formation and Polystyrene Nanoparticle Functionalisation on the Interaction with Dynamic Biomimetic Membranes Comprising of Integrin. Chembiochem 2024;25:e202400188. [PMID: 38743506 DOI: 10.1002/cbic.202400188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
216
Song X, Bao L, Feng C, Huang Q, Zhang F, Gao X, Han R. Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information. Nat Commun 2024;15:5538. [PMID: 38956032 PMCID: PMC11219796 DOI: 10.1038/s41467-024-49858-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 06/20/2024] [Indexed: 07/04/2024]  Open
217
Dorafshan Tabatabai AS, Dehghanian E, Mansouri-Torshizi H, Feizi-Dehnayebi M. Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM. J Biomol Struct Dyn 2024;42:5447-5469. [PMID: 37349936 DOI: 10.1080/07391102.2023.2226715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
218
Jalan A, Sangeet S, Pradhan AK, Moyon NS. Exploring the interaction of a potent anti-cancer drug Selumetinib with bovine serum albumin: Spectral and computational attributes. J Mol Recognit 2024;37:e3084. [PMID: 38596890 DOI: 10.1002/jmr.3084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/05/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
219
Wang Y, Song Y, Xu L, Zhou W, Wang W, Jin Q, Xie Y, Zhang J, Liu J, Wu W, Li H, Liang L, Wang J, Yang Y, Chen X, Ge S, Gao T, Zhang L, Xie M. A Membrane-Targeting Aggregation-Induced Emission Probe for Monitoring Lipid Droplet Dynamics in Ischemia/Reperfusion-Induced Cardiomyocyte Ferroptosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2309907. [PMID: 38696589 PMCID: PMC11234465 DOI: 10.1002/advs.202309907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/01/2024] [Indexed: 05/04/2024]
220
Yang R, Bernardino K, Xiao X, Gomes WR, Mattoso DA, Kotov NA, Bogdan P, de Moura AF. Graph Theoretical Description of Phase Transitions in Complex Multiscale Phases with Supramolecular Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402464. [PMID: 38952077 DOI: 10.1002/advs.202402464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/15/2024] [Indexed: 07/03/2024]
221
Khademi Dehkordi M, Hoveida L, Fani N. Structure-based virtual screening, molecular docking, and molecular dynamics simulation approaches for identification of new potential inhibitors of class a β-lactamase enzymes. J Biomol Struct Dyn 2024;42:5631-5641. [PMID: 37534493 DOI: 10.1080/07391102.2023.2227724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/14/2023] [Indexed: 08/04/2023]
222
Zeneli E, Lange JJ, Holm R, Kuentz M. A study of hydrophobic domain formation of polymeric drug precipitation inhibitors in aqueous solution. Eur J Pharm Sci 2024;198:106791. [PMID: 38705420 DOI: 10.1016/j.ejps.2024.106791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/07/2024]
223
Feng P, Zhang D, Zhang G, Li C, Wang Y, Chen G, Gan Y. SEM Electron-Beam-Induced Ultrathin Carbon Deposition Layer on Cu Substrate: Improved Dry Oxidation Protection Performance than CVD Single Layer Graphene. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024;20:e2309285. [PMID: 38402441 DOI: 10.1002/smll.202309285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/14/2024] [Indexed: 02/26/2024]
224
Lee W. Mechanistic Insight into how β-Ketoacyl ACP Synthase I (KasA) Recognizes the Fatty Acid Chain Length of its Substrate. Chempluschem 2024;89:e202300568. [PMID: 37983623 DOI: 10.1002/cplu.202300568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
225
Zhong Z, Du G, Ma L, Wang Y, Jiang J. Self-Assembly of Lamellae-in-Lamellae by Double-Tail Cationic Surfactants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2401210. [PMID: 38751126 PMCID: PMC11267300 DOI: 10.1002/advs.202401210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/25/2024] [Indexed: 07/25/2024]
226
Liang Y, Ormazabal-Toledo R, Yao S, Shi YS, Herrera-Molina R, Montag D, Lin X. Deafness causing neuroplastin missense variants fail to promote plasma membrane Ca2+-ATPase levels and Ca2+ transient regulation in brain neurons. J Biol Chem 2024;300:107474. [PMID: 38879011 PMCID: PMC11264175 DOI: 10.1016/j.jbc.2024.107474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/06/2024] [Accepted: 06/09/2024] [Indexed: 07/08/2024]  Open
227
Cheng K, Xu X, Song J, Chen Y, Kan Z, Li C. Molecular dynamics simulations of choline chloride and ascorbic acid deep eutectic solvents: Investigation of structural and dynamics properties. J Mol Graph Model 2024;130:108784. [PMID: 38692127 DOI: 10.1016/j.jmgm.2024.108784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
228
Mazzaferro S, Kang G, Natarajan K, Hibbs RE, Sine SM. Structural bases for stoichiometry-selective calcium potentiation of a neuronal nicotinic receptor. Br J Pharmacol 2024;181:1973-1992. [PMID: 38454578 DOI: 10.1111/bph.16321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 03/09/2024]  Open
229
Davidson DS, Lemkul JA. Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β-peptide. Proteins 2024;92:842-853. [PMID: 38436541 PMCID: PMC11147713 DOI: 10.1002/prot.26677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
230
Senoo N, Chinthapalli DK, Baile MG, Golla VK, Saha B, Oluwole AO, Ogunbona OB, Saba JA, Munteanu T, Valdez Y, Whited K, Sheridan MS, Chorev D, Alder NN, May ER, Robinson CV, Claypool SM. Functional diversity among cardiolipin binding sites on the mitochondrial ADP/ATP carrier. EMBO J 2024;43:2979-3008. [PMID: 38839991 PMCID: PMC11251061 DOI: 10.1038/s44318-024-00132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024]  Open
231
Madsen JJ, Ohkubo YZ. Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM. PLoS Comput Biol 2024;20:e1011421. [PMID: 38976709 PMCID: PMC11257402 DOI: 10.1371/journal.pcbi.1011421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 07/18/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024]  Open
232
Cappelluti F, Gontrani L, Mariani A, Galliano S, Carbone M, Bonomo M. Voronoi Tessellation as a Tool for Predicting the Formation of Deep Eutectic Solvents. J Chem Inf Model 2024. [PMID: 38950140 DOI: 10.1021/acs.jcim.3c01738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
233
Abramov-Harpaz K, Lan-Mark S, Miller Y. Structural packing of the non-amyloid component core domain in α-synuclein plays a role in the stability of the fibrils. Biophys Chem 2024;310:107239. [PMID: 38663121 DOI: 10.1016/j.bpc.2024.107239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/23/2024]
234
Hoff SE, Thomasen FE, Lindorff-Larsen K, Bonomi M. Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. PLoS Comput Biol 2024;20:e1012180. [PMID: 39008528 PMCID: PMC11271924 DOI: 10.1371/journal.pcbi.1012180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 07/25/2024] [Accepted: 05/20/2024] [Indexed: 07/17/2024]  Open
235
Rigobello L, Lugli F, Caporali L, Bartocci A, Fadanni J, Zerbetto F, Iommarini L, Carelli V, Ghelli AM, Musiani F. A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory complex I. Int J Biol Macromol 2024;273:133086. [PMID: 38871105 DOI: 10.1016/j.ijbiomac.2024.133086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
236
Zhang H, Zhang J, Zhang HX. Effect of quercetin on the protein-substrate interactions in SIRT6: Insight from MD simulations. J Mol Graph Model 2024;130:108778. [PMID: 38652998 DOI: 10.1016/j.jmgm.2024.108778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/28/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
237
Skrdla PJ, Coscia BJ, Gavartin J, Browning A, Shelley J, Sanders JM. Complexation Mechanisms of Aqueous Amylose: Molecular Dynamics Study Using 3-Pentadecylphenol. Mol Pharm 2024;21:3540-3552. [PMID: 38900044 DOI: 10.1021/acs.molpharmaceut.4c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
238
Ray S, Gupta S, Panda G, Chatterjee P, Das A, Patawri P, Hosseinzadeh P, Ray A, Banerjee S. Identification of pseudobaptigenin as a novel polyphenol-based multi-target antagonist of different hormone receptors for breast cancer therapeutics. J Biomol Struct Dyn 2024;42:5502-5514. [PMID: 37409735 DOI: 10.1080/07391102.2023.2226750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023]
239
Mondal S, Karmakar T. Insights into the mechanism of peptide fibril growth on gold surface. Biophys Chem 2024;310:107237. [PMID: 38640598 DOI: 10.1016/j.bpc.2024.107237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/24/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
240
Sun Q, Chen YN, Liu YZ. The Effects of External Interfaces on Hydrophobic Interactions I: Smooth Surface. Molecules 2024;29:3128. [PMID: 38999080 PMCID: PMC11243484 DOI: 10.3390/molecules29133128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/14/2024]  Open
241
Asmare MM, Krishnaraj C, Radhakrishnan S, Kim BS, Yoon JS, Yun SI. In silico modelling of ciprofloxacin specific aptamer for the development of high-performance biosensor. J Mol Graph Model 2024;130:108787. [PMID: 38749234 DOI: 10.1016/j.jmgm.2024.108787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
242
Ruzmetov T, Hung TI, Jonnalagedda SP, Chen SH, Fasihianifard P, Guo Z, Bhanu B, Chang CEA. Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592587. [PMID: 38979147 PMCID: PMC11230202 DOI: 10.1101/2024.05.05.592587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
243
Lupi L, Gallo P. Mode coupling behavior and fragile to strong transition of trehalose in a binary mixture with water upon supercooling. J Chem Phys 2024;160:244501. [PMID: 38912627 DOI: 10.1063/5.0218369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024]  Open
244
Ngoc Toan V, Son Hai D, Thi Kim Van H, Minh Tri N, Ngoc Toan D, Thi Thanh Mai N, Dinh Thanh N. Design, synthesis, inhibitory activity, and molecular simulations study for d-glucose-conjugated thioureas containing pyrimidine ring as multitarget inhibitors against α-amylase, α-glucosidase, DDP-4, and PTP1B in Type 2 diabetes mellitus. RSC Med Chem 2024:d4md00334a. [PMID: 39185455 PMCID: PMC11342126 DOI: 10.1039/d4md00334a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/24/2024] [Indexed: 08/27/2024]  Open
245
Al Qaraghuli MM, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Exploiting the Fc base of IgG antibodies to create functional nanoparticle conjugates. Sci Rep 2024;14:14832. [PMID: 38937649 PMCID: PMC11211340 DOI: 10.1038/s41598-024-65822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]  Open
246
Costanzo A, Fata F, Freda I, De Sciscio ML, Gugole E, Bulfaro G, Di Renzo M, Barbizzi L, Exertier C, Parisi G, D'Abramo M, Vallone B, Savino C, Montemiglio LC. Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure 2024:S0969-2126(24)00223-5. [PMID: 38971159 DOI: 10.1016/j.str.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
247
Deng Y, Carnevale V, Ditchfield R, Pletneva EV. Applications of the Newly Developed Force-Field Parameters Uncover a Dynamic Nature of Ω-Loop C in the Lys-Ligated Alkaline Form of Cytochrome c. J Phys Chem B 2024;128:5935-5949. [PMID: 38864552 DOI: 10.1021/acs.jpcb.4c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
248
Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024;128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
249
Kowalczyk A, Dziubak D, Kasprzak A, Sobczak K, Ruzycka-Ayoush M, Bamburowicz-Klimkowska M, Sęk S, Rios-Mondragon I, Żołek T, Runden-Pran E, Shaposhnikov S, Cimpan MR, Dusinska M, Grudzinski IP, Nowicka AM. Surface-Bioengineered Extracellular Vesicles Seeking Molecular Biotargets in Lung Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2024;16:31997-32016. [PMID: 38869318 PMCID: PMC11212023 DOI: 10.1021/acsami.4c04265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
250
Pinto AV, Ferreira P, Cunha AV, Havenith RWA, Magalhães AL, Ramos MJ, Fernandes PA. Revisiting the reaction pathways for phospholipid hydrolysis catalyzed by phospholipase A2 with QM/MM methods. Chem Sci 2024;15:9793-9805. [PMID: 38939148 PMCID: PMC11206408 DOI: 10.1039/d4sc02315c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/17/2024] [Indexed: 06/29/2024]  Open
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