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Publications enabled by research that made use of Anton or Anton 2  at PSC:

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Ahmed T, Nisler CR, Fluck EC, Walujkar S, Sotomayor M, Moiseenkova-Bell VY. Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium. Structure. 2022;30: 139–155.e5. doi:10.1016/j.str.2021.08.003

Araya MK, Gorfe AA. Phosphatidylserine and Phosphatidylethanolamine Asymmetry Have a Negligible Effect on the Global Structure, Dynamics, and Interactions of the KRAS Lipid Anchor. J Phys Chem B. 2022;126: 4491–4500. doi:10.1021/acs.jpcb.2c01253

Corradi V, Bukiya AN, Miranda WE, Cui M, Plant LD, Logothetis DE, et al. A molecular switch controls the impact of cholesterol on a Kir channel. Proceedings of the National Academy of Sciences. 2022;119: e2109431119. doi:10.1073/pnas.2109431119

Feng S, Pumroy RA, Protopopova AD, Moiseenkova‐Bell VY, Im W. Modulation of TRPV2 by Endogenous and Exogenous Ligands: A Computational Study. Protein Sci. 2022. doi:10.1002/pro.4490

Govind Kumar V, Ogden DS, Isu UH, Polasa A, Losey J, Moradi M. Prefusion Spike Protein Conformational Changes Are Slower in SARS-CoV-2 than in SARS-CoV-1. J Biol Chem. 2022; 101814. doi:10.1016/j.jbc.2022.101814

Han K, Kim SH, Venable RM, Pastor RW. Design principles of PI(4,5)P 2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy. Proceedings of the National Academy of Sciences. 2022;119: e2202647119. doi:10.1073/pnas.2202647119

Hashemi M, Banerjee S, Lyubchenko YL. Free Cholesterol Accelerates Aβ Self-Assembly on Membranes at Physiological Concentration. Int J Mol Sci. 2022;23: 2803. doi:10.3390/ijms23052803

Itagi P, Kante A, Lagunes L, Deeds EJ. Understanding the Separation of Timescales in Rhodococcus erythropolis Proteasome Core Particle Assembly. Biophys J. 2022; S0006349522006828. doi:10.1016/j.bpj.2022.08.022

Jalali S, Yang Y, Mahmoudinobar F, Singh SM, Nilsson BL, Dias C. Using all-atom simulations in explicit solvent to study aggregation of amphipathic peptides into amyloid-like fibrils. J Mol Liq. 2022;347: 118283. doi:10.1016/j.molliq.2021.118283

Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, et al. Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature. 2022. doi:10.1038/s41586-022-05314-8

Knapp BD, Ward MD, Bowman GR, Shi H, Casey Huang K. Multiple conserved states characterize the twist landscape of the bacterial actin homolog MreB. Comput Struct Biotechnol J. 2022; S200103702200455X. doi:10.1016/j.csbj.2022.10.008

Kudaibergenova M, Guo J, Khan HM, Lees-Miller J, Mouasei M, Miranda W, et al. The Voltage Sensing Domain of a hERG1 mutant is a Cation-Selective Channel. Biophys J. 2022; S0006349522008700. doi:10.1016/j.bpj.2022.10.032

Li J, Remington JM, Liao C, Parsons RL, Schneebeli S, Braas KM, et al. GPCR Intracellular Loop Regulation of Beta-Arrestin-Mediated Endosomal Signaling Dynamics. J Mol Neurosci. 2022;72: 1358–1373. doi:10.1007/s12031-022-02016-8

Li Z-L, Mattos C, Buck M. Computational studies of the principle of dynamic-change-driven protein interactions. Structure. 2022; S0969212622000892. doi:10.1016/j.str.2022.03.008

Liao S, Pino MJ, Deleon C, Lindner-Jackson M, Wu C. Interaction analyses of hTAAR1 and mTAAR1 with antagonist EPPTB. Life Sci. 2022;300: 120553. doi:10.1016/j.lfs.2022.120553

Ngo VA, Queralt-Martín M, Khan F, Bergdoll L, Abramson J, Bezrukov SM, et al. The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating. J Am Chem Soc. 2022; jacs.2c03316. doi:10.1021/jacs.2c03316

Pshetitsky Y, Mendelman N, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: N–H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry. J Phys Chem B. 2022; acs.jpcb.2c03431. doi:10.1021/acs.jpcb.2c03431

Rice A, Haldar S, Wang E, Blank PS, Akimov SA, Galimzyanov TR, et al. Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration. Nat Commun. 2022;13: 7336. doi:10.1038/s41467-022-34576-z

Rickard MM, Luo H, De Lio A, Gruebele M, Pogorelov TV. Impact of the Cellular Environment on Adenosine Triphosphate Conformations. J Phys Chem Lett. 2022; 9809–9814. doi:10.1021/acs.jpclett.2c02375

Tajima N, Simorowski N, Yovanno RA, Regan MC, Michalski K, Gómez R, et al. Development and characterization of functional antibodies targeting NMDA receptors. Nat Commun. 2022;13: 923. doi:10.1038/s41467-022-28559-3

Tan et. al. Structure of the Shaker Kv channel and mechanism of slow C-type inactivation. Science Advances. 2022;8: eabm7814.

Tyagi A, Ahmed T, Jian S, Bajaj S, Ong ST, Goay SSM, et al. Rearrangement of a unique Kv1.3 selectivity filter conformation upon binding of a drug. Proceedings of the National Academy of Sciences. 2022;119: e2113536119. doi:10.1073/pnas.2113536119

Wilson MA, Pohorille A. Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel. J Phys Chem B. 2022; acs.jpcb.2c05965. doi:10.1021/acs.jpcb.2c05965

Yang MY, Kim S-K, Goddard WA. G protein coupling and activation of the metabotropic GABAB heterodimer. Nat Commun. 2022;13: 4612. doi:10.1038/s41467-022-32213-3

Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci. 2022; acschemneuro.2c00446. doi:10.1021/acschemneuro.2c00446

Yelshanskaya MV, Patel DS, Kottke CM, Kurnikova MG, Sobolevsky AI. Opening of glutamate receptor channel to subconductance levels. Nature. 2022. doi:10.1038/s41586-022-04637-w

Yovanno RA, Chou TH, Brantley SJ, Furukawa H, Lau AY. Excitatory and inhibitory D-serine binding to the NMDA receptor. Elife. 2022;11: e77645. doi:10.7554/eLife.77645

Yuan Y, Deng J, Cui Q. Molecular Dynamics Simulations Establish the Molecular Basis for the Broad Allostery Hotspot Distributions in the Tetracycline Repressor. J Am Chem Soc. 2022;144: 10870–10887. doi:10.1021/jacs.2c03275

Zhao R, Shen R, Dai H, Perozo E, Goldstein SAN. Molecular determinants of inhibition of the human proton channel hHv1 by the designer peptide C6 and a bivalent derivative. Proceedings of the National Academy of Sciences. 2022;119: e2120750119. doi:10.1073/pnas.2120750119


Agrawal S, Govind Kumar V, Gundampati RK, Moradi M, Kumar TKS. Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor. Sci Rep. 2021;11: 15579. doi:10.1038/s41598-021-95050-2

Banerjee S, Hashemi M, Zagorski K, Lyubchenko YL. Cholesterol in Membranes Facilitates Aggregation of Amyloid β Protein at Physiologically Relevant Concentrations. ACS Chem Neurosci. 2021;12: 506–516. doi:10.1021/acschemneuro.0c00688

Bavi N, Clark MD, Contreras GF, Shen R, Reddy BG, Milewski W, et al. Prestin’s conformational cycle underlies outer hair cell electromotility. Nature. 2021. doi:10.1038/s41586-021-04152-4

Brady J, Vasin A, Bykhovskaia M. The Accessory Helix of Complexin Stabilizes a Partially Unzippered State of the SNARE Complex and Mediates the Complexin Clamping Function in Vivo. eneuro. 2021; ENEURO.0526–20.2021. doi:10.1523/ENEURO.0526-20.2021

Bykhovskaia M. SNARE complex alters the interactions of the Ca2+ sensor synaptotagmin 1 with lipid bilayers. Biophys J. 2021;120: 642–661. doi:10.1016/j.bpj.2020.12.025

Canner SW, Feller SE, Wassall SR. Molecular Organization of a Raft-like Domain in a Polyunsaturated Phospholipid Bilayer: A Supervised Machine Learning Analysis of Molecular Dynamics Simulations. J Phys Chem B. 2021;125: 13158–13167. doi:10.1021/acs.jpcb.1c06511

DeMarco KR, Yang P-C, Singh V, Furutani K, Dawson JRD, Jeng M-T, et al. Molecular determinants of pro-arrhythmia proclivity of d- and l-sotalol via a multi-scale modeling pipeline. J Mol Cell Cardiol. 2021;158: 163–177. doi:10.1016/j.yjmcc.2021.05.015

Gao L, Zou Y, Liu X, Yang J, Du X, Wang J, et al. Enzymatic control of endo- and exo-stereoselective Diels–Alder reactions with broad substrate scope. Nature Catalysis. 2021. doi:10.1038/s41929-021-00717-8

Geragotelis AD, Freites JA, Tobias DJ. Anomalous Diffusion of Peripheral Membrane Signaling Proteins from All-Atom Molecular Dynamics Simulations. J Phys Chem B. 2021; acs.jpcb.1c04905. doi:10.1021/acs.jpcb.1c04905

Govind Kumar V, Agrawal S, Kumar TKS, Moradi M. Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding. J Phys Chem B. 2021;125: 12690–12697. doi:10.1021/acs.jpcb.1c07772

Jiang W, Lin Y-C, Botello-Smith W, Contreras JE, Harris AL, Maragliano L, et al. Free energy and kinetics of cAMP permeation through connexin26 via applied voltage and milestoning. Biophys J. 2021;120: 2969–2983. doi:10.1016/j.bpj.2021.06.024

Jiang W, Del Rosario JS, Botello-Smith W, Zhao S, Lin Y-C, Zhang H, et al. Crowding-induced opening of the mechanosensitive Piezo1 channel in silico. Communications Biology. 2021;4: 84. doi:10.1038/s42003-020-01600-1

Kasahara K, Re S, Nawrocki G, Oshima H, Mishima-Tsumagari C, Miyata-Yabuki Y, et al. Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nat Commun. 2021;12: 4099. doi:10.1038/s41467-021-24349-5

Khan HM, Guo J, Duff HJ, Tieleman DP, Noskov SY. Refinement of a cryo-EM structure of hERG: Bridging structure and function. Biophys J. 2021;120: 738–748. doi:10.1016/j.bpj.2021.01.011

Leung L, Liao S, Wu C. To Probe the Binding Interactions between Two FDA Approved Migraine Drugs (Ubrogepant and Rimegepant) and Calcitonin-Gene Related Peptide Receptor (CGRPR) Using Molecular Dynamics Simulations. ACS Chem Neurosci. 2021;12: 2629–2642. doi:10.1021/acschemneuro.1c00135

Li J, Shen R, Reddy B, Perozo E, Roux B. Mechanism of C-type inactivation in the hERG potassium channel. Science Advances. 2021;7: eabd6203. doi:10.1126/sciadv.abd6203

Li J, Shen R, Rohaim A, Mendoza Uriarte R, Fajer M, Perozo E, et al. Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel. J Gen Physiol. 2021;153: e202112875. doi:10.1085/jgp.202112875

Li Z-L, Müller-Greven J, Kim S, Tamagnone L, Buck M. Plexin-Bs enhance their GAP activity with a novel activation switch loop generating a cooperative enzyme. Cell Mol Life Sci. 2021;78: 1101–1112. doi:10.1007/s00018-020-03571-2

Mafi A, Kim S-K, Chou KC, Güthrie B, Goddard WA. Predicted Structure of Fully Activated Tas1R3/1R3′ Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars. J Am Chem Soc. 2021; jacs.1c08839. doi:10.1021/jacs.1c08839

Monje-Galvan V, Voth GA. Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2. Faraday Discuss. 2021;232: 49–67. doi:10.1039/D1FD00031D

Mugnai ML, Thirumalai D. Step-Wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor. J Phys Chem B. 2021;125: 1107–1117. doi:10.1021/acs.jpcb.0c10004

Muller C, Lynch DL, Hurst DP, Reggio PH. TRPV1 Activation by Anandamide via a Unique Lipid Pathway. J Chem Inf Model. 2021;61: 5742–5746. doi:10.1021/acs.jcim.1c00893

Nierzwicki Ł, Palermo G. Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Frontiers in Molecular Biosciences. 2021;8: 641208. doi:10.3389/fmolb.2021.641208

Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput. 2021; acs.jctc.1c00550. doi:10.1021/acs.jctc.1c00550

Packer MR, Parker JA, Chung JK, Li Z, Lee YK, Cookis T, et al. Raf promotes dimerization of the Ras G-domain with increased allosteric connections. Proceedings of the National Academy of Sciences. 2021;118: e2015648118. doi:10.1073/pnas.2015648118

Pajak J, Dill E, Reyes-Aldrete E, White MA, Kelch BA, Jardine PJ, et al. Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor. Nucleic Acids Res. 2021; gkab372. doi:10.1093/nar/gkab372

Prakash P, Gorfe AA. Determinants of Membrane Orientation Dynamics in Lipid-Modified Small GTPases. JACS Au. 2021; jacsau.1c00426. doi:10.1021/jacsau.1c00426

Ramirez-Mondragon CA, Nguyen ME, Milicaj J, Hassan BA, Tucci FJ, Muthyala R, et al. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. Int J Mol Sci. 2021;22: 4619. doi:10.3390/ijms22094619

Sepehri A, Nepal B, Lazaridis T. Lipid interactions of an actinoporin pore-forming oligomer. Biophys J. 2021; S0006349521001521. doi:10.1016/j.bpj.2021.02.015

Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, et al. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences. 2021;118: e2103674118. doi:10.1073/pnas.2103674118

Tang PK, Manandhar A, Hu W, Kang M, Loverde SM. The interaction of supramolecular anticancer drug amphiphiles with phospholipid membranes. Nanoscale Advances. 2021;3: 370–382. doi:10.1039/D0NA00697A

Thirman J, Rui H, Roux B. Elusive Intermediate State Key in the Conversion of ATP Hydrolysis into Useful Work Driving the Ca 2+ Pump SERCA. J Phys Chem B. 2021; acs.jpcb.1c00558. doi:10.1021/acs.jpcb.1c00558

Tyagi V, Vasquez-Montes V, Freites JA, Kyrychenko A, Tobias DJ, Ladokhin AS. Effects of Cardiolipin on the Conformational Dynamics of Membrane-Anchored Bcl-xL. Int J Mol Sci. 2021;22: 9388. doi:10.3390/ijms22179388

Uba AI, Scorese N, Dean E, Liu H, Wu C. Activation Mechanism of Corticotrophin Releasing Factor Receptor Type 1 Elucidated Using Molecular Dynamics Simulations. ACS Chem Neurosci. 2021;12: 1674–1687. doi:10.1021/acschemneuro.1c00126

Wang B, Su Z, Wu Y. Characterizing the function of domain linkers in regulating the dynamics of multi‐domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence. Proteins: Struct Funct Bioinf. 2021; rot.26066. doi:10.1002/prot.26066

Wang W, Tsirulnikov K, Zhekova HR, Kayık G, Khan HM, Azimov R, et al. Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE. Nat Commun. 2021;12: 5690. doi:10.1038/s41467-021-25998-2

Wu X, Ramentol R, Perez ME, Noskov SY, Larsson HP. A second S4 movement opens hyperpolarization-activated HCN channels. Proceedings of the National Academy of Sciences. 2021;118: e2102036118. doi:10.1073/pnas.2102036118

Yang MY, Mafi A, Kim S-K, Goddard WA, Guthrie B. Predicted structure of fully activated human bitter taste receptor TAS2R4 complexed with G protein and agonists. QRB Discovery. 2021;2: e3. doi:10.1017/qrd.2021.1

Yazdi S, Nikesjö J, Miranda W, Corradi V, Tieleman DP, Noskov SY, et al. Identification of PUFA interaction sites on the cardiac potassium channel KCNQ1. J Gen Physiol. 2021;153: e202012850. doi:10.1085/jgp.202012850

Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, et al. A Multiscale Coarse-Grained Model of the SARS-CoV-2 Virion. Biophys J. 2021. doi:10.1016/j.bpj.2020.10.048

Zhang L. Interaction of Human β Defensin Type 3 (hBD-3) with Different PIP2-Containing Membranes, a Molecular Dynamics Simulation Study. J Chem Inf Model. 2021; acs.jcim.1c00805. doi:10.1021/acs.jcim.1c00805

Zimmer MH, Niesen MJM, Miller TF. Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides. Biophys J. 2021;120: 2425–2435. doi:10.1016/j.b


Baral S, Levental I, Lyman E. Composition dependence of cholesterol flip-flop rates in physiological mixtures. Chem Phys Lipids. 2020;232: 104967. doi:10.1016/j.chemphyslip.2020.104967

Biggers L, Elhabashy H, Ackad E, Yousef MS. Molecular dynamics simulations of an engineered T4 lysozyme exclude helix to sheet transition, and provide insights into long distance, intra‐protein switchable motion. Protein Sci. 2020;29: 542–554. doi:10.1002/pro.3780

Clark MD, Contreras GF, Shen R, Perozo E. Electromechanical coupling in the hyperpolarization-activated K+ channel KAT1. Nature. 2020. doi:10.1038/s41586-020-2335-4

Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM. Ball-and-chain inactivation in a calcium-gated potassium channel. Nature. 2020;580: 288–293. doi:10.1038/s41586-020-2116-0

Geragotelis AD, Wood ML, Göddeke H, Hong L, Webster PD, Wong EK, et al. Voltage-dependent structural models of the human Hv1 proton channel from long-timescale molecular dynamics simulations. Proceedings of the National Academy of Sciences. 2020;117: 13490–13498. doi:10.1073/pnas.1920943117

Guros NB, Balijepalli A, Klauda JB. Microsecond-timescale simulations suggest 5-HT–mediated preactivation of the 5-HT 3A serotonin receptor. Proceedings of the National Academy of Sciences. 2020;117: 405–414. doi:10.1073/pnas.1908848117

Han K, Pastor RW, Fenollar–Ferrer C. PLD2–PI(4,5)P2 interactions in fluid phase membranes: Structural modeling and molecular dynamics simulations. PLoS One. 2020;15: e0236201. doi:10.1371/journal.pone.0236201

Karandur D, Bhattacharyya M, Xia Z, Lee YK, Muratcioglu S, McAffee D, et al. Breakage of the oligomeric CaMKII hub by the regulatory segment of the kinase. Elife. 2020;9. doi:10.7554/eLife.57784

Khelashvili G, Cheng X, Falzone ME, Doktorova M, Accardi A, Weinstein H. Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins. J Comput Chem. 2020;41: 538–551. doi:10.1002/jcc.26105

Kudaibergenova M, Guo J, Khan HM, Zahid F, Lees-Miller J, Noskov SY, et al. Allosteric Coupling Between Drug Binding and the Aromatic Cassette in the Pore Domain of the hERG1 Channel: Implications for a State-Dependent Blockade. Front Pharmacol. 2020;11: 914. doi:10.3389/fphar.2020.00914

Kumar V, Hoag H, Sader S, Scorese N, Liu H, Wu C. GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β 2 Adrenergic Receptor. J Chem Inf Model. 2020;60: 4064–4075. doi:10.1021/acs.jcim.0c00432

Lev B, Allen TW. Simulating ion channel activation mechanisms using swarms of trajectories. J Comput Chem. 2020;41: 387–401. doi:10.1002/jcc.26102

Li Z, Buck M. Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface. J Chem Inf Model. 2020;60: 306–315. doi:10.1021/acs.jcim.9b00690

Lolicato M, Natale AM, Abderemane-Ali F, Crottès D, Capponi S, Duman R, et al. K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions. Science Advances. 2020;6: eabc9174. doi:10.1126/sciadv.abc9174

Miranda WE, DeMarco KR, Guo J, Duff HJ, Vorobyov I, Clancy CE, et al. Selectivity filter modalities and rapid inactivation of the hERG1 channel. Proceedings of the National Academy of Sciences. 2020;117: 2795–2804. doi:10.1073/pnas.1909196117

Monje-Galvan V, Voth GA. Binding mechanism of the matrix domain of HIV-1 Gag to lipid membranes. Elife. 2020;9. doi:10.7554/eLife.58621

Muller C, Lynch DL, Hurst DP, Reggio PH. A Closer Look at Anandamide Interaction With TRPV1. Frontiers in Molecular Biosciences. 2020;7: 144. doi:10.3389/fmolb.2020.00144

Nangia S, Boyd KJ, May ER. Molecular dynamics study of membrane permeabilization by wild-type and mutant lytic peptides from the non-enveloped Flock House virus. Biochimica et Biophysica Acta (BBA) – Biomembranes. 2020;1862: 183102. doi:10.1016/j.bbamem.2019.183102

Nierzwicki Ł, Arantes PR, Saha A, Palermo G. Establishing the allosteric mechanism in CRISPR‐Cas9. WIREs Computational Molecular Science. 2020. doi:10.1002/wcms.1503

Palmer NJ, Eskici G, Axelsen PH. Non-Equilibrium Mass Exchange in AOT Reverse Micelles. J Phys Chem B. 2020;124: 144–148. doi:10.1021/acs.jpcb.9b08511

Pattis JG, May ER. Markov State Model of Lassa Virus Nucleoprotein Reveals Large Structural Changes during the Trimer to Monomer Transition. Structure. 2020;28: 548–554.e3. doi:10.1016/j.str.2020.03.002

Paul F, Thomas T, Roux B. Diversity of Long-Lived Intermediates along the Binding Pathway of Imatinib to Abl Kinase Revealed by MD Simulations. J Chem Theory Comput. 2020;16: 7852–7865. doi:10.1021/acs.jctc.0c00739

Rickard MM, Zhang Y, Pogorelov TV, Gruebele M. Crowding, Sticking, and Partial Folding of GTT WW Domain in a Small Cytoplasm Model. J Phys Chem B. 2020. doi:10.1021/acs.jpcb.0c02536

Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol. 2020;253: 287–298. doi:10.1007/s00232-020-00124-3

Schachter I, Allolio C, Khelashvili G, Harries D. Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties. J Phys Chem B. 2020;124: 7166–7175. doi:10.1021/acs.jpcb.0c03374

Sepehri A, PeBenito L, Pino-Angeles A, Lazaridis T. What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives. Biophys J. 2020;118: 1901–1913. doi:10.1016/j.bpj.2020.02.024

Shi H, Quint DA, Grason GM, Gopinathan A, Huang KC. Chiral twisting in a bacterial cytoskeletal polymer affects filament size and orientation. Nat Commun. 2020;11: 1408. doi:10.1038/s41467-020-14752-9

Suppahia A, Itagi P, Burris A, Kim FMG, Vontz A, Kante A, et al. Cooperativity in Proteasome Core Particle Maturation. iScience. 2020;23: 101090. doi:10.1016/j.isci.2020.101090

Winogradoff D, John S, Aksimentiev A. Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly. Nanoscale. 2020;12: 5422–5434. doi:10.1039/C9NR09135A

Wolska A, Lo L, Sviridov DO, Pourmousa M, Pryor M, Ghosh SS, et al. A dual apolipoprotein C-II mimetic–apolipoprotein C-III antagonist peptide lowers plasma triglycerides. Sci Transl Med. 2020;12: eaaw7905. doi:10.1126/scitranslmed.aaw7905

Yang P-C, DeMarco KR, Aghasafari P, Jeng M-T, Dawson JRD, Bekker S, et al. A Computational Pipeline to Predict Cardiotoxicity: From the Atom to the Rhythm. Circ Res. 2020;126: 947–964. doi:10.1161/CIRCRESAHA.119.316404

Yu A, Lee EMY, Jin J, Voth GA. Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP 6 ). Science Advances. 2020;6: eabc6465. doi:10.1126/sciadv.abc6465

Zhang L. Disulfide Bonds Affect the Binding Sites of Human β Defensin Type 3 On Negatively Charged Lipid Membranes. J Phys Chem B. 2020;11: 2088–2100. doi:10.1021/acs.jpcb.9b10529

Zheng W, Dignon GL, Jovic N, Xu X, Regy RM, Fawzi NL, et al. Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations. J Phys Chem B. 2020;124: 11671–11679. doi:10.1021/acs.jpcb.0c10489


Balusek, Curtis, Hyea Hwang, Chun Hon Lau, Karl Lundquist, Anthony Hazel, Anna Pavlova, Diane L. Lynch, Patricia H. Reggio, Yi Wang, and James C. Gumbart. “Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.” Journal of Chemical Theory and Computation, June 20, 2019. https://doi.org/10.1021/acs.jctc.9b00160.

Biggers, Laurence, Hadeer Elhabashy, Edward Ackad, and Mohammad S. Yousef. “Molecular Dynamics Simulations of an Engineered T4 Lysozyme Exclude Helix to Sheet Transition, and Provide Insights into Long Distance, Intra‐Protein Switchable Motion.” Protein Science, November 8, 2019. https://doi.org/10.1002/pro.3780.

Boiteux, Céline, Emelie Flood, and Toby W. Allen. “Comparison of Permeation Mechanisms in Sodium-Selective Ion Channels.” Neuroscience Letters 700 (May 2019): 3–8. https://doi.org/10.1016/j.neulet.2018.05.036.

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Anton 2 at PSC is supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM116961. This content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.