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Davit Potoyan, Ph.D. - Publications

Affiliations: 
2011 Chemical Physics University of Maryland, College Park, College Park, MD 
Area:
Physical Chemistry, General Biophysics
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21/44 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
2022 Laghmach R, Di Pierro M, Potoyan D. A Liquid State Perspective on Dynamics of Chromatin Compartments. Frontiers in Molecular Biosciences. 8: 781981. PMID 35096966 DOI: 10.3389/fmolb.2021.781981  0.336
2018 Di Pierro M, Potoyan DA, Wolynes PG, Onuchic JN. Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987017 DOI: 10.1073/Pnas.1806297115  0.44
2018 Wang Z, Potoyan DA, Wolynes PG. Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs). Bmc Systems Biology. 12: 4. PMID 29382384 DOI: 10.1186/S12918-018-0525-6  0.384
2018 Wang Z, Potoyan DA, Wolynes PG. Stochastic resonances in a distributed genetic broadcasting system: the NFκB/IκB paradigm. Journal of the Royal Society, Interface. 15. PMID 29343631 DOI: 10.1098/Rsif.2017.0809  0.477
2017 Potoyan DA, Wolynes PG. Stochastic dynamics of genetic broadcasting networks. Physical Review. E. 96: 052305. PMID 29347696 DOI: 10.1016/J.Bpj.2016.11.3080  0.534
2017 Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG. Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. Journal of the American Chemical Society. PMID 29183131 DOI: 10.1021/Jacs.7B08741  0.533
2016 Wang Z, Potoyan DA, Wolynes PG. Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network. Journal of the Royal Society, Interface. 13. PMID 27683001 DOI: 10.1098/Rsif.2016.0606  0.464
2016 Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA. PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites. The Journal of Physical Chemistry. B. PMID 27098223 DOI: 10.1021/Acs.Jpcb.6B02359  0.488
2015 Potoyan DA, Zheng W, Komives EA, Wolynes PG. Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network. Proceedings of the National Academy of Sciences of the United States of America. PMID 26699500 DOI: 10.1073/Pnas.1520483112  0.546
2015 Potoyan DA, Wolynes PG. Dichotomous noise models of gene switches. The Journal of Chemical Physics. 143: 195101. PMID 26590554 DOI: 10.1063/1.4935572  0.456
2015 Winogradoff D, Echeverria I, Potoyan DA, Papoian GA. The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects. Journal of the American Chemical Society. 137: 6245-53. PMID 25905561 DOI: 10.1021/Jacs.5B00235  0.619
2015 Potoyan D, Wolynes P. Path Attractors and the Origins of Stochastic Bifrucation and Dephasing in Genetic Networks Biophysical Journal. 108: 464a. DOI: 10.1016/J.Bpj.2014.11.2531  0.486
2014 Potoyan DA, Wolynes PG. On the dephasing of genetic oscillators. Proceedings of the National Academy of Sciences of the United States of America. 111: 2391-6. PMID 24469814 DOI: 10.1073/Pnas.1323433111  0.446
2013 Papoian G, Potoyan D. Acetylations of Lysines of the H4 Histone Tail Lead to Functionally Important Remodeling of its Energy Landscape Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.055  0.516
2013 Potoyan DA, Savelyev A, Papoian GA. Recent successes in coarse-grained modeling of DNA Wiley Interdisciplinary Reviews: Computational Molecular Science. 3: 69-83. DOI: 10.1002/wcms.1114  0.554
2012 Potoyan DA, Papoian GA. Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. Proceedings of the National Academy of Sciences of the United States of America. 109: 17857-62. PMID 22988066 DOI: 10.1073/pnas.1201805109  0.643
2012 Potoyan DA, Zhuravlev PI, Papoian GA. Computing free energy of a large-scale allosteric transition in adenylate kinase using all atom explicit solvent simulations. The Journal of Physical Chemistry. B. 116: 1709-15. PMID 22212071 DOI: 10.1021/jp209980b  0.562
2011 Potoyan DA, Papoian GA. Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. Journal of the American Chemical Society. 133: 7405-15. PMID 21517079 DOI: 10.1021/ja1111964  0.628
2011 Potoyan D, Papoian G. Impact of Covalent Modifications on Binding and Conformational Propensities of Histone Tails Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.518  0.522
2010 Zhuravlev PI, Wu S, Potoyan DA, Rubinstein M, Papoian GA. Computing free energies of protein conformations from explicit solvent simulations. Methods (San Diego, Calif.). 52: 115-21. PMID 20493264 DOI: 10.1016/J.Ymeth.2010.05.003  0.55
2010 Potoyan D, Papoian G. Energy Landscape Analysis Reveals Residual Order in Histone Tail Dynamics Biophysical Journal. 98: 257a. DOI: 10.1016/J.Bpj.2009.12.1395  0.644
Low-probability matches (unlikely to be authored by this person)
2021 Laghmach R, Di Pierro M, Potoyan DA. The interplay of chromatin phase separation and lamina interactions in nuclear organization. Biophysical Journal. PMID 34653387 DOI: 10.1016/j.bpj.2021.10.012  0.282
2019 Roche J, Potoyan DA. Disorder Mediated Oligomerization of DISC1 Proteins Revealed by Coarse-Grained Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 31614085 DOI: 10.1021/Acs.Jpcb.9B07467  0.274
2023 Sedinkin SL, Burns D, Shukla D, Potoyan DA, Venditti V. Solution Structure Ensembles of the Open and Closed Forms of the ∼130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR. Journal of the American Chemical Society. 145: 13347-13356. PMID 37278728 DOI: 10.1021/jacs.3c03425  0.267
2019 Laghmach R, Di Pierro M, Potoyan DA. Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes. Biophysical Journal. PMID 31623887 DOI: 10.1016/j.bpj.2019.09.013  0.247
2024 Alshareedah I, Singh A, Yang S, Ramachandran V, Quinn A, Potoyan DA, Banerjee PR. Determinants of viscoelasticity and flow activation energy in biomolecular condensates. Science Advances. 10: eadi6539. PMID 38363841 DOI: 10.1126/sciadv.adi6539  0.243
2018 Lin YT, Hufton PG, Lee EJ, Potoyan DA. A stochastic and dynamical view of pluripotency in mouse embryonic stem cells. Plos Computational Biology. 14: e1006000. PMID 29451874 DOI: 10.1371/Journal.Pcbi.1006000  0.242
2021 Mueterthies J, Potoyan DA. Solvent Exposure and Ionic Condensation Drive Fuzzy Dimerization of Disordered Heterochromatin Protein Sequence. Biomolecules. 11. PMID 34203110 DOI: 10.3390/biom11060915  0.241
2020 Laghmach R, Potoyan D. Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm. Physical Biology. PMID 33113512 DOI: 10.1088/1478-3975/abc5ad  0.222
2023 Singh A, Burns D, Sedinkin SL, Van Veller B, Potoyan DA, Venditti V. Protein Conformational Dynamics Underlie Selective Recognition of Thermophilic over Mesophilic Enzyme I by a Substrate Analogue. Biomolecules. 13. PMID 36671545 DOI: 10.3390/biom13010160  0.2
2020 Dotas RR, Nguyen TT, Stewart CE, Ghirlando R, Potoyan DA, Venditti V. Hybrid thermophilic/mesophilic enzymes reveal a role for conformational disorder in regulation of bacterial Enzyme I. Journal of Molecular Biology. PMID 32504625 DOI: 10.1016/J.Jmb.2020.05.024  0.19
2022 Burns D, Singh A, Venditti V, Potoyan DA. Temperature-sensitive contacts in disordered loops tune enzyme I activity. Proceedings of the National Academy of Sciences of the United States of America. 119: e2210537119. PMID 36375052 DOI: 10.1073/pnas.2210537119  0.173
2022 Laghmach R, Malhotra I, Potoyan DA. Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium. Methods in Molecular Biology (Clifton, N.J.). 2563: 117-133. PMID 36227470 DOI: 10.1007/978-1-0716-2663-4_5  0.166
2024 Marijan D, Momchilova EA, Burns D, Chandhok S, Zapf R, Wille H, Potoyan DA, Audas TE. Protein thermal sensing regulates physiological amyloid aggregation. Nature Communications. 15: 1222. PMID 38336721 DOI: 10.1038/s41467-024-45536-0  0.155
2023 Levengood JD, Potoyan D, Penumutchu S, Kumar A, Wang Y, Hansen AL, Kutluay S, Roche J, Tolbert BS. Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions. Biorxiv : the Preprint Server For Biology. PMID 37645738 DOI: 10.1101/2023.08.17.553700  0.148
2021 Alshareedah I, Moosa MM, Pham M, Potoyan DA, Banerjee PR. Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides. Nature Communications. 12: 6620. PMID 34785657 DOI: 10.1038/s41467-021-26733-7  0.14
2023 Burns D, Venditti V, Potoyan DA. Temperature-Sensitive Contact Modes Allosterically Gate TRPV3. Biorxiv : the Preprint Server For Biology. PMID 36711981 DOI: 10.1101/2023.01.02.522497  0.137
2023 Burns D, Venditti V, Potoyan DA. Temperature sensitive contact modes allosterically gate TRPV3. Plos Computational Biology. 19: e1011545. PMID 37831724 DOI: 10.1371/journal.pcbi.1011545  0.135
2023 Malhotra I, Potoyan DA. Re-entrant transitions of locally stiff RNA chains in the presence of polycations leads to gelated architectures. Soft Matter. 19: 5622-5629. PMID 37449795 DOI: 10.1039/d3sm00320e  0.133
2022 Laghmach R, Alshareedah I, Pham M, Raju M, Banerjee PR, Potoyan DA. RNA chain length and stoichiometry govern surface tension and stability of protein-RNA condensates. Iscience. 25: 104105. PMID 35378855 DOI: 10.1016/j.isci.2022.104105  0.12
2024 Brown WH, Potoyan DA. Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores. Biophysical Journal. PMID 38163950 DOI: 10.1016/j.bpj.2023.12.027  0.113
2021 Kaur T, Raju M, Alshareedah I, Davis RB, Potoyan DA, Banerjee PR. Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies. Nature Communications. 12: 872. PMID 33558506 DOI: 10.1038/s41467-021-21089-4  0.111
2020 Alshareedah I, Moosa MM, Raju M, Potoyan DA, Banerjee PR. Phase transition of RNA-protein complexes into ordered hollow condensates. Proceedings of the National Academy of Sciences of the United States of America. PMID 32571937 DOI: 10.1073/pnas.1922365117  0.108
2022 Badaczewska-Dawid AE, Uversky VN, Potoyan DA. BIAPSS: A Comprehensive Physicochemical Analyzer of Proteins Undergoing Liquid-Liquid Phase Separation. International Journal of Molecular Sciences. 23. PMID 35682883 DOI: 10.3390/ijms23116204  0.107
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