Garegin A. (Garyk) Papoian - Publications

Affiliations: 
2004-2010 University of North Carolina, Chapel Hill, Chapel Hill, NC 
 2010- Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
Area:
computational methods, to study biological processes
Website:
http://www.chem.umd.edu/faculty-staff-directory/facultydirectory/garegin-papoian

79 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
2020 Li X, Ni Q, He X, Kong J, Lim SM, Papoian GA, Trzeciakowski JP, Trache A, Jiang Y. Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry. Plos Computational Biology. 16: e1007693. PMID 32520928 DOI: 10.1371/journal.pcbi.1007693  0.64
2020 Jin S, Contessoto VG, Chen M, Schafer NP, Lu W, Chen X, Bueno C, Hajitaheri A, Sirovetz BJ, Davtyan A, Papoian GA, Tsai MY, Wolynes PG. AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Research. PMID 32383764 DOI: 10.1093/nar/gkaa356  1
2020 Floyd C, Papoian GA, Jarzynski C. Gibbs free energy change of a discrete chemical reaction event. The Journal of Chemical Physics. 152: 084116. PMID 32113353 DOI: 10.1063/1.5140980  0.32
2020 Pitman M, Dalal Y, Papoian GA. Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes. Biophysical Journal. PMID 32097625 DOI: 10.1016/j.bpj.2020.01.042  0.96
2019 Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y. Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners. Proceedings of the National Academy of Sciences of the United States of America. PMID 31712435 DOI: 10.1073/pnas.1911880116  0.96
2019 Ni Q, Papoian GA. Turnover versus Treadmilling in Actin Network Assembly and Remodeling. Cytoskeleton (Hoboken, N.J.). PMID 31525282 DOI: 10.1002/cm.21564  0.64
2019 Floyd C, Papoian GA, Jarzynski C. Quantifying dissipation in actomyosin networks. Interface Focus. 9: 20180078. PMID 31065344 DOI: 10.1098/rsfs.2018.0078  0.32
2019 Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophysical Journal. PMID 31005236 DOI: 10.1016/j.bpj.2019.03.021  1
2018 Wu H, Wolynes PG, Papoian GA. AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 30091924 DOI: 10.1021/acs.jpcb.8b05791  0.01
2017 Bui M, Pitman M, Nuccio A, Roque S, Donlin-Asp PG, Nita-Lazar A, Papoian GA, Dalal Y. Internal modifications in the CENP-A nucleosome modulate centromeric dynamics. Epigenetics & Chromatin. 10: 17. PMID 28396698 DOI: 10.1186/s13072-017-0124-6  0.96
2016 Zhao H, Winogradoff D, Bui M, Dalal Y, Papoian GA. Promiscuous histone mis-assembly is actively prevented by chaperones. Journal of the American Chemical Society. PMID 27454815 DOI: 10.1021/jacs.6b05355  1
2016 Zhang B, Zheng W, Papoian GA, Wolynes PG. Exploring the Free Energy Landscape of Nucleosomes. Journal of the American Chemical Society. PMID 27300314 DOI: 10.1021/jacs.6b02893  1
2016 Dobramysl U, Papoian GA, Erban R. Steric Effects Induce Geometric Remodeling of Actin Bundles in Filopodia. Biophysical Journal. 110: 2066-75. PMID 27166814 DOI: 10.1016/j.bpj.2016.03.013  1
2016 Popov K, Komianos J, Papoian GA. MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks. Plos Computational Biology. 12: e1004877. PMID 27120189 DOI: 10.1371/journal.pcbi.1004877  1
2016 Davtyan A, Platkov M, Gruebele M, Papoian GA. Stochastic Resonance in Protein Folding Dynamics. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 26992148 DOI: 10.1002/cphc.201501125  1
2015 Gruebele M, Dave K, Davtyan A, Papoian GA, Platkov M. Environmental fluctuations and stochastic resonance in protein folding. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 26711088 DOI: 10.1002/cphc.201501041  1
2015 Winogradoff D, Zhao H, Dalal Y, Papoian GA. Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome. Scientific Reports. 5: 17038. PMID 26602160 DOI: 10.1038/srep17038  1
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  1
2015 Echeverria I, Papoian GA. DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates. Plos Computational Biology. 11: e1003980. PMID 25675216 DOI: 10.1371/journal.pcbi.1003980  1
2014 Echeverria I, Makarov DE, Papoian GA. Concerted dihedral rotations give rise to internal friction in unfolded proteins. Journal of the American Chemical Society. 136: 8708-13. PMID 24844314 DOI: 10.1021/ja503069k  1
2014 Erban R, Flegg MB, Papoian GA. Multiscale stochastic reaction-diffusion modeling: application to actin dynamics in filopodia. Bulletin of Mathematical Biology. 76: 799-818. PMID 23640574 DOI: 10.1007/s11538-013-9844-3  1
2014 Echeverria I, Papoian GA. Structural heterogeneity and dynamics of the unfolded ensemble Israel Journal of Chemistry. DOI: 10.1002/ijch.201400030  1
2013 Popov KI, Papoian GA. Capsid deformations reveal complex mechano-chemistry. Biophysical Journal. 105: 2233-4. PMID 24268133 DOI: 10.1016/j.bpj.2013.09.055  1
2013 Hu L, Papoian GA. Molecular transport modulates the adaptive response of branched actin networks to an external force. The Journal of Physical Chemistry. B. 117: 13388-96. PMID 23962335 DOI: 10.1021/jp405179e  1
2013 Ma D, Bettis SE, Hanson K, Minakova M, Alibabaei L, Fondrie W, Ryan DM, Papoian GA, Meyer TJ, Waters ML, Papanikolas JM. Interfacial energy conversion in Ru(II) polypyridyl-derivatized oligoproline assemblies on TiO2. Journal of the American Chemical Society. 135: 5250-3. PMID 23514453 DOI: 10.1021/ja312143h  1
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  1
2012 Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG. Predictive energy landscapes for protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. 109: 19244-9. PMID 23129648 DOI: 10.1073/pnas.1216215109  1
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  1
2012 Zhuravlev PI, Lan Y, Minakova MS, Papoian GA. Theory of active transport in filopodia and stereocilia. Proceedings of the National Academy of Sciences of the United States of America. 109: 10849-54. PMID 22711803 DOI: 10.1073/pnas.1200160109  0.6
2012 Wilger DJ, Bettis SE, Materese CK, Minakova M, Papoian GA, Papanikolas JM, Waters ML. Tunable energy transfer rates via control of primary, secondary, and tertiary structure of a coiled coil peptide scaffold. Inorganic Chemistry. 51: 11324-38. PMID 22679929 DOI: 10.1021/ic300669t  1
2012 Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. The Journal of Physical Chemistry. B. 116: 8494-503. PMID 22545654 DOI: 10.1021/jp212541y  1
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  1
2012 Rubinstein M, Papoian GA. Polyelectrolytes in biology and soft matter Soft Matter. 8: 9265-9267. DOI: 10.1039/c2sm90104h  1
2011 Savelyev A, Materese CK, Papoian GA. Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions? Journal of the American Chemical Society. 133: 19290-3. PMID 22039974 DOI: 10.1021/ja207984z  1
2011 Zhuravlev PI, Papoian GA. Protein fluxes along the filopodium as a framework for understanding the growth-retraction dynamics: the interplay between diffusion and active transport. Cell Adhesion & Migration. 5: 448-56. PMID 21975554 DOI: 10.4161/cam.5.5.17868  1
2011 Hu L, Papoian GA. How does the antagonism between capping and anti-capping proteins affect actin network dynamics? Journal of Physics. Condensed Matter : An Institute of Physics Journal. 23: 374101. PMID 21862844 DOI: 10.1088/0953-8984/23/37/374101  1
2011 Minakova M, Savelyev A, Papoian GA. Nonequilibrium water transport in a nonionic microemulsion system. The Journal of Physical Chemistry. B. 115: 6503-8. PMID 21528855 DOI: 10.1021/jp201431u  1
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  1
2011 Bettis S, Wilger D, Materese C, Minakova M, Papoian G, Papanikolas JM, Waters ML. Energy transfer in ruthenium and osmium functionalized coiled-coil peptides Acs National Meeting Book of Abstracts 1
2010 Savelyev A, Papoian GA. Chemically accurate coarse graining of double-stranded DNA. Proceedings of the National Academy of Sciences of the United States of America. 107: 20340-5. PMID 21059937 DOI: 10.1073/pnas.1001163107  1
2010 Zhuravlev PI, Papoian GA. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Quarterly Reviews of Biophysics. 43: 295-332. PMID 20819242 DOI: 10.1017/S0033583510000119  1
2010 Oklejas V, Zong C, Papoian GA, Wolynes PG. Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice? Methods (San Diego, Calif.). 52: 84-90. PMID 20561998 DOI: 10.1016/j.ymeth.2010.05.006  1
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  1
2010 Zhuravlev PI, Der BS, Papoian GA. Design of active transport must be highly intricate: a possible role of myosin and Ena/VASP for G-actin transport in filopodia. Biophysical Journal. 98: 1439-48. PMID 20409462 DOI: 10.1016/j.bpj.2009.12.4325  1
2010 Hu L, Papoian GA. Mechano-chemical feedbacks regulate actin mesh growth in lamellipodial protrusions. Biophysical Journal. 98: 1375-84. PMID 20409456 DOI: 10.1016/j.bpj.2009.11.054  1
2010 Tanaka N, Papoian GA. Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations. Journal of Theoretical Biology. 264: 490-500. PMID 20171230 DOI: 10.1016/j.jtbi.2010.02.022  1
2010 Zhuravlev PI, Papoian GA. Functional versus folding landscapes: the same yet different. Current Opinion in Structural Biology. 20: 16-22. PMID 20102791 DOI: 10.1016/j.sbi.2009.12.010  1
2009 Materese CK, Savelyev A, Papoian GA. Counterion atmosphere and hydration patterns near a nucleosome core particle. Journal of the American Chemical Society. 131: 15005-13. PMID 19778017 DOI: 10.1021/ja905376q  1
2009 Zhuravlev PI, Papoian GA. Molecular noise of capping protein binding induces macroscopic instability in filopodial dynamics. Proceedings of the National Academy of Sciences of the United States of America. 106: 11570-5. PMID 19556544 DOI: 10.1073/pnas.0812746106  1
2009 Zhuravlev PI, Materese CK, Papoian GA. Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. The Journal of Physical Chemistry. B. 113: 8800-12. PMID 19453123 DOI: 10.1021/jp810659u  1
2009 Savelyev A, Papoian GA. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. Biophysical Journal. 96: 4044-52. PMID 19450476 DOI: 10.1016/j.bpj.2009.02.067  1
2009 Savelyev A, Papoian GA. Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl. The Journal of Physical Chemistry. B. 113: 7785-93. PMID 19425537 DOI: 10.1021/jp9005058  1
2008 Lan Y, Elston TC, Papoian GA. Elimination of fast variables in chemical Langevin equations. The Journal of Chemical Physics. 129: 214115. PMID 19063552 DOI: 10.1063/1.3027499  1
2008 Wu S, Zhuravlev PI, Papoian GA. High resolution approach to the native state ensemble kinetics and thermodynamics. Biophysical Journal. 95: 5524-32. PMID 18805918 DOI: 10.1529/biophysj.108.136697  1
2008 Papoian GA. Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm. Proceedings of the National Academy of Sciences of the United States of America. 105: 14237-8. PMID 18799750 DOI: 10.1073/pnas.0807977105  1
2008 Materese CK, Goldmon CC, Papoian GA. Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions. Proceedings of the National Academy of Sciences of the United States of America. 105: 10659-64. PMID 18664578 DOI: 10.1073/pnas.0801850105  1
2008 Savelyev A, Papoian GA. Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers. The Journal of Physical Chemistry. B. 112: 9135-45. PMID 18597519 DOI: 10.1021/jp801448s  1
2008 Lan Y, Papoian GA. The stochastic dynamics of filopodial growth. Biophysical Journal. 94: 3839-52. PMID 18234810 DOI: 10.1529/biophysj.107.123778  1
2007 Lan Y, Papoian GA. Stochastic resonant signaling in enzyme cascades. Physical Review Letters. 98: 228301. PMID 17677882 DOI: 10.1103/PhysRevLett.98.228301  1
2007 Lan Y, Papoian GA. Evolution of complex probability distributions in enzyme cascades. Journal of Theoretical Biology. 248: 537-45. PMID 17631318 DOI: 10.1016/j.jtbi.2007.06.008  1
2007 Savelyev A, Papoian GA. Inter-DNA electrostatics from explicit solvent molecular dynamics simulations. Journal of the American Chemical Society. 129: 6060-1. PMID 17455935 DOI: 10.1021/ja070207t  1
2007 Lätzer J, Papoian GA, Prentiss MC, Komives EA, Wolynes PG. Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. Journal of Molecular Biology. 367: 262-74. PMID 17257619 DOI: 10.1016/j.jmb.2006.12.006  1
2007 Savelyev A, Papoian GA. Free energy calculations of counterion partitioning between DNA and chloride solutions Mendeleev Communications. 17: 97-99. DOI: 10.1016/j.mencom.2007.03.015  1
2006 Savelyev A, Papoian GA. Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+). Journal of the American Chemical Society. 128: 14506-18. PMID 17090034 DOI: 10.1021/ja0629460  1
2006 Lan Y, Papoian GA. The interplay between discrete noise and nonlinear chemical kinetics in a signal amplification cascade. The Journal of Chemical Physics. 125: 154901. PMID 17059287 DOI: 10.1063/1.2358342  1
2006 Lan Y, Wolynes PG, Papoian GA. A variational approach to the stochastic aspects of cellular signal transduction. The Journal of Chemical Physics. 125: 124106. PMID 17014165 DOI: 10.1063/1.2353835  1
2006 Zong C, Papoian GA, Ulander J, Wolynes PG. Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins. Journal of the American Chemical Society. 128: 5168-76. PMID 16608353 DOI: 10.1021/ja058589v  1
2004 Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Water in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 101: 3352-7. PMID 14988499 DOI: 10.1073/pnas.0307851100  1
2004 Levy Y, Papoian GA, Onuchic JN, Wolynes PG. Energy landscape analysis of protein dimers Israel Journal of Chemistry. 44: 281-297. DOI: 10.1560/XGCB-WUHN-JRJC-BV0Y  1
2003 Papoian GA, Ulander J, Wolynes PG. Role of water mediated interactions in protein-protein recognition landscapes. Journal of the American Chemical Society. 125: 9170-8. PMID 15369374 DOI: 10.1021/ja034729u  1
2003 Papoian GA, Wolynes PG. The physics and bioinformatics of binding and folding-an energy landscape perspective. Biopolymers. 68: 333-49. PMID 12601793 DOI: 10.1002/bip.10286  1
2003 Papoian GA, DeGrado WF, Klein ML. Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor. Journal of the American Chemical Society. 125: 560-9. PMID 12517172 DOI: 10.1021/ja028161l  1
2001 Ienco A, Hoffmann R, Papoian G. Electron-rich bonding and the importance of s,p mixing as one moves across a period: a lesson from the LiSn system. Journal of the American Chemical Society. 123: 2317-25. PMID 11456880 DOI: 10.1021/ja0032576  1
2001 Papoian G, Hoffmann R. Electron-rich rods as building blocks for Sb strips and Te sheets. Journal of the American Chemical Society. 123: 6600-8. PMID 11439046 DOI: 10.1021/ja003420x  1
2000 Papoian G, Nørskov JK, Hoffmann R. A comparative theoretical study of the hydrogen, methyl, and ethyl chemisorption on the Pt(111) surface Journal of the American Chemical Society. 122: 4129-4144. DOI: 10.1021/ja993483j  1
2000 Papoian GA, Hoffmann R. Hypervalent bonding in one, two, and three dimensions: Extending the Zintl-Klemm concept to nonclassical electron-rich networks Angewandte Chemie - International Edition. 39: 2408-2448. DOI: 10.1002/1521-3773(20000717)39:14<2408::AID-ANIE2408>3.0.CO;2-U  1
2000 Seo DK, Papoian G, Hoffmann R. Generalized Perturbational Molecular Orbital (PMO) Theory International Journal of Quantum Chemistry. 77: 408-420.  1
1999 Glassey WV, Papoian GA, Hoffmann R. Total energy partitioning within a one-electron formalism: A Hamilton population study of surface-CO interaction in the c(2x2)-CO/Ni(100) chemisorption system Journal of Chemical Physics. 111: 893-910.  1
1998 Papoian G, Hoffmann R. Building up Complexity from Strips and Sheets: The Electronic Structure of the La12Mn2Sb30Alloy Journal of Solid State Chemistry. 139: 8-21. DOI: 10.1006/jssc.1998.7773  1
Show low-probability matches.