Publications

Peer Reviewed Publications

  • Tonddast-Navaei, Sam, & Stan, George (2013). Mechanism of transient binding and release of substrate protein during the allosteric cycle of the p97 nanomachine. Journal of the American Chemical Society, 135(39), 14627-36.
  • Jayasinghe, Manori, Shrestha, Pooja, Wu, Xiongwu, Tehver, Riina, & Stan, George (2012). Weak intra-ring allosteric communications of the archaeal chaperonin thermosome revealed by normal mode analysis. Biophysical journal, 103(6), 1285-95.
  • S. M. Doyle, S. Shastry, A. N Kravats, Y.-H. Shih, M. Miot, J. R. Hoskins, G. Stan, and S. Wickner (2015), Interplay between E. coli DnaK, ClpB and GrpE during protein disaggregation, J. Mol. Biol. 427, 312-327.
  • H.-Y. Kim, S. M. Gatica, G. Stan, and M. W. Cole (2009) Effects of substrate relaxation on adsorption in pores, J. Low Temp. Phys. 156, 1-8.
  • Jayasinghe, Manori, Tewmey, Cody, & Stan, George (2010). Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT. Proteins, 78(5), 1254-65.
  • O'Brien, Edward P, Stan, George, Thirumalai, D, & Brooks, Bernard R (2008). Factors governing helix formation in peptides confined to carbon nanotubes. Nano letters, 8(11), 3702-8.
  • Stan, George, Lorimer, George H, Thirumalai, D, & Brooks, Bernard R (2007). Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein. Proceedings of the National Academy of Sciences of the United States of America, 104(21), 8803-8.
  • Stan, George, Brooks, Bernard R, Lorimer, George H, & Thirumalai, D (2006). Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state. Proceedings of the National Academy of Sciences of the United States of America, 103(12), 4433-8.
  • Stan, George, Brooks, Bernard R, & Thirumalai, D (2005). Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations. Journal of molecular biology, 350(4), 817-29.
  • Stan, George, Brooks, Bernard R, Lorimer, George H, & Thirumalai, D (2005). Identifying natural substrates for chaperonins using a sequence-based approach. Protein science : a publication of the Protein Society, 14(1), 193-201.
  • Stan, George, Thirumalai, D, Lorimer, George H, & Brooks, Bernard R (2003). Annealing function of GroEL: structural and bioinformatic analysis. Biophysical chemistry, 100(1-3), 453-67.
  • Kravats, Andrea, Jayasinghe, Manori, & Stan, George (2011). Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase. Proceedings of the National Academy of Sciences of the United States of America 108 (1) 2234-2239.
  • S. M. Gatica, M. M. Calbi, G. Stan, R. A. Trasca, and M. W. Cole (2010) Quasi-one dimensional fluids that exhibit higher dimensional behavior, Int. J. Mod. Phys. B. 24(25-26), 5051-59.
  • Abdolreza Javidialesaadi and George Stan, "Asymmetric Conformational Transitions in AAA+ Biological Nanomachines Modulate Directional-Dependent Substrate Protein Unfolding Mechanisms" (under review)

Invited Publication

  • Andrea N. Kravats, Sam Tonddast-Navaei, and George Stan (2016), Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines, PLOS Comp. Biol. 12(1): e1004675, 1-24 (accepted Nov. 25, 2015; published online Jan. 6, 2016)
  • G. Stan (2009) Condensation of a Quasi-one Dimensional Gas Within a Single Wall Carbon Nanotube, J. Low Temp. Phys. 157, 374-381.
  • Kravats, Andrea N, Tonddast-Navaei, Sam, Bucher, Ryan J, & Stan, George (2013). Asymmetric processing of a substrate protein in sequential allosteric cycles of AAA+ nanomachines. The Journal of chemical physics, 139(12), 121921.

Review

  • Maurizi, Michael R, & Stan, George (2013). ClpX shifts into high gear to unfold stable proteins. Cell, 155(3), 502-4.

Presentations & Lectures

Invited Presentations

  • George Stan (03/12/2010). Computer simulations of protein unfolding and translocation by Clp ATPase nanomachines Department of Chemistry, Wright State University.
  • George Stan (02/26/2010). Computer simulations of protein unfolding and translocation by Clp ATPase nanomachines Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati.
  • George Stan (02/12/2010). Protein quality control mechanisms: protein unfolding and translocation by biological nanomachines Department of Chemistry, Xavier University.
  • George Stan (04/02/2009). Biological nanomachines at work: chaperonin-mediated protein folding Department of Chemistry, Central State University.
  • George Stan (02/06/2009). Biological nanomachines at work: chaperonin-mediated protein folding Department of Chemistry, Indiana University Purdue University Fort Wayne.
  • George Stan (03/18/2011). Computer simulations of unfolding and translocation of substrate proteins mediated by allosteric pores Department of Chemistry, Central State Univ..
  • George Stan (04/04/2011). Computer simulations of unfolding and translocation of substrate proteins mediated by allosteric pores Department of Chemistry, Fisk Univ..
  • George Stan (04/04/2011). Computational modeling of unfolding and translocation of substrate proteins by AAA biological nanomachines Department of Chemical Engineering, Vanderbilt Univ..
  • George Stan (10/18/2011). Protein quality control mechanisms: protein unfolding and translocation by biological nanomachines' Department of Chemistry, Indiana State Univ..
  • George Stan (10/19/2011). Protein quality control mechanisms: protein unfolding and translocation by biological nanomachines Department of Chemistry, Rose-Hulman Institute of Technology.
  • George Stan (12/18/2012). Computational Modeling of Unfolding and Translocation of Substrate Proteins by Clp ATPases Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati.
  • George Stan (11/01/2012). Computer Simulations of Protein Unfolding and Translocation by Clp ATPases in the Protein Degradation Pathway National Cancer Institute, Lambda Lunch Seminar Series, National Institutes of Health.
  • George Stan (10/05/2012). Computational Modeling of Unfolding and Translocation of Substrate Proteins by Ring-Shaped Biological Machines Department of Physics, Biophysics Seminar, Ohio State University.
  • George Stan (07/05/2012). Computational Modeling of Unfolding and Translocation of Substrate Proteins by Ring-Shaped Biological Machines Department of Physics, Technical University Munich.
  • George Stan (02/10/2012). Computational Modeling of Unfolding and Translocation of Substrate Proteins by AAA Biological Machines Department of Chemistry, Central State University.
  • George Stan (09/23/2013). Computer simulations of protein unfolding and translocation by AAA+ nanomachines National Heart, Lung, and Blood Institute, National Institutes of Health.
  • George Stan (09/24/2013). Computer simulations of protein unfolding and translocation by AAA+ nanomachines National Cancer Institute, National Institutes of Health.
  • George Stan (05/07/2014). Computational studies of protein unfolding and translocation by AAA+ nanomachines School of Life Sciences, Technical University Munich, Munich, Germany.
  • George Stan (04/28/2014). Computational studies of protein unfolding and translocation by AAA+ nanomachines Department of Chemistry, Technical University Munich, Munich, Germany.
  • George Stan (03/31/2014). Computer simulations of protein unfolding and translocation by AAA+ nanomachines Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
  • George Stan (12/11/2014). Computer simulations of protein unfolding and translocation by AAA+ biological nanomachines Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana.
  • George Stan (10/01/2014). Computer simulations of protein unfolding and translocation by AAA+ nanomachines Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, Indiana.
  • George Stan (09/03/2014). Computer simulations of protein unfolding and translocation by AAA+ nanomachines National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
  • George Stan (11/21/2016). Multiscale computational modeling of protein unfolding and translocation by AAA+ nanomachines in the degradation pathway University of Texas, Austin, Austin, TX.
  • George Stan (09/08/2016). Coarse-grained and implicit solvent modeling of protein unfolding and translocation in the degradation pathway. National Cancer Institute, National Institutes of Health, Bethesda, MD.
  • George Stan (09/19/2017). Multiscale computational modeling of protein unfolding and translocation by AAA+ nanomachines in the degradation pathway National Cancer Institute, National Institutes of Health, Bethesda, MD.

Paper Presentations

  • Shannon M. Doyle, Andrea N. Kravats, Joel R. Hoskins, Yu-Hsuan Shih, George Stan and Sue Wickner (06/10/2015). Interaction and collaboration between DnaK and ClpB during protein disaggregation. Albany 2015: the 19th Conversation , SUNY at Albany.
  • Yu-Hsuan Shih, Shannon M. Doyle, Andrea N. Kravats, Joel R. Hoskins, George Stan and Sue Wickner (05/17/2015). Computational studies of collaboration between E. coli ClpB and cofactors DnaK/GrpE during protein disaggregation . From Computational Biophysics to Systems Biology (CBSB2015), Norman, OK.
  • Abdolreza Javidialesaadi and George Stan (05/19/2016). Coarse - grained simulations of mechanical threading of Immunoglobulin domains through non - allosteric ClpY ATPase pore. 47th Central Regional Meeting of ACS, Covington, KY.
  • M. Jayasinghe , Q. Wang, A. Schirmer, G. Stan, S. Paula (05/19/2016). Investigation of inhibitory potency of BHQ derivatives as SERCA inhibitors to use as potential drugs as well as tools to study the SERCA function: Binding free energy computation using FEP/ MD . . 47th Central Regional Meeting of ACS, Covington, KY.
  • Abdolreza Javidialesaadi and George Stan (10/28/2016). Atomistic simulations of unfolding and translocation of the Immunoglobulin domain I27 in repetitive cycles of the ClpY Biological Nanomachines . Oesper Symposium, University of Cincinnati.
  • Yu-Hsuan Shih, Shannon M. Doyle, Andrea N. Kravats, Joel R. Hoskins , Sue Wickner and George Stan (10/28/2016). Computational Studies of Dyn amic Collaboration between ClpB and co-factor DnaK during Protein Disaggregation . Oesper Symposium, University of Cincinnati.
  • Rui Jiang and George Stan Effect of Force Directionality on ClpB-mediated Unfolding Mechanisms of GFP and superfolder GFP. Oesper Symposium, University of Cincinnati.
  • Allison Talley, Reza Javidi, George Stan (10/28/2016). Small Molecule Effects on Surfactant Microstructure and Dynamics: A Case Where MD and NMR Can Drive Understanding in How Partitioning Influences Physical Properties . Oesper Symposium, University of Cincinnati.
  • Qi Wang, Riina Tehver and George Stan (10/28/2016). Normal Mode Analysis of Conformational Changes in the ClpP Peptidase . Oesper Symposium, University of Cincinnati.

Poster Presentations

  • Allison Talley, Andrea Kravats, Sam Tonddast‐Navaei, George Stan Elucidation of binding and unfolding pathways of biopolymers at interfaces via molecular dynamics simulations 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Rui Jiang, Sam Tonddast‐Navaei, Andrea Kravats, and George Stan Probing Unfolding Mechanisms of GFP by ClpB Using All‐atom Simulation 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Qi Wang and George Stan Mechanical unfolding and translocation of protein L and protein G through nonallosteric ClpY chaperone 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Huan Wang and George Stan Unfolding and translocation mechanism of peptides with diverse structures by ClpY ATPase 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Yu‐Hsuan Shih, Shannon M. Doyle, Shankar Shastry, Andrea Kravats, Marika Miot, Joel R. Hoskings, George Stan and Sue Wickner Computational studies of functional interactions between E. coli. ClpB, DnaK and GrpE during protein disaggregation 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Abdolreza Javidialesaadi and George Stan Structural Analysis of Constant Domains of IgG Antibodies 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Nathan Smith, Pooja Shrestha and George Stan Confinement Effects on the Kinetics of a Multi‐Domain Protein Folding in a Nanotube 2014 Ralph&Helen Oesper Symposium, Cincinnati Section of the American Chemical Society, University of Cincinnati.
  • Yu-Hsuan Shih, Shannon M. Doyle, Shankar Shastry, Andrea Kravats, Marika Miot, Joel R. Hoskings, George Stan and Sue Wickner Computational studies of functional interactions of the multi-chaperone ClpB/DnaK/GrpE system for protein disaggregation Academy of Computational Life Sciences Summer School, Purdue University, West Lafayette, Indiana.
  • Rui Jiang, Sam Tonddast‐Navaei, Andrea Kravats, and George Stan Mechanisms of Protein Disaggregation by Bacterial Proteases Academy of Computational Life Sciences Summer School, Purdue University, West Lafayette, Indiana.
  • Jessica C McKinley, Andrea Kravats, Huan Wang, George Stan Computer simulations of peptide translocation by ClpY nanomachines ACS National Meeting March 2014, Dallas, TX.
  • Abdolreza Javidialesaadi and George Stan (11/13/2015). Molecular Dynamics Simulation of the Folding Properties of IgG Antibody 2015 Ralph&Helen Oesper Symposium, Cincinnati section of the American Chemical Society, University of Cincinnati.
  • Rui Jiang, Andrea Kravats, and George Stan (11/13/2015). Effect of Force Directionality on Unfolding and Translocation Pathways of the Green Fluorescent Protein by the ClpB Biological Nanomachine 2015 Ralph&Helen Oesper Symposium, Cincinnati section of the American Chemical Society, University of Cincinnati.
  • Yu-Hsuan Shih, Shannon M. Doyle, Andrea N. Kravats, Joel R. Hoskins, George Stan and Sue Wickner (11/13/2015). Identification of interaction and collaboration between DnaK system and ClpB hexamer during protein disaggregation 2015 Ralph&Helen Oesper Symposium, Cincinnati section of the American Chemical Society, University of Cincinnati.
  • Nathan Smith and George Stan (11/13/2015). Normal Mode Analysis of a Protein-Unfolding Biological Nanomachine 2015 Ralph&Helen Oesper Symposium, Cincinnati section of the American Chemical Society, University of Cincinnati.
  • Qi Wang, George Stan (11/13/2015). Multi-scale modeling: unfolding and translocation of FtsZ and repA through molecular chaperone 2015 Ralph&Helen Oesper Symposium, Cincinnati section of the American Chemical Society, University of Cincinnati.
  • Kyle Vieth, Yu-Hsuan Shih and George Stan (04/24/2015). Mechanistic Insights into Disaggregation and Unfolding Functions of Bacterial Clp ATPase Nanomachines 2015 Undergraduate Conference: Research, Scholarship & Creative Work, University of Cincinnati.
  • Alex Mason, Abdolreza Javidialesaadi and George Stan (04/24/2015). Constant Domains of Antigen-Binding Fragment of IgG Antibody: A Bioinformatic Analysis 2015 Undergraduate Conference: Research, Scholarship & Creative Work, University of Cincinnati.
  • Rui Jiang, Andrea Kravats, and George Stan (05/20/2016). ClpB-mediated Unfolding Mechanisms of GFP: Two Different Pathways Breakdown and the Effect of Force Directionality 47th Central Regional Meeting of ACS, Covington, KY.
  • Qi Wang, George Stan (05/20/2016). Normal mode analysis of conformational changes in the ClpP peptidase 47th Central Regional Meeting of ACS, Covington, KY.
  • Y. Shih , G. Stan (05/20/2016). Molecular Dynamics Simulations of Protein Unfolding and Translocation by the ClpY ATPase in the Protein Degradation Pathway 47th Central Regional Meeting of ACS, Covington, KY.

Symposium

  • George Stan (10/01/2010). Computer simulations of protein unfolding and translocation mediated by allosteric pores. The 10th KIAS Conference on Protein Structure and Function, Seoul, South Korea. Professional Meeting. Level: International.
  • George Stan (08/23/2010). Unfolding and translocation of substrate proteins mediated by allosteric pores. The Berder Summerschool 2010 "Biosensing with channels'', Berder Island, France. Professional Meeting. Level: International.
  • George Stan (12/06/2011). Development of coarse-grained models of unfolding and translocation of substrate proteins by AAA+ nanomachines. The Zing Conference ``Protein and RNA Structure Prediction 2011'', Xcaret, Mexico. Professional Meeting. Level: International.
  • George Stan (12/15/2015). Role of confinement in chaperone-mediated protein remodeling. 3rd International Conference on Protein and RNA Structure Prediction, Punta Cana, Dominican Republic. Professional Meeting. Level: International.
  • George Stan (01/11/2012). Proteins in Action. Gordon Research Conference on Protein Folding Dynamics, Ventura, CA. Professional Meeting. Level: International.
  • George Stan (07/26/2016). Coarse-grained and implicit solvent modeling of protein unfolding and translocation in the degradation pathway. Telluride workshop on Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules 4, Telluride, CO. Professional Meeting. Level: International.
  • George Stan (03/26/2012). Computational Modeling of Unfolding and Translocation of Substrate Proteins by AAA Biological Machines. Nanobiomotors mini-symposium, University of Kentucky. Professional Meeting. Level: National.
  • George Stan (06/28/2012). Computational Modeling of Unfolding and Translocation of Substrate Proteins by Ring-Shaped Biological Machines. Protein and Peptide Interactions in Cellular Environments, Telluride, CO. Workshop. Level: International.
  • George Stan (07/26/2012). Coarse-grained models of substrate protein unfolding and translocation by AAA+ biological nanomachines. Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules, Telluride, CO. Workshop. Level: International.
  • George Stan (10/23/2012). Atomistic simulations of peptide unfolding and translocation by AAA+ biological nanomachines. Material Science-2012, Chicago, IL. Professional Meeting. Level: International.
  • George Stan (12/05/2012). Computer Simulations of Protein Unfolding and Translocation by Ring Nanomachines in the Degradation Pathway. Zing Conference ``Mathematical and Computational Medicine Conference'', Xcaret, Mexico. Professional Meeting. Level: International.
  • George Stan Computer simulations of protein unfolding and translocation by AAA+ chaperones. Biomolecules and Nanostructures meeting, 4th edition, Pultusk, Poland. Professional Meeting. Level: International.
  • George Stan Computational studies of protein unfolding and translocation through repetitive pulling in allosteric cycles of AAA+ motors. T elluride "Rise of the Machines" workshop, Telluride, Colorado. Workshop. Level: International.
  • George Stan Topology-dependent mechanisms of protein unfolding and translocation by AAA+ nanomachines. 2nd Zing Protein & RNA Structure Prediction Conference, Xcaret, Mexico. Professional Meeting. Level: International.
  • George Stan (02/03/2014). Computer simulations of protein unfolding and translocation by AAA+ nanomachines. XVI Linz Winter Workshop, Linz, Austria. Professional Meeting. Level: International.
  • George Stan (06/24/2014). Mechanisms of substrate protein unfolding and translocation in repetitive cycles of AAA+ nanomachines. Telluride workshop on "Protein and Peptide Interactions in Cellular Environments", Telluride, Colorado. Professional Meeting. Level: International.
  • George Stan (06/09/2014). Computational Studies of Protein Unfolding and Translocation in Allosteric Cycles of AAA+ Nanomachines. 7th World Congress of Biomechanics, Boston, Massachusetts. Professional Meeting. Level: International.
  • George Stan (08/06/2014). Protein unfolding and translocation by repetitive forces in the degradation pathway. Telluride workshop on "Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules 3", Telluride, Colorado. Professional Meeting. Level: International.
  • George Stan (08/15/2014). Development of computational models of protein unfolding and translocation mechanisms by bacterial proteases. Academy of Computational Life Sciences Summer School, Purdue University, West Lafayette, Indiana. Professional Meeting. Level: International.
  • George Stan (03/19/2014). Computational studies of actin folding within cylindrical nanopores. Technical University Munich Biophysics Winterschool Professional Meeting. Level: International.