Challenges of Water in Biological Systems
 
September 13-17, 2010
Papers will be posted as soon as they are received. Please send your papers to Prof. Steve Berry (berry @ uchicago.edu) and Prof. Ka Yee Lee (kayeelee @ uchicago.edu) to make them available to other workshop participants.
 
Zip folder of the first 24 papers.     papers.zip
Zip folder of the papers 25-43.       papers2.zip      
 
New Papers added 09/07/2010 - please scroll down to download #44, 45, 46, and 47.
Cover photo from PNAS March 9, 2004
G. A. Papoian et al. PNAS 2004; 101: 3352-3357
List of Papers Nonstandard dielectric response - L. Ridgway Scott PDF The Origin of Long-Range Attraction between Hydrophobes in Water - Florin Despa and R. Stephen Berry, Biophys J (2007) 92: 373-378. PDF Hydration Profiles of Amyloidogenic Molecular Structures - Florin Despa, Ariel Fernández, L. Ridgway Scott, R. Stephen Berry, J Biol Phys (2008) 34: 577-590. PDF A unified model of protein dynamics - Hans Frauenfelder, Guo Chen, Joel Berendzen, Paul W. Fenimore, Helén Jansson, Benjamin H. McMahon, Izabela R. Stroe, Jan Swenson, and Roberto D. Young, PNAS (2009) 106: 5129-5134 PDF Coincidence of Dynamical Transitions in a Soluble Protein and Its Hydration Water: Direct Measurements by Neutron Scattering and MD Simulations - Kathleen Wood, Andreas Frölich, Alessandro Paciaroni, Martine Moulin, Michael Härtlein, Giuseppe Zaccai, Douglas J. Tobias, and Martin Weik, JACS (2008) 130: 4586-4587 PDF Coupling of protein and hydration-water dynamics in biological membranes. K. Wood, M. Plazanet, F. Gabel, B. Kessler, D. Oesterhelt, D. J. Tobias, G. Zaccai, and M. Weik, PNAS (2007) 104: 18049-18054 PDF Protein Hydration Dynamics and Molecular Mechanism of Coupled Water-Protein Fluctuations - Luyuan Zhang, Yi Yang, Ya-Ting Kao, Lijuan Wang, and Dongping Zhong, JACS (2009) 131: 10677-10691 PDF Protein surface hydration mapped by site-specific mutations - Weihong Qiu, Ya-Ting Kao, Luyuan Zhang, Lijuan Wang, Wesley E. Stites, Dongping Zhong, and Ahmed H. Zewail, PNAS (2006) 103: 13979-13984 PDF Mapping hydration dynamics around a protein surface - Luyuan Zhang, Lijuan Wng, Ya-Ting Kao, Weihong Qiu, Yi Yang, Oghaghare Okobiah, and Dongping Zhong, PNAS (2007) 104: 18461-18466 PDF Using a Charging Coordinate in Studies of Ionization Induced Partial Unfolding - Mitsunori Kato and Arieh Warshel, J Phys Chem B (2006) 110: 11566-11570 PDF Modeling electrostatic effects in proteins -Arieh Warshel, Pankaz K. Sharma, Mitsunori Kato, William W. Parson, BBA (2006) 1764: 1647-1676 PDF Specific Na+ and K+ cation effects on the interfacial water molecules at the air/aqueous salt solution interfaces probed with resonant second harmonic generation - Hong-tao Bian, Ran-ran Feng, Yuan Guo, and Hong-fei Wang, JCP (2009) 130:134709 PDF Water penetration/accommodation and phase behavior of the neutral langmuir monolayer at the air/water interface probed with sum frequency generation vibrational spectroscopy (SFG-VS) - Zhen Zhang, De-sheng Zheng, Yuan Guo, and Hong-fei Wang, Phys Chem Chem Phys (2009) 11: 991-1002 PDF Effect of Radiant Energy on Near-Surface Water - Binghua Chai, Hyok Yoo, and Gerald H. Pollack, JPCB (2009) 113: 13953-13958 PDF Surfaces and interfacial water: Evidence that hydrophilic surfaces have long-range impact - Jian-ming Zheng, Wei-Chun Chin, Eugene Khijniak, Eugene Khijniak Jr, Gerald H. Pollack, Advances in Colloid and Interface Science (2006) 127: 19-27 PDF Cells, Gels and the Engines of Life, G. H. Pollack, Ebner and Sons, Seattle, 2001. University of Washington 32nd Annual Faculty Lecture by Prof. Gerald Pollack 2008: Water, Energy, and Life: Fresh Views from the Water’s Edge Link Molecular self-assembly in a model amphiphile system - Lorna Dougan, Jason Crain, John L. Finney and Alan K. Soper, Phys. Chem. Chem. Phys. (2010) Advanced Article DOI:10.1039/C003407J PDF Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions - Murielle Lopez, Vandana Kurkal-Siebert, Rachel V. Dunn, Moeava Tehei, John L. Finney, Jeremy C. Smith, and Roy M. Daniel, Biophys J Lett, in press PDF Water? What’s so special about it? - John L. Finney, Phil. Trans. R. Soc. Lond. B (2004) 359: 1145-1165 PDF Transcript of final discussion, Phil. Trans. R. Soc. Lond. B (2004) 359: 1323-1328 PDF Calculation of the free energy of solvation of the Li+ and Na+ ions in water and chloroform - Peter V. Maye, Mihaly Mezei, J. of Molecular Structure (Theochem) (1996) 362: 317-324 PDF Structure-Guided Optimization of Small Molecules Inhibiting Human Immunodeficiency Virus 1 Tat Association with the Human Coactivator p300/CREB Binding Protein-Associated Factor - Chongfeng Pan, Mihaly Mezei, Shiraz Mujtaba, Michaela Muller, Lei Zeng, Jiaming Li, Zhiyong Wang, and Ming-Ming Zhou, J. Med. Chem (2007) 50: 2285-2288 PDF Water confined in reverse micelles - probe tool in biomedical informatics - Florin Despa, Phys. Chem. Chem. Phys (2008) 10: 4740-4747. PDF Cholic acid micelles - controlling the size of the aqueous cavity by PEGylation - F. Despa, J. T. Luo, J. Li, Y. Duan, and K. S. Lam - Phys. Chem. Chem. Phys. (2010) 12: 1589-1594. PDF Modeling the Hydration Layer around Proteins: HyPred - Jouko J. Virtanen, Lee Makowski, Tobin R. Sosnick, and Karl F. Freed, Biophys J (2010) doi: 10.1016/j.bpf.2010.06.027 PDF Mechanistic Elements of Protein Cold Denaturation - Carlos F. Lopez, Richard K. Darst, and Peter J. Rossky, J. Phys. Chem. B (2008) 112: 5961-5967. PDF Hydrophobicity of protein surfaces: Separating geometry from chemistry - Nicolas Giovambattista, Carlos F. Lopez, Peter J. Rossky, and Pablo G. Debenedetti, PNAS (2008) 105: 2274-2269. PDF The Physics and Bioinformatics of Binding and Folding - An Energy Landscape Perspective - Garegin A. Papoian and Peter G. Wolynes, Biopolymers (2003) 68: 333-349. PDF Role of Water Mediated Interactions in Protein-Protein Recognition Landscapes - Garegin A. Papoian, Johan Ulander, and Peter G. Wolynes, JACS (2003) 125: 9170-9178. PDF Water in protein structure prediction - Garegin A. Papoian, Johan Ulander, Michael P. Eastwood, Zaida Luthey-Schulten, and Peter G. Wolynes, PNAS (2004) 101: 3352-3357. PDF Counterfactual Biomolecular Physics: Protein Folding and Molecular Recognition in Water and Other Fluid Environments - Peter G. Wolynes, in Water and Life: The Unique Properties of H2O. Editors Ruth M. Lynden-Bell, Simon Conway Morris, John D. Barrow, John L. Finney, Charles Harper (2010) p. 209-214. PDF Role of Topology, Nonadditivity, and Water-Mediated Interactions in Predicting the Structures of α/β Proteins - Chenghang Zong, Garegin A. Papoian, Johan Ulander, and Peter G. Wolynes, JACS (2006) 128: 5168-5176. PDF Localizing frustration in native proteins and protein assemblies - Diego U. Ferreiro, Joseph A. Hegler, Elizabeth A. Komives, and Peter G. Wolynes, PNAS (2007) 104: 19819-19824. PDF Consequences of localized frustration for the folding mechanism of the IM7 protein - Ludovico Sutto, Joachim Lätzer, Joseph A. Hegler, Diego U. Ferreiro, and Peter G. Wolynes, PNAS (2007) 104: 19825-19830. PDF Protein Structure Prediction: Do Hydrogen Bonding and Water-Mediated Interactions Suffice? - Vanessa Oklejas, Chenghang Zong, Garegin A. Papoian, Peter G. Wolynes. PDF Dissecting the Assembly of Aβ16-22 Amyloid Peptides into Antiparallel β Sheets - Dmitri K. Klimov and D. Thirumalai, Structure (2003) 11: 295-307. PDF Aqueous urea solution destabilizes Aβ16-22 Oligomers - D. K. Klimov, John E. Straub, and D. Thirumalai, PNAS (2004) 101: 14760-14765. PDF Dynamics of locking peptides onto growing amyloid fibrils - Govardhan Reddy, John E. Straub, and D. Thirumalai, PNAS (2009) 106: 11948-11953. PDF Principles governing oligomer formation in amyloidogenic peptides - John E. Straub and Devarajan Thirumalai, Current Opinion in Structural Biology (2010) 20: 187-195. PDF Molecular Dynamics Simulations of End-to-End Contact Formation in Hydrocarbon Chains in Water and Aqueous Urea Solution - Raymond D. Mountain and D. Thirumalai, JACS (2003) 125: 1950-1957. PDF Hydrophobic and Ionic Interactions in Nanosized Water Droplets - S. Vaitheeswaran and D. Thirumalai, JACS (2006) 128: 13490-13496. PDF Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability, S. Vaitheeswaran and D. Thirumalai, PNAS (2008) 105: 17636-17641. PDF Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores - S. Vaitheeswaran, G. Reddy, and D. Thirumalai, JCP (2009) 130: 094502. PDF Quantum vibration analysis of hydrated ions using an an initio potential - Eugene Kamarchik and Joel M. Bowman. PDF Glass Transitions in Biomolecules and the Liquid-Liquid Critical Point of Water - Pradeep Kumar, Z. Yan, L. Xu, M. G. Mazza, S. V. Buldyrev, S.-H. Chen, S. Sastry, and H. E. Stanley, PRL (2006) 97: 177802. PDF Phase transitions in confined water nanofilms - Sungho Han, M. Y. Choi, Pradeep Kumar, and H. Eugene Stanley, Nature Physics (2010) 6: 685-689. PDF A practical method to avoid zero-point leak in molecular dynamics calculations: Application to the water dimer - Gábor Czakó, Alexey L. Kaledin, and Joel M. Bowman, JCP (2010) 132: 164103. PDF Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems - Gregory A. Voth, Acc. Chem. Res. (2006) 39: 143-150. 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