CMB: List of publications

List of publications


		2007 L. MEINHOLD and J.C. SMITH. Liquid-like and solid-like dynamics in crystalline proteins. Biophysical Journal In Press. L. MEINHOLD, J.C. SMITH, A. KITAO and A.H. ZEWAIL. Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. Proceedings of the National Academy of Sciences (U.S.A.) 104 44 17261-17265 (2007). L. MEINHOLD, F. MERZEL and J.C. SMITH. Lattice dynamics of a protein crystal. Physical Review Letters 99 (13) 138101 (2007). I. DAIDONE, M. ULMSCHNEIDER, A. DI NOLA, A. AMADEI and J.C. SMITH. Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proceedings of the National Academy of Sciences (U.S.A.) 104 39 15230-15235 (2007). X. DE HATTEN, Z. COURNIA, I. HUC, J.C. SMITH and N. METZLER-NOLTE. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics. Chemistry 13(29) 8139-8152 (2007). K. MORITSUGU and J.C. SMITH. Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian. Biophysical Journal 93 3460-3469 (2007). S. KOPPOLE, J.C. SMITH and S. FISCHER. The structural coupling between ATPase activation and recovery stroke in the Myosin II motor. Structure 15 825-837 (2007). D.R. NUTT and J.C. SMITH. Choosing an Appropriate Water Model for Use in Biomolecular Simulations. In Physics and Chemistry of Ice RSC Publishing, 451-458 (2007). C.M. TOPHAM and J.C. SMITH. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form. Biophysical Journal 92 769-786 (2007). D.R. NUTT and J.C. SMITH. Molecular dynamics simulations of proteins: Can the explicit water model be varied? Journal of Chemical Theory and Computation 3(4) 1550-1560 (2007). F. NOE, I. HORENKO, C. SCHÜTTE and J.C. SMITH. Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states. The Journal of Chemical Physics 126 155102 (2007). L. MEINHOLD and J.C. SMITH. Protein Dynamics from X-ray Crystallography: Anisotropic, Global Motion in Diffuse Scattering Patterns. Proteins: Structure, Function, and Bioinformatics 66 941-953 (2007). F. NOE and J.C. SMITH. Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science. In: Mathematical Modeling of Biological Systems, Volume I. A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (eds). Birkhäuser, Boston, 125-144 (2007). S. MESENTEAN, S. KOPPOLE, J.C. SMITH and S. FISCHER. The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. Journal of Molecular Biology 367 591-602 (2007). A.N. BONDAR, S. SUHAI, S. FISCHER, J.C. SMITH and M. ELSTNER. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements. Journal of Structural Biology 157 454-469 (2007). Z. COURNIA, G.M. ULLMANN and J.C. SMITH. Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulations Study. The Journal of Physical Chemistry B 111 1786-1801 (2007). 2006 F. NOE, M. OSWALD, G. REINELT, S. FISCHER and J.C. SMITH. Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the α_L ↔ β ↔ α_R Transitions in Octaalanine. Journal of Multiscale Modelling and Simulation 5 393-419 (2006). S. KOPPOLE, J.C. SMITH and S. FISCHER. Simulations of the Myosin II Motor Reveal a Nucleotide-state Sensing Element that Controls the Recovery Stroke. Journal of Molecular Biology 361 604-616 (2006). V. KURKAL-SIEBERT, R. DANIEL, J.L. FINNEY, M. TEHEI, R.V. DUNN and J.C. SMITH. Enzyme hydration, activity and flexibility: A neutron scattering approach. Journal of Noncrystalline Solids 352 4387-4393 (2006). E. BALOG, J.C. SMITH and D. PERAHIA. Conformational heterogeneity and low-frequency vibrational modes of proteins. Physical Chemistry Chemical Physics 8 (47) 5543-5548 (2006). P. IMHOF, F. NOE, S. FISCHER and J.C. SMITH. AM1/d Parameters for Magnesium in Metalloenzymes. Journal of Chemical Theory and Computation 2 1050-1056 (2006). A.N. BONDAR, J.C. SMITH and S. FISCHER. Structural and energetic determinants of proton transfer in bacteriorhodopsin. Photochemical and Photobiological Sciences. 5 547-552 (2006). S. MESENTEAN, S. FISCHER and J.C. SMITH. Analyzing Large-Scale Structural Change in Proteins: Comparison of Principal Component Projection and Sammon Mapping. Proteins: Structure, Function and Bioinformatics 64 210-218 (2006). F. NOE, D. KRACHTUS, J.C. SMITH and S. FISCHER. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. Journal of Chemical Theory and Computation 2 840-857 (2006). S.M. SCHWARZL, J.C. SMITH and S. FISCHER. Insights into the Chemo-mechanical Coupling of the Myosin Motor from Simulation of its ATP Hydrolysis Mechanism. Biochemistry 45 5830-5847 (2006). J.C. SMITH. Tight in Titin. Structure 14 389-392 (2006). K. MORITSUGU and J.C. SMITH. Temperature-Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description. The Journal of Physical Chemistry B 110 5807-5816 (2006). L. WALEWSKI, D. KRACHTUS, S. FISCHER, J.C. SMITH, P. BALA and B. LESYNG. SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene. International Journal of Quantum Chemistry 106 636-640 (2006). J.C. SMITH, T. BECKER, S. FISCHER, F. NOE, A.L. TOURNIER, G.M. ULLMANN and V. KURKAL. Physical and functional aspects of protein dynamics. Soft Condensed Matter Physics in Molecular and Cell Biology 225-241 ed. W.C.K. Poon and D. Andelman, Taylor&Francis (2006). T. EFFERTH, S.M. SCHWARZL, J.C. SMITH and R. OSIEKA. Role of glucose-6-phosphate dehydrogenase for oxidative stress and apoptosis. Cell Death and Differentiation 13 527-528 (2006). M. TEHEI, J.C. SMITH, C. MONK, J. OLLIVIER, M. OETTL, V. KURKAL, J.L. FINNEY and R.M. DANIEL. Dynamics of Immobilized and Native Escherichia coli Dihydrofolate Reductase by Quasieleastic Neutron Scattering. Biophysical Journal. 90 1090-1097 (2006). V. KURKAL-SIEBERT and J.C. SMITH. Low-Temperature Protein Physics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K. Journal of the American Chemical Society (JACS) 128 2356-2364 (2006). 2005 F. MERZEL and J.C. SMITH. High-Density Hydration Layer of Lysozyme: Molecular Dynamics Decomposition of Solution Scattering Data. Journal of Chemical Information and Modelling. 45(6) 1593-1599 (2005). J. BAUDRY and J.C. SMITH. Can proteins and crystals self-catalyze methyl rotations? The Journal of Physical Chemistry B 109(43) 20572-20578 (2005). S.M. SCHWARZL, J.C. SMITH, B. KAINA, and T. EFFERTH. Molecular Modeling of O⁶-Methylguanine-DNA Methyltransferase Mutant Proteins Encoded by Single Nucleotide Polymorphisms. International Journal of Molecular Medicine. 16 553-557 (2005). L. MEINHOLD and J.C. SMITH. Correlated dynamics determining X-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. Physical Review Letters 95:218103 (2005). A.N. BONDAR, J.C. SMITH and S. FISCHER. QM/MM investigation of the hydrogen-bonding interactions in putative K and early-M intermediates of the bacteriorhodopsin photocycle. Phase Transitions 78 9-11 671-675 (2005). L. MEINHOLD and J.C. SMITH. Pressure-dependent transition in protein dynamics at ~4 kbar revealed by molecular dynamics simulation. Physical Review E 72:061908 (2005). M. HAMMEL, H.-P. FIEROBE, M. CZJZEK, V. KURKAL, J.C. SMITH, E.A. BAYER, S. FINET, and V. RECEVEUR-BRECHOT. Structural basis of cellulosome efficiency explored by small angle X-ray scattering. The Journal of Biological Chemistry 280 46 38562-38568 (2005). Z. COURNIA, J.C. SMITH and G.M. ULLMANN. Development and Validation of a Force-Field for Biologically Important Sterols in Biomembranes. Lecture Series on Computer and Computational Sciences, Brill Academic Publishers, Vol. 4, 949-953 (2005). M. JAGODA, S. WARZESKA, H. PRITZKOW, H. WADEPOHL, P. IMHOF, J.C. SMITH and R. KRÄMER. Catalytic Transesterification of Dialkyl Phosphates by a Bioinspired Dicopper(II) Macrocyclic Complex. Journal of the American Chemical Society (JACS) 127 15061-15070 (2005). A.N. BONDAR, S. FISCHER, S. SUHAI and J.C. SMITH. Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps. The Journal of Physical Chemistry B 109 14786-14788 (2005). Z. COURNIA, J.C. SMITH and G.M. ULLMANN. A Molecular Mechanics Force Field for Biologically Important Sterols. Journal of Computational Chemistry 26 1383-1399 (2005). F. GRÄTER, S.M. SCHWARZL, A. DEJAEGERE, S. FISCHER and J.C. SMITH. Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics / Molecular Mechanics. The Journal of Physical Chemistry B 109 10474-10483 (2005). V. KURKAL, R.M. DANIEL, J.L. FINNEY, M. TEHEI, R.V. DUNN and J.C. SMITH. Low frequency enzyme dynamics as a function of temperature and hydration: A neutron scattering study. Chemical Physics 317 267-273 (2005). V. KURKAL, R. DANIEL, J. FINNEY, M. TEHEI, R.V. DUNN and J.C. SMITH. Enzyme activity and flexibility at very low hydration. Biophysical Journal 89 1282-1287 (2005). K. MORITSUGU and J.C. SMITH. Langevin model of the temperature and hydration dependence of protein vibrational dynamics. The Journal of Physical Chemistry B 109 12182-12194 (2005). S.M. SCHWARZL, D. HUANG, J.C. SMITH and S. FISCHER. Non-Uniform Charge Scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins. Journal of Computational Chemistry 26 131359-1371 (2005). S. FISCHER, B. WINDSHÜGEL, D. HORAK, K.C. HOLMES and J.C. SMITH. Structural mechanism of the recovery stroke in the Myosin molecular motor. Proceedings of the National Academy of Sciences (U.S.A.) 102 19 6873-6878 (2005). D. SENGUPTA, R. NATH BEHERA, J.C. SMITH and G.M. ULLMANN. The α-Helix Dipole - Screened Out? Structure 13 849-855 (2005). A.D. GRUIA, A.-N. BONDAR, J.C. SMITH and S. FISCHER. Mechanism of a molecular valve in halorhodopsin chloride pump. Structure 13 617-627 (2005). F. NOE, F. ILLE, J.C. SMITH and S. FISCHER. Automated Computation of Low-Energy Pathways for Complex Rearrangements in Proteins: Application to the conformational switch of Ras p21. Proteins: Structure, Function and Bioinformatics 59 534-544 (2005). D. SENGUPTA, L. MEINHOLD, D. LANGOSCH, G.M. ULLMANN and J.C. SMITH. Understanding the energetics of helical peptide orientation in membranes. Proteins: Structure, Function and Bioinformatics 58 913-922 (2005). L. MEINHOLD and J.C. SMITH. Fluctuations and Correlations in Crystalline Protein Dynamics: a Simulation Analysis of Staphylococcal Nuclease. Biophysical Journal 88 2554-2563 (2005). A.C. VAIANA, Z. COURNIA, I.B. COSTESCU and J.C. SMITH. AFMM: A Molecular Mechanics Force Field Vibrational Parametrization Program. Computer Physics Communications 167 34-42 (2005). A.-N. BONDAR, M. ELSTNER, S. SUHAI, S. FISCHER and J.C. SMITH. Direct proton transfer in a putative L-state intermediate of the bacteriorhodopsin photocycle. Phase Transitions 78 5-9 (2005). 2004 A.L. TOURNIER, J.L. FINNEY, R.M. DANIEL and J.C. SMITH. Temperature and timescale dependence of protein dynamics in methanol:water mixtures. Physical Chemistry Chemical Physics, B416103C (2004). P. IMHOF, S. FISCHER, R. KRÄMER and J.C. SMITH. Density Functional Theory Analysis of Dimethylphopshate Hydrolysis: effect of Solvation and Nucleophile Variation. Journal of Molecular Structure: THEOCHEM 713/1-3 1-5 (2004). A.-N. BONDAR, S. FISCHER, J.C. SMITH, M. ELSTNER and S. SUHAI. Key Role of Electrostatic Interactions in Bacteriorhodopsin Proton Transfer. Journal of the American Chemical Society (JACS) 126 14668-14677 (2004). T. EFFERTH, E.B. BACHLI, S.M. SCHWARZL, J.S. GOEDE, C. WEST, J.C. SMITH and E. BEUTLER. Glucose-6-phosphate dehydrogenase (G6PD) deficiency-type Zurich: a splice site mutation as an uncommon mechanism producing enzyme deficiency. Blood 104 8 2608 (2004). T. BECKER, J. HAYWARD, J.L. FINNEY, R.M. DANIEL and J.C. SMITH. Neutron frequency windows and the protein dynamical transition. Biophysical Journal 87 (3) 1436-1444 (2004). C. PFISTERER, D. MIHAILESCU, J.C. SMITH and J. REED. Common Pharmacophoric Footprint for AIDS Vaccine Design. Journal of Medicinal Chemistry 47(15) 3723-3729 (2004). J.C. SMITH, F. MERZEL, A.-N. BONDAR, A. TOURNIER and S. FISCHER. Structure, dynamics and reactions of protein hydration water. Philosophical Transactions: Biological Sciences 359 1181-1190 (2004). E. BALOG, T. BECKER, M. OETTL, R. LECHNER, R. DANIEL, J.L. FINNEY and J.C. SMITH. Direct determination of Vibrational Density of States Change on Ligand Binding to a Protein. Physical Review Letters 93 2 028103 (2004). L. MEINHOLD, S. LAMMERS, T. BECKER and J.C. SMITH. Convergence properties of X-ray scattering calculated from protein crystal molecular dynamics simulations. Physica B. 350 127-131 (2004) A.-N. BONDAR, M. ELSTNER, S. SUHAI, J.C. SMITH and S. FISCHER. Multiple Pathways for the Primary Proton Transfer Step in Bacteriorhodopsin. Structure. 12 1281-1288 (2004). V. KURKAL and J.C. SMITH. The protein glass transition. In: Physics meets Biology - From Soft Matter to Cell Biology (Lecture notes of the 35^th Spring School of the Institut für Festkörperforschung Jülich, Schriften des Forschungszentrums Jülich Reihe Matter and Materials Vol. 19, Ch. C5 (2004). D. MIHAILESCU and J.C. SMITH. Computer simulation of energy-transducing proteins and peptide:membrane interactions. ACS Proceedings. Symposium Series No. 883 Molecular Bioenergetics - Simulations of Electronic, Proton and Energy Transfer, Ed. R.A. Wheeler, Ch. 11, 175-186 (2004). J.C. SMITH, Z. COURNIA, A. TALY, A.L. TOURNIER, D. MIHAILESCU and G.M. ULLMANN. Conformational Transitions in Proteins and Membranes. In: Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations. Eds. J. Samios, V.A. Durov, Kluwer Academic Publishers, Dordrecht: 485-502 (2004). A. GRUIA, S. FISCHER and J.C. SMITH. Kinetics of breaking a salt-bridge critical in protein unfolding. Chemical Physics Letters. 385:337-340 (2004). Abstract Z. COURNIA, A.C. VAIANA, G.M. ULLMANN and J.C. SMITH. Derivation of a Molecular Mechanics Force Field for Cholesterol. Pure and Applied Chemistry. 76(1):189-196 (2004). Abstract N. BONDAR, M. ELSTNER, S. FISCHER, J.C. SMITH and S. SUHAI. Can coordinate driving describe the first proton transfer step in bacteriorhodopsin ? Phase Transitions. 77(1-2):47-52 (2004). Abstract 2003 A.C. VAIANA, H. NEUWEILER, A. SCHULZ, J. WOLFRUM, M. SAUER and J.C. SMITH. Fluorescence Quenching of Dyes by Tryptophan: Interactions at Atomic Detail from Combination of Experiment and Computer Simulation. Journal of the American Chemical Society. 125(47):14564-72 (2003) Abstract A. TOURNIER and J.C. SMITH. Principal Components of the Protein Dynamical Transition. Physical Review Letters. 91:208106 (2003). Abstract F. NOE, S.M. SCHWARZL, S. FISCHER and J.C. SMITH. Computational tools for analyzing structural changes in proteins in solution. Applied Bioinformatics. 2(3):S11-S17 (2003). Abstract A. TOURNIER, J. XU and J.C. SMITH. Translational hydration water dynamics drives the protein glass transition. Biophysical Journal. 85(3):1871-5 (2003). Abstract G.M. ULLMANN. Relations between Protonation Constants and Titration Curves in Polyprotic Acids: A Critical View. Journal of Physical Chemistry B. 107:1263-1271 (2003). Abstract J.A. HAYWARD, J.L. FINNEY, R. DANIEL and J.C. SMITH. Use of computer simulation for understanding elastic neutron scattering from complex systems: a small protein in various solvents. Chemical Physics. 292:389-396 (2003). J.A. HAYWARD, J.L. FINNEY, R. DANIEL and J.C. SMITH. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophysical Journal. 85(2):679-85. (2003). Abstract D. MIHAILESCU, J. REED and J.C. SMITH. Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore. Biopolymers. 70(2):121-133 (2003). Abstract T. BECKER, S. FISCHER, F. NOE, A.L. TOURNIER, G.M. ULLMANN and J.C. SMITH. Protein Dynamics: Glass Transition and Mechanical Function. Advances in Solid State Physics. 43:677-694 (2003). Abstract M. KATAOKA, H. KAMIKUBO, H. NAKAGAWA, S.F. PARKER and J.C. SMITH. Neutron Inelastic Scattering as a High-Resolution Vibrational Spectroscopy: New Tool for the Study of Protein Dynamics. Spectroscopy. 17:529-535 (2003). S.M. SCHWARZL, D. HUANG, J.C. SMITH and S. FISCHER. How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin. In Silico Biology. 3:0016 (2003). Abstract T. BECKER and J.C. SMITH. Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. Physical Review E. 67:021904 (2003). Abstract A. TALY, P. SEBBAN, J.C. SMITH and G.M. ULLMANN. The position of Q_B in the photosynthetic reaction center depends on pH: a theoretical analysis of the proton uptake upon Q_B reduction. Biophysical Journal. 84(3):2090-2098 (2003). Abstract A.C. VAIANA, A. SCHULZ, J. WOLFRUM, M. SAUER and J.C. SMITH. Molecular Mechanics Force Field Parameterization of the Fluorescent Probe Rhodamine 6G using Automated Frequency Matching. Journal of Computational Chemistry. 24:632-639 (2003). Abstract R.M. DANIEL, R.V. DUNN, J.L. FINNEY and J.C. SMITH. The Role of Dynamics in Enzyme Activity. Annual Review of Biophysics & Biomolecular Structure. 32:69-92 (2003). Abstract A.D. GRUIA, S. FISCHER and J.C. SMITH. Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in the unfolding of truncated Staphylococcal nuclease. Proteins: Structure, Function, and Genetics. 50:507-515 (2003). Abstract A.L. TOURNIER, J. XU and J.C. SMITH. Solvent Caging of Internal Motions in Myoglobin at Low Temperatures. Phys. Chem. Comm. 6(2):6-8 (2003). Abstract 2002 R. DUTZLER, T. SCHIRMER, M. KARPLUS and S. FISCHER. Translocation mechanism of long sugar chains across the maltoporin membrane channel. Structure. 10:1273-1284 (2002). Abstract G. M ULLMANN, L. NOODLEMAN and D A. CASE. Density Functional Calculation of pKa values & Redox Potentials in the Bovine Rieske Iron-Sulfur Protein. J. Biol. Inorg. Chem. 7:632-639 (2002). Abstract R. GREBE, M. GUMBEL, M. KNAPP, G.M. ULLMANN and J. LANGOWSKI. Modellierung biologischer Prozesse. In: Handbuch Medizinische Informatik. T. Lehmann and E. M. zu Bexten (Eds.), 179-223; Carl Hanser Verlag, München, (2002). H. NEUWEILER, A. SCHULZ, A.C. VAIANA, J.C. SMITH, S. KAUL, J. WOLFRUM and M. SAUER. Detection of Individual p53-Autoantibodies Using Quenched Peptide-Based Molecular Probes. Angewandte Chemie (Intl. Ed.) 41(24):4769-73 (2002). Abstract J.C. SMITH, F. MERZEL, C.S. VERMA and S. FISCHER. Protein hydration water: structure and thermodynamics. Journal of Molecular Liquids. 101(1-3):27-33 (2002). Abstract P. MANIVET, B. SCHNEIDER, J.C. SMITH, D.-S. CHOI, L. MAROTEAUX, O. KELLERMANN and J.-M. LAUNAY. The serotonin binding site of human and murine 5-HT_2B receptors: molecular modelling and site-directed mutagenesis. Journal of Biological Chemistry. 277(19):17170-8 (2002). Abstract R.M. DANIEL, J.L. FINNEY and J.C. SMITH. The dynamic transition in enzymes may have a simple explanation. Faraday Discusssions. 122:163-169 (2002). Abstract A. TOURNIER, S. SCHWARZL, D. HUANG, S. FISCHER and J.C. SMITH. Time-resolved computational protein biochemistry: solvent effects on interactions, conformational transitions and equilibrium fluctuations. Faraday Discussions. 122:243-251 (2002). Abstract T. HUYNH, J.C. SMITH and A. SANSON. Protein Unfolding Transitions in an Intrinsically Unstable Annexin Domain: Molecular Dynamics Simulation and Comparison with Nuclear Magnetic Resonance Data. Biophysical Journal. 83(2):681-698 (2002). Abstract S.M. SCHWARZL, T. TSCHOPP, J.C. SMITH and S. FISCHER. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? Journal of Computational Chemistry. 23:1143-1149 (2002). Abstract F. MERZEL and J.C. SMITH. Calculation of small angle scattering intensities from molecular dynamics simulation. Cellular and Molecular Biology Letters. 7(1):134-5 (2002). Abstract F. MERZEL and J.C. SMITH. Is the first hydration shell of lysozyme of higher density than bulk water? Proceedings of the National Academy of Sciences (U.S.A.) 99(8):5378-5383 (2002). Abstract A.D. GRUIA, S. FISCHER and J.C. SMITH. Computer Simulation of Protein Unfolding. Proceedings of High-Performance Computing in Science and Engineering ´01, Eds. E. Krause and W. Jäger, Springer-Verlag, 260-268 (2002). D. MIHAILESCU, J.C. SMITH and J. REED. Solution structure of a putative HIV1 immunogenic peptide: computer simulation of the principal CD4 binding domain of gp120. Journal of Medicinal Chemistry. 45:1019-1025 (2002). Abstract J. HAYWARD and J.C. SMITH. Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophysical Journal 82:1216-1225 (2002). Abstract F. MERZEL and J.C. SMITH. SASSIM: A method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallographica Section D 58:242-249 (2002). Abstract 2001 M. CRNOGORAC, G.M. ULLMANN and N. M. KOSTIC. Aspects of pH on Protein Association: The Case of Zinc Cytochrome c and Plastocyanin. Extension of the Proton Linkage Model and Experimental Verification of the Extended Model. J. Amer. Chem. Soc. 123:10789-10798 (2001). Abstract G.M. ULLMANN. Charge Transfer Properties of Photosynthetic & Respiratory Proteins. In: Supramolecular Photosensitive and Electroactive Materials. H. S. Nalwa (Ed.) pg. 525-584, Academic Press, New York (2001). A. ONUFRIEV, D.A. CASE and G.M. ULLMANN. A Novel View of pH Titration in Biomolecules. Biochemistry. 40:3413-3419 (2001). Abstract S. FISCHER, J.C. SMITH and C. VERMA. Dissecting the vibrational entropy change on protein-ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor. Journal of Physical Chemistry B. 105:8050-8055 (2001). Abstract S. DELLERUE, A.-J. PETRESCU, J.C. SMITH and M.-C. BELLISSENT-FUNEL. Radially softening diffusive motions in a globular protein. Biophysical Journal. 81:1666-1676 (2001). Abstract A.-N. BONDAR, R. DANIEL, J.L. FINNEY, S. FISCHER, M. KATAOKA, A. PETRESCU and J.C. SMITH. Protein Folding and Dynamics - New Insights from Computer Simulation and Scattering Experiments. Journal of the Physical Society of Japan. 70 Suppl. A (Proc. Int. Symp. ASR-2000) Eds. S. Katano, N. Metoki, Y. Morii and Y. Ishii. 392-395 (2001). J.C. SMITH. Motions in Biomolecules - Comparing Simulation with Experiment. In: Spectroscopic Techniques in Biophysics. Eds. G.M. Giacometti & G. Giacometti. IOS Press, Amsterdam. 179-195 (2001). J.C. SMITH. X-ray & Neutron Scattering as Probes of the Dynamics of Biological Molecules. In: Computational Biochemistry and Biophysics. Eds. O. Becker, A.D. MacKerell, B. Roux and M. Watanabe. Marcel Dekker, New York. 237-251 (2001). 2000 J. SOPKOVA-DE OLIVEIRA SANTOS, F.K. OLING, S. RETY, A. BRISSON, J.C. SMITH and A. LEWIT-BENTLEY. S100 protein-annexin interactions: a model of the (Anx2-p11)₂ heterotetramer complex. Biochimica et Biophysica Acta. 1498:181-191 (2000). Abstract J. SOPKOVA-DE OLIVEIRA SANTOS, S. FISCHER, C. GUILBERT, A. LEWIT-BENTLEY and J.C. SMITH. Pathway for large-scale conformational change in Annexin V. Biochemistry. 39(46):14065-14074 (2000). Abstract S. DELLERUE, A.J. PETRESCU, J.C. SMITH, S. LONGEVILLE and M.-C. BELLISSENT-FUNEL. Collective dynamics of a photosynthetic protein probed by neutron spin-echo spectroscopy and molecular dynamics simulation. Physica B. 276-278:514-515 (2000). Abstract D. MIHAILESCU and J.C. SMITH. Atomic Detail Peptide-Membrane Interactions: Molecular Dynamics Simulation of Gramicidin S in a DMPC Bilayer. Biophysical Journal. 79(4):1718-1730 (2000). Abstract C. GUILBERT, F. RICARD and J.C. SMITH. Dynamic Simulation of the Mouse Prion Protein. Biopolymers. 54(6):406-415 (2000). Abstract J. BAUDRY, S. CROUZY, B. ROUX and J.C. SMITH. From Sequence to Structure and Function: Modelling and Simulation of Light-Activated Membrane Proteins. In: Genomics and Proteomics. Ed. S. Suhai. Kluwer/Plenum. 141-147 (2000). V. REAT, R. DUNN, M. FERRAND, J.L. FINNEY, R.M. DANIEL and J.C. SMITH. Solvent dependence of dynamic transitions in protein solutions. Proceedings of the National Academy of Sciences (U.S.A.) 97(18):9961-9966 (2000). Abstract A.-J. PETRESCU, P. CALMETTES, D. DURAND, V. RECEVEUR and J.C. SMITH. Change in backbone torsion angle distribution on protein folding. Protein Science. 9:1129-1136 (2000). Abstract C. TENETTE-SOUAILLE and J.C. SMITH. Structure of the Mα2-3/toxin α antibody-antigen complex: combination of modelling with functional mapping experimental results. Protein Engineering. 13(5):345-351 (2000). Abstract J.C. SMITH. Inelastic & quasielastic neutron scattering: complementarity with biomolecular simulation. In: Structure and Dynamics of Biomolecules: Neutron and Synchrotron Radiation for Condensed Matter Studies. Volume IV. Oxford University Press. 161-180 (2000). R. DUNN, V. REAT, J.L. FINNEY, M. FERRAND, J.C. SMITH and R.M. DANIEL. Enzyme Dynamics and Activity: Xylanase Activity in the absence of fast anharmonic motions. Biochemical Journal. 346:355-358 (2000). Abstract V. REAT, J.L. FINNEY, W.A. STEER, M.A. ROBERTS, J.C. SMITH, R. DUNN, M. PETERSON and R.M. DANIEL. Cryosolvents useful for protein and enzyme studies below -100^oC. Journal of Biochemical and Biophysical Methods. 42:97-103 (2000). Abstract 1999 S. CROUZY, J. BAUDRY, J.C. SMITH and B. ROUX. Efficient Calculation of Two-Dimensional Adiabatic and Free Energy Maps: Application to the Isomerization of the C13=C14 and C15=N16 Bonds in the Retinal of Bacteriorhodopsin. Journal of Computational Chemistry. 20(15):1644-1658 (1999). Abstract M. KATAOKA, M. FERRAND, A.V. GOUPIL-LAMY, H. KAMIKUBO, J. YUNOKI, T. OKA and J.C. SMITH. Dynamical and structural modifications of staphylococcal nuclease on C-terminal truncation. Physica B. 266:20-26 (1999). Abstract \| C.M. TOPHAM and J.C. SMITH. The Influence of Helix Morphology on Cooperative Polyamide Backbone Conformational Flexibility in Peptide Nucleic Acid Complexes. Journal of Molecular Biology. 292(5):1017-1038 (1999). Abstract R. DANIEL, J.L. FINNEY, V. REAT, R. DUNN, M. FERRAND and J.C. SMITH. Enzyme Dynamics and Activity: Timescale-Dependence of the Dynamical Transitions in Glutamate Dehydrogenase Solution. Biophysical Journal. 77:2184-2190 (1999). Abstract J. BAUDRY, S. CROUZY, B. ROUX and J.C. SMITH. Simulation Analysis of the Retinal Conformational Equilibrium in Dark-Adapted Bacteriorhodopsin. Biophysical Journal. 76(4):1909-1917 (1999). Abstract D. MIHAILESCU and J.C. SMITH. Molecular Dynamics Simulation of the Cyclic Decapeptide Antibiotic, Gramicidin S, in Dimethyl Sulfoxide Solution. Journal of Physical Chemistry B. 103(9):1586-1594 (1999). Abstract T. HUYNH, G. MUSAT, J.-M. NEUMANN, J.C. SMITH and A. SANSON. Molecular dynamics simulations of the Isolated Domain I of annexin I. Theoretical Chemistry Accounts. 101:82-86 (1999). Abstract
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