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Research Publications

Below are select publications from the last two years that highlight the research and activity of our faculty, postdocs, graduate, and undergraduate students.

Comprehensive list of BCMB publications (dating back to 2004).

In Press

Binder BM, Schaller GE, Chang, C. (2011) Perception of Ethylene by Plants- Ethylene Receptors. IN: The Plant Hormone Ethylene (MT McManus, ed.). Wiley-Blackwell. In press.

publication5

(From Jenson, J.K., et al. 2011)

T Berezniak, A. Jaeschke, J.C. Smith & P. Imhof. Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study. Journal of Computational Chemistry. In Press.

Brager A, Prosser RA, and Glass DJ (2011) Acamprosate-responsive brain sites for suppression of ethanol intake and preference. Am.J.Physiology (in press).

Brager A, Prosser RA, and Glass DJ, 2011 Circadian and acamprosate modulation of elevated ethanol drinking in mPer2 clock gene mutant mice. Am.J.Physiology, in press

Brager AJ, Ruby CL, Prosser, RA, Glass, JD, 2011 Acute ethanol disrupts photic and serotonergic circadian clock phase resetting in the mouse. Alcoholism, in press

S.R. Ellingson and J. Baudry (2011) High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud. Concurrency and Computation: Practice and Experience, in press

publication1

(From S.L. Madison, A. Nebenführ. 2011)

Kim BH, Malek P, Waloszek,  andvon Arnim AG. “Arabidopsis BPG2: A phytochrome regulated gene whose protein product binds to plastid ribosomal RNAs” Planta (in press).

Klein, H., Cheng, X., Smith, J.C., &Shen, T. (2011) Transfer matrix approach to the hydrogen-bonding incelluloseI-a fibrils describes the recalcitrance to thermal deconstruction. J. Phys. Chem., in press

M. Krishnan & J.C. Smith Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters. Journal of Physical Chemistry B. In Press.

S.L. MadisonA. Nebenführ (2011) Live-cell imaging of dual-labeled Golgi stacks in tobacco BY-2 cells reveals similar behaviors for different cisternae during movement and brefeldin A treatment. Molecular Plant, 4(5), in press

biophys-j-cover6

(From Y. Miao and J. Baudry . 2011)

Noe F, Doose S, Daidone I, Lollmann M, Sauer M, Chodera J, and Smith J.C. (2011) Dynamical Fingerprints: Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiments. Proceedings of the National Academy of Sciences, in press

Parks J, Imhof P, and Smith J.C. Understanding Enzyme Catalysis Using Computer Simulation. Wiley. Encyclopedia of Catalysis, 2nd edition. (in press)

R. PoolL, K.A. Feenstra, M. Hoefling, R. Schulz, J.C. Smith & J. Heringa. Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy Python Interface module to the GROMACS simulation C-library. Journal of Computational Chemistry. In press.

Serpersu, E. H. and Norris, A. L. (2012) Effect of protein dynamics and solvent in ligand recognition by promiscuous aminoglycoside-modifying enzymes. Adv. Carbohydr. Chem. Biochem. (in press)

Siuti, P., C. S. Green, A. N. Edwards, M. Doktycz and G. Alexandre. (2011) The chemotaxis-like Che1 pathway has an indirect role in adhesive cell properties of Azospirillum brasilense. FEMS Microbiology Letters, in press

 2012

Berezniak T, Jaeschke A, Smith JC, and Imhof P (2012). Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study. Journal of Computational Chemistry, 33(19):1603-1614.

Cheng X, Parks JM, Petridis L, Lindner B, Schulz R, Guo HB, Srinivas G, and Smith JC (2012). Molecular Simulation in the Energy Biosciences. In: Innovations in Biomolecular Modeling and Simulations, ed. by T. Schlick. RSC Publishing, chap. 5, pp. 87-114. (ISBN: 978-1-84973-504-9 ).

Daidone I, Iacobucci C, McLain SE, and Smith JC (2012). Alteration of Water Structure by Peptide Clusters Revealed by Neutron Scattering in the Small-Angle Region (below 1 Å^?1). Biophysical Journal, 103(7):1518-1524.

Glass DC, Moritsugu K, Cheng X, and Smith JC (2012). REACH Coarse-Grained Simulation of a Cellulose Fiber. Biomacromolecules, 13(9):2634–2644.

Guo HB, He F, Gu B, Liang L, and Smith JC (2012). Time-Dependent Density Functional Theory Assessment of UV Absorption of Benzoic Acid Derivatives. The Journal of Physical Chemistry A, 116(48):11870–11879.

Hong L, Glass DC, and Smith JC (2012). Surface Hydration Amplifies Single-Well Protein Atom Diffusion Propagating into the Macromolecular Core. Physical Review Letters, 108(23):238102.

Krishnan M, and Smith JC (2012). Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters. The Journal of Physical Chemistry B, 116(14):4124-4133.

Langan P, Evans BR, Foston M, Heller WT, O’Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, and Davison BH (2012). Neutron Technologies for Bioenergy Research. Industrial Biotechnology, 8(4):209-216.

Merzel F, Johnson MR, and Smith JC (2012). Normal Modes and Neutrons: Defining Collective, Functional Biomolecular Motions. Neutron News, 3(23):26-30.

Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, and Smith JC (2012). Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein. Journal of the American Chemical Society, 134(48):19576-19579.

Nickels JD, O’Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, and Sokolov AP (2012). Dynamics of a Protein and Its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP. Biophysical Journal, 104(7):1566-1575.

Pool R, Heringa J, Hoefling M, Schulz R, and Smith JC (2012). Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of GROMACS through the GromPy Python Interface Module to the GROMACS Simulation C-library. Journal of Computational Chemistry, 33(12):1207-1214.

Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, and Smith JC (2012). Radical Coupling Reactions in Lignin Synthesis: A Density Functtional Theory Study. The Journal of Physical Chemistry B, 116(16):4760-4768.

Tschaplinski TJ, Standaert RF, Engle NL, Martin MZ, Sangha AK, Parks JM, Smith JC, Samuel R, Pu Y, Ragauskas AJ, Hamilton CY, Fu C, Wang ZY, Davison BH, Dixon RA, and Mielenz JR (2012). Down-Regulation of the Caffeic Acid O-Methyltransferase Gene in Switchgrass Reveals a Novel Monolignol Analog. Biotechnology for Biofuels, 5:71.

Ulmschneider JP, Smith JC, Ulmschneider MB, Ulrich AS, and Strandberg E (2012). Reorientation and Dimerization of the Membrane-Bound Antimicrobial PeptidePGLa from Microsecond All-Atom MD Simulations. Biophysical Journal, 103(3):472-482.

Yi Z, Miao Y, Baudry J, Jain N, and Smith JC (2012). Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering. The Journal of Physical Chemistry B, 116(16):5028-5036.

“VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy.” M.C. Brothers , A.E. Nesbitt, M.J. Hallock, S.G. Rupasinghe, M. Tang, J. Harris J. Baudry, M.A. Schuler, and C.M. Rienstra. J. Biomolecular NMR.  2012, 52, 41-56

Balananda-Dhurjati K. Putcha, Edward Wright, Joseph S. Brunzelle, and Elias J. Fernandez, (2012) Proc. Natl. Acad. Sci USA, in press. Structural basis for negative cooperativity within agonist-bound TR- RXR Heterodimers

M. Biswas, T. Wocjan, J. Langowski & J.C. Smith. DNA bending potentials for loop-mediated nucleosome repositioning by M. Biswas, EPL 97 38004 (2012)

Neuropeptide Y-induced phase shifts of PER2::LUC rhythms are mediated by long-term suppression of neuronal excitability in a phase-specific manner. Besing RC, Hablitz LM, Paul JR, Johnson RL, Prosser RA, Gamble KL. Chronobiol Int. 2012 Mar;29(2):91-102.

Duff, Jr., M.R., Grubbs, J., Serpersu, E.H., and Howell, E.E. (2012) “Weak Interactions between Folate and Osmolytes in Solution,” Biochemistry 51, 2309?2318.

Cocaine modulates pathways for photic and nonphotic entrainment of the mammalian SCN circadian clock. Glass JD, Brager AJ, Stowie AC, Prosser RA. Am J Physiol Regul Integr Comp Physiol. 2012 Mar;302(6):R740-50.

Jayaraman, M., Kodali, R., Sahoo, B.,Thakur, A.K., Mayasundari, A., Mishra, R., Peterson, C. B.,  and Wetzel, R. (2012) J. Mol. Biol, in press.  “Slow Amyloid Nucleation via ?-helix-rich Oligomeric Intermediates in Short Polyglutamine-containing Huntingtin Fragments.”

Kong D, Karve R, Willet A, Chen MK, Oden J, and Shpak ED. (2012) Regulation of plasmodesmatal permeability and stomatal patterning by a glycosyltransferase-like protein KOBITO1. Plant Physiology (accepted)

B. Lindner and J.C. Smith. Sassena – X-ray and Neutron Scattering Calculations from Molecular Dynamics Trajectories using Massively Parallel Computers. Computer Physics Communications. 183(7) 1491-1501 (2012)

Lipid Droplet De Novo Formation and Fission Are Linked to the Cell Cycle in Fission Yeast,” (2012) Traffic, 1-10. Allan P. Long1, Anna K. Manneschmidt1, BobbyVerBrugge1, Mary R. Dortch1, Steven C. Minkin2, Keith E. Prater2, John P. Biggerstaff2, John R. Dunlap3 and Paul Dalhaimer

Muday G, Rahman A., Binder BM (2012) Auxin and Ethylene: Collaborators or Competitors? Trends in Plant Science. 17: 181-195.

Peckys, D.B. and P. Mazur. 2012. Regulatory volume decrease in COS-7 cells at 22 °C and influence on the Boyle van’t Hoff relation and the determination of the osmotically inactive volume. Cryobiology (Accepted 26 Mar 2012)

A. K. Sangha, L. Petridis, J. C. Smith, A. Ziebell and J. M. Parks. Molecular simulation as a tool for studying lignin Environmental Progress and Sustainable Energy. 31 (1) 47-54 (2012)

Seki, S. and P. Mazur. 2012. Ultra-rapid warming yields high survival of mouse oocytes cooled to –196°C in dilute vitrification solutions. PLoS One (Accepted 29 March 2012)

Seki, S., B. Jin, and P. Mazur. 2012. Ultra-rapid warming yields yields high functional survival of 8-cell mouse embryos even when suspended in a half-strength vitrification solution and cooled at moderate rates to –196°C. Biol. Reprod. (submitted 04/10/12).

N. Smolin, R. Biehl, G.R. Kneller, D. Richter & J.C. Smith. Functional Domain Motions in Proteins on the ~1-100ns Timescale: Comparison of Neutron Spin Echo Spectroscopy of Phosphoglycerate Kinase with Molecular Dynamics Simulation. Biophysical Journal. 102(5), 1108-1117 (2012).

K. Voltz, J. Trylska, N. Calimet, J.C. Smith and J. Langowski. Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophysical Journal. 102(4):849-58 (2012)

2011

E. Balog, D. Perahia, J.C. Smith & F. Merzel. (2011). Vibrational Softening of a Protein on Ligand Binding. Journal of Physical Chemistry B. 115(21):6811-7.

Behrens, M. A., Botkjaer, K. A., Goswami, S., Oliveira, C. L., Jensen, J. K., Schar, C. R., Declerck, P. J., Peterson, C. B., Andreasen, P. A., and Pedersen, J. S. (2011) J Mol Biol 411, 417-429. “Activation of the zymogen to urokinase-type plasminogen activator is associated with increased interdomain flexibility”

M. Biswas, K. Voltz, J. C. Smith and J. Langowski. Role of Histone Tails in Structural Stability of the Nucleosome. PLoS Computational Biology. 7 (12) e1002279  (2011)

A.N. Bondar, S. Fischer & J.C. Smith. (2011). Water pathways in the bacteriorhodopsin proton pump Journal of Membrane Biology: 239 1 73

A.-N. Bondar, M Knapp-Mohammady, S. Fischer & J.C. Smith. Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins. Theoretical Chemistry Accounts. 130 4-6, 1169-1183 (2011)

S. D. Brown, A. M. Guss, T.V. Karpinets, J. M. Parks, N. Smolin, S. Yang, M. L. Land, D. M. Klingeman, A. Bhandiwad, M. Rodriguez, B.  Raman, X. Shao, J. R. Mielenz, J. C.. Smith, M. Keller & L. R. Lynd. (2011). Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proceedings of the National Academy of Sciences (U.S.A.). 108(33):13752-7.

B. Collignon, R. Schulz, J.C. Smith and J. Baudry (2011) Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J. Comput. Chem., 32(6), 1202–1209

I. Daidone, A. Di Nola & J.C. Smith. (2011). Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophysical Journal. 100(12):3000-7

Duff, Jr., M.R., Grubbs, J., and Howell, E.E. (2011) “Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity,” Journal of Visualized Experiments

Edwards, A. N., P. Siuti, A. N. Bible, G. Alexandre, S. T. Retterer, M. J. Doktycz and J. L. Morrell-Falvey (2011). Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy. FEMS Microbiology Letters 314(2):131-139.

S. R. Ellingson and J. Baudry (2011). High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud. ECMLS 2011 Proceedings of the second international workshop on Emerging computational methods for the life sciences.

Hembree_Baudry_11

(From Hembree and Baudry. 2010)

Fairman, J. W., Wijerathna, S. R., Ahmad, M. F., Xu, H., Nakano, R., Jha, S., Prendergast, J., Welin, R. M., Flodin, S., Roos, A., Nordlund, P., Li, Z., Walz, T., and Dealwis, C. G. (2011) Nat Struct Mol Biol 18, 316-322. “Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization”

A. Godec, J.C. Smith and F. Merzel. Increase of both order and disorder in first hydration shell with increasing solute polarity. Physical Review Letters. 107, 267801 (2011).

Grubbs, J.Rahmanian, S., DeLuca, A., Padmashali, C., Jackson, M., andHowell, E.E. (2011) “Thermodynamicsand Solvent Effects on Substrate andCofactor Binding in E. coli Chromosomal Dihydrofolate Reductase,”Biochemistry 50, 3673-3685.

H.B. Guo, J.M. Parks, A. Johs & J.C. Smith. Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage in Modeling of Molecular Properties. Ed. Comba Wiley. 311–324, (2011).

W.I. Hembree and J. Baudry (2011) Three-dimensional mapping of micro-environmental control of methyl rotational barriers. J Phys Chem B. 2011 115(26), 8575-80

L. Hong, B. Lindner, N. Smolin, A. Sokolov & J.C. Smith. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Physical Review Letters. 107, 148102 (2011)

Hu, X., Elgobashi-Meinhardt, N., Gembris, D. & Smith, J.C. Response of Water to Electric Fields at Temperatures below the Glass Transition: A Molecular Dynamics Analysis. Journal of Chemical Physics. 135(13):134507 (2011).

Hu, X., Norris, A., Baudry, J. and Serpersu, E. H. (2011) Coenzyme-A Binding to the Aminoglycoside Acetyltransferase (3)-IIIb Increases Conformational Sampling of Antibiotic Binding Site. Biochemistry 50,10559-10565.

Iwuchukwu, I.J., Iwuchukwu, E., Le, R., Paquet, C., Sawhney, R., Bruce, B., and Frymier, P. (2011) Optimization of photosynthetic hydrogen yield from platinized photosystem I complexes using response surface methodology.International Journal of Hydrogen Energy, 36(18), 11684-11692.

Jensen, J. K., Thompson, L. C., Nissen, P., Gettins, P. G. W., Peterson, C. B., Andreasen, P. A., and Morth, J. P. (2011) J. Biol. Chem., 286, 29709-29717. “Crystal Structure of Plasminogen Activator Inhibitor-1 in a Metastable Active Conformation.”

A. Johs, I.M. Harwood, J.M. Parks, J.C. Smith, L. Liang & S.M. Miller. Structural characterization of intramolecular Hg2+ transfer between flexibly-linked domains of mercuric ion reductase. Journal of Molecular Biology. 413(3):639-56 (2011).

Karve R., Liu W., Willet S. G., Torii K.U., and Shpak E. D. (2011). The presence of multiple introns is essential forERECTA expression in Arabidopsis.RNA (Aug 31. [Epub ahead of print])

publication3

(From Li, T, et al. 2011)

Kim H, Helmbrecht E, Stalans MBSchmitt CLPatel N, Wen C-K, Wang W, Binder BM (2011) Domain Requirements for Different Roles of the ETR1 Ethylene Receptor. Plant Physiology. 156, 417-429.

Klein, H., Cheng, X., Smith, J.C., & Shen, T. (2011) Transfer matrix approach to the hydrogen-bonding incelluloseI-a fibrils describes the recalcitrance to thermal deconstruction. Journal of Chemical Physics. 135, 085106 (2011)

Lee G, Wang Z, Sehgal R, Chen C-H, Kikuno K, Hay B, Park JH (2011) Drosophila caspases involved in developmentally regulated programmed cell death of peptidergic neurons during early metamorphosis. Journal of Comparative Neurology, 519, 34-48.

Li, L-Y,  Jiang, XL, Guan, HS, Wang, P., Guo, H. (2011) “Three Alginate Lyases from Marine Bacterium
Pseudomonas fluorescens HZJ216: Purification and Characterization” Appl. Biochem. Biotechnol.
164, 305-317.

Tian Li, Won-Gyu Choi, Ian S. WallaceJerome Baudry, and Daniel M. Roberts (2011) Arabidopsis thaliana NIP7;1: An Anther-Specific Boric Acid Transporter of the Aquaporin Superfamily Regulated by an Unusual Tyrosine in Helix 2 of the Transport Pore. Biochemistry 50(31), 6633–6641

“Active site hydration and water diffusion in cytochrome P450cam: a highly dynamic process.” Y. Miao and J. Baudry  Biophysical Journal, (2011), 101 (6): 1493-1503.  This paper has received publicity through NICS, ORNL and UT’s Quest magazine

B. Mostofian, J. C. SmithX. Cheng The Solvation Structures of Cellulose Microfibrils in Ionic Liquids Interdisciplinary Sciences- Computational Life Sciences 3: 1-13 (2011)

Mukherjee, D., Vaughn, M., Khomami, B., and Bruce, B.D. (2011) Modulation of cyanobacterial photosystem I deposition properties on alkanethiolate Au substrate by various experimental conditions. Colloids and Surfaces (Biointerfaces). 88(1):181-90.

T. Neusius, I. Daidone, I. Sokolov & J.C. Smith. (2011). Configurational subdiffusion of peptides: A Network Study. Physical Review E. 83, 021902

F. Noe, S. Doose, I, Daidone, M, Lollmann, M. Sauer, J.D. Chodera & J.C. Smith. (2011). Dynamical Fingerprints: Probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proceedings of the National Academy of Sciences (U.S.A.) 108(12):4822-7.

Norris, A. L. and Serpersu, E. H. (2011) Antibiotic Selection by the Promiscuous Aminoglycoside Acetyltransferase-(3)-IIIb is Thermodynamically Achieved Through Control of Solvent Rearrangement. Biochemistry 50,9309-9317.

E. ParkA. Nebenführ (2011) Cytoskeleton and Root Hair Growth. in: The Plant Cytoskeleton (Ed. B. Liu) Advances in Plant Biology 2:259-275.

L. Petridis, S.V. Pingali, V. Urban, W. T. Heller,  H. M. O’ Neill, M. Foston, A. Ragauskas & J.C. Smith. (2011). Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Physical Review E. 83(6-1):061911.

L. Petridis, R. Schulz & J.C. Smith. Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics. Journal of the American Chemical Society 133 (50)  20277-20287 (2011)

L. Petridis, J. Xu, M. Crowley, J.C. Smith and X. Cheng. (2011). Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes In  Computational Modeling in Lignocellulosic Biofuel Production Eds: M. R. Nimlos, M. F. Crowley American Chemical Society Symposium Series 1052, 55-73

S. V. Pingali, H. M. O’neil, J. McGaughey, V. S. Urban, C. S. Rempe, L. Petridis, J. C. Smith, B. R. Evans  and W. T. Heller. Small-angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reeseicellobiohydrolase I: Implications for enzymatic activity. Journal of Biological Chemistry. 286(37):32801-9 (2011).

V. Philip, J. Harris, R, Adams, D. Nguyen, J. Spiers, J. Baudry, E.E. Howell and R.J. Hinde. (2011) A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-pairs. Biochemistry, 50(14), 2939-2950 (Note: this paper was chosen to be highlighted on the journal home page)

J-H Prinz, J. Chodera, V. Pande, W. Swope, J.C. Smith & F. Noe. (2011). Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. Journal of Chemical Physics. 134, 244108.

J.-H. Prinz, M. Held, J.C. Smith & F. Noe. Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Modeling and Simulation. 9(2)  545-567 (2011)

publication2

(From V.Philip, et al. 2011)

Roy, B., Copenhaver, G.P., and von Arnim, A.G. (2011). Fluorescence-tagged transgenic lines reveal genetic defects in pollen growth – application to the eIF3 complex. Plos One 6:e17640.

Ruiqiang C, Binder BM, Garrett WM, Tucker ML, Cooper B, and Chang C (2011) Proteomic Responses in Arabidopsis thaliana Seedlings Treated with Ethylene.Molecular Biosystems. In press. DOI: 10.1039/c1mb05159h

M. Saharay, H.-B. Guo, J.C. Smith and H. Guo. QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates. In  Computational Modeling in Lignocellulosic Biofuel Production Eds: M. R. Nimlos, M. F. Crowley. American Chemical Society Symposium Series 1052, 135-154 (2011).

J.C. Smith, M. Krishnan, L. Petridis, N. Smolin. Integration of Neutron Scattering with Computer Simulation to Study the Structure and Dynamics of Biological Systems in Dynamics of Biological Macromolecules by Neutron Scattering. Eds. Magazu and Migliardo. Bentham. 99-108 (2011)

T. Splettstoesser, K.C. Holmes, F. Noe & J.C. Smith. (2011). Structural Modeling and Molecular Dynamics Simulation of the Actin Filament PROTEINS: Structure, Function, and Bioinformatics. 79(7):2033-43.

G. Srinivas, X. Cheng & J.C. Smith. A solvent-free coarse-grain model for crystalline and amorphous cellulose fibrils” Journal of Computational Chemistry. 7 (8) 2539-2548 (2011)

Suresh, A. K., Doktycz, M. J., Wang, W., Moon, Ji-Won., Gu, B.,  Meyer III H. M.,  Hensley D. K., Allison, D. P., Phelps T. J., Pelletier D. A. (2011) “Monodispersed biocompatible siilver sulfide nanoparticles; facile extracellular biofabrication using the ?-proteobacterium.” Shewanella oneidensis. Acta Biomaterialia, 7(12): 4253-4258.

Suresh A. K., Pelletier D. A., Wang W., Broich M. L., Gu B. H., Allison D. P., Joy D. C., Phelps T. J., Docktyz M. J. (2011), “Biofabrication of Discrete Spherical Gold Nanoparticles using Metal-reducing Bacterium Shewanella Oneidensis, Acta Biomater. 7, 2148-2152

Thompson, L. C., Goswami, S., Ginsberg, D. S., Day, D. E., Verhamme, I. M. and Peterson, C. B. (2011) Metals Affect the Structure and Activity of Human Plasminogen Activator Inhibitor-1: I. Modulation of stability and protease inhibition. Protein Sci. 20, 353-365.

Thompson, L. C.Goswami, S., and Peterson, C. B. (2011) Metals Affect the Structure and Activity of Human Plasminogen Activator Inhibitor-1: II. Binding Affinity and Conformational Effects. Protein Sci. 20, 366-378.

L. Thukral, I. Daidone & J.C. Smith. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations. PLoS Computational Biology. 7(9):e1002137 (2011).

Tsai, J. H., and McKee, B. D. (2011) Homologous pairing and the role of pairing centers in meiosis. J Cell Sci 124, 1955-1963.

Tsai J. H., Yan R, McKee B. D. (2011). Homolog pairing and sister chromatid cohesion in heterochromatin in Drosophila male meiosis I. Chromosoma 120:335-351.

J. Ulmschneider, J.C. Smith, S. White & M. Ulmschneider. In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides Under Equilibrium Conditions. Journal of the American Chemical Society. 133(39):15487-95 (2011).

Wang, S.S., Shen, T., & Wolynes, P.G. (2011) The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics, J. Chem. Phys. 134(1), 014510

Wieninger, S. A, Serpersu, E. H. and Ullmann, G. M. (2011) ATP Binding Enables Broad Antibiotic Selectivity of Aminoglycoside Phosphotransferase(3?)-IIIa– An Elastic Network Analysis. J. Mol. Biol. 409, 450-465.

Wright, E., Busby, S.A., Wisecarver, S.Vincent, J., Griffin, P.R., Fernandez, E. J. (2011) Helix 11 Dynamics Is Critical for Constitutive Androstane Receptor Activity. Structure (Cell Press) 19(1), 37-44.

Wright, E. and Serpersu, E. H. (2011) Effects of Proton Linkage on Thermodynamic Properties of Enzyme–Antibiotic Complexes of the Aminoglycoside Nucleotidyltransferase(2?)-Ia.  J. Thermodyn.  Catal.  2,105-111.

Xu, Q., Yao, J-Z., Wlodawer, A. and Guo, H. (2011) “Clarification of the Mechanism of Acylation Reaction and Origin of Substrate Specificity of the Serine-Carboxyl Peptidase Sedolisin through QM/MM Free Energy Simulations” J. Phys. Chem. B, 115, 2470-2476.

Yao, J., Nellas, R., Glover, M.M., & Shen, T. (2011) Stability and sugar recognition ability of ricin-like carbohydrate binding domains. Biochemistry 50(19), 4097-4104.

Yao, J-Z., Xu, Q., Chen, F. and Guo, H. (2011) “QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity” J. Phys. Chem. B.115, 389-396.

Zmijewski, J. W., Bae, H. B., Deshane, J. S., Peterson, C. B., Chaplin, D. D., and Abraham, E. (2011) Am J Physiol Lung Cell Mol Physiol 301, L247-254. “Inhibition of neutrophil apoptosis by PAI-1”
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M. Zahran, T. Berezniak, P. Imhof & J.C. Smith. Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease. FEBS Letters. 585 2739–2743 (2011).

 

2010

Alexandre, G. (2010) Coupling metabolism and chemotaxis-dependent behaviours by energy taxis receptors. Microbiology 156, 2283-2293

Banerjee, P., Schoenfeld, B.P., Bell, A.J., Choi, C.H., Bradley, M.P., Hinchey P., Kollaros, M., Park J.H., McBride, S.M.J., and Dockendorff, T.C. (2010) Short and long-term memory are modulated by multiple isoforms of the fragile X mental retardation protein. J. Neurosci. 30, 6782-6792.

Bellesia, G., Asztalos, A., Shen, T., Langan, P., Redondoe, A., & Gnanakaran, S. (2010) Computational studies of crystalline cellulose and its degradation by enzymes, Acta Cryst. D66 1184-1188

Figure 6

(From Binder BM, Rodriguez FI, Bleecker AB, 2010)

Berezniak T, Zahran M, Imhof P, Jaeschke A, and Smith J.C.(2010) Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme. Journal of the American Chemical Society, 132(36),12587–12596.

Binder BM, Rodriguez FI, Bleecker AB. (2010). The Copper Transporter RESPONSIVE-TO-ANTAGONIST1 (RAN1) is Essential for the Biogenesis of Ethylene Receptors in Arabidopsis. Journal of Biological Chemistry. 285, 37263-37270

Bondar AN, Smith J.C., and Elstner M. Mechanism of a Proton Pump Analyzed with Computer Simulations. Theoretical Chemistry Accounts, 125(3-6):353-363. (2010)

Brager AJ, Ruby CL, Prosser RA and Glass JD (2010) Chronic ethanol disrupts circadian photic entrainment and daily locomotor activity in the mouse. Alcohol.Clin.Expt.Res. 34: 1266-1273.

Buchan, A., Crombie, B. and G. M. Alexandre (2010) Temporal dynamics and genetic diversity of chemotactic-competent microbial populations in the rhizosphere. Environnmental Microbiology12 (12): 3171-3184.

Chen Y-F, Gao Z, Kerris RJ, Wang W, Binder BM, Schaller GE (2010) Ethylene Receptors Function as Components of High-Molecular-Mass Protein Complexes in Arabidopsis. PLoS ONE. 5:e8640. doi:10.1371/journal.pone.0008640.

Cho D, Zheng M, Min C, Ma L, Kurose H, Park JH, Kim K-M. 2010. Agonist-induced endocytosis and receptor phosphorylation mediate resensitization of dopamine receptors. Molecular Endocrinology 24: 574-586.

Chu, Y., Xu, Q and Hong Guo (2010) Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations: What Causes the Stop of Methyl Addition during Histone Lysine Methylation? J. Chem. Theory Comput., 2010, 6, 1380-1389.

Chung, E., H. Kweon, S. Yiacoumi, I. Lee, D.C. Joy, A.V. Palumbo, and C. Tsouris, “Adhesion of Spores of Bacillusthuringiensis on a Planar Surface,” Environmental Science & Technology, 44, 290-296 (2010)

Daidone I, Neuweiler H, Doose S, Sauer M, and Smith J.C. Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains. PLoS Computational Biology, 6(1):e1000645. (2010)

Human TLRs 10 and 1 share common mechanisms of innate immune sensing but not signaling. Y. Guan, D.R.E. Ranoa, S. Jiang,. S.K. Mutha, X. Li, J. Baudry, and R.I. Tapping. Journal Immunol. (2010)  184: 5094–5103

Feng, J., Grubbs, J., Dave, A., Goswami, S.Horner, CG., and Howell, E.E. (2010) Radical Redesign of a Tandem Array of Four R67 Dihydrofolate Reductase Genes Yields a Functional, Folded Protein Possessing 45 Substitutions. Biochemistry 49, 7384–7392.

Glass D, Krishnan M, Nutt D, and Smith J.C. Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models. Journal of Chemical Theory and Computation, 6(4):1390-1400. (2010)

Guo HB, Johs A, Parks J, Oliff L, Miller S, Summers A, Liang L, and Smith J.C. Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II). Journal of Molecular Biology, 398(4), 555-568. (2010)

Hammer SB, Ruby CL, Brager AJ, Prosser RA and Glass JD (2010) Environmental modulation of alcohol intake in hamsters: effects of wheel-running and constant light exposure. Alcohol.Clin.Expt.Res 34, 1651-1658.

Hwang, J. H., Ellingson, S. R., and Roberts, D. M. (2010) FEBS Lett 584, 4339-4343. “Ammonia permeability of the soybean nodulin 26 channel”

Iwuchukwu, I., Vaughn, M., Myers, N., O’Neill, H., Frymier, P., & Bruce, B. D. (2010) Selfassembled Photosynthetic Nanoparticle for Cell-free Hydrogen Production. Nature Nanotechnology, 5, 73-79.

Kamath, G., Howell, E.E. and Agarwal, P.K. (2010) The Tail Wagging the Dog: Insights into Catalysis in R67 Dihydrofolate Reductase. Biochemistry 49, 9078–9088.

Kim, B.H. and von Arnim, A.G. (2010). Molecular approaches to the study of plant development. In: Plant Development and Biotechnology, Robert N. Trigiano and Dennis J. Gray, eds. Taylor and Francis Group, Boca Raton, FL.

J.-F. Li, A. Nebenführ (2010) FAST Technique for Agrobacterium-Mediated Transient Gene Expression in Seedlings of Arabidopsis and Other Plant Species. Cold Spring Harbor Protocols doi:10.1101/pdb.prot5428

Lopez M, Kurkal-Siebert V, Dunn R, Tehei M, Finney J, Smith J.C., and Daniel R. Activity and Dynamics of an Enzyme, Pig Liver Esterase, in Near-Anhydrous Conditions. Biophysical Journal, 99(8):L62-L64. (2010)

Johnson, Q., Doshi, U., Shen, T., & Hamelberg, D. (2010) Water’s contribution to the energetic roughness from peptide dynamics. J. Chem. Theo. Comput. 6(9), 2591-2597.

Joy, D C, Michael J, Griffin B J, (2010), “Evaluating SEM Performance from the Contrast Transfer Function”, Proc. SPIE 7638, 3J1 – 8(429)

Joy, D C, “Protons, Ions, Electrons and the future of the SEM”, J.Phys:Conference Series 241, 012002 (2010)  (see http://iopscience.iop.org/1742-6596/241/1/01002)

publication6

(From Masalkar, P et al., 2010)

Lynch, R.M., Rong, R., Li, B., Shen, T., Honnen, W., Mulenga, J., Allen, S., Pinter, A., Gnanakaran, S., Derdeyn, C. A. (2010) Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection, Virol. 404(1), 59-70.

Masalkar, P., Wallace, I. S., Hwang, J. H., and Roberts, D. M.(2010) “Interaction of cytosolic glutamine synthetase of soybean root nodules with the C-terminal domain of the symbiosome membrane nodulin 26 aquaglyceroporin. J Biol Chem 285, 23880-23888. (Note: this paper was selected for as a featured “paper of the week”)

R. Morra, S. Kuruganti, V. Lam, J. C. Lucchesi and R. Ganguly (2010) Functional analysis of the cis-acting elements responsible for the induction of the Cyp6a8 and Cyp6g1 genes of Drosophila melanogaster by DDT, phenobarbital and caffeine. Insect Molecular Biology 19, 121–130

Moritsugu K, Njunda B, and Smith J.C. Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding. Journal of Physical Chemistry B, 114(3):1479–1485. (2010)

Mukherjee, D., May, M., Vaughn, M., Bruce, B.D. and Khomami, B. (2010) Controlling the morphology of Photosystem I assembly on thiol-activated Au substrates. Langmuir, 26(20):16048-54.

Norris, A.L., Özen, C., and Serpersu, E.H. (2010) Thermodynamics and Kinetics of Antibiotic Association with the Aminoglycoside Acetyltransferase(3)-IIIb: A Resistance Causing Enzyme. Biochemistry. 49, 4027-4035.

Norris, A.L. and Serpersu, E.H. (2010) Coenzyme A Interactions with the Aminoglycoside Acetyltransferase(3)-IIIb and Thermodynamics of a Ternary System. Biochemistry. 49, 4036-4042.

John Notte IV, Raymond Hill, Sean McVey, Ranjan Ramachandra, Brendan Griffin, David Joy, (2010) Diffraction Imaging in a He+ Ion Beam Scanning Transmission Microscope. Microscopy and Microanalysis 16, 1 – 5

Pelletier D A, Suresh A K, Holton G A,  McKeown C K, Wang W, Gu B, Motensen N P, Allison DP, Joy D C, Allison M R, Brown S D, Phelps T J, and Doctycz M J, (2010), “Effect of Engineered Cerium Oxide Nanoparticles on Bacterial Growth and Viability”, Applied and Environmental Microbiology, 76, 7981-7989

Roberts DMHwang JH and Choi WG (2010) Strategies for adaptation to waterlogging and hypoxia in nitrogen fixing nodules of legumes. in Waterlogging Signalling and Tolerance in Plants. (S. Mancuso and S. Shabala, eds.). Springer-Verlag Berlin Heidelberg, pp. 37-59.

Roy, B., Vaughn, J.N., Kim, B.H.Zhou, F., Gilchrist, M.A., and von Arnim, A.G. (2010). The h subunit of eIF3 controlsreinitiation on mRNAs harboring upstream open reading frames. RNA 16, 748-761.

Saharay M, Guo H, and Smith J.C. Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS. PLos ONE, 5(10):e12947. (2010)

Saharay, M., Guo, H-B., Smith, J.C. and Guo, H. (2010) “QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates” in Computational Modeling in Lignocellulosic Biofuel ProductionEditor(s): Mark R. Nimlos and Michael F. Crowley, ACS Symposium Series, Volume 1052, Chapter 7, Page 135-154.

Seki, S. and P. Mazur. (2010) The temperature and type of intracellular ice formation in preimplantation mouse embryos as a function of the developmental stage. Biology of Reproduction 82, 1198-1205.

Serpersu, E.H., Özen, C., Norris, A.L., Steren, C., and Whittemore, N. (2010) Backbone Resonance Assignments of a Promiscuous Aminoglycoside Antibiotic Resistance Enzyme: the Aminoglycoside Phosphotransferase(3’)-IIIa.Biomol. NMR Assign. 4, 9-12.

Schoborg TALabrador M. (2010) The phylogenetic distribution of non-CTCF protein insulators is limited to insects and reveals that insulator protein BEAF-32 is Drosophila lineage specific. Journal of Molecular evolution. Jan;70(1):74-84. Epub 2009 Dec 19.

Smith DA, Joy DC, and Rack P D, (2010) Monte Carlo Simulation of Helium Ion Beam Induced Deposition, Nanotechnology,21, 175302 (8pp)

Stahle, M.I., Kuehlich, J., Staron, L.A.von Arnim, A.G., and Golz, J.F. (2010). Role of YABBYs and the transcriptional co-repressors LEUNIG and LEUNIG HOMOLOG in maintaining leaf polarity and meristem activity in Arabidopsis. Plant Cell 21: 3105-3118.

Anil  K. Suresh,  Dale  A. Pelletier,  Wei  Wang, J I  Wonmoon  Baohuagu,  Ninnell, P. Mortensen, David  P. Allison,David C Joy, Tommy J. Phelps, and Mitchel J  Doktycz (2010), “Silver Nanocrystallites: Biofabrication using Shewanella oneidensis, and an Evaluation ofTheir Comparative Toxicity on Gram-negative and Gram-positiveBacteria”, Environmental Science and Technology 44, 5210-5215

Tsai, J. H., Yan, R., and McKee, B. D. (2010) Homolog pairing and sister chromatid cohesion in heterochromatin in Drosophila male meiosis I. Chromosoma 120, 335-351.

Ulmschneider M, Doux JP, Killian J, Smith J.C., and Ulmschneider J. Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides. Journal of the American Chemical Society, 132(10):3452–3460. (2010)

Ulmschneider M, Smith J.C., and Ulmschneider J. Peptide Partitioning Properties from Direct Insertion Studies. Biophysical Journal, 98(12):L60-L62. (2010)

Wallace HA, Plata MP, Kang HJ, Ross M, Labrador M. (2010) Chromatin insulators specifically associate with different levels of higher order chromatin organization in Drosophila. Chromosoma. Apr;119(2):177-94. Epub 2009 Dec 23.

Wang, W., Howe J Y, Li Y, Qiu X, Joy D C, Paranthaman MP, Doktycz M J, and Gu B,  (2010),”A surfactant and template-free route for synthesizing ceria nanocrystals with tunable morphologies”, J.of Materials Chemistry, 20, 7776-778

Xie, Z., Ulrich, L. E., Zhulin, I. B. and G. Alexandre (2010) PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis. Proceedings of the National Academy of Sciences USA 107(5), 2235-2240

Xu J, and Smith J.C. Probing the Mechanism of Cellulosome Attachment to the Clostridium thermocellum Cell Surface: Computer Simulation of the Type II Cohesin-Dockerin Complex and Its Variants. Protein Engineering, Design and Selection, 23(10):759-768. (2010)

Xu, Q., Li, L. and Hong Guo (2010) Understanding the mechanism of deacylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As: insights from QM/MM free energy simulations, J. Phys. Chem. B., Publication Date (Web): July 26, 2010

publication4

(From Yan, R., et al. 2010)

Xu, Q., Ye, X., Li, L.-Y, Cheng, Z. M., and Hong Guo (2010) Structural Basis for the Action of Xyloglucan Endotransglycosylases/hydrolases: Insights from Homology Modeling. Interdiscip. Sci., 2010; 2: 133-139.

Yan, R., Thomas, S. E., Tsai, J. H., Yamada, Y., and McKee, B. D.(2010) SOLO: a meiotic protein required for centromere cohesion, coorientation, and SMC1 localization in Drosophila melanogaster. J Cell Biol 188, 335-349.

Yang S, Land M, Klingeman D, Pelletier D, Lu TY, Martin S, Guo HB, Smith J.C., and Brown S. (2010) A Paradigm for Strain Improvement Identifies Sodium Acetate Tolerance Loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences USA, 107(23):10395-10400.

Zahran M, Daidone I, Smith J.C., and Imhof P.Mechanism of DNA Recognition by the Restriction Enzyme EcoRV. Journal of Molecular Biology, 401(3):415-432. (2010)

Zhou, F., Roy, B., and von Arnim, A.G. (2010). The translation initiation factor eIF3h cooperates with the large ribosomal subunit in mediating translation reinitiation on mRNAs harboring upstream open reading frames. BMC Plant Biology 10:193

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