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Tag pka [182 articles]

Recent papers classified by the tag pka.
  • A buried lysine that titrates with a normal pKa : Role of conformational flexibility at the protein-water interface as a determinant of pKa values
    Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 833-845.
    by Michael J Harms, Jamie L Schlessman, Michael S Chimenti, Gloria R Sue, Ana Damjanovic, Garcia-Moreno
    posted to prediction pka by zfekete on 2008-09-13 10:22:42 as **** along with 3 people and 2 groups sobolevnrm skoddet RamuAnandakrishnan baker-group Nielsen group
  • Benchmarking pKa prediction
    BMC Biochemistry, Vol. 7 (02 June 2006), 18.
    by Matthew N Davies, Christopher P Toseland, David S Moss, Darren R Flower
    posted to prediction pka by zfekete on 2008-09-13 10:11:19 as **** along with 4 people bicko cat_worth sim82 RamuAnandakrishnan
  • Predicting Hydrogen-Bond Strengths from Acid−Base Molecular Properties. The pKa Slide Rule: Toward the Solution of a Long-Lasting Problem
    Acc. Chem. Res. (16 October 2008)
    by Paola Gilli, Loretta Pretto, Valerio Bertolasi, Gastone Gilli
    posted to pka hb by yzlab on 2008-10-19 03:33:06 as ** along with 3 people zubatyuk bongo paulschlesinger
  • Neuromodulation of Na(+) Channel Slow Inactivation via cAMP-Dependent Protein Kinase and Protein Kinase C.
    Neuron, Vol. 49, No. 3. (2 February 2006), pp. 409-420.
    by Y Chen, FH Yu, DJ Surmeier, T Scheuer, WA Catterall
    posted to channel pka pkc by ykom on 2006-02-02 00:40:38 as **
  • AKAP150-anchored PKA activity is important for LTD during its induction phase
    J Physiol, Vol. 586, No. 17. (1 September 2008), pp. 4155-4164.
    by Yuan Lu, Mingxu Zhang, Indra A Lim, Duane D Hall, Margaret Allen, Yuliya Medvedeva, Stanley G Mcknight, Yuriy M Usachev, Johannes W Hell
    posted to synaptic_plasticity pka 090908 by tyrell_turing on 2008-09-08 18:21:02 as **
  • Design and synthesis of novel 6,7-imidazotetrahydroquinoline inhibitors of thymidylate synthase using iterative protein crystal structure analysis.
    J Med Chem, Vol. 35, No. 5. (6 March 1992), pp. 847-858.
    by SH Reich, MA Fuhry, D Nguyen, MJ Pino, KM Welsh, S Webber, CA Janson, SR Jordan, DA Matthews, WW Smith
    posted to pka tgt by trmr on 2007-06-28 18:06:36 as **
  • Development, validation, and application of adapted PEOE charges to estimate p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values of functional groups in protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2006), NA.
    by Paul Czodrowski, Ingo Dramburg, Christoph A Sotriffer, Gerhard Klebe
    posted to pka by trmr on 2006-09-06 11:54:35 as ** along with 1 person mschofie
  • HIP/PAP stimulates liver regeneration after partial hepatectomy and combines mitogenic and anti-apoptotic functions through the PKA signaling pathway
    FASEB J., Vol. 17, No. 11. (1 August 2003), pp. 1441-1450.
    by Marie-Therese Simon, Alain Pauloin, Guillaume Normand, Hanh-Tu Lieu, Helene Mouly, Gerard Pivert, Francoise Carnot, Guilherme J Tralhao, Christian Brechot, Laurence Christa
    posted to function hip pap pka signal by Trillian on 2006-10-03 10:46:50 as **
  • Calculating pKa values in enzyme active sites
    Protein Sci, Vol. 12, No. 9. (1 September 2003), pp. 1894-1901.
    by Jens E Nielsen, Andrew J Mccammon
    posted to catalysis enzyme pka by tny on 2007-04-02 13:56:40 as ** along with 3 people and 1 group boris_aguilar RamuAnandakrishnan qaiser_fatmi group
  • PKA mediates the effects of monoamine transmitters on the K+ current underlying the slow spike frequency adaptation in hippocampal neurons.
    Neuron, Vol. 11, No. 6. (December 1993), pp. 1023-1035.
    by P Pedarzani, JF Storm
    posted to bar ca1 pka by tmk on 2006-06-29 10:03:10 as ****
  • Ca(2+)-Stimulated Adenylyl Cyclases Regulate ERK-Dependent Activation of MSK1 during Fear Conditioning.
    Neuron, Vol. 53, No. 1. (4 January 2007), pp. 79-89.
    by CB Sindreu, ZS Scheiner, DR Storm
    posted to pka erk ca1 by tmk on 2007-01-18 06:04:58 as read
  • Both protein kinase A and mitogen-activated protein kinase are required in the amygdala for the macromolecular synthesis-dependent late phase of long-term potentiation.
    J Neurosci, Vol. 20, No. 17. (1 September 2000), pp. 6317-6325.
    by YY Huang, KC Martin, ER Kandel
    posted to amygdala la ltp mapk pka by tmk on 2006-06-29 12:28:35 as read
  • Regulation of hippocampal synaptic plasticity by cyclic AMP-dependent protein kinases.
    Prog Neurobiol, Vol. 71, No. 6. (December 2003), pp. 401-437.
    by PV Nguyen, NH Woo
    posted to ca1 ltp pka review by tmk on 2006-08-06 06:54:02 as **
  • Beta-adrenergic regulation of synaptic NMDA receptors by cAMP-dependent protein kinase.
    Neuron, Vol. 16, No. 2. (February 1996), pp. 415-421.
    by IM Raman, G Tong, CE Jahr
    posted to bar ca1 nmdar pka by tmk on 2006-06-21 11:38:51 as read
  • Inhibition of the cAMP pathway decreases early long-term potentiation at CA1 hippocampal synapses.
    J Neurosci, Vol. 20, No. 12. (15 June 2000), pp. 4446-4451.
    by NA Otmakhova, N Otmakhov, LH Mortenson, JE Lisman
    posted to ca1 ltp pka by tmk on 2006-06-13 11:24:32 as **
  • Downregulation of transient K+ channels in dendrites of hippocampal CA1 pyramidal neurons by activation of PKA and PKC.
    J Neurosci, Vol. 18, No. 10. (15 May 1998), pp. 3521-3528.
    by DA Hoffman, D Johnston
    posted to pka ca1 acurrent by tmk on 2007-01-19 11:34:36 as **
  • Regulation of distinct AMPA receptor phosphorylation sites during bidirectional synaptic plasticity.
    Nature, Vol. 405, No. 6789. (22 June 2000), pp. 955-959.
    by HK Lee, M Barbarosie, K Kameyama, MF Bear, RL Huganir
    posted to ampar_p ca1 kt pka by tmk on 2006-12-30 03:29:39 as **
  • Postsynaptic induction and PKA-dependent expression of LTP in the lateral amygdala.
    Neuron, Vol. 21, No. 1. (July 1998), pp. 169-178.
    by YY Huang, ER Kandel
    posted to la ltp pka by tmk on 2006-07-03 02:05:22 as read
  • Gating of CaMKII by cAMP-regulated protein phosphatase activity during LTP.
    Science, Vol. 280, No. 5371. (19 June 1998), pp. 1940-1942.
    by RD Blitzer, JH Connor, GP Brown, T Wong, S Shenolikar, R Iyengar, EM Landau
    posted to ca1 camkii ltp pka by tmk on 2006-06-29 12:00:19 as read
  • Involvement of a postsynaptic protein kinase A substrate in the expression of homosynaptic long-term depression.
    Neuron, Vol. 21, No. 5. (November 1998), pp. 1163-1175.
    by K Kameyama, HK Lee, MF Bear, RL Huganir
    posted to ampar_p ca1 kt pka by tmk on 2006-12-30 03:28:39 as **
  • Postsynaptic cAMP pathway gates early LTP in hippocampal CA1 region.
    Neuron, Vol. 15, No. 6. (December 1995), pp. 1403-1414.
    by RD Blitzer, T Wong, R Nouranifar, R Iyengar, EM Landau
    posted to ca1 ltp pka by tmk on 2006-06-29 11:59:47 as read
  • Protein kinase A regulates calcium permeability of NMDA receptors
    Nature Neuroscience, Vol. 9, No. 4. (12 March 2006), pp. 501-510.
    by Arvydas V Skeberdis, Vivien Chevaleyre, Geoffrey C Lau, Jesse H Goldberg, Diana L Pettit, Sylvia O Suadicani, Ying Lin, Michael VL Bennett, Rafael Yuste, Pablo E Castillo, Suzanne R Zukin
    posted to calcium nmda-receptor pka two-photon by tmiya on 2007-01-04 12:03:06 as **
  • Is Arginine Charged in a Membrane?
    Biophys. J., Vol. 94, No. 2. (15 January 2008), pp. L11-13.
    by Libo Li, Igor Vorobyov, Alexander D Mackerell, Toby W Allen
    posted to biomembranes electrostatics pka solvation by sobolevnrm on 2008-01-31 12:54:26 as read along with 1 group baker-group
  • Does Arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations
    Biophys. J. (16 January 2008), biophysj.107.122945.
    by Jejoong Yoo, Qiang Cui
    posted to biomembranes electrostatics pka solvation by sobolevnrm on 2008-02-25 12:11:49 as read along with 2 people and 1 group paulschlesinger sunhwan baker-group
  • Improved p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> prediction: Combining empirical and semimicroscopic methods
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Gernot Kieseritzky, EW Knapp
    posted to bioinformatics electrostatics pka solvation by sobolevnrm on 2008-06-27 18:08:01 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Electrostatic Effects in a Network of Polar and Ionizable Groups in Staphylococcal Nuclease
    Journal of Molecular Biology, Vol. 379, No. 5. (20 June 2008), pp. 1045-1062.
    by Kelli L Baran, Michael S Chimenti, Jamie L Schlessman, Carolyn A Fitch, Katie J Herbst, Bertrand E Garcia-Moreno
    posted to electrostatics pka solvation by sobolevnrm on 2008-06-03 17:12:13 as read along with 1 group baker-group
  • Linking folding with aggregation in Alzheimer's beta-amyloid peptides
    Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 16880-16885.
    by Jana Khandogin, Charles L Brooks
    posted to molecular_dynamics pka protein_folding by sobolevnrm on 2007-11-08 13:04:01 as read along with 2 people and 1 group Diego_Prada onufriev baker-group
  • On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel.
    Biophys J, Vol. 92, No. 12. (15 June 2007)
    by DL Bostick, CL Brooks
    posted to biomembranes ion_channels pka by sobolevnrm on 2008-04-01 12:16:21 as read along with 1 person and 1 group paulschlesinger baker-group
  • Mapping Local Protein Electrostatics by EPR of pH-Sensitive Thiol-Specific Nitroxide
    Biochemistry, Vol. 47, No. 20. (20 May 2008), pp. 5626-5637.
    by Maxim A Voinov, Andres Ruuge, Vladimir A Reznikov, Igor A Grigor&#x2019;ev, Alex I Smirnov
    posted to electrostatics pka solvation by sobolevnrm on 2008-05-27 01:52:16 as read along with 1 person and 2 groups skoddet baker-group Nielsen group
  • Optimizing pKa computation in proteins with pH adapted conformations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Gernot Kieseritzky, Ernst-Walter Knapp
    posted to electrostatics pka solvation by sobolevnrm on 2008-01-07 13:00:01 as read along with 3 people and 1 group sim82 RamuAnandakrishnan boris_aguilar baker-group
  • Probing electric fields in proteins in solution by NMR spectroscopy
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Mathias AS Hass, Malene R Jensen, Jens J Led
    posted to electrostatics nmr pka solvation by sobolevnrm on 2008-01-27 14:41:30 as read along with 1 group baker-group
  • Protein-protein binding is often associated with changes in protonation state
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron C Mason, Jan H Jensen
    posted to electrostatics pka protein-protein_interactions solvation by sobolevnrm on 2007-12-17 12:40:07 as read along with 5 people and 3 groups onufriev csrocha bicko RamuAnandakrishnan barry baker-group structural_bioinformatics McCammon
  • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Chresten R Sondergaard, Lawrence P Mcintosh, Gianluca Pollastri, Jens E Nielsen
    posted to electrostatics pka solvation by sobolevnrm on 2007-10-04 13:17:49 as read along with 3 people and 2 groups onufriev barry skoddet structural_bioinformatics baker-group
  • Role of Flexibility and Polarity as Determinants of the Hydration of Internal Cavities and Pockets in Proteins
    Biophys. J., Vol. 93, No. 8. (15 October 2007), pp. 2791-2804.
    by Ana Damjanovic, Jamie L Schlessman, Carolyn A Fitch, Angel E Garcia, Garcia-Moreno
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-23 21:18:26 as read along with 1 group baker-group
  • Electrostatic Contributions to the Stability of the GCN4 Leucine Zipper Structure
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by William M Matousek, Barbara Ciani, Carolyn A Fitch, Bertrand E Garcia-Moreno, Richard A Kammerer, Andrei T Alexandrescu
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-17 01:56:00 as read along with 1 person and 1 group cjeans baker-group
  • New and Original pKa Prediction Method Using Grid Molecular Interaction Fields
    J. Chem. Inf. Model. (2 October 2007)
    by F Milletti, L Storchi, G Sforna, G Cruciani
    posted to pka solvation drugdesign by sobolevnrm on 2007-10-08 12:24:55 as read along with 1 person and 1 group sim82 baker-group
  • Recent advances in implicit solvent-based methods for biomolecular simulations
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Jianhan Chen, Brooks, Jana Khandogin
    posted to electrostatics nonpolar pka solvation by sobolevnrm on 2008-04-15 11:47:07 as read along with 2 people and 1 group choonpeng onufriev baker-group
  • Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups
    Biophys. J. (4 January 2008), biophysj.107.122473.
    by Jamie L Schlessman, Colby Abe, Apostolos Gittis, Daniel A Karp, Michael A Dolan, Bertrand Garcia-Moreno
    posted to pka solvation by sobolevnrm on 2008-05-05 11:14:27 as read along with 2 people and 1 group paulschlesinger onufriev baker-group
  • Very fast prediction and rationalization of p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to bioinformatics electrostatics pka software solvation by sobolevnrm on 2008-07-22 11:48:46 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 673-685.
    by Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig
    posted to electrostatics pka protein-ligand_interactions solvation by sobolevnrm on 2008-04-03 11:57:01 as read along with 4 people and 1 group mijogiffin dmobley sunhwan boris_aguilar baker-group
  • Analysing the pH-dependent properties of proteins using pKa calculations
    Journal of Molecular Graphics and Modelling, Vol. 25, No. 5. (January 2007), pp. 691-699.
    by Jens E Nielsen
    posted to electrostatics pka software solvation by sobolevnrm on 2008-04-24 15:00:23 as read along with 1 group baker-group
  • Benchmarking pKa Prediction Methods for Residues in Proteins
    J. Chem. Theory Comput., Vol. 4, No. 6. (10 June 2008), pp. 951-966.
    by Courtney L Stanton, Kendall N Houk
    posted to electrostatics pka solvation by sobolevnrm on 2008-06-27 11:54:41 as read along with 1 person and 1 group onufriev baker-group
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Miguel Machuqueiro, António M Baptista
    posted to molecular_dynamics pka by sobolevnrm on 2008-02-25 12:09:47 as read along with 2 people and 1 group sunhwan skoddet baker-group
  • Electrostatic effects in unfolded staphylococcal nuclease
    Protein Sci, Vol. 17, No. 2. (1 February 2008), pp. 216-227.
    by Nicholas C Fitzkee, Garcia-Moreno
    posted to electrostatics pka protein_folding solvation by sobolevnrm on 2008-02-26 12:16:44 as read along with 1 group baker-group
  • Protonation free energy levels in complex molecular systems
    Biopolymers, Vol. 9999, No. 9999. (2007), NA.
    by Jan M Antosiewicz
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-06 13:15:31 as read along with 1 person and 2 groups barry baker-group McCammon
  • Proton Binding to Proteins: p<i>K</i><sub>a</sub> Calculations with Explicit and Implicit Solvent Models
    J. Am. Chem. Soc., Vol. 126, No. 13. (7 April 2004), pp. 4167-4180.
    by T Simonson, J Carlsson, DA Case
    posted to electrostatics molecular_dynamics pka solvation by sobolevnrm on 2008-03-28 10:50:31 as read along with 3 people and 1 group 6rheology RamuAnandakrishnan dmobley baker-group
  • Membrane Organization and Ionization Behavior of the Minor but Crucial Lipid Ceramide-1-Phosphate
    Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4320-4330.
    by Edgar E Kooijman, Jesus Sot, Montes, Alicia Alonso, Arne Gericke, Ben de Kruijff, Satyendra Kumar, Felix M Goni
    posted to biomembranes pka by sobolevnrm on 2008-07-08 12:07:18 as read along with 1 person and 1 group paulschlesinger baker-group
  • Calculation of the aqueous solvation free energy of the proton
    The Journal of Chemical Physics, Vol. 109, No. 12. (1998), pp. 4852-4863.
    by GJ Tawa, IA Topol, SK Burt, RA Caldwell, AA Rashin
    posted to electrostatics pka solvation by sobolevnrm on 2008-06-30 12:27:13 as read along with 1 group baker-group
  • Residue-Specific pKa Determination of Lysine and Arginine Side Chains by Indirect 15N and 13C NMR Spectroscopy: Application to apo Calmodulin
    J. Am. Chem. Soc., Vol. 129, No. 51. (26 December 2007), pp. 15805-15813.
    by I Andre, S Linse, FAA Mulder
    posted to nmr pka by sobolevnrm on 2008-01-31 12:52:27 as read along with 1 group baker-group
  • Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane
    Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 76-92.
    by Christian Fleck, Roland R Netz, Hans H von Grunberg
    posted to biomembranes electrostatics nucleic_acids pka solvation by sobolevnrm on 2008-07-16 16:02:20 as read along with 2 people and 1 group softsimu rok baker-group
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