thermodynamics

Summary

Summary: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)

Top Publications

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  2. ncbi GROMACS: fast, flexible, and free
    David van der Spoel
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S 75124 Uppsala, Sweden
    J Comput Chem 26:1701-18. 2005
  3. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
  4. ncbi Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Viktor Hornak
    Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
    Proteins 65:712-25. 2006
  5. ncbi Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004
  6. ncbi Development and testing of a general amber force field
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Comput Chem 25:1157-74. 2004
  7. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
  8. ncbi Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    Alexander D MacKerell
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
    J Comput Chem 25:1400-15. 2004
  9. ncbi Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    Raphael Guerois
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Mol Biol 320:369-87. 2002
  10. ncbi A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    J Comput Chem 25:1656-76. 2004

Detail Information

Publications347 found, 100 shown here

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
  2. ncbi GROMACS: fast, flexible, and free
    David van der Spoel
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S 75124 Uppsala, Sweden
    J Comput Chem 26:1701-18. 2005
    ..It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org...
  3. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
    ....
  4. ncbi Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Viktor Hornak
    Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
    Proteins 65:712-25. 2006
    ..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems...
  5. ncbi Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004
    ..Glide is also found to be more accurate than the recently described Surflex method...
  6. ncbi Development and testing of a general amber force field
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Comput Chem 25:1157-74. 2004
    ..The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching...
  7. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    ..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...
  8. ncbi Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    Alexander D MacKerell
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
    J Comput Chem 25:1400-15. 2004
    ..This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general...
  9. ncbi Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    Raphael Guerois
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Mol Biol 320:369-87. 2002
    ..FOLDEF is available via a web-interface at http://fold-x.embl-heidelberg.de..
  10. ncbi A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    J Comput Chem 25:1656-76. 2004
    ..The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed...
  11. ncbi The MARTINI force field: coarse grained model for biomolecular simulations
    Siewert J Marrink
    Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Phys Chem B 111:7812-24. 2007
    ..Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations...
  12. pmc The role of dynamic conformational ensembles in biomolecular recognition
    David D Boehr
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
    Nat Chem Biol 5:789-96. 2009
    ....
  13. ncbi UNAFold: software for nucleic acid folding and hybridization
    Nicholas R Markham
    Xerox Litigation Services, Albany, NY, USA
    Methods Mol Biol 453:3-31. 2008
    ..Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php ...
  14. ncbi Atomic-level characterization of the structural dynamics of proteins
    David E Shaw
    D E Shaw Research, 120 West 45th Street, New York, NY 10036, USA
    Science 330:341-6. 2010
    ....
  15. pmc Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    Bryson D Bennett
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Nat Chem Biol 5:593-9. 2009
    ..The data and analyses presented here highlight the ability to identify organizing metabolic principles from systems-level absolute metabolite concentration data...
  16. ncbi Macromolecular crowding: obvious but underappreciated
    R J Ellis
    Dept of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
    Trends Biochem Sci 26:597-604. 2001
    ..Positive results of crowding include enhancing the collapse of polypeptide chains into functional proteins, the assembly of oligomeric structures and the efficiency of action of some molecular chaperones and metabolic pathways...
  17. pmc A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    Adam M Feist
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    Mol Syst Biol 3:121. 2007
    ..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
  18. pmc Accurate SHAPE-directed RNA structure determination
    Katherine E Deigan
    Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599 3290, USA
    Proc Natl Acad Sci U S A 106:97-102. 2009
    ....
  19. ncbi Functional siRNAs and miRNAs exhibit strand bias
    Anastasia Khvorova
    Amgen, Inc, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
    Cell 115:209-16. 2003
    ..Together, these results suggest that the thermodynamic properties of siRNA play a critical role in determining the molecule's function and longevity, possibly biasing the steps involved in duplex unwinding and strand retention by RISC...
  20. pmc Escaping free-energy minima
    Alessandro Laio
    Centro Svizzero di Calcolo Scientifico, Via Cantonale, CH 6928 Manno, Switzerland
    Proc Natl Acad Sci U S A 99:12562-6. 2002
    ..We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution...
  21. pmc Sending signals dynamically
    Robert G Smock
    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
    Science 324:198-203. 2009
    ..The next stages in the signaling hierarchy-how multiple signals are integrated and how cellular signaling pathways are organized in space and time-present exciting challenges for the future, requiring bold multidisciplinary approaches...
  22. ncbi Design of a novel globular protein fold with atomic-level accuracy
    Brian Kuhlman
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Science 302:1364-8. 2003
    ..2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature...
  23. ncbi Exploring protein native states and large-scale conformational changes with a modified generalized born model
    Alexey Onufriev
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
    Proteins 55:383-94. 2004
    ..5 A after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 A relative to the crystal structure of the complex...
  24. ncbi Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    C Clementi
    Department of Physics, University of California at San Diego, La Jolla, CA 92093 0319, USA
    J Mol Biol 298:937-53. 2000
    ..This result clearly indicates that, as long as the protein sequence is sufficiently minimally frustrated, topology plays a central role in determining the folding mechanism...
  25. ncbi A systems approach to measuring the binding energy landscapes of transcription factors
    Sebastian J Maerkl
    Biochemistry and Molecular Biophysics Option, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
    Science 315:233-7. 2007
    ..With this platform we characterized DNA binding energy landscapes for four eukaryotic transcription factors; these landscapes were used to test basic assumptions about transcription factor binding and to predict their in vivo function...
  26. ncbi PRODRG: a tool for high-throughput crystallography of protein-ligand complexes
    Alexander W Schuttelkopf
    Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Scotland
    Acta Crystallogr D Biol Crystallogr 60:1355-63. 2004
    ..However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors...
  27. ncbi A semiempirical free energy force field with charge-based desolvation
    Ruth Huey
    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92102, USA
    J Comput Chem 28:1145-52. 2007
    ..The force field shows improvement in redocking simulations over the previous AutoDock3 force field...
  28. pmc Improved side-chain torsion potentials for the Amber ff99SB protein force field
    Kresten Lindorff-Larsen
    D E Shaw Research, New York, New York 10036, USA
    Proteins 78:1950-8. 2010
    ..The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data...
  29. ncbi Circular dichroism and guanine quadruplexes
    Michaela Vorlíčková
    Institute of Biophysics, Academy of Sciences of the Czech Republic, v v i, Kralovopolska 135, CZ 612 65 Brno, Czech Republic
    Methods 57:64-75. 2012
    ..This article aims to show that CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies...
  30. ncbi Stability effects of mutations and protein evolvability
    Nobuhiko Tokuriki
    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
    Curr Opin Struct Biol 19:596-604. 2009
    ..We describe ways of predicting and analyzing stability effects of mutations, and mechanisms that buffer or compensate for these destabilizing effects and thereby promote protein evolvabilty, in nature and in the laboratory...
  31. ncbi The role of site accessibility in microRNA target recognition
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:1278-84. 2007
    ..Our study thus demonstrates that target accessibility is a critical factor in microRNA function...
  32. ncbi Toward high-resolution de novo structure prediction for small proteins
    Philip Bradley
    University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA
    Science 309:1868-71. 2005
    ..5 angstroms) can be achieved for small protein domains (<85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling...
  33. pmc Stability and kinetics of G-quadruplex structures
    Andrew N Lane
    Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA
    Nucleic Acids Res 36:5482-515. 2008
    ..The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence...
  34. ncbi Unraveling hot spots in binding interfaces: progress and challenges
    Warren L DeLano
    Sunesis Pharmaceuticals Incorporated, 341 Oyster Point Boulevard South, San Francisco, CA 94080, USA
    Curr Opin Struct Biol 12:14-20. 2002
    ..Despite our current theoretical shortcomings, recent methodological advances provide efficient experimental means of probing hot spots and enable immediate applications for hot spots in drug discovery...
  35. pmc A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
    Wanjun Gu
    Key Laboratory of Child Development and Learning Science of Ministry of Education of China, Southeast University, Nanjing, Jiangsu, China
    PLoS Comput Biol 6:e1000664. 2010
    ..We suggest that the origin of this reduction is selection for efficient recognition of the start codon by initiator-tRNA...
  36. ncbi Thermofluor-based high-throughput stability optimization of proteins for structural studies
    Ulrika B Ericsson
    Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE 109 51, Sweden
    Anal Biochem 357:289-98. 2006
    ..This suggests that thermofluor constitutes an efficient generic high-throughput method for identification of protein properties predictive of crystallizability...
  37. ncbi Force fields for protein simulations
    Jay W Ponder
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Adv Protein Chem 66:27-85. 2003
  38. ncbi Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    Holger Gohlke
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 330:891-913. 2003
    ..This explains the finding of a conformational change in this region upon complex formation with Ras, and it may trigger a larger structural change in Raf, which is considered to be necessary for activation of the effector by Ras...
  39. pmc Structure of a beta1-adrenergic G-protein-coupled receptor
    Tony Warne
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 454:486-91. 2008
    ....
  40. ncbi Molecular code for transmembrane-helix recognition by the Sec61 translocon
    Tara Hessa
    Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
    Nature 450:1026-30. 2007
    ..The emerging picture of translocon-mediated transmembrane helix assembly is simple, with the critical sequence characteristics mirroring the physical properties of the lipid bilayer...
  41. pmc Group contribution method for thermodynamic analysis of complex metabolic networks
    Matthew D Jankowski
    Mayo Clinic, Rochester, Minnesota 55905, USA
    Biophys J 95:1487-99. 2008
    ..A web-based implementation of this new group contribution method is available free at http://sparta.chem-eng.northwestern.edu/cgi-bin/GCM/WebGCM.cgi...
  42. pmc Improved prediction of protein side-chain conformations with SCWRL4
    Georgii G Krivov
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 77:778-95. 2009
    ..The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs...
  43. ncbi Protein-protein docking with backbone flexibility
    Chu Wang
    Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    J Mol Biol 373:503-19. 2007
    ..The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models...
  44. pmc Specificity of microRNA target selection in translational repression
    John G Doench
    Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 18:504-11. 2004
    ..Thus, predicted miRNA:mRNA interactions must be viewed in the context of other potential interactions and cellular conditions...
  45. ncbi Recognition of transmembrane helices by the endoplasmic reticulum translocon
    Tara Hessa
    Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
    Nature 433:377-81. 2005
    ..Our results indicate that direct protein-lipid interactions are critical during translocon-mediated membrane insertion...
  46. pmc Nonequilibrium thermodynamics of thiol/disulfide redox systems: a perspective on redox systems biology
    Melissa Kemp
    The Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
    Free Radic Biol Med 44:921-37. 2008
    ....
  47. pmc I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
    Emidio Capriotti
    Laboratory of Biocomputing, CIRB Department of Biology, University of Bologna via Irnerio 42, 40126 Bologna, Italy
    Nucleic Acids Res 33:W306-10. 2005
    ..0 as a unique and valuable helper for protein design, even when the protein structure is not yet known with atomic resolution. Availability: http://gpcr.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi...
  48. ncbi Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules
    Donald Hamelberg
    NSF Center for Theoretical Biological Physics and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, USA
    J Chem Phys 120:11919-29. 2004
    ..We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution...
  49. pmc Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    Luba Katz
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 13:2042-51. 2003
    ..These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control...
  50. pmc Molecular dynamics and protein function
    M Karplus
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:6679-85. 2005
    ..We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems...
  51. pmc Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril
    Crystal N Nguyen
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 0736, USA
    J Chem Phys 137:044101. 2012
    The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process...
  52. pmc Targeted rescue of a destabilized mutant of p53 by an in silico screened drug
    Frank M Boeckler
    Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 0QH, United Kingdom
    Proc Natl Acad Sci U S A 105:10360-5. 2008
    ..We point out some general principles in relationships between binding constants, raising of melting temperatures, and increase of protein half-lives by stabilizing ligands...
  53. pmc NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
    Douglas H Turner
    Department of Chemistry and Center for RNA Biology, Box 0216, University of Rochester, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 38:D280-2. 2010
    ..The initial release covers parameters for predicting RNA folding free energy and enthalpy changes...
  54. pmc Inferring binding energies from selected binding sites
    Yue Zhao
    Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Comput Biol 5:e1000590. 2009
    ..We show that after a single round of selection our method can estimate binding parameters that give very good fits to the selected site distributions, much better than standard motif identification algorithms...
  55. ncbi Interfaces and the driving force of hydrophobic assembly
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 437:640-7. 2005
    ..Despite the basic principles underlying the hydrophobic effect being qualitatively well understood, only recently have theoretical developments begun to explain and quantify many features of this ubiquitous phenomenon...
  56. pmc De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
    Guillermo Rodrigo
    Institute of Systems and Synthetic Biology, Genopole Université d Évry Val d Essonne Centre National de la Recherche Scientifique CNRS UPS3509, 91030 Evry, France
    Proc Natl Acad Sci U S A 109:15271-6. 2012
    ..Our results demonstrate that a computational methodology based on first-principles can be used to engineer interacting RNAs with allosteric behavior in living cells...
  57. pmc Thermodynamic stability of wild-type and mutant p53 core domain
    A N Bullock
    Cambridge University Chemical Laboratory and Cambridge Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom
    Proc Natl Acad Sci U S A 94:14338-42. 1997
    ..Under certain denaturing conditions, the wild-type domain forms an aggregate that is relatively highly fluorescent at 340 nm on excitation at 280 nm. The destabilized mutants give this fluorescence under milder denaturation conditions...
  58. ncbi Macromolecular crowding: an important but neglected aspect of the intracellular environment
    R J Ellis
    Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
    Curr Opin Struct Biol 11:114-9. 2001
    ..It is proposed that the addition of crowding agents should become as routine as controlling pH and ionic strength if we are to meet the objective of studying biological molecules under more physiologically relevant conditions...
  59. ncbi Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    Renxiao Wang
    Medical Chemistry and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109 0934, USA
    J Comput Aided Mol Des 16:11-26. 2002
    ..Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking...
  60. ncbi Structures and metal-ion-binding properties of the Ca2+-binding helix-loop-helix EF-hand motifs
    Jessica L Gifford
    Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
    Biochem J 405:199-221. 2007
    ..A structural approach is used in this review to examine the diversity of family members, and a biophysical perspective provides insight into the ability of the EF-hand motif to bind Ca2+ with a wide range of affinities...
  61. pmc Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    Jason Gertz
    Center for Genome Sciences, Department of Genetics, Washington University in Saint Louis School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 457:215-8. 2009
    ..Quantitative analyses of synthetic promoter libraries will be an important tool in unravelling the rules underlying combinatorial cis-regulation...
  62. ncbi Small molecule inhibitors of aggregation indicate that amyloid beta oligomerization and fibrillization pathways are independent and distinct
    Mihaela Necula
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
    J Biol Chem 282:10311-24. 2007
    ..In addition, these data suggest that small molecule inhibitors are useful for clarifying the mechanisms underlying protein aggregation and may represent potential therapeutic agents that target fundamental disease mechanisms...
  63. ncbi Adaptive biasing force method for scalar and vector free energy calculations
    Eric Darve
    Mechanical Engineering Department, Stanford University, Stanford, California 94305 4040, USA
    J Chem Phys 128:144120. 2008
    ....
  64. ncbi Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy
    Niels Fischer
    3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Nature 466:329-33. 2010
    ..The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement...
  65. ncbi A general purpose model for the condensed phases of water: TIP4P/2005
    J L F Abascal
    Departamento de Quimica Fisica, Facultad de Ciencias Quimicas, Universidad Complutense, 28040 Madrid, Spain
    J Chem Phys 123:234505. 2005
    ..For example, it gives excellent predictions for the densities at 1 bar with a maximum density at 278 K and an averaged difference with experiment of 7 x 10(-4) g/cm3...
  66. pmc Protein stability promotes evolvability
    Jesse D Bloom
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 103:5869-74. 2006
    ..Our work establishes a crucial link between protein stability and evolution. We show that we can exploit this link to discover protein functions, and we suggest how natural evolution might do the same...
  67. pmc Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination
    Masoud Vedadi
    Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, ON, Canada M5G 1L5
    Proc Natl Acad Sci U S A 103:15835-40. 2006
    ..The methods are cost-effective, can be implemented in any laboratory, promise to increase the success rates of purifying and crystallizing human proteins significantly, and identify new ligands for these proteins...
  68. ncbi The structure of glycosaminoglycans and their interactions with proteins
    Neha S Gandhi
    Western Australian Biomedical Research Institute, Curtin University of Technology, Perth, WA 6845, Australia
    Chem Biol Drug Des 72:455-82. 2008
    ..New approaches to the development of GAG mimetics as possible new glycotherapeutics are also briefly covered...
  69. pmc Limitations in xylose-fermenting Saccharomyces cerevisiae, made evident through comprehensive metabolite profiling and thermodynamic analysis
    Mario Klimacek
    Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, Petersgasse 12 I, A 8010 Graz, Austria
    Appl Environ Microbiol 76:7566-74. 2010
    ..Coenzyme and ATP pools did not rate limit flux through xylose pathway enzymes...
  70. ncbi Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    J Wang
    Contribution from the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-0446, USA
    J Am Chem Soc 123:5221-30. 2001
    ..Therefore, molecular docking combined with MD simulations followed by MM-PBSA analysis is an attractive approach for modeling protein complexes a priori...
  71. pmc The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building
    Francois Yves Dupradeau
    CNRS UMR 6219 and UFR Pharmacie, Universite de Picardie Jules Verne, 1, rue des Louvels, F 80037 Amiens Cedex 1, France
    Phys Chem Chem Phys 12:7821-39. 2010
    ..Selected results related to non-polarizable charge models are presented and discussed...
  72. pmc A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands
    Deepak Koirala
    Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, USA
    Nat Chem 3:782-7. 2011
    ..We anticipate that this single-molecule platform can provide detailed insights into the mechanical, kinetic and thermodynamic properties of liganded bio-macromolecules, which have biological relevance...
  73. pmc Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms
    Chung Jung Tsai
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Mol Biosyst 5:207-16. 2009
    ..We further provide a range of examples illustrating mechanisms in protein allostery and their classification from the cellular functional standpoint...
  74. pmc Atomic accuracy in predicting and designing noncanonical RNA structure
    Rhiju Das
    Departments of Biochemistry and Physics, Stanford University, Stanford, California, USA
    Nat Methods 7:291-4. 2010
    ..Sequence redesign calculations recovered native bases at 65% of residues engaged in noncanonical interactions, and we experimentally validated mutations predicted to stabilize a signal recognition particle domain...
  75. pmc A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    J SantaLucia
    Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
    Proc Natl Acad Sci U S A 95:1460-5. 1998
    A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented...
  76. pmc The application of statistical physics to evolutionary biology
    Guy Sella
    Center for the Study of Rationality, Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
    Proc Natl Acad Sci U S A 102:9541-6. 2005
    ..Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift...
  77. pmc Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions
    Norma J Greenfield
    Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854 5635, USA
    Nat Protoc 1:2527-35. 2006
    ..Measurement of the spectra of five folded proteins and their unfolding curves at a single wavelength requires approximately 8 h...
  78. ncbi Thermodynamic stability of carbonic anhydrase: measurements of binding affinity and stoichiometry using ThermoFluor
    Daumantas Matulis
    Johnson and Johnson Pharmaceutical Research and Development, LLC, Eagleview Corporate Center, 665 Stockton Drive, Suite 104, Exton, Pennsylvania 19341, USA
    Biochemistry 44:5258-66. 2005
    ..The precise ligand effects depend on the thermodynamics of protein stability: in particular, the unfolding enthalpy...
  79. pmc Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements
    Xinghua Zhang
    BioSystems and Micromechanics BioSyM, Singapore MIT Alliance for Research and Technology, National University of Singapore, Singapore 117543
    Proc Natl Acad Sci U S A 109:8103-8. 2012
    ..Our results provide important insights into the thermodynamics of DNA overstretching and conformational structures of overstretched DNA that may play an important role in ..
  80. pmc Pollutant-induced modulation in conformation and β-lactamase activity of human serum albumin
    Ejaz Ahmad
    Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
    PLoS ONE 7:e38372. 2012
    ..We also show a correlation with non-microbial drug resistance as HSA is capable of self-hydrolysis of β-lactam drugs, which is further potentiated by pollutants due to conformational changes in HSA...
  81. pmc Predicting protein structures with a multiplayer online game
    Seth Cooper
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA
    Nature 466:756-60. 2010
    ....
  82. ncbi The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    Marc Parisien
    Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Universite de Montreal, PO Box 6128, Downtown Station, Montreal, Quebec H3C 3J7, Canada
    Nature 452:51-5. 2008
    ....
  83. pmc Low micromolar zinc accelerates the fibrillization of human tau via bridging of Cys-291 and Cys-322
    Zhong Ying Mo
    State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
    J Biol Chem 284:34648-57. 2009
    ....
  84. ncbi Improved treatment of the protein backbone in empirical force fields
    Alexander D MacKerell
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
    J Am Chem Soc 126:698-9. 2004
    ..The developed approach is suggested to lead to significant improvements in the accuracy of empirical force fields to treat peptides and proteins...
  85. pmc The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
    Ahmet Bakan
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
    Proc Natl Acad Sci U S A 106:14349-54. 2009
    ..The results suggest that simple but robust rules encoded in the protein structure play a dominant role in predefining the mechanisms of ligand binding, which may be advantageously exploited in designing inhibitors...
  86. pmc Slipknotting upon native-like loop formation in a trefoil knot protein
    Jeffrey K Noel
    Center for Theoretical Biological Physics, University of California at San Diego, Gilman Drive 9500, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 107:15403-8. 2010
    ....
  87. pmc Structure and folding of a designed knotted protein
    Neil P King
    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1569, USA
    Proc Natl Acad Sci U S A 107:20732-7. 2010
    ..The success of the design strategy--connecting two monomers of an intertwined homodimer into a single protein chain--supports a model for evolution of knotted structures via gene duplication...
  88. pmc Probing for DNA damage with β-hairpins: similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro
    Yang Liu
    Chemistry Department, New York University, New York, NY 10003, USA
    DNA Repair (Amst) 10:684-96. 2011
    ..These observations suggest that, in addition to recognition involving the initial modified duplexes, downstream events involving UvrC can also play a role in distinguishing and processing different lesions in prokaryotic NER...
  89. pmc Direct observation of hierarchical folding in single riboswitch aptamers
    William J Greenleaf
    Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
    Science 319:630-3. 2008
    ..These results provide an integrated view of hierarchical folding in an aptamer, demonstrating how complex folding can be resolved into constituent parts, and supply further insights into tertiary structure formation...
  90. ncbi Computer modeling of mitochondrial tricarboxylic acid cycle, oxidative phosphorylation, metabolite transport, and electrophysiology
    Fan Wu
    Biotechnology and Bioengineering Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    J Biol Chem 282:24525-37. 2007
    ....
  91. pmc The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    Ivelin Georgiev
    Department of Computer Science, Duke University, Durham, NC, USA
    J Comput Chem 29:1527-42. 2008
    ..Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design...
  92. pmc Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
    Justin B Kinney
    Department of Physics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 107:9158-63. 2010
    ..The principles of our method can also be applied to a wide range of other problems in molecular biology...
  93. pmc Protein stability imposes limits on organism complexity and speed of molecular evolution
    Konstantin B Zeldovich
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:16152-7. 2007
    ....
  94. ncbi Macromolecular modeling with rosetta
    Rhiju Das
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Annu Rev Biochem 77:363-82. 2008
    ..Emerging connections to crystallographic phasing, NMR modeling, and lower-resolution approaches are described and critically assessed...
  95. pmc Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli
    R M T Fleming
    Science Institute, University of Iceland, Reykjavik, Iceland
    Biophys Chem 145:47-56. 2009
    ..In vivo, the second law of thermodynamics requires that net macroscopic flux be forward, when the transformed reaction Gibbs energy is negative...
  96. ncbi Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
    Ajay N Jain
    Department of Biopharmaceutical Sciences, UCSF Cancer Research Institute, University of California San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 21:281-306. 2007
    ....
  97. pmc Computational analysis of missense mutations causing Snyder-Robinson syndrome
    Zhe Zhang
    Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina 29634, USA
    Hum Mutat 31:1043-9. 2010
    ..Specifically, the p.G56S mutation is predicted to greatly reduce the affinity of monomers to form a dimer, and therefore should have a dramatic effect on SMS function because dimerization is essential for SMS activity...
  98. pmc mRNA secondary structures fold sequentially but exchange rapidly in vivo
    Elisabeth M Mahen
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
    PLoS Biol 8:e1000307. 2010
    ..We find that a narrow thermodynamic threshold determines whether kinetics or thermodynamics govern RNA folding outcomes in vivo...
  99. pmc A statistical sampling algorithm for RNA secondary structure prediction
    Ye Ding
    Bioinformatics Center, Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12208, USA
    Nucleic Acids Res 31:7280-301. 2003
    ..The algorithm is applicable to the rational design of small interfering RNAs (siRNAs), antisense oligonucleotides, and trans-cleaving ribozymes in gene knock-down studies...
  100. ncbi Thermodynamics of beta-catenin-ligand interactions: the roles of the N- and C-terminal tails in modulating binding affinity
    Hee Jung Choi
    Department of Structural Biology, Stanford University School of Medicine, CA 94305 5126, USA
    J Biol Chem 281:1027-38. 2006
    ..The thermodynamics of beta-catenin binding to E-cadherin, Lef-1, APC, axin, and the transcriptional inhibitor ICAT have been ..
  101. ncbi Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
    Vladimir Potapov
    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
    Protein Eng Des Sel 22:553-60. 2009
    ..These results suggest that there is still room for improvement, which is crucial if we want forcefields to perform better in their various tasks...

Research Grants71

  1. Structure and Mechanism of SAM-responsive Riboswitches
    Robert T Batey; Fiscal Year: 2013
    ..features of the aptamer and expression domains play functional roles in regulation, and (4) do binding thermodynamics or kinetics dictate the regulatory response? To address these questions, a combination of approaches including ..
  2. NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINS
    FRANCES ANN WALKER; Fiscal Year: 2012
    ..The thermodynamics and kinetics of their function, and the roles that individual NP proteins play in making a suite of closely ..
  3. Allosteric regulation of the sensory protease DegS
    RANDALL VERNON MAULDIN; Fiscal Year: 2011
    ..Finally, a fluorescence assay will be developed to allow rigorous determination of the kinetics and thermodynamics of DegS activation as a function of activating peptide, substrate, and environmental conditions...
  4. Placental shape features, gestational timing and maternal and infant health
    Carolyn M Salafia; Fiscal Year: 2011
    ..shape based on well-established methodologies in mathematics (Fourier analysis) and physics (statistical thermodynamics) that are based on data derived from digital images of the placental chorionic surface and slices that could ..
  5. Toxic Metal Complexation by de Novo Designed Peptides
    Vincent L Pecoraro; Fiscal Year: 2013
    ..for understanding metal binding by metalloregulatory proteins and metallochaperones, (2) to understand the thermodynamics and kinetics of heavy metals in helical assemblies and (3) to prepare new designed peptides utilizing ..
  6. Using Microfluidic Affinity Analysis to Probe Transcriptional Regulation
    POLLY MORRELL FORDYCE; Fiscal Year: 2013
    ..high-throughput measurement of interaction affinities, this proposal seeks to systematically investigate the thermodynamics of transcriptional regulation at multiple scales, from individual interactions between transcription factors ..
  7. BIOINORGANIC COPPER COORDINATION CHEMISTRY
    Kenneth D Karlin; Fiscal Year: 2013
    ..process will be carried out, (2) the study of O2 and carbon monoxide (CO, as O2-surrogate) kinetics and thermodynamics of binding to tetradentate ligand CuI-chelates including with one thioether donor atom, that being ..
  8. Structural and Functional Studies of the Novel DBD Domain of MKP5
    Amjad Farooq; Fiscal Year: 2012
    ..aims: (i) To determine 3D structure and dynamics of MKP5 DBD domain in complex with AP1 oligo;(ii) To measure thermodynamics and kinetics of MKP5 DBD domain binding to AP1 oligo;and (iii) To analyze cellular consequences of MKP5 DBD ..
  9. Regulation of Rho family GTPases by heterotrimeric G proteins
    BARRY S KREUTZ; Fiscal Year: 2013
    ..3) Using surface plasmon resonance (SPR) we established a system to measure kinetics and thermodynamics of G13-LARG interaction...
  10. Regulation of nucleosome positions and transcription during CTL differentiation
    MATTHEW EUGENE PIPKIN; Fiscal Year: 2013
    ..cognate sites in vivo in order to change transcriptional programs;both enzymatic nucleosome remodeling and the thermodynamics of nucleosome:DNA and transcription factor:DNA interactions are likely to determine transcription factor ..
  11. Role of Helix Formation in Mediating Protein-Protein Interactions
    George I Makhatadze; Fiscal Year: 2010
    ..A detailed statistical thermodynamics study of the factors that affect this transition (from coil to helix), and how these factors affect the ..
  12. Thermodynamics of Coupled Binding of Zn(II) and DNA to a Zinc Finger Tumor Suppre
    Brian R Gibney; Fiscal Year: 2013
    ..of artificial zinc finger protein (ZFP) transcription factor therapeutics by characterizing the fundamental thermodynamics of ZFP transcription factor interactions with zinc metal-ions and DNA...
  13. Understanding the impact of Antigen 85 complex substrate specificity on mycobacte
    DONALD RONNING; Fiscal Year: 2010
    ..This will offer two benefits. First, these compounds will be used to study the thermodynamics of complex formation and allow comparison of the three antigen 85 enzymes...
  14. Large-Scale Conformational Changes in Regulation of Transcription Initiation
    M Thomas Record; Fiscal Year: 2011
    ..Effects of temperature and solution variables on the thermodynamics of formation of a wrapped IHF-H'DNA interface will be measured by isothermal titration calorimetry (ITC) ..
  15. Biophysical Characterization of PDX1 interactions with DNA and other transcriptio
    Monique Bastidas; Fiscal Year: 2013
    ..The thermodynamics of PDX1 interactions with 11 gene promoter elements from 5 genes and interactions with other proteins will be ..
  16. Coordination Chemistry of Microbial Iron Transport Compounds
    Kenneth N Raymond; Fiscal Year: 2013
    ..This project seeks to understand siderophore transport systems: 1) from a structural level, studying the thermodynamics and kinetics of iron binding, 2) to a systemic level, following the recognition and transport of these ..
  17. Dynamic properties of a glutamate binding domain
    Robert E Oswald; Fiscal Year: 2013
    ..in the agonist binding site, and the goal will be to determine the effects of dimerization on dynamics and thermodynamics of agonist and antagonist binding...
  18. Computational modeling of viral assembly: encapsulation of nucleic acids and env
    Michael F Hagan; Fiscal Year: 2013
    ..Comparison of predicted assembly kinetics and thermodynamics for each model identifies the contributions of base-pairing to assembly...
  19. Multiscale Interaction of Pulmonary Gas Flow and Lung Tissue Mechanics
    Ching Long Lin; Fiscal Year: 2013
    ..stresses in terms of the regional distributions of PCL water level and calcium ion concentration together with thermodynamics for heat and moisture in the human lung...
  20. Probing the real-time kinetics and steady-state dynamics of gene expression
    Narendra Maheshri; Fiscal Year: 2013
    ..This relationship has traditionally been described using semi-empirical models based on the thermodynamics of protein-DNA interactions...
  21. Exploring tyrosine redox chemistry in model proteins
    MELISSA MARTINEZ-RIVERA; Fiscal Year: 2013
    ..For this reason, we have developed a series of model protein scaffolds with the characteristics necesary to investigate the relation between the thermodynamics of amino-acid redox chemistry and the surrounding protein environment.
  22. Development and Application of Multi-Spectroscopic, Site-Specific (MS3) Probes of
    EDWARD EMMETT FENLON; Fiscal Year: 2010
    ..long-term objective of the research is to significantly advance our understanding of nucleic acid structure, thermodynamics, and kinetics...
  23. Membrane Proteins of Normal and Abnormal Red Cells
    David W Speicher; Fiscal Year: 2013
    ..Structures of heterodimer and tetramer binding site complexes and elucidation of wild type interaction thermodynamics will provide a reference for determining how specific HE and HPP mutations disrupt spectrin self-assembly and ..
  24. Thermodynamics and kinetics of DNA-ligand binding probed by DNA overstretching
    Andreas Hanke; Fiscal Year: 2013
    ..The project will both enhance our knowledge of multiscale phenomena in fundamental biophysics and provide new insight into the anticancer function of ActD. ..
  25. Binding and Splicing mRNA
    DANIEL AALBERTS; Fiscal Year: 2009
    ..2) Improve models of mRNA splicing to understand the role of thermodynamics in alternative splicing and intron/exon segregation, and correlations in the codon frames where introns begin...
  26. TRAINING IN MOLECULAR PHYSICS OF BIOLOGICAL SYSTEMS
    Michelle D Wang; Fiscal Year: 2013
    ..undertake interdisciplinary studies with advanced courses in mathematics, quantum mechanics, statistical thermodynamics, biochemistry, molecular and cell biology, computation and instrumentation, and other special topics...
  27. STRUCTURE AND FUNCTION OF NUCLEIC ACID THERAPEUTICS
    Martin Egli; Fiscal Year: 2012
    ..Other approaches we will rely on to achieve our objectives are synthetic organic chemistry, biochemical and molecular biology tools as well as thermodynamics, kinetics and single-crystal NMC.
  28. DNA confined by surfaces
    Bernard Montgomery Pettitt; Fiscal Year: 2013
    ..around ten kilo-basepairs long, we will employ a multi scale technique to model the structure and consequent thermodynamics. We will refine a coarse-grained model of DNA from our previous work...
  29. Allostery in Hepatitis B Virus Capsid Assembly
    SARAH PALMER KATEN; Fiscal Year: 2010
    ..We will describe the mechanism of action of these molecules by observing their effects on the kinetics and thermodynamics of assembly...
  30. Biochemical Insight of Hyperphosphorylation of Replication Protein A
    Yue Zou; Fiscal Year: 2010
    ..on RPA interaction with DNA intermediates of biological significance;and (3) determine binding affinity and thermodynamics of the hyperphosphorylation-induced domain-domain interaction of RPA...
  31. Supporting RNAstructure: Software for RNA Analysis
    David H Mathews; Fiscal Year: 2013
    ..state-of-the-art algorithms for RNA structure prediction using the most current understanding of RNA folding thermodynamics. It also provides algorithms for finding the optimal secondary structure shared by two sequences, which is, on ..
  32. Houston Area Molecular Biophysics Program
    Theodore G Wensel; Fiscal Year: 2013
    ..electron microscopy, fluorescence, magnetic resonance and other types of macromolecular spectroscopy, thermodynamics, kinetics, molecular dynamics, theoretical biophysics, protein folding, nucleic acid structure, molecular ..
  33. 2013 MECHANISMS OF MEMBRANE TRANSPORT GRC
    Nancy Carrasco; Fiscal Year: 2013
    ..We will organize a highly innovative session focused on this approach, where we will discuss thermodynamics, kinetics, and conformational states during transport...
  34. ASSEMBLY AND ACTIVATION OF ENZYME-SSDNA COMPLEXES
    Scott W Morrical; Fiscal Year: 2012
    ..We will explore all three enzyme loading mechanisms using classical biochemical methods (kinetics, thermodynamics, fluorescence, sedimentation, crosslinking), single- molecule approaches (fluorescence imaging, force ..
  35. Machine Learning Analysis of Genetic Modulators of Vaccine Immune Response
    BRETT MCKINNEY; Fiscal Year: 2009
    ..optimization method called Evaporative Cooling (EC), which is based on information theory and the statistical thermodynamics of cooling a system of interacting particles by evaporation...
  36. NMR Studies of Protein Side-Chain Dynamics
    MARK A RANCE; Fiscal Year: 2012
    ..the contribution of amino acid side-chain dynamics to the physico-chemical mechanisms that determine the thermodynamics of recognition and association in protein/DNA interactions and the molecular basis of cooperativity of ion ..
  37. Multi-User, Isothermal Titration Microcalorimeter
    IVAN JULIAN DMOCHOWSKI; Fiscal Year: 2013
    ..Isothermal titration calorimetry (ITC) is one of the most straightforward methods for characterizing the thermodynamics and stoichiometry of molecular interactions involving small molecules, proteins and polypeptides, antibodies, ..
  38. Structure And Mechanism In Intracellular Notch Signaling
    DOUGLAS E BARRICK; Fiscal Year: 2013
    ..In this proposal, we use traditional biophysical, structural methods, and solution thermodynamics to characterize these aspects of Notch signaling, but also combine these methods with functional assays for ..
  39. Mechanistic Analysis of Intracellular RNA Folding
    Martha J Fedor; Fiscal Year: 2013
    ..intracellular assembly of RNA structures that integrates molecular biology and genetics with kinetics and thermodynamics. So far, this unique approach has enabled us to show that some kinetic and equilibrium parameters of ..
  40. Comparison of Morpholino and DNA Technologies for Surface-Based Diagnostics
    Rastislav Levicky; Fiscal Year: 2010
    ..Development of fundamental understanding of the kinetics and thermodynamics of Morpholino surface hybridization, and 3)...
  41. RNA folding: from global structure to atomic detail
    Lois Pollack; Fiscal Year: 2012
    ..experimental studies, we propose to develop efficient atomically detailed simulations of the kinetics and thermodynamics of RNA folding...
  42. Dynamics &energetics of p38a kinase regulation by ligands
    A Joshua Wand; Fiscal Year: 2013
    ..recent studies utilizing this approach that changes in conformational entropy can significantly influence the thermodynamics of the interaction of small molecule ligands with proteins...
  43. Single Molecule HIV-1 NC/Gag-DNA Interactions
    Mark C Williams; Fiscal Year: 2013
    ..To test this hypothesis, will examine the thermodynamics and kinetics of human APOBEC interactions with single- and double-stranded DNA...
  44. Protein-Crystal Molecular Recognition in Biomineralization
    Patrick S Stayton; Fiscal Year: 2012
    ..statherin structure that connects to the molecular mechanisms underlying hydroxyapatite adsorption thermodynamics and crystal engineering function...
  45. Isothermal Titration Calorimeter
    Robert S Hodges; Fiscal Year: 2013
    ..The MicroCal iTC200 is an instrument used to determine binding affinity and thermodynamics of biomolecular interactions...
  46. Energetics and dynamics in protease inhibitor function
    David Goldenberg; Fiscal Year: 2009
    ..In addition, the thermodynamics of the interactions will be studied by calorimetric and fluorescence methods, and x-ray crystal structures ..
  47. Atomic resolution structure and function of the ribosome
    JAMIE H CATE; Fiscal Year: 2013
    ..3. Probe the effects of macromolecular crowding on the kinetics and thermodynamics of ribosome recycling...
  48. CODA Assembly of Mutant Genes
    SHE PIN contact HUNG; Fiscal Year: 2010
    ..lies in applying computational optimization to mutant sequence assembly, in bringing cluster computing and thermodynamics to the wet-lab, in the integration of different methods, and in the general approach taken...
  49. MEMBRANE PROTEIN FOLDING
    Karen G Fleming; Fiscal Year: 2013
    ..computational prediction and design, molecular dynamics simulations, experimental analysis of the thermodynamics and kinetics of folding, directed evolution for stability, and in vivo folding...
  50. Functional Dynamics of Large Molecular Machines. The Primosome.
    W M BUJALOWSKI; Fiscal Year: 2012
    ..This will be accomplished through quantitative studies of the thermodynamics, kinetics, and structures of multiple protein-protein and protein-DNA complexes, using the analytical ..
  51. Sequence Effects of Arylamine-DNA Adducts: Repair and Replication
    Bongsup P Cho; Fiscal Year: 2013
    ..repair (NER) system and long-range sequence effects, (2) damage recognition (protein-DNA interaction) (3) the thermodynamics of sequence-dependent slippage-induced frameshift mutagenesis, and (4) replication fork conformational ..
  52. Mechanisms of amyloid nucleation
    RONALD B WETZEL; Fiscal Year: 2013
    ..will yield important parameters such as the thermodynamic driving force for nucleus formation, and the thermodynamics associated with simple fibril growth (elongation)...
  53. Fluorescence Correlation Quantitation of Insulin-like Growth Factor and Insulin R
    B George Barisas; Fiscal Year: 2013
    ..Aim 2: To evaluate the thermodynamics of IR and IGF1R homodimer and IR-IGF1R hybrid receptor formation...
  54. Fluctuations and entropy in the energetics and function of protein complexes
    A Joshua Wand; Fiscal Year: 2013
    ..Thus our general hypothesis is that the thermodynamics of protein-ligand interactions can be influenced via changes in the protein internal entropy...
  55. STRUCTURAL STUDY OF EPH RECEPTORS AND EPHRINS
    Dimitar B Nikolov; Fiscal Year: 2013
    ..Parallel to our crystallographic experiments will be our biophysical studies of the kinetics and thermodynamics of the ligand/receptor interactions...
  56. Impact of climate change on mosquito-borne arbovirus transmission
    C M Barker; Fiscal Year: 2011
    ..temperate latitudes, are especially vulnerable to climate change, because their transmission depends upon the thermodynamics of viral replication and dissemination within the poikilothermic arthropod vector and upon both arthropod ..
  57. Thermodynamics and energetics of voltage-gated ion channels
    Baron Chanda; Fiscal Year: 2013
    ....
  58. Using deep-cavity cavitands to study supramolecular chemistry in water
    Bruce C Gibb; Fiscal Year: 2013
    ..Furthermore, ITC and NMR spectroscopy allows the accurate determination of the thermodynamics of host-guest and host-anion binding...
  59. SEQUENCE SPECIFIC DNA PROTEIN INTERACTIONS
    Linda Jen Jacobson; Fiscal Year: 2010
    ..of unfavorable interactions relaxes specificity by modifying the structure of the protein-DNA interface, the thermodynamics of binding and/or the cleavage kinetics of the system...
  60. Understanding the thermodynamics and structure of RNA secondary structure motifs
    BRENT ZNOSKO; Fiscal Year: 2013
    ..In order to achieve this long-term objective, it is essential to understand RNA thermodynamics and structure and how these properties are related...
  61. Thermodynamics of the Conformational Activation of Von Willebrand Factor
    Matthew Auton; Fiscal Year: 2013
    ....
  62. Effect of Base Lesions on the DNA Duplex
    MEGAN NUNEZ; Fiscal Year: 2009
    ..The third aim is to measure the thermodynamics of DNA stability with and without lesions, to determine the extent to which the lesion weakens the integrity ..
  63. MOLECULAR RECOGNITION IN THE STREPTAVIDIN BIOTIN SYSTEM
    Patrick Stayton; Fiscal Year: 2001
    ..molecular insight into the structure-function relationships, which govern the high affinity equilibrium thermodynamics and the construction of the high activation barrier to dissociation...
  64. MOLECULAR RECOGNITION IN THE STREPTAVIDIN BIOTIN SYSTEM
    Patrick Stayton; Fiscal Year: 2002
    ..molecular insight into the structure-function relationships, which govern the high affinity equilibrium thermodynamics and the construction of the high activation barrier to dissociation...
  65. MECHANISMS OF COOPERATIVE PROTEIN-DNA INTERACTIONS
    Michael Brenowitz; Fiscal Year: 2006
    ..structural features of TBP and its complexes with DNA and regulatory proteins are reflected in equally unusual thermodynamics and kinetics of DNA binding...
  66. OPIOID RECEPTOR CONSTANTS IN VITRO--TEMPERATURE
    Frank Porreca; Fiscal Year: 1990
    ..This possible agonist-induced change in conformation is reflected by the reaction thermodynamics, with agonist and antagonists having different characteristics...
  67. Protein interactions underlying actin-based motility
    David Sept; Fiscal Year: 2006
    ..and disassembly, and (3) the binding of Arp 2/3 complex to actin filaments, as well as the kinetics and thermodynamics of Arp 2/3 mediated nucleation, and the capping of pointed ends by the complex...
  68. CHROMATOGRAPHIC STUDIES OF FUNCTIONAL PROTEOMICS
    DAVID HAGE; Fiscal Year: 2009
    ..affinity chromatography (HPAC) using immobilized HSA columns is a fast, precise tool for studying the thermodynamics and stoichiometries of these drug-protein interactions...
  69. Signaling Proteins: Binding Studies and Peptide Mimetics
    Mark Spaller; Fiscal Year: 2006
    ..From a biochemical point of view, there is a near-total absence of an understanding of the thermodynamics that governs the basic molecular recognition process involving PDZ domains...
  70. SINGLE PROTON EXCHANGE KINETICS IN PROTEINS
    Clare Woodward; Fiscal Year: 1999
    ..by this grant since the last competitive renewal produced a significant body of data on dynamics, folding thermodynamics and crystal structure for 8 variants of the small model protein, bovine pancreatic trypsin inhibitor (BPTI)...
  71. Splicing, Folding, and Stretching Nucleic Acids
    DANIEL AALBERTS; Fiscal Year: 2003
    ..1) Gene finding algorithms are currently statistics based. We, like cells, favor a thermodynamics-based approach to locating splice sites...