Research articles for Physical Biochemistry BIOL/CHEM 5312 project Spring 2008
You must select your article by April 3, and schedule a meeting with the instructor to discuss the outline of your paper.
This list will be updated periodically.
To see an abstract of the articles click the link in the title of the article. These papers are all available in full-text (pdf) format. From off-campus, you may need to go through the library's "Online Resources" page, as described here.
To select one of the articles, notify me.
The selected articles are shown in the Table below:
| Order | Student | Paper Selected | Paper received |
| 3 | Bahaa Bedair |
Kusumi A, Nakada C, Ritchie K, Murase K, Suzuki K, Murakoshi H, Kasai RS, Kondo J, Fujiwara T. |
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| 1 | Mallika Doss | Horn JR, Russell D, Lewis EA, Murphy KP. Van't Hoff and calorimetric enthalpies from isothermal titration calorimetry: are there significant discrepancies? Biochemistry. 2001 Feb 13;40(6):1774-8. |
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| 4 | Julius Ejiofor |
Prazeres DM. |
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| 2 | Michael Evans | Xu H, Dill KA. Water's hydrogen bonds in the hydrophobic effect: a simple model. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2005 Dec 15;109(49):23611-7. |
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| 7 | Shalla Hanson | Lim W, Feng YP. The stretched intermediate model of B-Z DNA transition. Biophys J. 2005 Mar;88(3):1593-607 |
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| 5 | Thoris Pan | Persikov AV, Xu Y, Brodsky B. Equilibrium thermal transitions of collagen model peptides. Protein Sci. 2004 Apr;13(4):893-902. Epub 2004 Mar 9 |
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| 6 | Kalie Van Ree |
Gambin Y, Lopez-Esparza R, Reffay M, Sierecki E, Gov NS, Genest M, Hodges RS, Urbach W. |
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| 8 | Gauri Verma | Hyeon C, Dima RI, Thirumalai D. Size, shape, and flexibility of RNA structures. J Chem Phys. 2006 Nov 21;125(19):194905 |
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Chapman R, Kulp Iii JL, Patgiri A, Kallenbach NR, Bracken C, Arora PS.
Trapping a Folding Intermediate of the alpha-Helix: Stabilization of the pi-Helix.
Biochemistry. 2008 Mar 13; [Epub ahead of print]
Sumiko Araki, Tonau Nakai, Kohji Hizume, Kunio Takeyasu and Kenichi Yoshikawa
Hydrodynamic radius of circular DNA is larger than that of linear DNA
Chem Phys Lett. 418: 255-259
Lee HT, Olsen CM, Waters L, Sukup H, Marky LA.
Thermodynamic contributions of the reactions of DNA intramolecular structures with their complementary strands.
Biochimie. 2008 Feb 8; [Epub ahead of print]
Loregian A, Sinigalia E, Mercorelli B, Palù G, Coen DM.
Binding parameters and thermodynamics of the interaction of the human cytomegalovirus DNA polymerase accessory protein, UL44, with DNA: implications for the processivity mechanism.
Nucleic Acids Res. 2007;35(14):4779-91
Meier M, Seelig J.
Length dependence of the coil <--> beta-sheet transition in a membrane environment.
J Am Chem Soc. 2008 Jan 23;130(3):1017-24
Kaur H, Wengel J, Maiti S.
Thermodynamics of DNA-RNA heteroduplex formation: effects of locked nucleic acid nucleotides incorporated into the DNA strand.
Biochemistry. 2008 Jan 29;47(4):1218-27
Liu CC, Richard AJ, Datta K, Licata V.
Prevalence of Temperature Dependent Heat Capacity Changes in Protein-DNA Interactions.
Biophys J. 2008 Jan 16; [Epub ahead of print]
Gong H, Rose GD.
Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model.
Proc Natl Acad Sci U S A. 2008 Feb 27; [Epub ahead of print]
Zhao H, Streaker E, Pan W, Beckett D.
Protein-protein interactions dominate the assembly thermodynamics of a transcription repression complex.
Biochemistry. 2007 Nov 27;46(47):13667-7
Tang KH, Niebuhr M, Aulabaugh A, Tsai MD.
Solution structures of 2 : 1 and 1 : 1 DNA polymerase-DNA complexes probed by ultracentrifugation and small-angle X-ray scattering.
Nucleic Acids Res. 2008 Feb;36(3):849-60
Ghirlando R, Felsenfeld G.
Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn.
J Mol Biol. 2008 Mar 7;376(5):1417-25
Kohlheyer D, Eijkel JC, van den Berg A, Schasfoort RB.
Miniaturizing free-flow electrophoresis - a critical review.
Electrophoresis. 2008 Jan 29;29(5):977-993
Kohlheyer D, Eijkel JC, Schlautmann S, van den Berg A, Schasfoort RB.
Microfluidic high-resolution free-flow isoelectric focusing.
Anal Chem. 2007 Nov 1;79(21):8190-8.
Szyma?ski J, Patkowski A, Wilk A, Garstecki P, Holyst R.
Diffusion and viscosity in a crowded environment: from nano- to macroscale.
J Phys Chem B. 2006 Dec 28;110(51):25593-7
Wolgemuth CW, Sun SX.
Elasticity of alpha-helical coiled coils.
Phys Rev Lett. 2006 Dec 15;97(24):248101
Bobrovnik S.
New capabilities in determining the binding parameters for ligand-receptor interaction.
J Biochem Biophys Methods. 2005 Oct 31;65(1):30-44. Epub 2005 Sep 13.
Zhang H, Yu H, Ren J, Qu X.
Reversible B-Z DNA transition under the low salt condition and non-B form polydApolydT selectivity by a cubane-like europium-L-aspartic acid complex.
Biophys J. 2006 Feb 10; [Epub ahead of print]
Wang M, Wales TE, Fitzgerald MC.
Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold.
Proc Natl Acad Sci U S A. 2006 Feb 10; [Epub ahead of print]
Graneli A, Yeykal CC, Robertson RB, Greene EC.
Long-distance lateral diffusion of human Rad51 on double-stranded DNA.
Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1221-6. Epub 2006 Jan 23.
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Gong H, Fleming PJ, Rose GD.
Building native protein conformation from highly approximate backbone torsion angles.
Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16227-32. Epub 2005 Oct 26.
Gowers DM, Wilson GG, Halford SE.
Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.
Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15883-8. Epub 2005 Oct 21.
Burak Y, Orland H.
Manning condensation in two dimensions.
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jan;73(1 Pt 1):010501. Epub 2006 Jan 9.
Velazquez-Campoy A.
Ligand binding to one-dimensional lattice-like macromolecules: analysis of the McGhee-von Hippel theory implemented in isothermal titration calorimetry.
Anal Biochem. 2006 Jan 1;348(1):94-104. Epub 2005 Oct 26.
Sikora CW, Turner RJ.
Investigation of ligand binding to the multidrug resistance protein EmrE by isothermal titration calorimetry.
Biophys J. 2005 Jan;88(1):475-82. Epub 2004 Oct 22
Barratt E, Bingham RJ, Warner DJ, Laughton CA, Phillips SE, Homans SW
Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water.
J Am Chem Soc. 2005 Aug 24;127(33):11827-34.
Menze MA, Hellmann N, Decker H, Grieshaber MK
Allosteric models for multimeric proteins: oxygen-linked effector binding in hemocyanin.
Biochemistry. 2005 Aug 2;44(30):10328-38
Lim W, Feng YP.
Applying the stochastic difference equation to DNA conformational transitions: a study of B-Z and B-A DNA transitions.
Biopolymers. 2005 Jun 15;78(3):107-20
Dell'Orco D, Xue WF, Thulin E, Linse S.
Electrostatic contributions to the kinetics and thermodynamics of protein assembly.
Biophys J. 2005 Mar;88(3):1991-2002. Epub 2004 Dec 13.
Richardson JM, Lopez MM, Makhatadze GI.
Enthalpy of helix-coil transition: missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues.
Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1413-8.
Sandstrom P, Akerman B.
Electrophoretic properties of DNA-modified colloidal gold nanoparticles.
Langmuir. 2004 May 11;20(10):4182-6.
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