Research articles for Physical Biochemistry BIOL/CHEM 5312 project Spring 2015

You must select your article by April , 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:

Friday, April 17, 2015 8:43 AM

DNA looping provides for "intersegmental hopping" by proteins: a mechanism for long-range site localization.
Pollak AJ, Chin AT, Brown FL, Reich NO.
J Mol Biol. 2014 Oct 23;426(21):3539-52.

Characterization of membrane protein interactions by isothermal titration calorimetry.
Situ AJ, Schmidt T, Mazumder P, Ulmer TS.
J Mol Biol. 2014 Oct 23;426(21):3670-80.

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.
Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL 3rd.
J Mol Biol. 2014 Sep 23;426(19):3201-13.

Diffusion of human replication protein A along single-stranded DNA.
Nguyen B, Sokoloski J, Galletto R, Elson EL, Wold MS, Lohman TM.
J Mol Biol. 2014 Sep 23;426(19):3246-61.

Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer.
Lee KS, Marciel AB, Kozlov AG, Schroeder CM, Lohman TM, Ha T.
J Mol Biol. 2014 Jun 26;426(13):2413-21.

Redefining the dry molten globule state of proteins.
Neumaier S, Kiefhaber T.
J Mol Biol. 2014 Jun 26;426(13):2520-8.

Folding pathways of the Tetrahymena ribozyme.
Mitchell D 3rd, Russell R.
J Mol Biol. 2014 Jun 12;426(12):2300-12.

Folding and unfolding pathways of the human telomeric G-quadruplex.
Gray RD, Trent JO, Chaires JB.
J Mol Biol. 2014 Apr 17;426(8):1629-50.

Thermodynamic and structural basis for relaxation of specificity in protein-DNA recognition.
Sapienza PJ, Niu T, Kurpiewski MR, Grigorescu A, Jen-Jacobson L.
J Mol Biol. 2014 Jan 9;426(1):84-104.

Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein.
Politis A, Park AY, Hall Z, Ruotolo BT, Robinson CV.
J Mol Biol. 2013 Nov 29;425(23):4790-801.

Three-dimensional structure and biophysical characterization of Staphylococcus aureus cell surface antigen-manganese transporter MntC.
Gribenko A, Mosyak L, Ghosh S, Parris K, Svenson K, Moran J, Chu L, Li S, Liu T, Woods VL Jr, Jansen KU, Green BA, Anderson AS, Matsuka YV.
J Mol Biol. 2013 Sep 23;425(18):3429-45.

Molecular crowding limits translation and cell growth.
Klumpp S, Scott M, Pedersen S, Hwa T.
Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16754-9. doi: 10.1073/pnas.1310377110. Epub 2013 Sep 30.

Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions.
Phelps C, Lee W, Jose D, von Hippel PH, Marcus AH.
Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17320-5. doi: 10.1073/pnas.1314862110. Epub 2013 Sep 23.

Protein-DNA binding in the absence of specific base-pair recognition.
Afek A, Schipper JL, Horton J, Gordân R, Lukatsky DB.
Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17140-5. doi: 10.1073/pnas.1410569111. Epub 2014 Oct 13.

Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding.
Baldwin RL.
Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13052-6. doi: 10.1073/pnas.1414556111. Epub 2014 Aug 25.

Modulation of DNA loop lifetimes by the free energy of loop formation.
Chen YJ, Johnson S, Mulligan P, Spakowitz AJ, Phillips R.
Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17396-401. doi: 10.1073/pnas.1415685111. Epub 2014 Nov 19.

Measurement of histidine pKa values and tautomer populations in invisible protein states.
Hansen AL, Kay LE.
Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):E1705-12. doi: 10.1073/pnas.1400577111. Epub 2014 Apr 14.

Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride.
Jha SK, Marqusee S.
Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4856-61. doi: 10.1073/pnas.1315453111. Epub 2014 Mar 17.

Effects of side chains in helix nucleation differ from helix propagation.
Miller SE, Watkins AM, Kallenbach NR, Arora PS.
Proc Natl Acad Sci U S A. 2014 May 6;111(18):6636-41. doi: 10.1073/pnas.1322833111. Epub 2014 Apr 21.

The heat released during catalytic turnover enhances the diffusion of an enzyme.
Riedel C, Gabizon R, Wilson CA, Hamadani K, Tsekouras K, Marqusee S, Pressé S, Bustamante C.
Nature. 2015 Jan 8;517(7533):227-30. doi: 10.1038/nature14043. Epub 2014 Dec 10.

Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein.
Robinson AC, Castañeda CA, Schlessman JL, García-Moreno EB.
Proc Natl Acad Sci U S A. 2014 Aug 12;111(32):11685-90. doi: 10.1073/pnas.1402900111. Epub 2014 Jul 29.

Experimental basis for a new allosteric model for multisubunit proteins.
Viappiani C, Abbruzzetti S, Ronda L, Bettati S, Henry ER, Mozzarelli A, Eaton WA.
Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12758-63. doi: 10.1073/pnas.1413566111. Epub 2014 Aug 19.

Thermodynamic mechanism for inhibition of lactose permease by the phosphotransferase protein IIAGlc.
Hariharan P, Balasubramaniam D, Peterkofsky A, Kaback HR, Guan L.
Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2407-12. doi: 10.1073/pnas.1500891112. Epub 2015 Feb 9.

Temperature-dependent solvation modulates the dimensions of disordered proteins.
Wuttke R, Hofmann H, Nettels D, Borgia MB, Mittal J, Best RB, Schuler B.
Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5213-8. doi: 10.1073/pnas.1313006111. Epub 2014 Mar 21.

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors.
Priest DG, Cui L, Kumar S, Dunlap DD, Dodd IB, Shearwin KE.
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):349-54. doi: 10.1073/pnas.1317817111. Epub 2013 Dec 16.

Gene regulation by substoichiometric heterocomplex formation of undecameric TRAP and trimeric anti-TRAP.
Ihms EC, Zhou M, Zhang Y, Kleckner IR, McElroy CA, Wysocki VH, Gollnick P, Foster MP.
Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3442-7. doi: 10.1073/pnas.1315281111. Epub 2014 Feb 18.

Three-dimensional cell migration does not follow a random walk.
Wu PH, Giri A, Sun SX, Wirtz D.
Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):3949-54. doi: 10.1073/pnas.1318967111. Epub 2014 Mar 4.

Role of substrate unbinding in Michaelis-Menten enzymatic reactions.
Reuveni S, Urbakh M, Klafter J.
Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4391-6. doi: 10.1073/pnas.1318122111. Epub 2014 Mar 10.

Shape matters in protein mobility within membranes.
Quemeneur F, Sigurdsson JK, Renner M, Atzberger PJ, Bassereau P, Lacoste D.
Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5083-7. doi: 10.1073/pnas.1321054111. Epub 2014 Mar 24.

Eur Biophys J. 2012 Jun;41(6):505-26. doi: 10.1007/s00249-012-0806-8. Epub 2012 Apr 7.
On the simple random-walk models of ion-channel gate dynamics reflecting long-term memory.
Wawrzkiewicz A, Pawelek K, Borys P, Dworakowska B, Grzywna ZJ.

Eur Biophys J. 2012 Jul;41(7):607-14. doi: 10.1007/s00249-012-0828-2. Epub 2012 Jul 12.
Probing the catalytic allosteric mechanism of rabbit muscle pyruvate kinase by tryptophan fluorescence quenching.
Li F, Yu T, Zhao Y, Yu S.

Eur Biophys J. 2012 Nov;41(11):991-1001. doi: 10.1007/s00249-012-0862-0. Epub 2012 Oct 5.
Thermodynamics of strongly allosteric inhibition: a model study of HIV-1 protease.
Kimura S, Broglia RA, Tiana G.

Eur Biophys J. 2012 Dec;41(12):1055-64. doi: 10.1007/s00249-012-0864-y. Epub 2012 Oct 13.
Simultaneous diffusion and brightness measurements and brightness profile visualization from single fluorescence fluctuation traces of GFP in living cells.
Skakun VV, Engel R, Borst JW, Apanasovich VV, Visser AJ.

Eur Biophys J. 2013 Apr;42(4):281-90. doi: 10.1007/s00249-012-0873-x. Epub 2012 Dec 15.
The effect of ligand affinity on integrins' lateral diffusion in cultured cells.
Mainali D, Smith EA.

BMC Biophys. 2011 Mar 2;4:6. doi: 10.1186/2046-1682-4-6.
Brownian dynamics simulation of analytical ultracentrifugation experiments.
Díez A, Ortega A, Garcia de la Tore J.

BMC Biophys. 2011 May 31;4:13. doi: 10.1186/2046-1682-4-13.
An upper limit for macromolecular crowding effects.
Miklos AC, Li C, Sorrell CD, Lyon LA, Pielak GJ.

BMC Biophys. 2012 Aug 29;5:17. doi: 10.1186/2046-1682-5-17.
Physical constraints on the establishment of intracellular spatial gradients in bacteria.
Tropini C, Rabbani N, Huang KC.

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Biophys J. 2011 Dec 7;101(11):2782-9. doi: 10.1016/j.bpj.2011.09.033.
Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results.
Marcos E, Mestres P, Crehuet R.

Biophys J. 2011 Oct 19;101(8):1807-15. doi: 10.1016/j.bpj.2011.07.025.
Measurement and perturbation of morphogen lifetime: effects on gradient shape.
Drocco JA, Grimm O, Tank DW, Wieschaus E.

Biophys J. 2011 Oct 5;101(7):1569-79. doi: 10.1016/j.bpj.2011.08.041.
Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation.
Geisel N, Gerland U.

Biophys J. 2011 Sep 7;101(5):1139-47. doi: 10.1016/j.bpj.2011.07.016.
The binding process of a nonspecific enzyme with DNA.
Chen C, Pettitt BM.

Biophys J. 2011 Sep 7;101(5):1130-8. doi: 10.1016/j.bpj.2011.07.003.
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration.
Beierlein FR, Kneale GG, Clark T.

Biophys J. 2011 Sep 7;101(5):1123-9. doi: 10.1016/j.bpj.2011.07.041.
High-affinity quasi-specific sites in the genome: how the DNA-binding proteins cope with them.
Chakrabarti J, Chandra N, Raha P, Roy S.

Biophys J. 2011 Aug 17;101(4):875-84. doi: 10.1016/j.bpj.2011.06.058.
Electrostatic braiding and homologous pairing of DNA double helices.
Cortini R, Kornyshev AA, Lee DJ, Leikin S.

Biophys J. 2011 Dec 21;101(12):2882-91. doi: 10.1016/j.bpj.2011.10.053. Epub 2011 Dec 20.
Effects of macromolecular crowding on genetic networks.
Morelli MJ, Allen RJ, Wolde PR.

Biophys J. 2011 Aug 3;101(3):727-35. doi: 10.1016/j.bpj.2011.06.033.
Interactions of cations with RNA loop-loop complexes.
Singh A, Sethaphong L, Yingling YG.

Biophys J. 2011 Jul 6;101(1):100-9. doi: 10.1016/j.bpj.2011.05.047.
Thermodynamic profiling of peptide membrane interactions by isothermal titration calorimetry: a search for pores and micelles.
Henriksen JR, Andresen TL.

Biophys J. 2011 Jul 6;101(1):70-9. doi: 10.1016/j.bpj.2011.05.034.
Origins and consequences of velocity fluctuations during DNA passage through a nanopore.
Lu B, Albertorio F, Hoogerheide DP, Golovchenko JA.

Biophys J. 2011 Jun 22;100(12):2974-80. doi: 10.1016/j.bpj.2011.05.007.
Long dwell-time passage of DNA through nanometer-scale pores: kinetics and sequence dependence of motion.
Jetha NN, Feehan C, Wiggin M, Tabard-Cossa V, Marziali A.

Biophys J. 2011 Jun 8;100(11):2745-53. doi: 10.1016/j.bpj.2011.04.038.
Theory for RNA folding, stretching, and melting including loops and salt.
Einert TR, Netz RR.

Biophys J. 2011 Apr 20;100(8):2006-15. doi: 10.1016/j.bpj.2011.02.049.
Condensation prevails over B-A transition in the structure of DNA at low humidity.
Hormeño S, Moreno-Herrero F, Ibarra B, Carrascosa JL, Valpuesta JM, Arias-Gonzalez JR.

Biophys J. 2011 Feb 16;100(4):1139-48. doi: 10.1016/j.bpj.2010.08.080.
Rotational diffusion of the α(2a) adrenergic receptor revealed by FlAsH labeling in living cells.
Spille JH, Zürn A, Hoffmann C, Lohse MJ, Harms GS.

Biophys J. 2011 Feb 16;100(4):1049-57. doi: 10.1016/j.bpj.2011.01.014.
Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair.
Spiriti J, Binder JK, Levitus M, van der Vaart A.

Biophys J. 2011 Feb 16;100(4):904-11. doi: 10.1016/j.bpj.2010.12.3739.
Mapping heat exchange in an allosteric protein.
Gupta S, Auerbach A.

Biophys J. 2011 Feb 2;100(3):611-9. doi: 10.1016/j.bpj.2010.12.3708.
Brownian dynamics simulations of ion transport through the VDAC.
Lee KI, Rui H, Pastor RW, Im W.

Biophys J. 2011 Feb 2;100(3):602-10. doi: 10.1016/j.bpj.2010.12.3711.
Molecular dynamics studies of ion permeation in VDAC.
Rui H, Lee KI, Pastor RW, Im W.

Biophys J. 2011 Jan 19;100(2):459-68. doi: 10.1016/j.bpj.2010.11.087.
An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability.
Linhananta A, Hadizadeh S, Plotkin SS.

Biophys J. 2011 Jan 5;100(1):22-31. doi: 10.1016/j.bpj.2010.11.044.
Protein diffusion in the periplasm of E. coli under osmotic stress.
Sochacki KA, Shkel IA, Record MT, Weisshaar JC.

Biophys J. 2012 Apr 4;102(7):1685-91. doi: 10.1016/j.bpj.2012.02.030. Epub 2012 Apr 3.
Single-image diffusion coefficient measurements of proteins in free solution.
Zareh SK, DeSantis MC, Kessler JM, Li JL, Wang YM.

Biophys J. 2012 Apr 4;102(7):1656-65. doi: 10.1016/j.bpj.2012.02.029. Epub 2012 Apr 3.
Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis.
Mueller F, Morisaki T, Mazza D, McNally JG.

Biophys J. 2012 Apr 4;102(7):1636-45. doi: 10.1016/j.bpj.2012.02.048. Epub 2012 Apr 3.
Highly perturbed pKa values in the unfolded state of hen egg white lysozyme.
Bradley J, O'Meara F, Farrell D, Nielsen JE.

Biophys J. 2012 Apr 4;102(7):1590-7. doi: 10.1016/j.bpj.2012.02.021. Epub 2012 Apr 3.
Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation.
Shi C, Wallace JA, Shen JK.

Biophys J. 2012 Mar 7;102(5):1194-203. doi: 10.1016/j.bpj.2012.02.003. Epub 2012 Mar 6.
Measurement of the mitochondrial membrane potential and pH gradient from the redox poise of the hemes of the bc1 complex.
Kim N, Ripple MO, Springett R.

Biophys J. 2012 Feb 8;102(3):552-60. doi: 10.1016/j.bpj.2011.11.4023. Epub 2012 Feb 7.
Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)?.
Wheatley EG, Pieniazek SN, Mukerji I, Beveridge DL.

Biophys J. 2012 Jan 4;102(1):101-11. doi: 10.1016/j.bpj.2011.11.4017. Epub 2012 Jan 3.
A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics.
Kuznetsov SV, Ansari A.

Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):17876-82. doi: 10.1073/pnas.1114477108. Epub 2011 Oct 17.
Physical limits of cells and proteomes.
Dill KA, Ghosh K, Schmit JD.

Eur Biophys J. 2011 May;40(5):673-85. doi: 10.1007/s00249-011-0673-8. Epub 2011 Jan 28.
Stability and folding dynamics of polyglutamic acid.
Krejtschi C, Hauser K.

Biophys Chem. 2011 Jun;156(1):88-95. doi: 10.1016/j.bpc.2011.02.001. Epub 2011 Feb 15.
The effect of hydrostatic pressure on the thermal stability of DNA hairpins.
Amiri AR, Macgregor RB Jr.

Biophys Chem. 2011 Nov;159(1):162-71. doi: 10.1016/j.bpc.2011.06.006. Epub 2011 Jun 21.
Melting behavior and ligand binding of DNA intramolecular secondary structures.
Maiti S, Kankia B, Khutsishvili I, Marky LA.

J Chem Phys. 2012 Jun 7;136(21):215101. doi: 10.1063/1.4723871.
Crowding effect on helix-coil transition: beyond entropic stabilization.
Koutsioubas A, Lairez D, Combet S, Fadda GC, Longeville S, Zalczer G.

Biopolymers. 2012 Oct;97(10):807-17. doi: 10.1002/bip.22077.
Thermal stability of DNA with interstrand crosslinks.
Chang CL, Lando DY, Fridman AS, Hu CK.

Phys Rev Lett. 2012 Aug 10;109(6):068101. Epub 2012 Aug 7.
Osmotic Pressure Induced Coupling between Cooperativity and Stability of a Helix-Coil Transition.
Badasyan A, Tonoyan S, Giacometti A, Podgornik R, Parsegian VA, Mamasakhlisov Y, Morozov V.

Eur Phys J E Soft Matter. 2011 Dec;34(12):1-18. doi: 10.1140/epje/i2011-11132-6. Epub 2011 Dec 23.
Counterion condensation theory of attraction between like charges in the absence of multivalent counterions.
Manning GS.

J Phys Chem B. 2011 Aug 18;115(32):9864-72. doi: 10.1021/jp204915y. Epub 2011 Jul 26.
Theoretical assessment of the oligolysine model for ionic interactions in protein-DNA complexes.
Fenley MO, Russo C, Manning GS.

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Biochemistry. 2010 Nov 16;49(45):9820-9. doi: 10.1021/bi101136d. Epub 2010 Oct 22.
Effect of temperature on the self-assembly of the Escherichia coli ClpA molecular chaperone.
Veronese PK, Lucius AL.

Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19808-13. doi: 10.1073/pnas.1005267107. Epub 2010 Nov 1.
Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP.
Khan MQ, Sweeting B, Mulligan VK, Arslan PE, Cashman NR, Pai EF, Chakrabartty A.

PLoS Biol. 2010 Dec 7;8(12):e1000555. doi: 10.1371/journal.pbio.1000555.
S. aureus MscL is a pentamer in vivo but of variable stoichiometries in vitro: implications for detergent-solubilized membrane proteins.
Dorwart MR, Wray R, Brautigam CA, Jiang Y, Blount P.

Biochemistry. 2011 Sep 20;50(37):7868-80. doi: 10.1021/bi200753b. Epub 2011 Aug 26.
Self-assembly of Escherichia coli MutL and its complexes with DNA.
Niedziela-Majka A, Maluf NK, Antony E, Lohman TM.

J Pharm Sci. 2012 Jan;101(1):92-101. doi: 10.1002/jps.22755. Epub 2011 Sep 15.
Resolving the challenge of measuring ligand binding to membrane proteins by combining analytical ultracentrifugation and light scattering photometry.
Doran JD, Mohanty AK, Fox T.

Anal Biochem. 2012 Mar 1;422(1):28-32. doi: 10.1016/j.ab.2011.12.010. Epub 2011 Dec 13.
Allowance for effects of thermodynamic nonideality in sedimentation equilibrium distributions reflecting protein dimerization.
Wills PR, Scott DJ, Winzor DJ.

Biochemistry. 2012 Jun 5;51(22):4541-50. Epub 2012 May 22.
Mg(2+)-linked self-assembly of FtsZ in the presence of GTP or a GTP analogue involves the concerted formation of a narrow size distribution of oligomeric species.
Monterroso B, Ahijado-Guzmán R, Reija B, Alfonso C, Zorrilla S, Minton AP, Rivas G.

Biophys J. 2012 Jul 18;103(2):303-12. doi: 10.1016/j.bpj.2012.05.041. Epub 2012 Jul 17. (email the author for a copy)
Bovine β-lactoglobulin is dimeric under imitative physiological conditions: dissociation equilibrium and rate constants over the pH range of 2.5-7.5.
Mercadante D, Melton LD, Norris GE, Loo TS, Williams MA, Dobson RC, Jameson GB.

Biochim Biophys Acta. 2012 Dec;1818(12):3090-7. doi: 10.1016/j.bbamem.2012.08.004. Epub 2012 Aug 18.
Oligomeric state study of prokaryotic rhomboid proteases.
Sampathkumar P, Mak MW, Fischer-Witholt SJ, Guigard E, Kay CM, Lemieux MJ.

Biochemistry. 2012 Nov 13;51(45):9147-55. doi: 10.1021/bi301126g. Epub 2012 Nov 2.
Thermodynamic characterization of a thermostable antibiotic resistance enzyme, the aminoglycoside nucleotidyltransferase (4').
Jing X, Wright E, Bible AN, Peterson CB, Alexandre G, Bruce BD, Serpersu EH.

Eur Biophys J. 2013 Mar 20. [Epub ahead of print]
Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B12-based photosensory regulator.
Díez AI, Ortiz-Guerrero JM, Ortega A, Elías-Arnanz M, Padmanabhan S, García de la Torre J.

Eur Phys J E Soft Matter. 2012 Nov;35(11):118. doi: 10.1140/epje/i2012-12118-6. Epub 2012 Nov 21.
Beyond Saffman-Delbruck approximation: a new regime for 2D diffusion of α-hemolysin complexes in supported lipid bilayer.
Harb F, Sarkis J, Ferte N, Tinland B.

Cell Mol Life Sci. 2013 Apr;70(8):1483-92. doi: 10.1007/s00018-012-1219-7. Epub 2012 Dec 8.
Diffusion of D-glucose measured in the cytosol of a single astrocyte.
Kreft M, Lukši? M, Zorec TM, Prebil M, Zorec R.

J Chem Phys. 2012 Dec 7;137(21):215104. doi: 10.1063/1.4768956.
Single molecule diffusion in critical lipid bilayers.
McConnell H.

Eur Phys J E Soft Matter. 2012 Dec;35(12):9806. doi: 10.1140/epje/i2012-12130-x. Epub 2012 Dec 14.
Translational diffusion coefficients of macromolecules.
Rodríguez Schmidt R, Hernández Cifre JG, García de la Torre J.

Elife. 2012;1:e00067. doi: 10.7554/eLife.00067. Epub 2012 Dec 13.
RecA filament sliding on DNA facilitates homology search.
Ragunathan K, Liu C, Ha T.

Eur Biophys J. 2013 Apr;42(4):281-90. doi: 10.1007/s00249-012-0873-x. Epub 2012 Dec 15.
The effect of ligand affinity on integrins' lateral diffusion in cultured cells.
Mainali D, Smith EA.

Chem Commun (Camb). 2013 Jan 30;49(9):907-9. doi: 10.1039/c2cc37517f.
Quantum dot-DNA origami binding: a single particle, 3D, real-time tracking study.
Du K, Ko SH, Gallatin GM, Yoon HP, Liddle JA, Berglund AJ.

Biochim Biophys Acta. 2013 Apr;1828(4):1259-70. doi: 10.1016/j.bbamem.2013.01.005. Epub 2013 Jan 16.
Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells.
Andoh Y, Okazaki S, Ueoka R.

Langmuir. 2013 Feb 19;29(7):2289-98. doi: 10.1021/la3043473. Epub 2013 Feb 4.
Solvation dynamics of biological water in a single live cell under a confocal microscope.
Sasmal DK, Ghosh S, Das AK, Bhattacharyya K.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3847-52. doi: 10.1073/pnas.1300596110. Epub 2013 Feb 13.
Elasticity, structure, and relaxation of extended proteins under force.
Stirnemann G, Giganti D, Fernandez JM, Berne BJ.

Colloids Surf B Biointerfaces. 2013 Jun 1;106:22-7. doi: 10.1016/j.colsurfb.2013.01.017. Epub 2013 Jan 19.
Lateral diffusion of lipids separated from rotational and translational diffusion of a fluid large unilamellar vesicle.
Yoshii N, Emoto T, Okamura E.

Rev Sci Instrum. 2013 Feb;84(2):023904. doi: 10.1063/1.4790567.
Translational diffusion of probe molecules under high pressure: A study by fluorescence recovery after photobleaching technique.
Bonetti M, Roger M.

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J Mol Biol. 2013 Feb 8;425(3):647-61. doi: 10.1016/j.jmb.2012.11.041. Epub 2012 Dec 7.
Impact of mutations on the allosteric conformational equilibrium.
Weinkam P, Chen YC, Pons J, Sali A.

Biochim Biophys Acta. 2013 Feb 1. pii: S1570-9639(13)00035-6. doi: 10.1016/j.bbapap.2013.01.024. [Epub ahead of print]
Thermodynamics of allostery paves a way to allosteric drugs.
Berezovsky IN.

J Mol Biol. 2013 Mar 19. pii: S0022-2836(13)00162-9. doi: 10.1016/j.jmb.2013.03.014. [Epub ahead of print]
Derivation of the Crick-Wyman Equation for Allosteric Proteins Defining the Difference between the Number of Binding Sites and the Hill Coefficient.
Poitevin F, Edelstein SJ.

J Mol Biol. 2013 Mar 21. pii: S0022-2836(13)00158-7. doi: 10.1016/j.jmb.2013.03.011. [Epub ahead of print]
Cooperativity of Allosteric Receptors.
Edelstein SJ, Le Novère N.

Science. 2013 Feb 15;339(6121):816-9. doi: 10.1126/science.1229223.
Probing allostery through DNA.
Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS.

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An energetic representation of protein architecture that is independent of primary and secondary structure.
Vertrees J, Wrabl JO, Hilser VJ.
Biophys J. 2009 Sep 2;97(5):1461-70.

Crowding effects on association reactions at membranes.
Kim JS, Yethiraj A.
Biophys J. 2010 Mar 17;98(6):951-8.

Hydration potential of lysozyme: protein dehydration using a single microparticle technique.
Rickard DL, Duncan PB, Needham D.
Biophys J. 2010 Mar 17;98(6):1075-84.

Statistics and physical origins of pK and ionization state changes upon protein-ligand binding.
Aguilar B, Anandakrishnan R, Ruscio JZ, Onufriev AV.
Biophys J. 2010 Mar 3;98(5):872-80.

Ion conduction in ligand-gated ion channels: Brownian dynamics studies of four recent crystal structures.
Song C, Corry B.
Biophys J. 2010 Feb 3;98(3):404-11.

Salt-dependent folding energy landscape of RNA three-way junction.
Chen G, Tan ZJ, Chen SJ.
Biophys J. 2010 Jan 6;98(1):111-20.

Helix/coil nucleation: a local response to global demands.
Vorov OK, Livesay DR, Jacobs DJ.
Biophys J. 2009 Dec 2;97(11):3000-9.

E. coli superdiffusion and chemotaxis-search strategy, precision, and motility.
Matthäus F, Jagodic M, Dobnikar J.
Biophys J. 2009 Aug 19;97(4):946-57.

Sequence dependencies of DNA deformability and hydration in the minor groove.
Yonetani Y, Kono H.
Biophys J. 2009 Aug 19;97(4):1138-47.

Common crowding agents have only a small effect on protein-protein interactions.
Phillip Y, Sherman E, Haran G, Schreiber G.
Biophys J. 2009 Aug 5;97(3):875-85.

Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures.
Novak IL, Kraikivski P, Slepchenko BM.
Biophys J. 2009 Aug 5;97(3):758-67.

Thermodynamics of forming a parallel DNA crossover.
Spink CH, Ding L, Yang Q, Sheardy RD, Seeman NC.
Biophys J. 2009 Jul 22;97(2):528-38.

Diffusion and partitioning of fluorescent lipid probes in phospholipid monolayers.
Gudmand M, Fidorra M, Bjørnholm T, Heimburg T.
Biophys J. 2009 Jun 3;96(11):4598-609.

Protein dynamics explain the allosteric behaviors of hemoglobin.
Yonetani T, Laberge M.
Biochim Biophys Acta. 2008 Sep;1784(9):1146-58. Epub 2008 May 8. Review.

RNA folding on the 3D triangular lattice.
Gillespie J, Mayne M, Jiang M.
BMC Bioinformatics. 2009 Nov 5;10:369.

Fluorescence recovery after photobleaching: the case of anomalous diffusion.
Lubelski A, Klafter J.
Biophys J. 2008 Jun;94(12):4646-53. Epub 2008 Mar 7.

Downhill versus two-state protein folding in a statistical mechanical model.
Bruscolini P, Pelizzola A, Zamparo M.
J Chem Phys. 2007 Jun 7;126(21):215103.

Correcting for Heat Capacity and 5'-TA Type Terminal Nearest Neighbors Improves Prediction of DNA Melting Temperatures Using Nearest-Neighbor Thermodynamic Models.
Hughesman CB, Turner RF, Haynes C.
Biochemistry. 2011 Mar 8. [Epub ahead of print]

Thermophoretic melting curves quantify the conformation and stability of RNA and DNA.
Wienken CJ, Baaske P, Duhr S, Braun D.
Nucleic Acids Res. 2011 Feb 4. [Epub ahead of print]

Single-molecule derivation of salt dependent base-pair free energies in DNA.
Huguet JM, Bizarro CV, Forns N, Smith SB, Bustamante C, Ritort F.
Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15431-6. Epub 2010 Aug 17.

Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation.
Lee J, Kim YG, Kim KK, Seok C.
J Phys Chem B. 2010 Aug 5;114(30):9872-81. (pdf)

The interaction between a charged wall and its counterions: a condensation theory.
Manning GS.
J Phys Chem B. 2010 Apr 29;114(16):5435-40.

Divalent counterion-induced condensation of triple-strand DNA.
Qiu X, Parsegian VA, Rau DC.
Proc Natl Acad Sci U S A. 2010 Nov 22. [Epub ahead of pr

Conformation parameters of linear macromolecules from velocity sedimentation and other hydrodynamic methods.
Pavlov GM, Perevyazko IY, Okatova OV, Schubert US.
Methods. 2011 Feb 12. [Epub ahead of print]

Evaluating the stoichiometry of macromolecular complexes using multisignal sedimentation velocity.
Padrick SB, Brautigam CA.
Methods. 2011 Jan 20. [Epub ahead of print]

Beyond the second virial coefficient: Sedimentation equilibrium in highly non-ideal solutions.
Rivas G, Minton AP.
Methods. 2010 Nov 26. [Epub ahead of print]

Diffusion and sedimentation interaction parameters for measuring the second virial coefficient and their utility as predictors of protein aggregation.
Saluja A, Fesinmeyer RM, Hogan S, Brems DN, Gokarn YR.
Biophys J. 2010 Oct 20;99(8):2657-65.

Diffusion of the reaction boundary of rapidly interacting macromolecules in sedimentation velocity.
Schuck P.
Biophys J. 2010 Jun 2;98(11):2741-51.

Methods and tools for the prediction of hydrodynamic coefficients and other solution properties of flexible macromolecules in solution. A tutorial minireview.
García de la Torre J, Ortega A, Amorós D, Rodríguez Schmidt R, Hernández Cifre JG.
Macromol Biosci. 2010 Jul 7;10(7):721-30. Review.

Size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy.
Erickson HP.
Biol Proced Online. 2009 May 15;11:32-51.

Gel chromatography and analytical ultracentrifugation to determine the extent of detergent binding and aggregation, and Stokes radius of membrane proteins using sarcoplasmic reticulum Ca2+-ATPase as an example.
le Maire M, Arnou B, Olesen C, Georgin D, Ebel C, Møller JV.
Nat Protoc. 2008;3(11):1782-95. (pdf)

Molecular studies of pH-dependent ligand interactions with the low-density lipoprotein receptor.
Yamamoto T, Chen HC, Guigard E, Kay CM, Ryan RO.
Biochemistry. 2008 Nov 4;47(44):11647-52. Epub 2008 Oct 11.

Interactions between two touching spherical particles in sedimentation.
Sun R, Chwang AT.
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Oct;76(4 Pt 2):046316. Epub 2007 Oct 31.

Using prior knowledge in the determination of macromolecular size-distributions by analytical ultracentrifugation.
Brown PH, Balbo A, Schuck P.
Biomacromolecules. 2007 Jun;8(6):2011-24. Epub 2007 May 24.

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

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

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.

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Copyright 2015, Steven B. Vik, Southern Methodist University