U.S. Department of Health and Human Services

Laboratory of Chemical Physics

William A. Eaton, M.D., Ph.D., Chief

​Publications

A selection of recent and significant publications can be viewed below.

Publications
Schwieters CD, Clore GM. Using small angle solution scattering data in Xplor-NIH structure calculations.Prog Nucl Magn Reson Spectrosc. 2014 Jul; 80C (80C; 2014 Jul) :1-11. [Full Text/Abstract]
Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S. Encounter complexes and dimensionality reduction in protein-protein association.Elife. 2014 Apr 8; 3 (3; 2014 Apr 8) :e01370. [Full Text/Abstract]
Clore GM. Interplay between conformational selection and induced fit in multidomain protein-ligand binding probed by paramagnetic relaxation enhancement.Biophys Chem. 2014 Feb; 186 (186; 2014 Feb) :3-12. [Full Text/Abstract]
Deshmukh L, Ghirlando R, Clore GM. Investigation of the structure and dynamics of the capsid-spacer peptide 1-nucleocapsid fragment of the HIV-1 gag polyprotein by solution NMR spectroscopy.Angew Chem Int Ed Engl. 2014 Jan 20; 53 (4; 53; 2014 Jan 20) :1025-8. [Full Text/Abstract]
Best RB. Folding and Binding: When the Force is Against You.Biophys J. 2013 Dec 17; 105 (105; 2013 Dec 17; 12) :2611-2. [Full Text/Abstract]
Clore GM. Seeing the invisible by paramagnetic and diamagnetic NMR.Biochem Soc Trans. 2013 Dec; 41 (6; 2013 Dec; 41) :1343-54. [Full Text/Abstract]
Tsytlonok M, Craig PO, Sivertsson E, Serquera D, Perrett S, Best RB, Wolynes PG, Itzhaki LS. Complex energy landscape of a giant repeat protein.Structure. 2013 Nov 5; 21 (21; 2013 Nov 5; 11) :1954-65. [Full Text/Abstract]
Carter JW, Baker CM, Best RB, De Sancho D. Engineering folding dynamics from two-state to downhill: application to λ-repressor.J Phys Chem B. 2013 Oct 31; 117 (43; 117; 2013 Oct 31) :13435-43. [Full Text/Abstract]
Deshmukh L, Schwieters CD, Grishaev A, Ghirlando R, Baber JL, Clore GM. Structure and dynamics of full-length HIV-1 capsid protein in solution.J Am Chem Soc. 2013 Oct 30; 135 (2013 Oct 30; 43; 135) :16133-47. [Full Text/Abstract]
Henry ER, Best RB, Eaton WA. Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.Proc Natl Acad Sci U S A. 2013 Oct 29; 110 (110; 2013 Oct 29; 44) :17880-5. [Full Text/Abstract]
Best RB, Hummer G, Eaton WA. Native contacts determine protein folding mechanisms in atomistic simulations.Proc Natl Acad Sci U S A. 2013 Oct 29; 110 (110; 2013 Oct 29; 44) :17874-9. [Full Text/Abstract]
Best RB. How well does a funneled energy landscape capture the folding mechanism of spectrin domains?J Phys Chem B. 2013 Oct 24; 117 (117; 42; 2013 Oct 24) :13235-44. [Full Text/Abstract]
Clore GM, Venditti V. Structure, dynamics and biophysics of the cytoplasmic protein-protein complexes of the bacterial phosphoenolpyruvate: sugar phosphotransferase system.Trends Biochem Sci. 2013 Oct; 38 (38; 2013 Oct; 10) :515-30. [Full Text/Abstract]
Cope SM, Shinde S, Best RB, Ghirlanda G, Vaiana SM. Cyclic N-terminal loop of amylin forms non amyloid fibers.Biophys J. 2013 Oct 1; 105 (105; 7; 2013 Oct 1) :1661-9. [Full Text/Abstract]
Sirur A, Knott M, Best RB. Effect of interactions with the chaperonin cavity on protein folding and misfolding.Phys Chem Chem Phys. 2013 Sep 27 (2013 Sep 27) . [Full Text/Abstract]
Tycko R, Wickner RB. Molecular Structures of Amyloid and Prion Fibrils: Consensus versus Controversy.Acc. Chem. Res. 2013 Jul 16; 46 (46; 7; 2013 Jul 16) :1487-96. [Full Text/Abstract]
Libich DS, Fawzi NL, Ying J, Clore GM. Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR.Proc Natl Acad Sci U S A. 2013 Jul 9; 110 (28; 110; 2013 Jul 9) :11361-6. [Full Text/Abstract]
Anthis NJ, Clore GM. The length of the calmodulin linker determines the extent of transient interdomain association and target affinity.J Am Chem Soc. 2013 Jul 3; 135 (2013 Jul 3; 135; 26) :9648-51. [Full Text/Abstract]
Palomaki GE, Knight GJ, Ashwood ER, Best RG, Haddow JE. Screening for down syndrome in the United States: results of surveys in 2011 and 2012.Arch Pathol Lab Med. 2013 Jul; 137 (7; 137; 2013 Jul) :921-6. [Full Text/Abstract]
Baker CM, Best RB. Matching of additive and polarizable force fields for multiscale condensed phase simulations.J Chem Theory Comput. 2013 Jun 11; 9 (6; 9; 2013 Jun 11) :2826-2837. [Full Text/Abstract]
Anthis NJ, Clore GM. Sequence-specific determination of protein and peptide concentrations by absorbance at 205 nm.Protein Sci. 2013 Jun; 22 (6; 22; 2013 Jun) :851-8. [Full Text/Abstract]
Clore GM. Generating accurate contact maps of transient long-range interactions in intrinsically disordered proteins by paramagnetic relaxation enhancement.Biophys J. 2013 Apr 16; 104 (2013 Apr 16; 104; 8) :1635-6. [Full Text/Abstract]
Best RB. A "slow" protein folds quickly in the end.Proc Natl Acad Sci U S A. 2013 Apr 9; 110 (110; 15; 2013 Apr 9) :5744-5. [Full Text/Abstract]
Shim J, Zhu X, Best RB, MacKerell AD Jr. (Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters.J Comput Chem. 2013 Mar 15; 34 (2013 Mar 15; 7; 34) :593-603. [Full Text/Abstract]
Sirur A, Best RB. Effects of interactions with the GroEL cavity on protein folding rates.Biophys J. 2013 Mar 5; 104 (104; 5; 2013 Mar 5) :1098-106. [Full Text/Abstract]
Ross LF, Saal HM, David KL, Anderson RR, American Academy of Pediatrics, American College of Medical Genetics and Genomics. Technical report: Ethical and policy issues in genetic testing and screening of children.Genet Med. 2013 Mar; 15 (2013 Mar; 15; 3) :234-45. [Full Text/Abstract]
McMahon DM, Liu J, Zhang H, Torres ME, Best RG. Maternal obesity, folate intake, and neural tube defects in offspring.Birth Defects Res A Clin Mol Teratol. 2013 Feb; 97 (2; 97; 2013 Feb) :115-22. [Full Text/Abstract]
Thurber KR, Potapov A, Yau WM, Tycko R. Solid state nuclear magnetic resonance with magic-angle spinning and dynamic nuclear polarization below 25 K.J. Magn. Reson. 2013 Jan; 226 (226; 2013 Jan) :100-6. [Full Text/Abstract]
Lorieau JL, Louis JM, Schwieters CD, Bax A. pH-triggered, activated-state conformations of the influenza hemagglutinin fusion peptide revealed by NMR.Proc. Natl. Acad. Sci. U.S.A. 2012 Dec 4; 109 (109; 49; 2012 Dec 4) :19994-9. [Full Text/Abstract]
Bermejo GA, Clore GM, Schwieters CD. Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures.Protein Sci. 2012 Dec; 21 (2012 Dec; 12; 21) :1824-36. [Full Text/Abstract]