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    22841 Publications
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    20 Edited Profiles

    Marqusee, Susan

    TitleBiologist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/642-7678

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Koulechova DA, Tripp KW, Horner G, Marqusee S. When the Scaffold Cannot Be Ignored: The Role of the Hydrophobic Core in Ligand Binding and Specificity. J Mol Biol. 2015 Oct 9; 427(20):3316-26.
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      2. Petzold C, Marceau AH, Miller KH, Marqusee S, Keck JL. Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity. J Biol Chem. 2015 Jun 5; 290(23):14626-36.
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      3. Guinn EJ, Jagannathan B, Marqusee S. Single-molecule chemo-mechanical unfolding reveals multiple transition state barriers in a small single-domain protein. Nat Commun. 2015; 6:6861.
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      4. Rosen LE, Marqusee S. Autonomously Folding Protein Fragments Reveal Differences in the Energy Landscapes of Homologous RNases H. PLoS One. 2015; 10(3):e0119640.
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      5. Bowman GR, Bolin ER, Hart KM, Maguire BC, Marqusee S. Discovery of multiple hidden allosteric sites by combining Markov state models and experiments. Proc Natl Acad Sci U S A. 2015 Mar 3; 112(9):2734-9.
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      6. Riedel C, Gabizon R, Wilson CA, Hamadani K, Tsekouras K, Marqusee S, Pressé S, Bustamante C. The heat released during catalytic turnover enhances the diffusion of an enzyme. Nature. 2015 Jan 8; 517(7533):227-30.
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      7. Hart KM, Harms MJ, Schmidt BH, Elya C, Thornton JW, Marqusee S. Thermodynamic system drift in protein evolution. PLoS Biol. 2014 Nov; 12(11):e1001994.
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      8. Rosen LE, Kathuria SV, Matthews CR, Bilsel O, Marqusee S. Non-Native Structure Appears in Microseconds during the Folding of E. coli RNase H. J Mol Biol. 2015 Jan 30; 427(2):443-53.
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      9. Rosen LE, Connell KB, Marqusee S. Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule. Proc Natl Acad Sci U S A. 2014 Oct 14; 111(41):14746-51.
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      10. Pressé S, Peterson J, Lee J, Elms P, MacCallum JL, Marqusee S, Bustamante C, Dill K. Single molecule conformational memory extraction: p5ab RNA hairpin. J Phys Chem B. 2014 Jun 19; 118(24):6597-603.
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      11. Jha SK, Marqusee S. Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride. Proc Natl Acad Sci U S A. 2014 Apr 1; 111(13):4856-61.
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      12. Jagannathan B, Marqusee S. Protein folding and unfolding under force. Biopolymers. 2013 Nov; 99(11):860-9.
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      13. Dimster-Denk D, Tripp KW, Marini NJ, Marqusee S, Rine J. Mono and dual cofactor dependence of human cystathionine ß-synthase enzyme variants in vivo and in vitro. G3 (Bethesda). 2013 Oct; 3(10):1619-28.
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      14. Hu W, Walters BT, Kan ZY, Mayne L, Rosen LE, Marqusee S, Englander SW. Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry. Proc Natl Acad Sci U S A. 2013 May 7; 110(19):7684-9.
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      15. Udgaonkar J, Marqusee S. Folding and binding. Curr Opin Struct Biol. 2013 Feb; 23(1):1-3.
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      16. Elms PJ, Chodera JD, Bustamante CJ, Marqusee S. Limitations of constant-force-feedback experiments. Biophys J. 2012 Oct 3; 103(7):1490-9.
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      17. Jagannathan B, Elms PJ, Bustamante C, Marqusee S. Direct observation of a force-induced switch in the anisotropic mechanical unfolding pathway of a protein. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17820-5.
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      18. Elms PJ, Chodera JD, Bustamante C, Marqusee S. The molten globule state is unusually deformable under mechanical force. Proc Natl Acad Sci U S A. 2012 Mar 6; 109(10):3796-801.
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      19. Miller KH, Marqusee S. Propensity for C-terminal domain swapping correlates with increased regional flexibility in the C-terminus of RNase A. Protein Sci. 2011 Oct; 20(10):1735-44.
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      20. Bernstein R, Schmidt KL, Harbury PB, Marqusee S. Structural and kinetic mapping of side-chain exposure onto the protein energy landscape. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10532-7.
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      21. Cecconi C, Shank EA, Marqusee S, Bustamante C. DNA molecular handles for single-molecule protein-folding studies by optical tweezers. Methods Mol Biol. 2011; 749:255-71.
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      22. Hanes MS, Ratcliff K, Marqusee S, Handel TM. Protein-protein binding affinities by pulse proteolysis: application to TEM-1/BLIP protein complexes. Protein Sci. 2010 Oct; 19(10):1996-2000.
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      23. Ratcliff K, Marqusee S. Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues. Biochemistry. 2010 Jun 29; 49(25):5167-75.
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      24. Shank EA, Cecconi C, Dill JW, Marqusee S, Bustamante C. The folding cooperativity of a protein is controlled by its chain topology. Nature. 2010 Jun 3; 465(7298):637-40.
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      25. Miller KH, Karr JR, Marqusee S. A hinge region cis-proline in ribonuclease A acts as a conformational gatekeeper for C-terminal domain swapping. J Mol Biol. 2010 Jul 16; 400(3):567-78.
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      26. Ratcliff K, Corn J, Marqusee S. Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues. Biochemistry. 2009 Jun 30; 48(25):5890-8.
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      27. Connell KB, Miller EJ, Marqusee S. The folding trajectory of RNase H is dominated by its topology and not local stability: a protein engineering study of variants that fold via two-state and three-state mechanisms. J Mol Biol. 2009 Aug 14; 391(2):450-60.
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      28. Connell KB, Horner GA, Marqusee S. A single mutation at residue 25 populates the folding intermediate of E. coli RNase H and reveals a highly dynamic partially folded ensemble. J Mol Biol. 2009 Aug 14; 391(2):461-70.
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      29. Cecconi C, Shank EA, Dahlquist FW, Marqusee S, Bustamante C. Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers. Eur Biophys J. 2008 Jul; 37(6):729-38.
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      30. Cellitti J, Bernstein R, Marqusee S. Exploring subdomain cooperativity in T4 lysozyme II: uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway. Protein Sci. 2007 May; 16(5):852-62.
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      31. Cellitti J, Llinas M, Echols N, Shank EA, Gillespie B, Kwon E, Crowder SM, Dahlquist FW, Alber T, Marqusee S. Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment. Protein Sci. 2007 May; 16(5):842-51.
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      32. Park C, Zhou S, Gilmore J, Marqusee S. Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis. J Mol Biol. 2007 May 18; 368(5):1426-37.
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      33. Young TA, Skordalakes E, Marqusee S. Comparison of proteolytic susceptibility in phosphoglycerate kinases from yeast and E. coli: modulation of conformational ensembles without altering structure or stability. J Mol Biol. 2007 May 18; 368(5):1438-47.
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      34. Park C, Marqusee S. Quantitative determination of protein stability and ligand binding by pulse proteolysis. Curr Protoc Protein Sci. 2006 Dec; Chapter 20:Unit 20.11.
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      35. Freedman TS, Sondermann H, Friedland GD, Kortemme T, Bar-Sagi D, Marqusee S, Kuriyan J. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A. 2006 Nov 7; 103(45):16692-7.
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      36. Wildes D, Anderson LM, Sabogal A, Marqusee S. Native state energetics of the Src SH2 domain: evidence for a partially structured state in the denatured ensemble. Protein Sci. 2006 Jul; 15(7):1769-79.
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      37. de los Rios MA, Muralidhara BK, Wildes D, Sosnick TR, Marqusee S, Wittung-Stafshede P, Plaxco KW, Ruczinski I. On the precision of experimentally determined protein folding rates and phi-values. Protein Sci. 2006 Mar; 15(3):553-63.
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      38. Cecconi C, Shank EA, Bustamante C, Marqusee S. Direct observation of the three-state folding of a single protein molecule. Science. 2005 Sep 23; 309(5743):2057-60.
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      39. Park C, Marqusee S. Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding. Nat Methods. 2005 Mar; 2(3):207-12.
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      40. Maxwell KL, Wildes D, Zarrine-Afsar A, De Los Rios MA, Brown AG, Friel CT, Hedberg L, Horng JC, Bona D, Miller EJ, Vallée-Bélisle A, Main ER, Bemporad F, Qiu L, Teilum K, Vu ND, Edwards AM, Ruczinski I, Poulsen FM, Kragelund BB, Michnick SW, Chiti F, Bai Y, Hagen SJ, Serrano L, Oliveberg M, Raleigh DP, Wittung-Stafshede P, Radford SE, Jackson SE, Sosnick TR, Marqusee S, Davidson AR, Plaxco KW. Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci. 2005 Mar; 14(3):602-16.
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      41. Wildes D, Marqusee S. Hydrogen exchange and ligand binding: ligand-dependent and ligand-independent protection in the Src SH3 domain. Protein Sci. 2005 Jan; 14(1):81-8.
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      42. Park C, Marqusee S. Probing the high energy states in proteins by proteolysis. J Mol Biol. 2004 Nov 5; 343(5):1467-76.
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      43. Park C, Marqusee S. Analysis of the stability of multimeric proteins by effective DeltaG and effective m-values. Protein Sci. 2004 Sep; 13(9):2553-8.
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      44. Spudich GM, Miller EJ, Marqusee S. Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism. J Mol Biol. 2004 Jan 9; 335(2):609-18.
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      45. Wildes D, Marqusee S. Hydrogen-exchange strategies applied to energetics of intermediate processes in protein folding. Methods Enzymol. 2004; 380:328-49.
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      46. Robic S, Guzman-Casado M, Sanchez-Ruiz JM, Marqusee S. Role of residual structure in the unfolded state of a thermophilic protein. Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20):11345-9.
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      47. Kim R, Lai L, Lee HH, Cheong GW, Kim KK, Wu Z, Yokota H, Marqusee S, Kim SH. On the mechanism of chaperone activity of the small heat-shock protein of Methanococcus jannaschii. Proc Natl Acad Sci U S A. 2003 Jul 8; 100(14):8151-5.
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      48. Guzman-Casado M, Parody-Morreale A, Robic S, Marqusee S, Sanchez-Ruiz JM. Energetic evidence for formation of a pH-dependent hydrophobic cluster in the denatured state of Thermus thermophilus ribonuclease H. J Mol Biol. 2003 Jun 13; 329(4):731-43.
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      49. Miller EJ, Fischer KF, Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc Natl Acad Sci U S A. 2002 Aug 6; 99(16):10359-63.
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      50. Kern G, Pelton J, Marqusee S, Kern D. Structural properties of the histidine-containing loop in HIV-1 RNase H. Biophys Chem. 2002 May 2; 96(2-3):285-91.
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      51. Spudich G, Lorenz S, Marqusee S. Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state. Protein Sci. 2002 Mar; 11(3):522-8.
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      52. Nicholson EM, Mo H, Prusiner SB, Cohen FE, Marqusee S. Differences between the prion protein and its homolog Doppel: a partially structured state with implications for scrapie formation. J Mol Biol. 2002 Feb 22; 316(3):807-15.
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      53. Hollien J, Marqusee S. Comparison of the folding processes of T. thermophilus and E. coli ribonucleases H. J Mol Biol. 2002 Feb 15; 316(2):327-40.
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      54. Robic S, Berger JM, Marqusee S. Contributions of folding cores to the thermostabilities of two ribonucleases H. Protein Sci. 2002 Feb; 11(2):381-9.
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      55. Goedken ER, Marqusee S. Native-state energetics of a thermostabilized variant of ribonuclease HI. J Mol Biol. 2001 Dec 7; 314(4):863-71.
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      56. Parker MJ, Marqusee S. A kinetic folding intermediate probed by native state hydrogen exchange. J Mol Biol. 2001 Jan 19; 305(3):593-602.
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      57. Goedken ER, Marqusee S. Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site. J Biol Chem. 2001 Mar 9; 276(10):7266-71.
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      58. Goedken ER, Keck JL, Berger JM, Marqusee S. Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI. Protein Sci. 2000 Oct; 9(10):1914-21.
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      59. Spudich G, Marqusee S. A change in the apparent m value reveals a populated intermediate under equilibrium conditions in Escherichia coli ribonuclease HI. Biochemistry. 2000 Sep 26; 39(38):11677-83.
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      60. Fischer KF, Marqusee S. A rapid test for identification of autonomous folding units in proteins. J Mol Biol. 2000 Sep 22; 302(3):701-12.
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      61. Toth EA, Worby C, Dixon JE, Goedken ER, Marqusee S, Yeates TO. The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds. J Mol Biol. 2000 Aug 11; 301(2):433-50.
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      62. Parker MJ, Marqusee S. A statistical appraisal of native state hydrogen exchange data: evidence for a burst phase continuum? J Mol Biol. 2000 Jul 28; 300(5):1361-75.
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      63. Chamberlain AK, Marqusee S. Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. Adv Protein Chem. 2000; 53:283-328.
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      64. Hollien J, Marqusee S. Structural distribution of stability in a thermophilic enzyme. Proc Natl Acad Sci U S A. 1999 Nov 23; 96(24):13674-8.
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      65. Parker MJ, Marqusee S. The cooperativity of burst phase reactions explored. J Mol Biol. 1999 Nov 12; 293(5):1195-210.
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      66. Llinás M, Gillespie B, Dahlquist FW, Marqusee S. The energetics of T4 lysozyme reveal a hierarchy of conformations. Nat Struct Biol. 1999 Nov; 6(11):1072-8.
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      67. Goedken ER, Marqusee S. Metal binding and activation of the ribonuclease H domain from moloney murine leukemia virus. Protein Eng. 1999 Nov; 12(11):975-80.
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      68. Raschke TM, Kho J, Marqusee S. Confirmation of the hierarchical folding of RNase H: a protein engineering study. Nat Struct Biol. 1999 Sep; 6(9):825-31.
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      69. Liu H, Farr-Jones S, Ulyanov NB, Llinas M, Marqusee S, Groth D, Cohen FE, Prusiner SB, James TL. Solution structure of Syrian hamster prion protein rPrP(90-231). Biochemistry. 1999 Apr 27; 38(17):5362-77.
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      70. Hollien J, Marqusee S. A thermodynamic comparison of mesophilic and thermophilic ribonucleases H. Biochemistry. 1999 Mar 23; 38(12):3831-6.
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      71. Keck JL, Goedken ER, Marqusee S. Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition. J Biol Chem. 1998 Dec 18; 273(51):34128-33.
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      72. Goedken ER, Marqusee S. Folding the ribonuclease H domain of Moloney murine leukemia virus reverse transcriptase requires metal binding or a short N-terminal extension. Proteins. 1998 Oct 1; 33(1):135-43.
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      73. Kern G, Handel T, Marqusee S. Characterization of a folding intermediate from HIV-1 ribonuclease H. Protein Sci. 1998 Oct; 7(10):2164-74.
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      74. Chamberlain AK, Marqusee S. Molten globule unfolding monitored by hydrogen exchange in urea. Biochemistry. 1998 Feb 17; 37(7):1736-42.
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      75. Raschke TM, Marqusee S. Hydrogen exchange studies of protein structure. Curr Opin Biotechnol. 1998 Feb; 9(1):80-6.
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      76. Llinás M, Marqusee S. Subdomain interactions as a determinant in the folding and stability of T4 lysozyme. Protein Sci. 1998 Jan; 7(1):96-104.
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      77. Chamberlain AK, Marqusee S. Touring the landscapes: partially folded proteins examined by hydrogen exchange. Structure. 1997 Jul 15; 5(7):859-63.
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      78. Goedken ER, Raschke TM, Marqusee S. Importance of the C-terminal helix to the stability and enzymatic activity of Escherichia coli ribonuclease H. Biochemistry. 1997 Jun 10; 36(23):7256-63.
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      79. Raschke TM, Marqusee S. The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions. Nat Struct Biol. 1997 Apr; 4(4):298-304.
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      80. Dabora JM, Pelton JG, Marqusee S. Structure of the acid state of Escherichia coli ribonuclease HI. Biochemistry. 1996 Sep 17; 35(37):11951-8.
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      81. Chamberlain AK, Handel TM, Marqusee S. Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat Struct Biol. 1996 Sep; 3(9):782-7.
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      82. Keck JL, Marqusee S. The putative substrate recognition loop of Escherichia coli ribonuclease H is not essential for activity. J Biol Chem. 1996 Aug 16; 271(33):19883-7.
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      83. Keck JL, Marqusee S. Substitution of a highly basic helix/loop sequence into the RNase H domain of human immunodeficiency virus reverse transcriptase restores its Mn(2+)-dependent RNase H activity. Proc Natl Acad Sci U S A. 1995 Mar 28; 92(7):2740-4.
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      84. Marqusee S, Sauer RT. Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor. Protein Sci. 1994 Dec; 3(12):2217-25.
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      85. Dabora JM, Marqusee S. Equilibrium unfolding of Escherichia coli ribonuclease H: characterization of a partially folded state. Protein Sci. 1994 Sep; 3(9):1401-8.
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      86. Marqusee S, Regan L. Deconstructing protein structure. Curr Biol. 1991 Aug; 1(4):207-8.
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      87. Scholtz JM, Marqusee S, Baldwin RL, York EJ, Stewart JM, Santoro M, Bolen DW. Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci U S A. 1991 Apr 1; 88(7):2854-8.
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      88. Padmanabhan S, Marqusee S, Ridgeway T, Laue TM, Baldwin RL. Relative helix-forming tendencies of nonpolar amino acids. Nature. 1990 Mar 15; 344(6263):268-70.
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      89. Marqusee S, Robbins VH, Baldwin RL. Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci U S A. 1989 Jul; 86(14):5286-90.
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      90. Marqusee S, Baldwin RL. Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design. Proc Natl Acad Sci U S A. 1987 Dec; 84(24):8898-902.
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      91. Shoemaker KR, Kim PS, Brems DN, Marqusee S, York EJ, Chaiken IM, Stewart JM, Baldwin RL. Nature of the charged-group effect on the stability of the C-peptide helix. Proc Natl Acad Sci U S A. 1985 Apr; 82(8):2349-53.
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