Department of Chemistry

Jane Clarke Publications


2014


Coupled Folding and Binding of the Disordered Protein PUMA Does Not Require Particular Residual Structure
Joseph M Rogers, Chi T Wong, and Jane Clarke
Journal_of_the_American_Chemical_Society DOI: 10.1021/ja4125065


Mechanism of assembly of the non-covalent spectrin tetramerization domain from intrinsically disordered partners
Hill SA, Kwa LG, Shammas SL, Lee JC, Clarke J
Journal of Molecular Biology, 2014, 1, 21-35.

2013


The folding of a family of three-helix bundle proteins: spectrin r15 has a robust folding nucleus, unlike its homologous neighbours.
Kwa LG, Wensley BG, Alexander CG, Browning SJ, Lichman BR, Clarke J
J Mol Biol, 2014, 7, 1600-1610. DOI: 10.1016/j.jmb.2013.12.018


Remarkably fast coupled folding and binding of the intrinsically disordered transactivation domain of cMyb to CBP KIX.
Shammas SL, Travis AJ, Clarke J
J Phys Chem B, 2013, 42, 13346-13356. DOI: 10.1021/jp404267e


A mechanistic model for amorphous protein aggregation of immunoglobulin-like domains.
Borgia MB, Nickson AA, Clarke J, Hounslow MJ
J Am Chem Soc, 2013, 17, 6456-6464. DOI: 10.1021/ja308852b


Folding Upon Binding - Not a Simple Protein Folding Problem
Clarke J, Rogers JM, Hill SA, Shammas SL, Gruszka D, Steward A, Lee JC, Potts JR
BIOPHYSICAL JOURNAL, 2013, 2, 189A-189A.


Identity of Hinge Residues Defines Stability and Kinetics of Spectrin Tetramer Interaction
Hill SA, Lee JC, Clarke J
BIOPHYSICAL JOURNAL, 2013, 2, 369A-369A.


Folding and binding of an intrinsically disordered protein: fast, but not 'diffusion-limited'.
Rogers JM, Steward A, Clarke J
J Am Chem Soc, 2013, 4, 1415-1422. DOI: 10.1021/ja309527h


Understanding pathogenic single-nucleotide polymorphisms in multidomain proteins - Studies of isolated domains are not enough
Randles LG, Dawes GJS, Wensley BG, Steward A, Nickson AA, Clarke J
FEBS Journal, 2013, 4, 1018-1027.


Biophysics: Rough passage across a barrier
Schuler B, Clarke J
Nature, 2013, 7473, 632-633.

2012


Take home lessons from studies of related proteins.
Nickson AA, Wensley BG, Clarke J
Curr Opin Struct Biol, 2013-02, 1, 66-74. DOI: 10.1016/j.sbi.2012.11.009


Understanding pathogenic single-nucleotide polymorphisms in multidomain proteins--studies of isolated domains are not enough.
Randles LG, Dawes GJ, Wensley BG, Steward A, Nickson AA, Clarke J
FEBS J, 2013-02, 4, 1018-1027. DOI: 10.1111/febs.12094


Slow, reversible, coupled folding and binding of the spectrin tetramerization domain.
Shammas SL, Rogers JM, Hill SA, Clarke J
Biophys J, 2012, 10, 2203-2214. DOI: 10.1016/j.bpj.2012.10.012


Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy
Alessandro Borgia, Beth G Wensley, Andrea Soranno, Daniel Nettels, Madeleine B Borgia, Armin Hoffmann, Shawn H Pfeil, Everett A Lipman, Jane Clarke, Benjamin Schuler
Nature_Communications DOI: 10.1038/ncomms2204


Separating the effects of internal friction and transition state energy to explain the slow, frustrated folding of spectrin domains.
Wensley BG, Kwa LG, Shammas SL, Rogers JM, Browning S, Yang Z, Clarke J
Proc Natl Acad Sci U S A, 2012, 44, 17795-17799. DOI: 10.1073/pnas.1201793109


Protein folding: Adding a nucleus to guide helix docking reduces landscape roughness
Wensley BG, Kwa LG, Shammas SL, Rogers JM, Clarke J
Journal of Molecular Biology, 2012, 3, 273-283.


Two immunoglobulin tandem proteins with a linking β-strand reveal unexpected differences in cooperativity and folding pathways
Steward A, Chen Q, Chapman RI, Borgia MB, Rogers JM, Wojtala A, Wilmanns M, Clarke J
Journal of Molecular Biology, 2012, 1, 137-147.


Staphylococcal biofilm-forming protein has a contiguous rod-like structure
Gruszka DT, Wojdyla JA, Bingham RJ, Turkenburg JP, Manfield IW, Steward A, Leech AP, Geoghegan JA, Foster TJ, Clarke J, Potts JR
Proceedings of the National Academy of Sciences of the United States of America, 2012, 17, E1011-E1018.


Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy
Borgia A, Wensley BG, Soranno A, Nettels D, Borgia MB, Hoffmann A, Pfeil SH, Lipman EA, Clarke J, Schuler B
Nature Communications, 2012, -.


Learning from Nature to design new biomolecules
Clarke J, Schief W
Current Opinion in Structural Biology, 2012, 4, 395-396.

2011


Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP)
Armin Hoffmann, Daniel Nettels, Jennifer Clark, Alessandro Borgia, Sheena E Radford, Jane Clarke, Benjamin Schuler
PCCP DOI: 10.1039/C0CP01911A


Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins
Borgia MB, Borgia A, Best RB, Steward A, Nettels D, Wunderlich B, Schuler B, Clarke J
Nature, 2011, 7353, 662-665.


Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: Recurrence analysis of single particles (RASP)
Hoffmann A, Nettels D, Clark J, Borgia A, Radford SE, Clarke J, Schuler B
Physical Chemistry Chemical Physics, 2011, 5, 1857-1871.

2010


What lessons can be learned from studying the folding of homologous proteins?
Nickson AA, Clarke J
Methods, 2010-09, 1, 38-50. DOI: 10.1016/j.ymeth.2010.06.003


Protein engineering and design: from first principles to new technologies
Clarke J, Regan L
CURR OPIN STRUC BIOL, 2010-08, 4, 480-481. DOI: 10.1016/j.sbi.2010.07.001


Membrane protein folding makes the transition
Booth PJ, Clarke J
P NATL ACAD SCI USA, 2010, 9, 3947-3948. DOI: 10.1073/pnas.0914478107


Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family.
Wensley BG, Batey S, Bone FA, Chan ZM, Tumelty NR, Steward A, Kwa LG, Borgia A, Clarke J
Nature, 2010, 7281, 685-688. DOI: 10.1038/nature08743

2009


Non-native interactions are critical for mechanical strength in PKD domains.
Forman JR, Yew ZT, Qamar S, Sandford RN, Paci E, Clarke J
Structure, 2009, 12, 1582-1590. DOI: 10.1016/j.str.2009.09.013


Naturally occurring mutations alter the stability of polycystin-1 polycystic kidney disease (PKD) domains.
Ma L, Xu M, Forman JR, Clarke J, Oberhauser AF
J Biol Chem, 2009, 47, 32942-32949. DOI: 10.1074/jbc.M109.021832


Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
Wensley BG, Gärtner M, Choo WX, Batey S, Clarke J
J Mol Biol, 2009, 5, 1074-1085. DOI: 10.1016/j.jmb.2009.05.010


Topology is the principal determinant in the folding of a complex all-alpha Greek key death domain from human FADD.
Steward A, McDowell GS, Clarke J
J Mol Biol, 2009, 2, 425-437. DOI: 10.1016/j.jmb.2009.04.004

2008


Studying the folding of multidomain proteins.
Batey S, Nickson AA, Clarke J
HFSP J, 2008-12, 6, 365-377. DOI: 10.2976/1.2991513


Manipulating the stability of fibronectin type III domains by protein engineering
Ng SP, Billings KS, Randles LG, Clarke J
NANOTECHNOLOGY, 2008, 38, -. DOI: 10.1088/0957-4484/19/38/384023


Folding of a LysM domain: entropy-enthalpy compensation in the transition state of an ideal two-state folder.
Nickson AA, Stoll KE, Clarke J
J Mol Biol, 2008, 3, 557-569. DOI: 10.1016/j.jmb.2008.05.020


The folding pathway of a single domain in a multidomain protein is not affected by its neighbouring domain.
Batey S, Clarke J
J Mol Biol, 2008, 2, 297-301. DOI: 10.1016/j.jmb.2008.02.032


Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.
Geierhaas CD, Salvatella X, Clarke J, Vendruscolo M
Protein Eng Des Sel, 2008-03, 3, 215-222. DOI: 10.1093/protein/gzm092


Distinguishing specific and nonspecific interdomain interactions in multidomain proteins.
Randles LG, Batey S, Steward A, Clarke J
Biophys J, 2008, 2, 622-628. DOI: 10.1529/biophysj.107.119123


Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain.
Billings KS, Best RB, Rutherford TJ, Clarke J
J Mol Biol, 2008, 2, 560-571. DOI: 10.1016/j.jmb.2007.10.056


Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain.
Lappalainen I, Hurley MG, Clarke J
J Mol Biol, 2008, 2, 547-559. DOI: 10.1016/j.jmb.2007.09.088


Single-molecule studies of protein folding.
Borgia A, Williams PM, Clarke J
Annu Rev Biochem, 2008, 101-125. DOI: 10.1146/annurev.biochem.77.060706.093102


An effective strategy for the design of proteins with enhanced mechanical stability.
Borgia A, Steward A, Clarke J
Angew Chem Int Ed Engl, 2008, 36, 6900-6903. DOI: 10.1002/anie.200801761

2007


Experiments suggest that simulations may overestimate electrostatic contributions to the mechanical stability of a fibronectin type III domain.
Ng SP, Clarke J
J Mol Biol, 2007, 4, 851-854. DOI: 10.1016/j.jmb.2007.06.015


Designing an extracellular matrix protein with enhanced mechanical stability.
Ng SP, Billings KS, Ohashi T, Allen MD, Best RB, Randles LG, Erickson HP, Clarke J
Proc Natl Acad Sci U S A, 2007, 23, 9633-9637. DOI: 10.1073/pnas.0609901104


The folding and evolution of multidomain proteins.
Han JH, Batey S, Nickson AA, Teichmann SA, Clarke J
Nat Rev Mol Cell Biol, 2007-04, 4, 319-330. DOI: 10.1038/nrm2144


Mechanical unfolding of proteins: insights into biology, structure and folding.
Forman JR, Clarke J
Curr Opin Struct Biol, 2007-02, 1, 58-66. DOI: 10.1016/j.sbi.2007.01.006


Spectrin domains lose cooperativity in forced unfolding.
Randles LG, Rounsevell RW, Clarke J
Biophys J, 2007, 2, 571-577. DOI: 10.1529/biophysj.106.093690


Single molecule studies of protein folding using atomic force microscopy.
Ng SP, Randles LG, Clarke J
Methods Mol Biol, 2007, 139-167.


BPPred: a Web-based computational tool for predicting biophysical parameters of proteins.
Geierhaas CD, Nickson AA, Lindorff-Larsen K, Clarke J, Vendruscolo M
Protein Sci, 2007-01, 1, 125-134. DOI: 10.1110/ps.062383807

2006


Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains.
Batey S, Clarke J
Proc Natl Acad Sci U S A, 2006, 48, 18113-18118. DOI: 10.1073/pnas.0604580103


Using model proteins to quantify the effects of pathogenic mutations in Ig-like proteins.
Randles LG, Lappalainen I, Fowler SB, Moore B, Hamill SJ, Clarke J
J Biol Chem, 2006, 34, 24216-24226. DOI: 10.1074/jbc.M603593200


Structural comparison of the two alternative transition states for folding of TI I27.
Geierhaas CD, Best RB, Paci E, Vendruscolo M, Clarke J
Biophys J, 2006, 1, 263-275. DOI: 10.1529/biophysj.105.077057


The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment.
Scott KA, Randles LG, Moran SJ, Daggett V, Clarke J
J Mol Biol, 2006, 1, 159-173. DOI: 10.1016/j.jmb.2006.03.011


Complex folding kinetics of a multidomain protein.
Batey S, Scott KA, Clarke J
Biophys J, 2006, 6, 2120-2130. DOI: 10.1529/biophysj.105.072710

2005


The importance of sequence diversity in the aggregation and evolution of proteins.
Wright CF, Teichmann SA, Clarke J, Dobson CM
Nature, 2005, 7069, 878-881. DOI: 10.1038/nature04195


Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation.
Ng SP, Rounsevell RW, Steward A, Geierhaas CD, Williams PM, Paci E, Clarke J
J Mol Biol, 2005, 4, 776-789. DOI: 10.1016/j.jmb.2005.04.070


Cooperative folding in a multi-domain protein.
Batey S, Randles LG, Steward A, Clarke J
J Mol Biol, 2005, 5, 1045-1059. DOI: 10.1016/j.jmb.2005.04.028


The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction.
Forman JR, Qamar S, Paci E, Sandford RN, Clarke J
J Mol Biol, 2005, 4, 861-871. DOI: 10.1016/j.jmb.2005.04.008


Spectrin R16: broad energy barrier or sequential transition states?
Scott KA, Clarke J
Protein Sci, 2005-06, 6, 1617-1629. DOI: 10.1110/ps.051377105


What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.
Best RB, Clarke J, Karplus M
J Mol Biol, 2005, 1, 185-203. DOI: 10.1016/j.jmb.2005.03.001


Biophysical investigations of engineered polyproteins: implications for force data.
Rounsevell RW, Steward A, Clarke J
Biophys J, 2005-03, 3, 2022-2029. DOI: 10.1529/biophysj.104.053744


Energy landscapes and solved protein-folding problems - Discussion
Karplus M, Wolynes PG, Dobson CM, Zewail AH, Clarke J, Schon JC
PHILOS T ROY SOC A, 2005, 1827, 464-467.


The use of model proteins to study the effect of pathogenic mutations
Randles LG, Lappalainen I, Fowler SB, Moore B, Clarke J
BIOPHYSICAL JOURNAL, 2005-01, 1, 215A-215A.


The remarkable mechanical strength of polycystin-1 suggests a novel mechanism for mechanotransduction
Forman JR, Qamar S, Sandford RN, Clarke J
BIOPHYSICAL JOURNAL, 2005-01, 1, 585A-585A.


Single molecule studies of protein folding by atomic force microscopy(AFM)
Ng SP, Rounsevell R, Randles LG, Steward A, Clarke J
BIOPHYSICAL JOURNAL, 2005-01, 1, 184A-184A.


Protein unfolding and refolding under force using the biomembrane force probe
Brampton C, Zhang WK, Clarke J, Leung A, Evans E, Williams PM
BIOPHYSICAL JOURNAL, 2005-01, 1, 213A-213A.


Comparison of the different transition states for folding in TI 127
Geierhaas CD, Paci E, Vendruscolo M, Clarke J
BIOPHYSICAL JOURNAL, 2005-01, 1, 216A-216A.


Energy landscapes and solved protein-folding problems
Wolynes PG, Karplus M, Dobson CM, Zewail AH, Clarke J, Schön JC
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2005, 1827, 453-467.

2004


The folding of spectrin domains I: wild-type domains have the same stability but very different kinetic properties.
Scott KA, Batey S, Hooton KA, Clarke J
J Mol Biol, 2004, 1, 195-205. DOI: 10.1016/j.jmb.2004.09.037


The folding of spectrin domains II: phi-value analysis of R16.
Scott KA, Randles LG, Clarke J
J Mol Biol, 2004, 1, 207-221. DOI: 10.1016/j.jmb.2004.09.023


Comparison of the transition states for folding of two Ig-like proteins from different superfamilies.
Geierhaas CD, Paci E, Vendruscolo M, Clarke J
J Mol Biol, 2004, 4, 1111-1123. DOI: 10.1016/j.jmb.2004.08.100


Atomic force microscopy: mechanical unfolding of proteins.
Rounsevell R, Forman JR, Clarke J
Methods, 2004-09, 1, 100-111. DOI: 10.1016/j.ymeth.2004.03.007


The origin of protein sidechain order parameter distributions.
Best RB, Clarke J, Karplus M
J Am Chem Soc, 2004, 25, 7734-7735. DOI: 10.1021/ja049078w


The importance of loop length in the folding of an immunoglobulin domain.
Wright CF, Christodoulou J, Dobson CM, Clarke J
Protein Eng Des Sel, 2004-05, 5, 443-453. DOI: 10.1093/protein/gzh052


Thermodynamic characterisation of two transition states along parallel protein folding pathways.
Wright CF, Steward A, Clarke J
J Mol Biol, 2004, 3, 445-451. DOI: 10.1016/j.jmb.2004.02.062


Using dynamic force spectroscopy, protein engineering, structural studies and molecular dynamics simulations to investigate the effect of force on a protein unfolding landscape.
Clarke J
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2004, U476-U476.


Single molecule studies of protein folding by atomic force microscopy(AFM).
Ng S, Rounsevell R, Steward A, Randles L, Clarke J
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2004, U545-U545.


Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing.
Best RB, Rutherford TJ, Freund SM, Clarke J
Biochemistry, 2004, 5, 1145-1155. DOI: 10.1021/bi035658e


FnIII domains: Predicting mechanical stability
Rounsevell RWS, Clarke J
STRUCTURE, 2004-01, 1, 4-5. DOI: 10.1016/j.str.2003.12.006

2003


Parallel protein-unfolding pathways revealed and mapped.
Wright CF, Lindorff-Larsen K, Randles LG, Clarke J
Nat Struct Biol, 2003-08, 8, 658-662. DOI: 10.1038/nsb947


Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations.
Best RB, Fowler SB, Herrera JL, Steward A, Paci E, Clarke J
J Mol Biol, 2003, 4, 867-877.


Hidden complexity in the mechanical properties of titin
Williams PM, Fowler SB, Best RB, Toca-Herrera JL, Scott KA, Steward A, Clarke J
NATURE, 2003, 6930, 446-449. DOI: 10.1038/nature01517


Force mode atomic force microscopy as a tool for protein folding studies
Best RB, Brockwell DJ, Toca-Herrera JL, Blake AW, Smith DA, Radford SE, Clarke J
ANAL CHIM ACTA, 2003, 1, 87-105. DOI: 10.1016/S0003-2670(02)01572-6


Combining protein engineering and dynamic force microscopy to examine protein folding landscapes
Clarke J, Best RB, Fowler SF, Steward A, Toca-Herrera JL, Williams PM, Martin KS, Paci E
BIOPHYSICAL JOURNAL, 2003-02, 2, 308A-308A.


The hidden strength of titin
Williams PM, Clarke J
BIOPHYSICAL JOURNAL, 2003-02, 2, 337A-337A.


Folding and binding - new technologies and new perspectives - Editorial overview
Clarke J, Schreiber G
CURR OPIN STRUC BIOL, 2003-02, 1, 71-74. DOI: 10.1016/S0959-440X(03)00008-3


Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain.
Paci E, Clarke J, Steward A, Vendruscolo M, Karplus M
Proc Natl Acad Sci U S A, 2003, 2, 394-399. DOI: 10.1073/pnas.232704999

2002


Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering.
Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J
J Mol Biol, 2002, 4, 841-849.


A simple method for probing the mechanical unfolding pathway of proteins in detail.
Best RB, Fowler SB, Toca-Herrera JL, Clarke J
Proc Natl Acad Sci U S A, 2002, 19, 12143-12148. DOI: 10.1073/pnas.192351899


Versatile cloning system for construction of multimeric proteins for use in atomic force microscopy.
Steward A, Toca-Herrera JL, Clarke J
Protein Sci, 2002-09, 9, 2179-2183. DOI: 10.1110/ps.0212702


Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily.
Steward A, Adhya S, Clarke J
J Mol Biol, 2002, 4, 935-940. DOI: 10.1016/S0022-2836(02)00184-5


What can atomic force microscopy tell us about protein folding?
Best RB, Clarke J
Chem Commun (Camb), 2002, 3, 183-192.


Titin; a multidomain protein that behaves as the sum of its parts.
Scott KA, Steward A, Fowler SB, Clarke J
J Mol Biol, 2002, 4, 819-829. DOI: 10.1006/jmbi.2001.5260


What can atomic force microscopy tell us about protein folding?
Best RB, Clarke J
Chemical communications (Cambridge, England), 2002, 3, 183-192.

2001


Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation.
Best RB, Li B, Steward A, Daggett V, Clarke J
Biophys J, 2001-10, 4, 2344-2356. DOI: 10.1016/S0006-3495(01)75881-X


Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement of the transition state.
Fowler SB, Clarke J
Structure, 2001, 5, 355-366.


Extending AFM to globular proteins: A general method for constructing multidomain repeats applied to proteins without any structural function.
Best RB, Steward A, Fowler S, Clarke J
ABSTR PAP AM CHEM S, 2001, U345-U345.


"How far do protein structures dictate the pathway of folding? The ""fold approach""."
Clarke J, Cota E, Fowler SB, Hamill SJ, Steward A, Chothia C
ABSTR PAP AM CHEM S, 2001, U404-U404.


Cantilever physics in the mechanical unfolding of proteins.
Cleveland J, Proksch R, Steward A, Clarke J
ABSTR PAP AM CHEM S, 2001, U330-U331.


The folding nucleus of a fibronectin type III domain is composed of core residues of the immunoglobulin-like fold.
Cota E, Steward A, Fowler SB, Clarke J
J Mol Biol, 2001, 5, 1185-1194. DOI: 10.1006/jmbi.2000.4378


Folding and binding - Emerging themes in protein folding and assembly - Editorial overview
Clarke J, Dobson CM
CURR OPIN STRUC BIOL, 2001-02, 1, 67-69.


Folding and binding emerging themes in protein folding and assembly
Clarke J, Dobson CM
Current Opinion in Structural Biology, 2001, 1, 67-69.

2000


The effects of disulfide bonds on the denatured state of barnase.
Clarke J, Hounslow AM, Bond CJ, Fersht AR, Daggett V
Protein Sci, 2000-12, 12, 2394-2404. DOI: 10.1110/ps.9.12.2394


Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability.
Cota E, Hamill SJ, Fowler SB, Clarke J
J Mol Biol, 2000, 3, 713-725. DOI: 10.1006/jmbi.2000.4053


Atomic force microscopy reveals the mechanical design of a modular protein
Li HB, Oberhauser AF, Fowler SB, Clarke J, Fernandez JM
P NATL ACAD SCI USA, 2000, 12, 6527-6531.


The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology.
Hamill SJ, Steward A, Clarke J
J Mol Biol, 2000, 1, 165-178. DOI: 10.1006/jmbi.2000.3517


Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding.
Wong KB, Clarke J, Bond CJ, Neira JL, Freund SM, Fersht AR, Daggett V
J Mol Biol, 2000, 5, 1257-1282. DOI: 10.1006/jmbi.2000.3523


Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac.
Hamill SJ, Cota E, Chothia C, Clarke J
J Mol Biol, 2000, 3, 641-649. DOI: 10.1006/jmbi.1999.3360


Mechanical unfolding of titin is under kinetic control
Li H, Oberhauser A, Fowler S, Clarke J, Marszalek PE, Fernandez JM
BIOPHYS J, 2000-01, 1, 402A-402A.


Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module.
Cota E, Clarke J
Protein Sci, 2000-01, 1, 112-120. DOI: 10.1110/ps.9.1.112

1999


Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway.
Clarke J, Cota E, Fowler SB, Hamill SJ
Structure, 1999, 9, 1145-1153.


Mechanical and chemical unfolding of a single protein: A comparison
Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 7, 3694-3699.


The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.
Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C
EMBO J, 1999, 2, 297-305. DOI: 10.1093/emboj/18.2.297


AFM and chemical unfolding of a single protein follow the same pathway
Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM
BIOPHYS J, 1999-01, 1, A173-A173.

1998


A reply to Englander and Woodward
Clarke J, Itzhaki LS, Fersht AR
TRENDS BIOCHEM SCI, 1998-10, 10, 379-381.


The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin.
Meekhof AE, Hamill SJ, Arcus VL, Clarke J, Freund SM
J Mol Biol, 1998, 1, 181-194. DOI: 10.1006/jmbi.1998.2019


The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin.
Hamill SJ, Meekhof AE, Clarke J
Biochemistry, 1998, 22, 8071-8079. DOI: 10.1021/bi9801659


Characterisation of urea-denatured states of an immunoglobulin superfamily domain by heteronuclear NMR.
Fong S, Bycroft M, Clarke J, Freund SM
J Mol Biol, 1998, 2, 417-429. DOI: 10.1006/jmbi.1998.1702


Folding intermediates of wild-type and mutants of barnase. II. Correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate.
Dalby PA, Clarke J, Johnson CM, Fersht AR
J Mol Biol, 1998, 3, 647-656. DOI: 10.1006/jmbi.1997.1547


Hydrogen exchange and protein folding.
Clarke J, Itzhaki LS
Curr Opin Struct Biol, 1998-02, 1, 112-118.

1997


Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway
Bond CJ, Wong KB, Clarke J, Fersht AR, Daggett V
P NATL ACAD SCI USA, 1997, 25, 13409-13413.


Folding and stability of a fibronectin type III domain of human tenascin.
Clarke J, Hamill SJ, Johnson CM
J Mol Biol, 1997, 5, 771-778. DOI: 10.1006/jmbi.1997.1147


Thermodynamics of denaturation of mutants of barnase with disulfide crosslinks.
Johnson CM, Oliveberg M, Clarke J, Fersht AR
J Mol Biol, 1997, 1, 198-208. DOI: 10.1006/jmbi.1997.0928


Hydrogen exchange at equilibrium: a short cut for analysing protein-folding pathways?
Clarke J, Itzhaki LS, Fersht AR
Trends Biochem Sci, 1997-08, 8, 284-287.

1996


Structure and stability of an immunoglobulin superfamily domain from twitchin, a muscle protein of the nematode Caenorhabditis elegans.
Fong S, Hamill SJ, Proctor M, Freund SM, Benian GM, Chothia C, Bycroft M, Clarke J
J Mol Biol, 1996, 3, 624-639. DOI: 10.1006/jmbi.1996.0665


An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway.
Clarke J, Fersht AR
Fold Des, 1996, 4, 243-254.

1995


Disulfide mutants of barnase. II: Changes in structure and local stability identified by hydrogen exchange.
Clarke J, Hounslow AM, Fersht AR
J Mol Biol, 1995, 3, 505-513. DOI: 10.1006/jmbi.1995.0569


Disulfide mutants of barnase. I: Changes in stability and structure assessed by biophysical methods and X-ray crystallography.
Clarke J, Henrick K, Fersht AR
J Mol Biol, 1995, 3, 493-504. DOI: 10.1006/jmbi.1995.0568


Relationship between equilibrium amide proton exchange behavior and the folding pathway of barnase.
Perrett S, Clarke J, Hounslow AM, Fersht AR
Biochemistry, 1995, 29, 9288-9298.

1993


Local breathing and global unfolding in hydrogen exchange of barnase and its relationship to protein folding pathways.
Clarke J, Hounslow AM, Bycroft M, Fersht AR
Proc Natl Acad Sci U S A, 1993, 21, 9837-9841.


Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation.
Clarke J, Fersht AR
Biochemistry, 1993, 16, 4322-4329.