Department of Chemistry

Jane Clarke Publications

2013

Folding and binding of an intrinsically disordered protein: fast, but not 'diffusion-limited'.
Rogers JM, Steward A, Clarke J
J Am Chem Soc 2013, 135, 1415-1422. DOI: 10.1021/ja309527h

A Mechanistic Model for Amorphous Protein Aggregation of Immunoglobulin-like Domains
Madeleine B Borgia, Adrian A Nickson, Jane Clarke, and Michael J Hounslow
Journal_of_the_American_Chemical_Society DOI: 10.1021/ja308852b

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
2013, 1018-1027.

Take home lessons from studies of related proteins
Nickson AA, Wensley BG, Clarke J
2013, 66-74.

2012

Take home lessons from studies of related proteins.
Nickson AA, Wensley BG, Clarke J
Curr Opin Struct Biol 2012, -. 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 2012, -. 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, 103, 2203-2214. DOI: 10.1016/j.bpj.2012.10.012

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, 109, 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
J Mol Biol 2012, 423, 273-283. DOI: 10.1016/j.jmb.2012.08.003

Learning from Nature to design new biomolecules.
Clarke J, Schief W
Curr Opin Struct Biol 2012, 395-396. DOI: 10.1016/j.sbi.2012.07.001

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
J Mol Biol 2012, 416, 137-147. DOI: 10.1016/j.jmb.2011.12.012

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

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, 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, 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, 3, -.

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

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, 423, 273-283.

2011

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, 2, 662-665. DOI: 10.1038/nature10099

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, 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, 3, 1857-1871.

2010

What lessons can be learned from studying the folding of homologous proteins?
Nickson AA, Clarke J
Amino Acid Sequence, Homeodomain Proteins, Kinetics, Models, Molecular, Molecular Dynamics Simulation, Protein Folding, Protein Structure, Secondary, Proteins, Proto-Oncogene Proteins c-myb, Sequence Homology, Thermodynamics, Transcription Factors 2010, 52, 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, 20, 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, 107, 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
Entropy, Friction, Kinetics, Models, Chemical, Models, Molecular, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Spectrin, Viscosity 2010, 463, 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
Microscopy, Atomic Force, Molecular Dynamics Simulation, Protein Binding, Protein Conformation, Protein Denaturation, TRPP Cation Channels, Thermodynamics 2009, 7, 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
Amino Acid Sequence, Archaea, Cloning, Molecular, Humans, Kinetics, Microscopy, Atomic Force, Models, Molecular, Molecular Sequence Data, Mutation, Mutation, Missense, Phenotype, Protein Structure, Tertiary, Sequence Homology, Amino Acid, TRPP Cation Channels, Thermodynamics 2009, 7, 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
Amino Acid Sequence, Animals, Chickens, Humans, Kinetics, Molecular Sequence Data, Mutant Proteins, Mutation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Spectrin, Thermodynamics 2009, 7, 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
Fas-Associated Death Domain Protein, Humans, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary 2009, 5, 425-437. DOI: 10.1016/j.jmb.2009.04.004

2008

Studying the folding of multidomain proteins.
Batey S, Nickson AA, Clarke J
2008, 4, 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, 0, -. 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
Entropy, Escherichia coli, Escherichia coli Proteins, Hydrogen-Ion Concentration, Kinetics, Models, Molecular, Mutation, Protein Denaturation, Protein Engineering, Protein Folding, Protein Renaturation, Protein Structure, Tertiary, Temperature, Thermodynamics 2008, 6, 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
Animals, Chickens, Humans, Kinetics, Mutation, Protein Folding, Protein Structure, Tertiary, Spectrin 2008, 8, 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
Kinetics, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Protein Folding, Proteins, Thermodynamics 2008, 4, 215-222. DOI: 10.1093/protein/gzm092

Distinguishing specific and nonspecific interdomain interactions in multidomain proteins.
Randles LG, Batey S, Steward A, Clarke J
Animals, Chickens, Humans, Kinetics, Muscle Proteins, Protein Denaturation, Protein Folding, Protein Kinases, Protein Structure, Secondary, Protein Structure, Tertiary, Spectrin, Thermodynamics 2008, 5, 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
Amino Acid Sequence, Cell Adhesion, Fibronectins, Genetic Variation, Guanidines, Humans, Hydrogen, Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Isothiocyanates, Kinetics, Models, Chemical, Models, Molecular, Molecular Sequence Data, Mutant Chimeric Proteins, Mutation, Nuclear Magnetic Resonance, Biomolecular, Protein Folding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Surface Properties, Tenascin, Thermodynamics, Urea 2008, 8, 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
Amino Acid Sequence, Amino Acids, Aromatic, Bacillus, Chitinase, Conserved Sequence, Fibronectins, Humans, Hydrogen Bonding, Immunoglobulins, Kinetics, Models, Chemical, Models, Molecular, Molecular Sequence Data, Mutation, Protein Denaturation, Protein Folding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Tenascin, Thermodynamics 2008, 14, 547-559. DOI: 10.1016/j.jmb.2007.09.088

Single-molecule studies of protein folding.
Borgia A, Williams PM, Clarke J
Animals, Biochemistry, Dose-Response Relationship, Drug, Fluorescence Resonance Energy Transfer, Humans, Kinetics, Microscopy, Atomic Force, Nanotechnology, Protein Conformation, Protein Denaturation, Protein Folding, Proteins, Thermodynamics, Time Factors 2008, 75, 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
Amino Acid Sequence, Fibronectins, Humans, Mechanics, Microscopy, Atomic Force, Molecular Sequence Data, Protein Engineering, Protein Folding, Protein Structure, Tertiary 2008, 13, 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
Amino Acid Motifs, Computer Simulation, Fibronectins, Hydrogen-Ion Concentration, Models, Molecular, Protein Folding, Protein Structure, Tertiary 2007, 6, 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
Amino Acid Sequence, Biophysical Phenomena, Biophysics, Cell Adhesion, Crystallization, Fibronectins, Humans, Microscopy, Atomic Force, Models, Molecular, Molecular Sequence Data, Mutation, Protein Conformation, Protein Engineering, Protein Structure, Tertiary, Sequence Alignment, Tenascin 2007, 30, 9633-9637. DOI: 10.1073/pnas.0609901104

The folding and evolution of multidomain proteins.
Han JH, Batey S, Nickson AA, Teichmann SA, Clarke J
Amino Acid Sequence, Animals, Evolution, Molecular, Humans, Molecular Sequence Data, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Proteins 2007, 69, 319-330. DOI: 10.1038/nrm2144

Mechanical unfolding of proteins: insights into biology, structure and folding.
Forman JR, Clarke J
Mechanics, Mechanoreceptors, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Proteins 2007, 59, 58-66. DOI: 10.1016/j.sbi.2007.01.006

Spectrin domains lose cooperativity in forced unfolding.
Randles LG, Rounsevell RW, Clarke J
Computer Simulation, Microscopy, Atomic Force, Models, Chemical, Models, Molecular, Muscle Proteins, Protein Conformation, Protein Denaturation, Protein Folding, Protein Kinases, Protein Structure, Tertiary, Spectrin, Stress, Mechanical 2007, 18, 571-577. DOI: 10.1529/biophysj.106.093690

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins.
Geierhaas CD, Nickson AA, Lindorff-Larsen K, Clarke J, Vendruscolo M
Algorithms, Biophysics, Databases, Protein, Internet, Protein Denaturation, Protein Folding, Proteins, Thermodynamics 2007, 15, 125-134. DOI: 10.1110/ps.062383807

Single molecule studies of protein folding using atomic force microscopy.
Ng SP, Randles LG, Clarke J
Microscopy, Atomic Force, Protein Folding, Proteins 2007, 139-167.

2006

Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains.
Batey S, Clarke J
Kinetics, Models, Molecular, Mutation, Protein Folding, Protein Structure, Tertiary, Spectrin 2006, 103, 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
Genetic Predisposition to Disease, Humans, Immunoglobulins, Interleukin Receptor Common gamma Subunit, Models, Molecular, Mutation, Neural Cell Adhesion Molecule L1, Predictive Value of Tests, Protein Structure, Tertiary, Receptors, Interleukin, Sequence Analysis, Structure-Activity Relationship 2006, 281, 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, 91, 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
Amino Acid Sequence, Animals, Brain Chemistry, Chickens, Computer Simulation, Models, Molecular, Mutation, Protein Folding, Protein Structure, Tertiary, Spectrin 2006, 359, 159-173. DOI: 10.1016/j.jmb.2006.03.011

Complex folding kinetics of a multidomain protein.
Batey S, Scott KA, Clarke J
Binding Sites, Computer Simulation, Kinetics, Models, Chemical, Models, Molecular, Protein Binding, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Spectrin 2006, 90, 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, 438, 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, 350, 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, 349, 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, 349, 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, 14, 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, 349, 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, 88, 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, 363, 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, 88, 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, 88, 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, 88, 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, 88, 213A-213A.

Comparison of the different transition states for folding in TI 127
Geierhaas CD, Paci E, Vendruscolo M, Clarke J
BIOPHYSICAL JOURNAL 2005, 88, 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, 363, 453-467.

2004

The folding of spectrin domains II: phi-value analysis of R16.
Scott KA, Randles LG, Clarke J
Animals, Brain Chemistry, Chickens, Drug Stability, Kinetics, Models, Molecular, Mutagenesis, Site-Directed, Protein Denaturation, Protein Engineering, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant Proteins, Spectrin, Thermodynamics 2004, 30, 207-221. DOI: 10.1016/j.jmb.2004.09.023

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
Animals, Brain Chemistry, Chickens, Drug Stability, Kinetics, Models, Molecular, Protein Folding, Protein Structure, Tertiary, Recombinant Proteins, Spectrin, Thermodynamics 2004, 27, 195-205. DOI: 10.1016/j.jmb.2004.09.037

Comparison of the transition states for folding of two Ig-like proteins from different superfamilies.
Geierhaas CD, Paci E, Vendruscolo M, Clarke J
Amino Acid Sequence, Fibronectins, Humans, Molecular Sequence Data, Multigene Family, Muscle Proteins, Peptide Fragments, Protein Folding, Protein Kinases, Protein Structure, Secondary, Protein Structure, Tertiary, Tenascin 2004, 26, 1111-1123. DOI: 10.1016/j.jmb.2004.08.100

Atomic force microscopy: mechanical unfolding of proteins.
Rounsevell R, Forman JR, Clarke J
Cloning, Molecular, Microscopy, Atomic Force, Protein Folding, Proteins 2004, 33, 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, 33, 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
Amino Acid Sequence, Humans, Immunoglobulins, Molecular Sequence Data, Muscle Proteins, Mutation, Protein Folding, Protein Kinases, Protein Structure, Tertiary, Structural Homology, Protein 2004, 7, 443-453. DOI: 10.1093/protein/gzh052

Thermodynamic characterisation of two transition states along parallel protein folding pathways.
Wright CF, Steward A, Clarke J
Protein Folding, Protein Structure, Tertiary, Proteins, Temperature, Thermodynamics 2004, 18, 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, 0, 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, 0, 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, 24, 1145-1155. DOI: 10.1021/bi035658e

FnIII domains: Predicting mechanical stability
Rounsevell RWS, Clarke J
STRUCTURE 2004, 3, 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
Cytoskeletal Proteins, Humans, Kinetics, Models, Molecular, Muscle Proteins, Point Mutation, Protein Denaturation, Protein Folding, Protein Kinases, Protein Structure, Tertiary, Proteins, Recombinant Proteins 2003, 95, 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, 76, 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, 143, 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, 55, 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, 0, 308A-308A.

The hidden strength of titin
Williams PM, Clarke J
BIOPHYSICAL JOURNAL 2003, 0, 337A-337A.

Folding and binding - new technologies and new perspectives - Editorial overview
Clarke J, Schreiber G
CURR OPIN STRUC BIOL 2003, 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
Fibronectins, Protein Folding 2003, 35, 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, 322, 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, 99, 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, 11, 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, 318, 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, 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, 315, 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, 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, 81, 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, 9, 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, 221, 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, 221, U404-U404.

Cantilever physics in the mechanical unfolding of proteins.
Cleveland J, Proksch R, Steward A, Clarke J
ABSTR PAP AM CHEM S 2001, 221, 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, 305, 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, 11, 67-69.

Folding and binding emerging themes in protein folding and assembly
Clarke J, Dobson CM
Current Opinion in Structural Biology 2001, 11, 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, 9, 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, 302, 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, 97, 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, 297, 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, 296, 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, 295, 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, 78, 402A-402A.

Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module.
Cota E, Clarke J
Protein Sci 2000, 9, 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, 7, 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, 96, 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, 18, 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, 76, A173-A173.

1998

A reply to Englander and Woodward
Clarke J, Itzhaki LS, Fersht AR
TRENDS BIOCHEM SCI 1998, 23, 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, 282, 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, 37, 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, 278, 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, 276, 647-656. DOI: 10.1006/jmbi.1997.1547

Hydrogen exchange and protein folding.
Clarke J, Itzhaki LS
Curr Opin Struct Biol 1998, 8, 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, 94, 13409-13413.

Folding and stability of a fibronectin type III domain of human tenascin.
Clarke J, Hamill SJ, Johnson CM
J Mol Biol 1997, 270, 771-778. DOI: 10.1006/jmbi.1997.1147

Hydrogen exchange at equilibrium: a short cut for analysing protein-folding pathways?
Clarke J, Itzhaki LS, Fersht AR
Trends Biochem Sci 1997, 22, 284-287.

Hydrogen exchange at equilibrium: a short cut for analysing protein-folding pathways?
Clarke J, Itzhaki LS, Fersht AR
Trends Biochem Sci 1997, 22, 284-287.

Thermodynamics of denaturation of mutants of barnase with disulfide crosslinks.
Johnson CM, Oliveberg M, Clarke J, Fersht AR
J Mol Biol 1997, 268, 198-208. DOI: 10.1006/jmbi.1997.0928

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, 264, 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, 1, 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, 253, 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, 253, 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, 34, 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, 90, 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, 32, 4322-4329.