| Year |
Citation |
Score |
| 2020 |
Staby L, Kemplen KR, Stein A, Ploug M, Clarke J, Skriver K, Heidarsson PO, Kragelund BB. Disorder in a two-domain neuronal Ca-binding protein regulates domain stability and dynamics using ligand mimicry. Cellular and Molecular Life Sciences : Cmls. PMID 32936312 DOI: 10.1007/S00018-020-03639-Z |
0.448 |
|
| 2020 |
Jensen MK, Samelson AJ, Steward A, Clarke J, Marqusee S. The folding and unfolding behavior of ribonuclease H on the ribosome. The Journal of Biological Chemistry. PMID 32527724 DOI: 10.1074/Jbc.Ra120.013909 |
0.497 |
|
| 2019 |
Boreikaite V, Wicky BIM, Watt IN, Clarke J, Walker JE. Extrinsic conditions influence the self-association and structure of IF, the regulatory protein of mitochondrial ATP synthase. Proceedings of the National Academy of Sciences of the United States of America. PMID 31064873 DOI: 10.1073/Pnas.1903535116 |
0.353 |
|
| 2018 |
Berthelot C, Clarke J, Desvignes T, Detrich HW, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Adaptation of proteins to the cold in Antarctic fish: A role for Methionine? Genome Biology and Evolution. PMID 30496401 DOI: 10.1093/Gbe/Evy262 |
0.395 |
|
| 2018 |
Tian P, Steward A, Kudva R, Su T, Shilling PJ, Nickson AA, Hollins JJ, Beckmann R, von Heijne G, Clarke J, Best RB. Folding pathway of an Ig domain is conserved on and off the ribosome. Proceedings of the National Academy of Sciences of the United States of America. PMID 30413621 DOI: 10.1073/Pnas.1810523115 |
0.708 |
|
| 2018 |
B da Silva F, Contessoto VG, Martins de Oliveira VM, Clarke J, Leite VBP. Non-Native Cooperative Interactions Modulate Protein Folding Rates. The Journal of Physical Chemistry. B. PMID 30407825 DOI: 10.1021/Acs.Jpcb.8B08990 |
0.479 |
|
| 2018 |
Marsden AP, Hollins JJ, O'Neill C, Ryzhov P, Higson S, Mendonca CATF, Kwan TO, Kwa LG, Steward A, Clarke J. Investigating the Effect of Chain Connectivity on the Folding of a Beta-Sheet Protein on and off the Ribosome. Journal of Molecular Biology. PMID 30365950 DOI: 10.1016/J.Jmb.2018.10.011 |
0.521 |
|
| 2018 |
Crabtree MD, Mendonça CATF, Bubb QR, Clarke J. Folding and binding pathways of BH3-only proteins are encoded within their intrinsically disordered sequence, not templated by partner proteins. The Journal of Biological Chemistry. PMID 29716994 DOI: 10.1074/Jbc.Ra118.002791 |
0.52 |
|
| 2018 |
Dahal L, Kwan TOC, Hollins JJ, Clarke J. Promiscuous and selective: How intrinsically disordered BH3-proteins interact with their pro-survival partner MCL-1. Journal of Molecular Biology. PMID 29654795 DOI: 10.1016/J.Jmb.2018.04.004 |
0.415 |
|
| 2018 |
Tian P, Steward A, Clarke J, Best RB. Conservation of Folding Mechanism in Cotranslational Folding of Titin I27 Biophysical Journal. 114: 593a. DOI: 10.1016/J.Bpj.2017.11.3242 |
0.443 |
|
| 2017 |
Dahal L, Kwan TOC, Shammas SL, Clarke J. pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions. Biophysical Journal. 113: 2713-2722. PMID 29262364 DOI: 10.1016/J.Bpj.2017.10.016 |
0.449 |
|
| 2017 |
Dahal L, Shammas SL, Clarke J. Phosphorylation of the IDP KID Modulates Affinity for KIX by Increasing the Lifetime of the Complex. Biophysical Journal. 113: 2706-2712. PMID 29262363 DOI: 10.1016/J.Bpj.2017.10.015 |
0.379 |
|
| 2017 |
Paul F, Wehmeyer C, Abualrous ET, Wu H, Crabtree MD, Schöneberg J, Clarke J, Freund C, Weikl TR, Noé F. Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nature Communications. 8: 1095. PMID 29062047 DOI: 10.1038/S41467-017-01163-6 |
0.41 |
|
| 2017 |
Wicky BIM, Shammas SL, Clarke J. Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure. Proceedings of the National Academy of Sciences of the United States of America. PMID 28847960 DOI: 10.1073/Pnas.1705105114 |
0.376 |
|
| 2017 |
Crabtree MD, Borcherds W, Poosapati A, Shammas SL, Daughdrill GW, Clarke J. Conserved helix-flanking prolines modulate IDP:target affinity by altering the lifetime of the bound complex. Biochemistry. PMID 28425697 DOI: 10.1021/Acs.Biochem.7B00179 |
0.386 |
|
| 2017 |
Chu WT, Clarke J, Shammas SL, Wang J. Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1. Plos Computational Biology. 13: e1005468. PMID 28369057 DOI: 10.1371/Journal.Pcbi.1005468 |
0.402 |
|
| 2017 |
Clarke J, Pappu RV. Editorial overview: Protein Folding and Binding, Complexity Comes of Age. Current Opinion in Structural Biology. 42: v-vii. PMID 28351535 DOI: 10.1016/J.Sbi.2017.03.004 |
0.385 |
|
| 2017 |
Nilsson OB, Nickson AA, Hollins JJ, Wickles S, Steward A, Beckmann R, von Heijne G, Clarke J. Cotranslational folding of spectrin domains via partially structured states. Nature Structural & Molecular Biology. PMID 28112730 DOI: 10.1038/Nsmb.3355 |
0.535 |
|
| 2017 |
Crabtree MD, Mendonca CA, Bubb Q, Shammas SL, Clarke J. What Encodes Coupled Folding and Binding Reactions: IDPS or Partner Proteins? Biophysical Journal. 112: 481a. DOI: 10.1016/J.Bpj.2016.11.2603 |
0.491 |
|
| 2016 |
Gruszka DT, Mendonça CA, Paci E, Whelan F, Hawkhead J, Potts JR, Clarke J. Disorder drives cooperative folding in a multidomain protein. Proceedings of the National Academy of Sciences of the United States of America. PMID 27698144 DOI: 10.1073/Pnas.1608762113 |
0.498 |
|
| 2016 |
Harmon TS, Crabtree MD, Shammas SL, Posey AE, Clarke J, Pappu RV. GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins. Protein Engineering, Design & Selection : Peds. PMID 27503953 DOI: 10.1093/Protein/Gzw034 |
0.387 |
|
| 2016 |
Shammas SL, Crabtree MD, Dahal L, Wicky BI, Clarke J. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies. The Journal of Biological Chemistry. PMID 26851275 DOI: 10.1074/Jbc.R115.692715 |
0.427 |
|
| 2016 |
Smock RG, Yadid I, Dym O, Clarke J, Tawfik DS. De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints. Cell. PMID 26806127 DOI: 10.1016/J.Cell.2015.12.024 |
0.475 |
|
| 2016 |
Valle Aramburu I, Mercadante D, Milles S, Ringkjøbing M, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas SL, Blackledge M, Gräter F, Lemke EA. Plasticity of Nucleoporin Nuclear Transport Receptor Interactions - Molecular Description of a Highly Dynamic, Ultrafast Interaction Mechanism Biophysical Journal. 110: 357a. DOI: 10.1016/J.Bpj.2015.11.1927 |
0.345 |
|
| 2016 |
Clarke J. The Role of Disorder in Protein Folding Biophysical Journal. 110: 196a. DOI: 10.1016/J.Bpj.2015.11.1095 |
0.464 |
|
| 2015 |
Borgia A, Kemplen KR, Borgia MB, Soranno A, Shammas S, Wunderlich B, Nettels D, Best RB, Clarke J, Schuler B. Transient misfolding dominates multidomain protein folding. Nature Communications. 6: 8861. PMID 26572969 DOI: 10.1038/Ncomms9861 |
0.672 |
|
| 2015 |
Milles S, Mercadante D, Aramburu IV, Jensen MR, Banterle N, Koehler C, Tyagi S, Clarke J, Shammas SL, Blackledge M, Gräter F, Lemke EA. Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors. Cell. 163: 734-45. PMID 26456112 DOI: 10.1016/J.Cell.2015.09.047 |
0.337 |
|
| 2015 |
Gruszka DT, Whelan F, Farrance OE, Fung HK, Paci E, Jeffries CM, Svergun DI, Baldock C, Baumann CG, Brockwell DJ, Potts JR, Clarke J. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nature Communications. 6: 7271. PMID 26027519 DOI: 10.1038/Ncomms8271 |
0.48 |
|
| 2015 |
Kemplen KR, De Sancho D, Clarke J. The response of Greek key proteins to changes in connectivity depends on the nature of their secondary structure. Journal of Molecular Biology. 427: 2159-65. PMID 25861761 DOI: 10.1016/J.Jmb.2015.03.020 |
0.739 |
|
| 2015 |
Borgia A, Kemplen KR, Borgia MB, Best RB, Soranno A, Nettels D, Wunderlich B, Clarke J, Schuler B. Surprising Abundance of Misfolding during Refolding of Multidomain Proteins Biophysical Journal. 108: 501a. DOI: 10.1016/J.Bpj.2014.11.2746 |
0.46 |
|
| 2015 |
Gruszka DT, Whelan F, Paci E, Brockwell DJ, Potts JR, Clarke J. The Folding of SasG: A Long and Remarkably Strong Monomeric Protein Responsible for Biofilm Formation is a Highly Cooperative System Biophysical Journal. 108: 346a. DOI: 10.1016/J.Bpj.2014.11.1897 |
0.45 |
|
| 2015 |
Shammas SL, Rogers J, Crabtree M, Clarke J. IDPs that Fold Upon Binding: What is the Role of the Partner Protein? Biophysical Journal. 108: 228a. DOI: 10.1016/J.Bpj.2014.11.1257 |
0.469 |
|
| 2014 |
Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR, Zhang X, Steward A, Reuter N, Clarke J, Teichmann SA. Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science (New York, N.Y.). 346: 1254346. PMID 25525255 DOI: 10.1126/Science.1254346 |
0.429 |
|
| 2014 |
Rogers JM, Oleinikovas V, Shammas SL, Wong CT, De Sancho D, Baker CM, Clarke J. Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. Proceedings of the National Academy of Sciences of the United States of America. 111: 15420-5. PMID 25313042 DOI: 10.1073/Pnas.1409122111 |
0.746 |
|
| 2014 |
Shammas SL, Travis AJ, Clarke J. Allostery within a transcription coactivator is predominantly mediated through dissociation rate constants. Proceedings of the National Academy of Sciences of the United States of America. 111: 12055-60. PMID 25092343 DOI: 10.1073/Pnas.1405815111 |
0.395 |
|
| 2014 |
Rogers JM, Wong CT, Clarke J. Coupled folding and binding of the disordered protein PUMA does not require particular residual structure. Journal of the American Chemical Society. 136: 5197-200. PMID 24654952 DOI: 10.1021/Ja4125065 |
0.483 |
|
| 2014 |
Kwa LG, Wensley BG, Alexander CG, Browning SJ, Lichman BR, Clarke J. The folding of a family of three-helix bundle proteins: spectrin R15 has a robust folding nucleus, unlike its homologous neighbours. Journal of Molecular Biology. 426: 1600-10. PMID 24373753 DOI: 10.1016/J.Jmb.2013.12.018 |
0.411 |
|
| 2014 |
Hill SA, Kwa LG, Shammas SL, Lee JC, Clarke J. Mechanism of assembly of the non-covalent spectrin tetramerization domain from intrinsically disordered partners. Journal of Molecular Biology. 426: 21-35. PMID 24055379 DOI: 10.1016/J.Jmb.2013.08.027 |
0.448 |
|
| 2014 |
Tiwari SP, Perica T, Kondo Y, McLaughlin S, Steward A, Clarke J, Teichmann SA, Reuter N. Studying the Role of Protein Flexibility in Allosteric and Evolutionary Changes as Seen in PyrR Protein Family Biophysical Journal. 106: 466a. DOI: 10.1016/J.Bpj.2013.11.2639 |
0.441 |
|
| 2014 |
Shammas SL, Clarke J. Speed Dating with KIX: A Single Domain that has Many Partners Biophysical Journal. 106: 426a. DOI: 10.1016/J.Bpj.2013.11.2401 |
0.469 |
|
| 2014 |
Clarke J. Folding Upon Binding - Is it just a Simple Protein Folding Problem? Biophysical Journal. 106: 4a. DOI: 10.1016/J.Bpj.2013.11.056 |
0.504 |
|
| 2013 |
Schuler B, Clarke J. Biophysics: Rough passage across a barrier. Nature. 502: 632-3. PMID 24153181 DOI: 10.1038/Nature12697 |
0.352 |
|
| 2013 |
Shammas SL, Travis AJ, Clarke J. Remarkably fast coupled folding and binding of the intrinsically disordered transactivation domain of cMyb to CBP KIX. The Journal of Physical Chemistry. B. 117: 13346-56. PMID 23875714 DOI: 10.1021/Jp404267E |
0.47 |
|
| 2013 |
Borgia MB, Nickson AA, Clarke J, Hounslow MJ. A mechanistic model for amorphous protein aggregation of immunoglobulin-like domains. Journal of the American Chemical Society. 135: 6456-64. PMID 23510407 DOI: 10.1021/Ja308852B |
0.405 |
|
| 2013 |
Rogers JM, Steward A, Clarke J. Folding and binding of an intrinsically disordered protein: fast, but not 'diffusion-limited'. Journal of the American Chemical Society. 135: 1415-22. PMID 23301700 DOI: 10.1021/Ja309527H |
0.431 |
|
| 2013 |
Nickson AA, Wensley BG, Clarke J. Take home lessons from studies of related proteins. Current Opinion in Structural Biology. 23: 66-74. PMID 23265640 DOI: 10.1016/J.Sbi.2012.11.009 |
0.495 |
|
| 2013 |
Randles LG, Dawes GJ, Wensley BG, Steward A, Nickson AA, Clarke J. Understanding pathogenic single-nucleotide polymorphisms in multidomain proteins--studies of isolated domains are not enough. The Febs Journal. 280: 1018-27. PMID 23241237 DOI: 10.1111/Febs.12094 |
0.424 |
|
| 2013 |
Hill SA, Lee JC, Clarke J. Identity of Hinge Residues Defines Stability and Kinetics of Spectrin Tetramer Interaction Biophysical Journal. 104: 369a. DOI: 10.1016/J.Bpj.2012.11.2052 |
0.46 |
|
| 2013 |
Clarke J, Rogers JM, Hill SA, Shammas SL, Gruszka D, Steward A, Lee JC, Potts JR. Folding Upon Binding - Not a Simple Protein Folding Problem Biophysical Journal. 104: 189a. DOI: 10.1016/J.Bpj.2012.11.1069 |
0.559 |
|
| 2012 |
Shammas SL, Rogers JM, Hill SA, Clarke J. Slow, reversible, coupled folding and binding of the spectrin tetramerization domain. Biophysical Journal. 103: 2203-14. PMID 23200054 DOI: 10.1016/J.Bpj.2012.10.012 |
0.487 |
|
| 2012 |
Borgia A, Wensley BG, Soranno A, Nettels D, Borgia MB, Hoffmann A, Pfeil SH, Lipman EA, Clarke J, Schuler B. Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nature Communications. 3: 1195. PMID 23149740 DOI: 10.1038/Ncomms2204 |
0.522 |
|
| 2012 |
Wensley BG, Kwa LG, Shammas SL, Rogers JM, Clarke J. Protein folding: adding a nucleus to guide helix docking reduces landscape roughness. Journal of Molecular Biology. 423: 273-83. PMID 22917971 DOI: 10.1016/J.Jmb.2012.08.003 |
0.334 |
|
| 2012 |
Wensley BG, Kwa LG, Shammas SL, Rogers JM, Browning S, Yang Z, Clarke J. Separating the effects of internal friction and transition state energy to explain the slow, frustrated folding of spectrin domains. Proceedings of the National Academy of Sciences of the United States of America. 109: 17795-9. PMID 22711800 DOI: 10.1073/Pnas.1201793109 |
0.356 |
|
| 2012 |
Gruszka DT, Wojdyla JA, Bingham RJ, Turkenburg JP, Manfield IW, Steward A, Leech AP, Geoghegan JA, Foster TJ, Clarke J, Potts JR. Staphylococcal biofilm-forming protein has a contiguous rod-like structure. Proceedings of the National Academy of Sciences of the United States of America. 109: E1011-8. PMID 22493247 DOI: 10.1073/Pnas.1119456109 |
0.425 |
|
| 2012 |
Steward A, Chen Q, Chapman RI, Borgia MB, Rogers JM, Wojtala A, Wilmanns M, Clarke J. Two immunoglobulin tandem proteins with a linking β-strand reveal unexpected differences in cooperativity and folding pathways. Journal of Molecular Biology. 416: 137-47. PMID 22197372 DOI: 10.1016/J.Jmb.2011.12.012 |
0.386 |
|
| 2011 |
Borgia MB, Borgia A, Best RB, Steward A, Nettels D, Wunderlich B, Schuler B, Clarke J. Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature. 474: 662-5. PMID 21623368 DOI: 10.1038/Nature10099 |
0.664 |
|
| 2010 |
Clarke J, Regan L. Protein engineering and design: from first principles to new technologies. Current Opinion in Structural Biology. 20: 480-1. PMID 20708403 DOI: 10.1016/J.Sbi.2010.07.001 |
0.421 |
|
| 2010 |
Nickson AA, Clarke J. What lessons can be learned from studying the folding of homologous proteins? Methods (San Diego, Calif.). 52: 38-50. PMID 20570731 DOI: 10.1016/J.Ymeth.2010.06.003 |
0.458 |
|
| 2010 |
Booth PJ, Clarke J. Membrane protein folding makes the transition. Proceedings of the National Academy of Sciences of the United States of America. 107: 3947-8. PMID 20173094 DOI: 10.1073/Pnas.0914478107 |
0.45 |
|
| 2010 |
Wensley BG, Batey S, Bone FA, Chan ZM, Tumelty NR, Steward A, Kwa LG, Borgia A, Clarke J. Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family. Nature. 463: 685-8. PMID 20130652 DOI: 10.1038/Nature08743 |
0.506 |
|
| 2009 |
Forman JR, Yew ZT, Qamar S, Sandford RN, Paci E, Clarke J. Non-native interactions are critical for mechanical strength in PKD domains. Structure (London, England : 1993). 17: 1582-90. PMID 20004162 DOI: 10.1016/J.Str.2009.09.013 |
0.491 |
|
| 2009 |
Ma L, Xu M, Forman JR, Clarke J, Oberhauser AF. Naturally occurring mutations alter the stability of polycystin-1 polycystic kidney disease (PKD) domains. The Journal of Biological Chemistry. 284: 32942-9. PMID 19759016 DOI: 10.1074/Jbc.M109.021832 |
0.356 |
|
| 2009 |
Wensley BG, Gärtner M, Choo WX, Batey S, Clarke J. Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms. Journal of Molecular Biology. 390: 1074-85. PMID 19445951 DOI: 10.1016/J.Jmb.2009.05.010 |
0.363 |
|
| 2009 |
Steward A, McDowell GS, Clarke J. Topology is the principal determinant in the folding of a complex all-alpha Greek key death domain from human FADD. Journal of Molecular Biology. 389: 425-37. PMID 19362094 DOI: 10.1016/J.Jmb.2009.04.004 |
0.71 |
|
| 2008 |
Ng SP, Billings KS, Randles LG, Clarke J. Manipulating the stability of fibronectin type III domains by protein engineering. Nanotechnology. 19: 384023. PMID 21832582 DOI: 10.1088/0957-4484/19/38/384023 |
0.45 |
|
| 2008 |
Batey S, Nickson AA, Clarke J. Studying the folding of multidomain proteins. Hfsp Journal. 2: 365-77. PMID 19436439 DOI: 10.2976/1.2991513 |
0.555 |
|
| 2008 |
Borgia A, Steward A, Clarke J. An effective strategy for the design of proteins with enhanced mechanical stability. Angewandte Chemie (International Ed. in English). 47: 6900-3. PMID 18666188 DOI: 10.1002/Anie.200801761 |
0.498 |
|
| 2008 |
Nickson AA, Stoll KE, Clarke J. Folding of a LysM domain: entropy-enthalpy compensation in the transition state of an ideal two-state folder. Journal of Molecular Biology. 380: 557-69. PMID 18538343 DOI: 10.1016/J.Jmb.2008.05.020 |
0.482 |
|
| 2008 |
Borgia A, Williams PM, Clarke J. Single-molecule studies of protein folding. Annual Review of Biochemistry. 77: 101-25. PMID 18412537 DOI: 10.1146/annurev.biochem.77.060706.093102 |
0.347 |
|
| 2008 |
Batey S, Clarke J. The folding pathway of a single domain in a multidomain protein is not affected by its neighbouring domain. Journal of Molecular Biology. 378: 297-301. PMID 18371978 DOI: 10.1016/J.Jmb.2008.02.032 |
0.477 |
|
| 2008 |
Geierhaas CD, Salvatella X, Clarke J, Vendruscolo M. Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values. Protein Engineering, Design & Selection : Peds. 21: 215-22. PMID 18299294 DOI: 10.1093/Protein/Gzm092 |
0.607 |
|
| 2008 |
Billings KS, Best RB, Rutherford TJ, Clarke J. Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain. Journal of Molecular Biology. 375: 560-71. PMID 18035373 DOI: 10.1016/J.Jmb.2007.10.056 |
0.686 |
|
| 2008 |
Lappalainen I, Hurley MG, Clarke J. Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain. Journal of Molecular Biology. 375: 547-59. PMID 18022190 DOI: 10.1016/J.Jmb.2007.09.088 |
0.499 |
|
| 2008 |
Randles LG, Batey S, Steward A, Clarke J. Distinguishing specific and nonspecific interdomain interactions in multidomain proteins. Biophysical Journal. 94: 622-8. PMID 17890397 DOI: 10.1529/Biophysj.107.119123 |
0.491 |
|
| 2007 |
Ng SP, Clarke J. Experiments suggest that simulations may overestimate electrostatic contributions to the mechanical stability of a fibronectin type III domain. Journal of Molecular Biology. 371: 851-4. PMID 17594907 DOI: 10.1016/J.Jmb.2007.06.015 |
0.424 |
|
| 2007 |
Ng SP, Billings KS, Ohashi T, Allen MD, Best RB, Randles LG, Erickson HP, Clarke J. Designing an extracellular matrix protein with enhanced mechanical stability. Proceedings of the National Academy of Sciences of the United States of America. 104: 9633-7. PMID 17535921 DOI: 10.1073/Pnas.0609901104 |
0.683 |
|
| 2007 |
Han JH, Batey S, Nickson AA, Teichmann SA, Clarke J. The folding and evolution of multidomain proteins. Nature Reviews. Molecular Cell Biology. 8: 319-30. PMID 17356578 DOI: 10.1038/Nrm2144 |
0.55 |
|
| 2007 |
Forman JR, Clarke J. Mechanical unfolding of proteins: insights into biology, structure and folding. Current Opinion in Structural Biology. 17: 58-66. PMID 17251000 DOI: 10.1016/J.Sbi.2007.01.006 |
0.45 |
|
| 2007 |
Geierhaas CD, Nickson AA, Lindorff-Larsen K, Clarke J, Vendruscolo M. BPPred: a Web-based computational tool for predicting biophysical parameters of proteins. Protein Science : a Publication of the Protein Society. 16: 125-34. PMID 17123959 DOI: 10.1110/Ps.062383807 |
0.549 |
|
| 2007 |
Randles LG, Rounsevell RW, Clarke J. Spectrin domains lose cooperativity in forced unfolding. Biophysical Journal. 92: 571-7. PMID 17085494 DOI: 10.1529/Biophysj.106.093690 |
0.416 |
|
| 2007 |
Ng SP, Randles LG, Clarke J. Single molecule studies of protein folding using atomic force microscopy. Methods in Molecular Biology (Clifton, N.J.). 350: 139-67. PMID 16957322 DOI: 10.1385/1-59745-189-4:139 |
0.414 |
|
| 2006 |
Batey S, Clarke J. Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains. Proceedings of the National Academy of Sciences of the United States of America. 103: 18113-8. PMID 17108086 DOI: 10.1073/Pnas.0604580103 |
0.547 |
|
| 2006 |
Randles LG, Lappalainen I, Fowler SB, Moore B, Hamill SJ, Clarke J. Using model proteins to quantify the effects of pathogenic mutations in Ig-like proteins. The Journal of Biological Chemistry. 281: 24216-26. PMID 16760466 DOI: 10.1074/Jbc.M603593200 |
0.359 |
|
| 2006 |
Scott KA, Randles LG, Moran SJ, Daggett V, Clarke J. The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment. Journal of Molecular Biology. 359: 159-73. PMID 16618492 DOI: 10.1016/J.Jmb.2006.03.011 |
0.445 |
|
| 2006 |
Geierhaas CD, Best RB, Paci E, Vendruscolo M, Clarke J. Structural comparison of the two alternative transition states for folding of TI I27. Biophysical Journal. 91: 263-75. PMID 16603501 DOI: 10.1529/Biophysj.105.077057 |
0.717 |
|
| 2006 |
Batey S, Scott KA, Clarke J. Complex folding kinetics of a multidomain protein. Biophysical Journal. 90: 2120-30. PMID 16387757 DOI: 10.1529/Biophysj.105.072710 |
0.551 |
|
| 2005 |
Wright CF, Teichmann SA, Clarke J, Dobson CM. The importance of sequence diversity in the aggregation and evolution of proteins. Nature. 438: 878-81. PMID 16341018 DOI: 10.1038/Nature04195 |
0.493 |
|
| 2005 |
Ng SP, Rounsevell RW, Steward A, Geierhaas CD, Williams PM, Paci E, Clarke J. Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation. Journal of Molecular Biology. 350: 776-89. PMID 15964016 DOI: 10.1016/J.Jmb.2005.04.070 |
0.482 |
|
| 2005 |
Scott KA, Clarke J. Spectrin R16: broad energy barrier or sequential transition states? Protein Science : a Publication of the Protein Society. 14: 1617-29. PMID 15930007 DOI: 10.1110/Ps.051377105 |
0.361 |
|
| 2005 |
Batey S, Randles LG, Steward A, Clarke J. Cooperative folding in a multi-domain protein. Journal of Molecular Biology. 349: 1045-59. PMID 15913648 DOI: 10.1016/J.Jmb.2005.04.028 |
0.498 |
|
| 2005 |
Forman JR, Qamar S, Paci E, Sandford RN, Clarke J. The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction. Journal of Molecular Biology. 349: 861-71. PMID 15894330 DOI: 10.1016/J.Jmb.2005.04.008 |
0.467 |
|
| 2005 |
Best RB, Clarke J, Karplus M. What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. Journal of Molecular Biology. 349: 185-203. PMID 15876377 DOI: 10.1016/J.Jmb.2005.03.001 |
0.605 |
|
| 2005 |
Rounsevell RW, Steward A, Clarke J. Biophysical investigations of engineered polyproteins: implications for force data. Biophysical Journal. 88: 2022-9. PMID 15613637 DOI: 10.1529/Biophysj.104.053744 |
0.478 |
|
| 2005 |
Rounsevell R, Forman JR, Clarke J. Atomic force microscopy: mechanical unfolding of proteins. Methods (San Diego, Calif.). 34: 100-11. PMID 15283919 DOI: 10.1016/J.Ymeth.2004.03.007 |
0.351 |
|
| 2004 |
Scott KA, Randles LG, Clarke J. The folding of spectrin domains II: phi-value analysis of R16. Journal of Molecular Biology. 344: 207-21. PMID 15504412 DOI: 10.1016/J.Jmb.2004.09.023 |
0.484 |
|
| 2004 |
Scott KA, Batey S, Hooton KA, Clarke J. The folding of spectrin domains I: wild-type domains have the same stability but very different kinetic properties. Journal of Molecular Biology. 344: 195-205. PMID 15504411 DOI: 10.1016/J.Jmb.2004.09.037 |
0.504 |
|
| 2004 |
Geierhaas CD, Paci E, Vendruscolo M, Clarke J. Comparison of the transition states for folding of two Ig-like proteins from different superfamilies. Journal of Molecular Biology. 343: 1111-23. PMID 15476825 DOI: 10.1016/J.Jmb.2004.08.100 |
0.661 |
|
| 2004 |
Best RB, Clarke J, Karplus M. The origin of protein sidechain order parameter distributions. Journal of the American Chemical Society. 126: 7734-5. PMID 15212494 DOI: 10.1021/Ja049078W |
0.582 |
|
| 2004 |
Wright CF, Christodoulou J, Dobson CM, Clarke J. The importance of loop length in the folding of an immunoglobulin domain. Protein Engineering, Design & Selection : Peds. 17: 443-53. PMID 15208402 DOI: 10.1093/Protein/Gzh052 |
0.505 |
|
| 2004 |
Wright CF, Steward A, Clarke J. Thermodynamic characterisation of two transition states along parallel protein folding pathways. Journal of Molecular Biology. 338: 445-51. PMID 15081803 DOI: 10.1016/J.Jmb.2004.02.062 |
0.47 |
|
| 2004 |
Best RB, Rutherford TJ, Freund SM, Clarke J. Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing. Biochemistry. 43: 1145-55. PMID 14756550 DOI: 10.1021/Bi035658E |
0.643 |
|
| 2004 |
Rounsevell RW, Clarke J. FnIII domains: predicting mechanical stability. Structure (London, England : 1993). 12: 4-5. PMID 14725758 DOI: 10.1016/J.Str.2003.12.006 |
0.385 |
|
| 2004 |
Wright CF, Lindorff-Larsen K, Randles LG, Clarke J. Parallel protein-unfolding pathways revealed and mapped. Nature Structural Biology. 10: 658-62. PMID 12833152 DOI: 10.1038/Nsb947 |
0.444 |
|
| 2003 |
Best RB, Fowler SB, Herrera JL, Steward A, Paci E, Clarke J. Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations. Journal of Molecular Biology. 330: 867-77. PMID 12850153 DOI: 10.1016/S0022-2836(03)00618-1 |
0.675 |
|
| 2003 |
Williams PM, Fowler SB, Best RB, Toca-Herrera JL, Scott KA, Steward A, Clarke J. Hidden complexity in the mechanical properties of titin. Nature. 422: 446-9. PMID 12660787 DOI: 10.1038/Nature01517 |
0.63 |
|
| 2003 |
Paci E, Clarke J, Steward A, Vendruscolo M, Karplus M. Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain. Proceedings of the National Academy of Sciences of the United States of America. 100: 394-9. PMID 12515856 DOI: 10.1073/Pnas.232704999 |
0.616 |
|
| 2003 |
Best RB, Brockwell DJ, Toca-Herrera JL, Blake AW, Smith D, Radford SE, Clarke J. Force mode atomic force microscopy as a tool for protein folding studies Analytica Chimica Acta. 479: 87-105. DOI: 10.1016/S0003-2670(02)01572-6 |
0.401 |
|
| 2002 |
Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J. Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. Journal of Molecular Biology. 322: 841-9. PMID 12270718 DOI: 10.1016/S0022-2836(02)00805-7 |
0.708 |
|
| 2002 |
Best RB, Fowler SB, Toca-Herrera JL, Clarke J. A simple method for probing the mechanical unfolding pathway of proteins in detail. Proceedings of the National Academy of Sciences of the United States of America. 99: 12143-8. PMID 12218181 DOI: 10.1073/Pnas.192351899 |
0.685 |
|
| 2002 |
Steward A, Toca-Herrera JL, Clarke J. Versatile cloning system for construction of multimeric proteins for use in atomic force microscopy. Protein Science : a Publication of the Protein Society. 11: 2179-83. PMID 12192073 DOI: 10.1110/Ps.0212702 |
0.367 |
|
| 2002 |
Best RB, Clarke J. What can atomic force microscopy tell us about protein folding? Chemical Communications (Cambridge, England). 183-92. PMID 12120362 DOI: 10.1039/B108159B |
0.672 |
|
| 2002 |
Steward A, Adhya S, Clarke J. Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily. Journal of Molecular Biology. 318: 935-40. PMID 12054791 DOI: 10.1016/S0022-2836(02)00184-5 |
0.456 |
|
| 2002 |
Scott KA, Steward A, Fowler SB, Clarke J. Titin; a multidomain protein that behaves as the sum of its parts. Journal of Molecular Biology. 315: 819-29. PMID 11812150 DOI: 10.1006/Jmbi.2001.5260 |
0.413 |
|
| 2001 |
Best RB, Li B, Steward A, Daggett V, Clarke J. Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophysical Journal. 81: 2344-56. PMID 11566804 DOI: 10.1016/S0006-3495(01)75881-X |
0.473 |
|
| 2001 |
Fowler SB, Clarke J. Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement of the transition state. Structure (London, England : 1993). 9: 355-66. PMID 11377196 DOI: 10.1016/S0969-2126(01)00596-2 |
0.529 |
|
| 2001 |
Cota E, Steward A, Fowler SB, Clarke J. The folding nucleus of a fibronectin type III domain is composed of core residues of the immunoglobulin-like fold. Journal of Molecular Biology. 305: 1185-94. PMID 11162123 DOI: 10.1006/Jmbi.2000.4378 |
0.507 |
|
| 2001 |
Clarke J, Dobson CM. Folding and binding Emerging themes in protein folding and assembly Current Opinion in Structural Biology. 11: 67-69. DOI: 10.1016/S0959-440X(00)00179-2 |
0.464 |
|
| 2000 |
Clarke J, Hounslow AM, Bond CJ, Fersht AR, Daggett V. The effects of disulfide bonds on the denatured state of barnase. Protein Science : a Publication of the Protein Society. 9: 2394-404. PMID 11206061 DOI: 10.1110/Ps.9.12.2394 |
0.402 |
|
| 2000 |
Cota E, Hamill SJ, Fowler SB, Clarke J. Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability. Journal of Molecular Biology. 302: 713-25. PMID 10986129 DOI: 10.1006/Jmbi.2000.4053 |
0.431 |
|
| 2000 |
Li H, Oberhauser AF, Fowler SB, Clarke J, Fernandez JM. Atomic force microscopy reveals the mechanical design of a modular protein Proceedings of the National Academy of Sciences of the United States of America. 97: 6527-6531. PMID 10823913 DOI: 10.1073/Pnas.120048697 |
0.447 |
|
| 2000 |
Cota E, Clarke J. Folding of beta-sandwich proteins: three-state transition of a fibronectin type III module. Protein Science : a Publication of the Protein Society. 9: 112-20. PMID 10739253 DOI: 10.1110/Ps.9.1.112 |
0.529 |
|
| 2000 |
Hamill SJ, Steward A, Clarke J. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. Journal of Molecular Biology. 297: 165-78. PMID 10704314 DOI: 10.1006/Jmbi.2000.3517 |
0.507 |
|
| 2000 |
Wong KB, Clarke J, Bond CJ, Neira JL, Freund SM, Fersht AR, Daggett V. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. Journal of Molecular Biology. 296: 1257-82. PMID 10698632 DOI: 10.1006/Jmbi.2000.3523 |
0.386 |
|
| 2000 |
Hamill SJ, Cota E, Chothia C, Clarke J. Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. Journal of Molecular Biology. 295: 641-9. PMID 10623553 DOI: 10.1006/Jmbi.1999.3360 |
0.508 |
|
| 1999 |
Clarke J, Cota E, Fowler SB, Hamill SJ. Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway. Structure (London, England : 1993). 7: 1145-53. PMID 10508783 DOI: 10.1016/S0969-2126(99)80181-6 |
0.454 |
|
| 1999 |
Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM. Mechanical and chemical unfolding of a single protein: a comparison. Proceedings of the National Academy of Sciences of the United States of America. 96: 3694-9. PMID 10097099 DOI: 10.1073/Pnas.96.7.3694 |
0.509 |
|
| 1999 |
Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C. The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. The Embo Journal. 18: 297-305. PMID 9889186 DOI: 10.1093/Emboj/18.2.297 |
0.478 |
|
| 1998 |
Meekhof AE, Hamill SJ, Arcus VL, Clarke J, Freund SM. The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin. Journal of Molecular Biology. 282: 181-94. PMID 9733649 DOI: 10.1006/Jmbi.1998.2019 |
0.397 |
|
| 1998 |
Hamill SJ, Meekhof AE, Clarke J. The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin. Biochemistry. 37: 8071-9. PMID 9609701 DOI: 10.1021/Bi9801659 |
0.463 |
|
| 1998 |
Fong S, Bycroft M, Clarke J, Freund SM. Characterisation of urea-denatured states of an immunoglobulin superfamily domain by heteronuclear NMR. Journal of Molecular Biology. 278: 417-29. PMID 9571061 DOI: 10.1006/Jmbi.1998.1702 |
0.426 |
|
| 1998 |
Dalby PA, Clarke J, Johnson CM, Fersht AR. 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. Journal of Molecular Biology. 276: 647-56. PMID 9551102 DOI: 10.1006/Jmbi.1997.1547 |
0.348 |
|
| 1998 |
Clarke J, Itzhaki LS. Hydrogen exchange and protein folding. Current Opinion in Structural Biology. 8: 112-8. PMID 9519304 DOI: 10.1016/S0959-440X(98)80018-3 |
0.453 |
|
| 1997 |
Bond CJ, Wong KB, Clarke J, Fersht AR, Daggett V. Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Proceedings of the National Academy of Sciences of the United States of America. 94: 13409-13. PMID 9391038 DOI: 10.1073/Pnas.94.25.13409 |
0.434 |
|
| 1997 |
Clarke J, Itzhaki LS, Fersht AR. Hydrogen exchange at equilibrium: a short cut for analysing protein-folding pathways? Trends in Biochemical Sciences. 22: 284-7. PMID 9270297 DOI: 10.1016/S0968-0004(97)01087-6 |
0.426 |
|
| 1997 |
Clarke J, Hamill SJ, Johnson CM. Folding and stability of a fibronectin type III domain of human tenascin. Journal of Molecular Biology. 270: 771-8. PMID 9245604 DOI: 10.1006/Jmbi.1997.1147 |
0.475 |
|
| 1997 |
Johnson CM, Oliveberg M, Clarke J, Fersht AR. Thermodynamics of denaturation of mutants of barnase with disulfide crosslinks. Journal of Molecular Biology. 268: 198-208. PMID 9149152 DOI: 10.1006/Jmbi.1997.0928 |
0.324 |
|
| 1997 |
Clarke J, Fersht AR. An evaluation of the use of hydrogen exchange at equilibrium to probe intermediates on the protein folding pathway. Folding & Design. 1: 243-54. PMID 9079387 DOI: 10.1016/S1359-0278(96)00038-7 |
0.384 |
|
| 1996 |
Fong S, Hamill SJ, Proctor M, Freund SM, Benian GM, Chothia C, Bycroft M, Clarke J. Structure and stability of an immunoglobulin superfamily domain from twitchin, a muscle protein of the nematode Caenorhabditis elegans. Journal of Molecular Biology. 264: 624-39. PMID 8969309 DOI: 10.1006/Jmbi.1996.0665 |
0.513 |
|
| 1995 |
Perrett S, Clarke J, Hounslow AM, Fersht AR. Relationship between equilibrium amide proton exchange behavior and the folding pathway of barnase. Biochemistry. 34: 9288-98. PMID 7626599 DOI: 10.1021/Bi00029A003 |
0.429 |
|
| 1995 |
Clarke J, Hounslow AM, Fersht AR. Disulfide mutants of barnase. II: Changes in structure and local stability identified by hydrogen exchange. Journal of Molecular Biology. 253: 505-13. PMID 7473730 DOI: 10.1006/Jmbi.1995.0569 |
0.408 |
|
| 1995 |
Clarke J, Henrick K, Fersht AR. Disulfide mutants of barnase. I: Changes in stability and structure assessed by biophysical methods and X-ray crystallography. Journal of Molecular Biology. 253: 493-504. PMID 7473729 DOI: 10.1006/Jmbi.1995.0568 |
0.448 |
|
| 1993 |
Clarke J, Fersht AR. Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation. Biochemistry. 32: 4322-9. PMID 8476861 DOI: 10.1021/Bi00067A022 |
0.514 |
|
| 1993 |
Clarke J, Hounslow AM, Bycroft M, Fersht AR. Local breathing and global unfolding in hydrogen exchange of barnase and its relationship to protein folding pathways. Proceedings of the National Academy of Sciences of the United States of America. 90: 9837-41. PMID 8234322 DOI: 10.1073/Pnas.90.21.9837 |
0.418 |
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