| Year |
Citation |
Score |
| 2022 |
Newaz K, Piland J, Clark PL, Emrich SJ, Li J, Milenković T. Multi-layer sequential network analysis improves protein 3D structural classification. Proteins. PMID 35441395 DOI: 10.1002/prot.26349 |
0.324 |
|
| 2021 |
Wright G, Rodriguez A, Li J, Milenkovic T, Emrich SJ, Clark PL. CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern. Protein Science : a Publication of the Protein Society. PMID 34738275 DOI: 10.1002/pro.4223 |
0.314 |
|
| 2020 |
Bowman MA, Riback JA, Rodriguez A, Guo H, Li J, Sosnick TR, Clark PL. Properties of protein unfolded states suggest broad selection for expanded conformational ensembles. Proceedings of the National Academy of Sciences of the United States of America. PMID 32879005 DOI: 10.1073/Pnas.2003773117 |
0.542 |
|
| 2020 |
Faisal FE, Newaz K, Chaney JL, Li J, Emrich SJ, Clark PL, Milenković T. Author Correction: GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. Scientific Reports. 10: 13455. PMID 32778675 DOI: 10.1038/S41598-020-69025-8 |
0.345 |
|
| 2020 |
Newaz K, Wright G, Piland J, Li J, Clark P, Emrich S, Milenković T. Network analysis of synonymous codon usage. Bioinformatics (Oxford, England). PMID 32609328 DOI: 10.1093/Bioinformatics/Btaa603 |
0.376 |
|
| 2020 |
Clark PL, Plaxco KW, Sosnick TR. Water as a good solvent for unfolded proteins: Folding and collapse are fundamentally different. Journal of Molecular Biology. PMID 32044346 DOI: 10.1016/J.Jmb.2020.01.031 |
0.459 |
|
| 2020 |
Walsh IM, Bowman MA, Soto Santarriaga IF, Rodriguez A, Clark PL. Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness. Proceedings of the National Academy of Sciences of the United States of America. PMID 32015130 DOI: 10.1073/Pnas.1907126117 |
0.528 |
|
| 2019 |
Clark PL. Proteins in the Cell. Protein Science : a Publication of the Protein Society. PMID 31152461 DOI: 10.1002/Pro.3665 |
0.434 |
|
| 2019 |
Riback JA, Bowman MA, Zmyslowski AM, Plaxco KW, Clark PL, Sosnick TR. Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proceedings of the National Academy of Sciences of the United States of America. PMID 30992378 DOI: 10.1073/Pnas.1813038116 |
0.4 |
|
| 2019 |
Sosnick TR, Riback JA, Bowman MA, Zmyslowski AM, Rodriguez A, Plaxco KW, Clark PL. The importance of measuring the solvent quality of unfolded proteins Acta Crystallographica Section a Foundations and Advances. 75: a419-a419. DOI: 10.1107/S0108767319095916 |
0.377 |
|
| 2018 |
Riback JA, Bowman MA, Zmyslowski A, Knoverek CR, Jumper J, Kaye EB, Freed KF, Clark PL, Sosnick TR. Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water". Science (New York, N.Y.). 361. PMID 30166460 DOI: 10.1126/Science.Aar7949 |
0.356 |
|
| 2018 |
Bartkiewicz M, Kazazić S, Krasowska J, Clark PL, Wielgus-Kutrowska B, Bzowska A. Non-fluorescent mutant of green fluorescent protein sheds light on the mechanism of chromophore formation. Febs Letters. PMID 29637558 DOI: 10.1002/1873-3468.13051 |
0.328 |
|
| 2018 |
Riback JA, Bowman MA, Zmyslowski AM, Plaxco KW, Clark PL, Sosnick TR. Saxs Confirms that FRET Dyes Promote Collapse of an Otherwise Fully Disordered Protein Biophysical Journal. 114: 368a. DOI: 10.1016/J.Bpj.2017.11.2040 |
0.365 |
|
| 2018 |
Bowman MA, Clark PL. Folding Proteins From One End to the Other Biophysical Journal. 114: 200a. DOI: 10.1016/J.Bpj.2017.11.1120 |
0.537 |
|
| 2017 |
Faisal FE, Newaz K, Chaney JL, Li J, Emrich SJ, Clark PL, Milenković T. GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. Scientific Reports. 7: 14890. PMID 29097661 DOI: 10.1038/S41598-017-14411-Y |
0.343 |
|
| 2017 |
Rodriguez A, Wright G, Emrich S, Clark PL. %MinMax: A Versatile Tool for Calculating and Comparing Synonymous Codon Usage and Its Impact on Protein Folding. Protein Science : a Publication of the Protein Society. PMID 29090506 DOI: 10.1002/Pro.3336 |
0.392 |
|
| 2017 |
Riback JA, Bowman MA, Zmyslowski AM, Knoverek CR, Jumper JM, Hinshaw JR, Kaye EB, Freed KF, Clark PL, Sosnick TR. Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science (New York, N.Y.). 358: 238-241. PMID 29026044 DOI: 10.1126/Science.Aan5774 |
0.421 |
|
| 2017 |
Chaney JL, Steele A, Carmichael R, Rodriguez A, Specht AT, Ngo K, Li J, Emrich S, Clark PL. Widespread position-specific conservation of synonymous rare codons within coding sequences. Plos Computational Biology. 13: e1005531. PMID 28475588 DOI: 10.1371/Journal.Pcbi.1005531 |
0.439 |
|
| 2017 |
Walsh IM, Li S, Elcock AH, Clark PL. Integrated In Vivo and In Silico Studies of Cotranslational Protein Folding as a Function of Translation Rate Biophysical Journal. 112: 40a. DOI: 10.1016/J.Bpj.2016.11.256 |
0.567 |
|
| 2017 |
Riback JA, Bowman MA, Zmyslowski A, Knoverek CR, Jumper J, Hinshaw J, Kaye EB, Freed KF, Clark PL, Sosnick TR. Measuring the (Good) Solvent Quality of Water for Disordered Proteins from a Single SAXS Measurement Biophysical Journal. 112: 316a. DOI: 10.1016/J.Bpj.2016.11.1712 |
0.443 |
|
| 2016 |
Wilson DN, Clark PL. Climbing to the peak of nascent-chain knowledge. Nature Structural & Molecular Biology. 23: 949-951. PMID 27814347 DOI: 10.1038/Nsmb.3314 |
0.454 |
|
| 2016 |
Braselmann E, Chaney JL, Champion MM, Clark PL. DegP Chaperone Suppresses Toxic Inner Membrane Translocation Intermediates. Plos One. 11: e0162922. PMID 27626276 DOI: 10.1371/Journal.Pone.0162922 |
0.48 |
|
| 2016 |
Clark PL, Elcock AH. Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis. Nature Structural & Molecular Biology. 23: 621-623. PMID 27384188 DOI: 10.1038/Nsmb.3255 |
0.424 |
|
| 2016 |
Jacobson GN, Clark PL. Quality over quantity: optimizing co-translational protein folding with non-'optimal' synonymous codons. Current Opinion in Structural Biology. 38: 102-110. PMID 27318814 DOI: 10.1016/J.Sbi.2016.06.002 |
0.505 |
|
| 2016 |
Clark PL. How to Build a Complex, Functional Propeller Protein From Parts. Trends in Biochemical Sciences. PMID 26971075 DOI: 10.1016/J.Tibs.2016.02.010 |
0.409 |
|
| 2015 |
Besingi RN, Clark PL. Extracellular protease digestion to evaluate membrane protein cell surface localization. Nature Protocols. 10: 2074-2080. PMID 26584447 DOI: 10.1038/Nprot.2015.131 |
0.787 |
|
| 2015 |
Cressiot B, Braselmann E, Oukhaled A, Elcock AH, Pelta J, Clark PL. Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore. Acs Nano. 9: 9050-61. PMID 26302243 DOI: 10.1021/Acsnano.5B03053 |
0.397 |
|
| 2015 |
Chaney JL, Clark PL. Roles for Synonymous Codon Usage in Protein Biogenesis. Annual Review of Biophysics. 44: 143-66. PMID 25747594 DOI: 10.1146/Annurev-Biophys-060414-034333 |
0.442 |
|
| 2015 |
Drobnak I, Braselmann E, Clark PL. Multiple driving forces required for efficient secretion of autotransporter virulence proteins. The Journal of Biological Chemistry. 290: 10104-16. PMID 25670852 DOI: 10.1074/jbc.M114.629170 |
0.393 |
|
| 2015 |
Drobnak I, Braselmann E, Chaney JL, Leyton DL, Bernstein HD, Lithgow T, Luirink J, Nataro JP, Clark PL. Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion. Molecular Microbiology. 95: 1-16. PMID 25345653 DOI: 10.1111/Mmi.12838 |
0.382 |
|
| 2015 |
Drobnak I, Braselmann E, Clark PL. Multiple Driving Forces Contribute to Translocation of Autotransporter Virulence Proteins Biophysical Journal. 108: 496a-497a. DOI: 10.1016/J.Bpj.2014.11.2717 |
0.501 |
|
| 2015 |
Cressiot B, Braselmann E, Oukhaled A, Pelta J, Clark PL. Dynamics and Energy Contributions for Transport of Pertactin through an Aerolysin Nanopore Biophysical Journal. 108: 481a. DOI: 10.1016/J.Bpj.2014.11.2629 |
0.502 |
|
| 2014 |
Brodsky JL, Clark PL. Protein folding in the cell, from atom to organism. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 28: 5034-8. PMID 25451678 DOI: 10.1096/Fj.14-1202Ufm |
0.519 |
|
| 2014 |
Sander IM, Chaney JL, Clark PL. Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design. Journal of the American Chemical Society. 136: 858-61. PMID 24392935 DOI: 10.1021/Ja411302M |
0.564 |
|
| 2014 |
Krasowska J, Uriginov KG, Clark PL, Sienkiewicz A, Bzowska A, Wielgus-Kutrowska B. Spectroscopic properties of two single-cysteine mutants of EGFP: C48S-EGFP and C70S-EGFP Biomedical Spectroscopy and Imaging. 3: 231-236. DOI: 10.3233/Bsi-140070 |
0.376 |
|
| 2014 |
Drobnak I, Clark PL. Driving Forces for Protein Secretion Across the Bacterial Outer Membrane Biophysical Journal. 106: 669a. DOI: 10.1016/J.Bpj.2013.11.3705 |
0.517 |
|
| 2013 |
Besingi RN, Chaney JL, Clark PL. An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C-terminal stable core. Molecular Microbiology. 90: 1028-45. PMID 24118465 DOI: 10.1111/Mmi.12414 |
0.812 |
|
| 2013 |
Braselmann E, Chaney JL, Clark PL. Folding the proteome. Trends in Biochemical Sciences. 38: 337-44. PMID 23764454 DOI: 10.1016/j.tibs.2013.05.001 |
0.434 |
|
| 2013 |
Clark PL. New Directions for Vectorial Protein Folding Biophysical Journal. 104: 3a. DOI: 10.1016/J.Bpj.2012.11.033 |
0.577 |
|
| 2012 |
Braselmann E, Clark PL. Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport. The Journal of Physical Chemistry Letters. 3: 1063-1071. PMID 23687560 DOI: 10.1021/jz201654k |
0.512 |
|
| 2012 |
Renn JP, Junker M, Besingi RN, Braselmann E, Clark PL. ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein. Chemistry & Biology. 19: 287-96. PMID 22209629 DOI: 10.1016/J.Chembiol.2011.11.009 |
0.784 |
|
| 2012 |
Sander IM, Clark PL. Expanding Anfinsen’s Principle: Controlling Protein Structure by Altering Local Translation Rate Biophysical Journal. 102: 219a. DOI: 10.1016/J.Bpj.2011.11.1199 |
0.555 |
|
| 2011 |
Bryan AW, Starner-Kreinbrink JL, Hosur R, Clark PL, Berger B. Structure-based prediction reveals capping motifs that inhibit β-helix aggregation. Proceedings of the National Academy of Sciences of the United States of America. 108: 11099-104. PMID 21685332 DOI: 10.1073/Pnas.1017504108 |
0.379 |
|
| 2011 |
Renn JP, Clark PL. Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo. Methods in Enzymology. 492: 233-51. PMID 21333794 DOI: 10.1016/B978-0-12-381268-1.00030-6 |
0.787 |
|
| 2011 |
Clark PL. Adding protease digestion to the membrane protein toolbox. Journal of Molecular Biology. 406: 543-4. PMID 21238458 DOI: 10.1016/J.Jmb.2011.01.023 |
0.371 |
|
| 2011 |
Renn JP, Junker M, Clark PL. Outer Membrane Secretion Efficiency of Autotransporter Virulence Proteins Correlates with Passenger Domain Folding Properties Biophysical Journal. 100: 516a. DOI: 10.1016/J.Bpj.2010.12.3021 |
0.805 |
|
| 2010 |
Ugrinov KG, Clark PL. Cotranslational folding increases GFP folding yield. Biophysical Journal. 98: 1312-20. PMID 20371331 DOI: 10.1016/J.Bpj.2009.12.4291 |
0.775 |
|
| 2010 |
Clarke TF, Clark PL. Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. Bmc Genomics. 11: 118. PMID 20167116 DOI: 10.1186/1471-2164-11-118 |
0.663 |
|
| 2010 |
Junker M, Clark PL. Slow formation of aggregation-resistant beta-sheet folding intermediates. Proteins. 78: 812-24. PMID 19847915 DOI: 10.1002/Prot.22609 |
0.66 |
|
| 2010 |
Krasowska J, Olasek M, Bzowska A, Clark PL, Wielgus-Kutrowska B. The comparison of aggregation and folding of enhanced green fluorescent protein (EGFP) by spectroscopic studies Spectroscopy. 24: 343-348. DOI: 10.3233/Spe-2010-0445 |
0.434 |
|
| 2009 |
Clark PL, Ugrinov KG. Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods in Enzymology. 466: 567-90. PMID 21609877 DOI: 10.1016/S0076-6879(09)66024-9 |
0.792 |
|
| 2009 |
Junker M, Besingi RN, Clark PL. Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion. Molecular Microbiology. 71: 1323-32. PMID 19170888 DOI: 10.1016/J.Bpj.2008.12.1677 |
0.82 |
|
| 2009 |
Clarke TF, Clark PL. Rare Codon Clustering: Implications for Protein Biogenesis Biophysical Journal. 96: 580a-581a. DOI: 10.1016/J.Bpj.2008.12.3036 |
0.705 |
|
| 2009 |
Braselmann E, Clark PL. Can An Autotransporter Protein Truly Transport Itself Across A Lipid Bilayer? Biophysical Journal. 96: 335a. DOI: 10.1016/J.Bpj.2008.12.1685 |
0.503 |
|
| 2008 |
Clarke TF, Clark PL. Rare codons cluster. Plos One. 3: e3412. PMID 18923675 DOI: 10.1371/Journal.Pone.0003412 |
0.695 |
|
| 2008 |
Evans MS, Sander IM, Clark PL. Cotranslational folding promotes beta-helix formation and avoids aggregation in vivo. Journal of Molecular Biology. 383: 683-92. PMID 18674543 DOI: 10.1016/J.Jmb.2008.07.035 |
0.515 |
|
| 2008 |
Renn JP, Clark PL. A conserved stable core structure in the passenger domain beta-helix of autotransporter virulence proteins. Biopolymers. 89: 420-7. PMID 18189304 DOI: 10.1002/Bip.20924 |
0.795 |
|
| 2007 |
Kutrowska BW, Narczyk M, Buszko A, Bzowska A, Clark PL. Folding and unfolding of a non-fluorescent mutant of green fluorescent protein. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 285223. PMID 20126640 DOI: 10.1088/0953-8984/19/28/285223 |
0.435 |
|
| 2006 |
Junker M, Schuster CC, McDonnell AV, Sorg KA, Finn MC, Berger B, Clark PL. Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 4918-23. PMID 16549796 DOI: 10.1073/Pnas.0507923103 |
0.712 |
|
| 2005 |
Evans MS, Ugrinov KG, Frese MA, Clark PL. Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro. Nature Methods. 2: 757-62. PMID 16179922 DOI: 10.1038/Nmeth790 |
0.766 |
|
| 2005 |
Jain M, Evans MS, King J, Clark PL. Monoclonal antibody epitope mapping describes tailspike beta-helix folding and aggregation intermediates. The Journal of Biological Chemistry. 280: 23032-40. PMID 15833745 DOI: 10.1074/Jbc.M501963200 |
0.454 |
|
| 2005 |
Evans MS, Clarke TF, Clark PL. Conformations of co-translational folding intermediates. Protein and Peptide Letters. 12: 189-95. PMID 15723645 DOI: 10.2174/0929866053005908 |
0.754 |
|
| 2004 |
Clark PL. Protein folding in the cell: reshaping the folding funnel. Trends in Biochemical Sciences. 29: 527-34. PMID 15450607 DOI: 10.1016/J.Tibs.2004.08.008 |
0.533 |
|
| 2002 |
Benton CB, King J, Clark PL. Characterization of the protrimer intermediate in the folding pathway of the interdigitated beta-helix tailspike protein. Biochemistry. 41: 5093-103. PMID 11955057 DOI: 10.1021/bi0115582 |
0.636 |
|
| 2001 |
Clark PL, King J. A newly synthesized, ribosome-bound polypeptide chain adopts conformations dissimilar from early in vitro refolding intermediates. The Journal of Biological Chemistry. 276: 25411-20. PMID 11319217 DOI: 10.1074/Jbc.M008490200 |
0.532 |
|
| 2001 |
Raso SW, Clark PL, Haase-Pettingell C, King J, Thomas GJ. Distinct cysteine sulfhydryl environments detected by analysis of Raman S-hh markers of Cys-->Ser mutant proteins. Journal of Molecular Biology. 307: 899-911. PMID 11273709 DOI: 10.1006/Jmbi.2001.4476 |
0.469 |
|
| 1998 |
Clark PL, Weston BF, Gierasch LM. Probing the folding pathway of a beta-clam protein with single-tryptophan constructs. Folding & Design. 3: 401-12. PMID 9806942 DOI: 10.1016/S1359-0278(98)00053-4 |
0.601 |
|
| 1997 |
Clark PL, Liu ZP, Rizo J, Gierasch LM. Cavity formation before stable hydrogen bonding in the folding of a beta-clam protein. Nature Structural Biology. 4: 883-6. PMID 9360599 DOI: 10.1038/Nsb1197-883 |
0.528 |
|
| 1997 |
Clark PL, Sukumar M, Liu ZP, Rizo J, Rotondi K, Gierasch LM. Folding of a predominantly beta sheet protein with a central cavity Faseb Journal. 11: A871. |
0.774 |
|
| 1996 |
Clark PL, Liu ZP, Zhang J, Gierasch LM. Intrinsic tryptophans of CRABPI as probes of structure and folding. Protein Science : a Publication of the Protein Society. 5: 1108-17. PMID 8762142 DOI: 10.1002/Pro.5560050613 |
0.5 |
|
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