Publications

Explore a collection of research articles and other publications authored by Patricia Clark's laboratory.

Jump to Career Development Articles Authored by Patricia Clark

Referreed Publications 

• Soto Santarriaga I.F. & Clark P.L.* (under review) Protein folding success depends on the direction and rate of polypeptide chain appearance.
• Luan Q. & Clark P.L.* (2025) Discovery of an on-pathway protein folding intermediate illuminates the kinetic competition between folding and misfolding. Proceedings of the National Academy of Sciences USA. (in press)
• Loughran G.*, Andreev D.E. Terenin I.M., Namy O., Mikl M., Yordanova M.M., McManus C.J., Firth A.E., Atkins J.F., Fraser C.S., Ignatova Z., Iwasaki S., Kufel J., Larsson O., Leidel S.A., Mankin A.S., Mariotti M., Tanenbaum M.E., Topisirovic I., Vázquez-Laslop N., Viero G., Caliskan N., Chen Y., Clark P.L., Dinman J.D., Farabaugh P.J., Gilbert W.V., Ivanov P., Kieft J.S., Mühlemann O., Sachs M.S., Shatsky I.N., Sonenberg N., Steckelberg A., Willis A.E., Woodside M.T., Valasek L.S.*, Dmitriev S.E.*, Baranov P.V.* (2025) Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nature Structural & Molecular Biology.
• Rodriguez A., Diehl J.D., Wright G.S., Bonar C.D., Lundgren T.J., Moss M.J., Li J., Milenkovic T., Huber P.W., Champion M.M., Emrich S.J. & Clark P.L.* (2024) Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA. Proceedings of the National Academy of Sciences USA. 121, e2405510121.
• Baxa M.C., Lin X., Mukinay C.D., Chakravathy S., Sachleban J.R., Antilla S., Hartramph N., Riback J.A., Gagnon I.A., Pentelute B.L., Clark P.L.* & Sosnick T.R.* (2024) How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Science. 33, e4986.
• Lundgren T.J., Clark P.L.* & Champion M.M.* (2024) Fit for purpose approach to evaluate detection of amino acid substitutions in shotgun proteomics. Journal of Proteome Research. 23, 1263-1271.
• Moss M.J., Chamness L. & Clark P.L.* (2024) The effects of codon usage on protein structure and folding. Annual Reviews of Biophysics 53, 87-108.
• Newaz, K., Piland, J., Li J., Emrich S.J., Clark P.L. & Milenkovic T.* (2022) Multi-layer sequential network analysis improves protein 3D structural classification. Proteins: Structure, Function & Bioinformatics 90, 1721-1731.
• Wright G., Rodriguez A., Li J., Milenkovic T., Emrich S.J.* & Clark P.L.* (2022) CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern. Protein Science 31, 221-231.
• Harkness R.W., Toyama Y., Ripstein Z.A., Zhao H., Sever A.I.M., Luan Q., Brady J.P., Clark P.L., Schuck P. & Kay, L.E.* (2021) Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP. Proceedings of the National Academy of Sciences USA 118, e2109732118.
• Bowman M.A., Riback J.A., Rodriguez, A., Gao H., Li J., Sosnick T.R.* & Clark P.L.* (2020) Properties of protein unfolded states suggests broad selection for expanded conformational ensembles. Proceedings of the National Academy of Sciences USA 117, 23356-23364.
• Newaz, K., Wright G., Piland, J., Li, J., Clark P.L., Emrich S.J. & Milenkovic T.* (2020) Network analysis of synonymous codon usage. Bioinformatics 36, 4876-4884.
• Wright G.*, Rodriguez A., Li J., Clark P.L. Milenkovic T. & Emrich S.J. (2020) Analysis of computational codon usage models and their association with translationally slow codons. PLoS ONE e:0232003.
• Clark P.L.*, Plaxco K.W.* & Sosnick T.R.* (2020) Water as a good solvent for unfolded proteins: Folding and collapse are fundamentally different. Journal of Molecular Biology 432, 2882-2889.
• Walsh I.M., Bowman M.A., Soto-Santarriaga I.F., Rodriguez A. & Clark P.L.* (2020) Synonymous codon substitutions perturb co-translational folding in vivo and impair cell fitness. Proceedings of the National Academy of Sciences USA 117, 3528-3534.
• Riback J.A., Bowman M.A., Zmyslowski A., Plaxco, K.W., Clark P.L.* & Sosnick T.R.* (2019) Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proceedings of the National Academy of Sciences USA 116, 8889-8894.
• Bartkiewicz M.*, Kazazic S., Krasowska J., Clark P.L., Wielgus-Kutrowska B. & Bzowska A.* (2018) Nonfluorescent mutant of green fluorescent protein sheds light on the mechanism of chromophore formation. FEBS Letters 592, 1516-1523.
• Rodriguez A., Wright, G., Emrich S. & Clark P.L.* (2018) %MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding. Protein Science 27, 356-362.
• Faisal F.E., Newaz K., Chaney J.L., Li J., Emrich S.J., Clark P.L. & Milenkovic, T.* (2017) GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. Scientific Reports 7, 14890.
• Riback J.A., Bowman M.A., Zmyslowski A., Knoverek C.R., Jumper J., Hinshaw J., Kaye E.B., Freed K.F., Clark P.L.* & Sosnick T.R.* (2017) Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science 358, 238-241.
• Chaney J.L., Steele A., Carmichael R., Rodriguez A., Specht A.T., Ngo K., Li J., Emrich S.* & Clark P.L.* (2017) Widespread position-specific conservation of synonymous rare codons within coding sequences. PLoS Computational Biology. 13, e1005531.
• Jacobson G.N. & Clark P.L.* (2016) Quality over quantity: Optimizing co-translational protein folding with non-‘optimal’ synonymous codons. Current Opinion in Structural Biology 38, 102-110.
• Braselmann E.*, Chaney J.L., Champion M.M. & Clark P.L. (2016) DegP chaperone suppresses toxic inner membrane translocation intermediates. PLoS ONE 11, e0162922.
• Besingi R.N. & Clark P.L.* (2015) Extracellular protease digestion to evaluate membrane protein cell surface localization. Nature Protocols 10, 2074-2080.
• Cressiot B., Braselmann E., Oukhaled A., Elcock A.H., Pelta J. & Clark P.L.* (2015) Dynamics and energy contributions for transport of unfolded pertactin through a protein nanopore. ACS Nano 9, 9050-9061.
• Chaney J.L. & Clark P.L.* (2015) Roles for synonymous codon usage in protein biogenesis. Annual Review of Biophysics 44,143-166.
• Drobnak I., Braselmann E. & Clark P.L.* (2015) Multiple driving forces required for efficient secretion of autotransporter virulence proteins. Journal of Biological Chemistry 290, 10104-10116.
• Drobnak I., Braselmann E., Chaney J.L., Leyton D., Bernstein H.D., Lithgow T., Luirink J., Nataro J.P. & Clark P.L.* (2015) Of linkers and autochaperones: An unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion. Molecular Microbiology 95, 1-16.
• Sander I.M., Chaney J.L. & Clark P.L.* (2014) Expanding Anfinsen’s principle: Contributions of synonymous codon selection to rational protein design. Journal of the American Chemical Society 136, 858-861.
• Besingi R.N., Chaney J.L. & Clark P.L.* (2013) An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C-terminal stable core. Molecular Microbiology 90, 1028-1045.
• Braselmann E., Chaney J.L. & Clark P.L.* (2013) Folding the proteome. Trends in Biochemical Sciences 38, 336-343.
• Braselmann E. & Clark P.L.* (2012) Autotransporters: The cellular environment reshapes a folding mechanism to promote protein transport. Journal of Physical Chemistry Letters 3, 1063-1071.
• Renn J.P., Junker M., Besingi R.N., Braselmann E. & Clark P.L.* (2012) ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein. Chemistry & Biology 19, 287-296.
• Bryan A.W., Starner-Kreinbrink J., Hosur R., Clark P.L.* & Berger B.* (2011) Structure-based prediction reveals capping motifs inhibit β-helix aggregation. Proceedings of the National Academy of Sciences USA 108, 11099-11104.
• Ugrinov K.G. & Clark P.L.* (2010) Co-translational folding increases GFP folding yield. Biophysical Journal 98, 1312-1320.
• Clarke T.F. IV & Clark P.L.* (2010) Increased incidence of rare codon clusters at 5’ and 3’ gene termini: Implications for function. BMC Genomics 11, 118.
• Krasowska, J., Olasek M., Bzowska A., Clark P.L. & Wielgus-Kutrowska B.* (2010) The comparison of aggregation and folding of enhanced green fluorescent protein (EGFP) by spectroscopic studies. Journal of Spectroscopy 24, 343-348.
• Junker M. & Clark P.L.* (2010) Slow formation of aggregation-resistant β-sheet folding intermediates. Proteins: Structure, Function & Bioinformatics 78, 812-824.
• Junker M., Besingi R.N. & Clark P.L.* (2009) Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion. Molecular Microbiology 71, 1323-1332.
• Clarke T.F. IV & Clark P.L.* (2008) Rare codons cluster. PLoS ONE 3, e3412.
• Evans M.S., Sander, I.M. & Clark P.L.* (2008) Co-translational folding promotes b-helix formation and prevents aggregation in vivo. Journal of Molecular Biology 383, 683-692.
• Renn J.P. & Clark P.L.* (2008) A conserved stable core structure in the passenger domain b-helix of autotransporter virulence proteins. Biopolymers 89, 420-427.
• Wielgus-Kutrowska B., Narczyk M., Buszko A., Bzowska A. & Clark P.L.* (2007) Folding and unfolding of a non-fluorescent mutant of green fluorescent protein. Journal of Physics: Condensed Matter 19, 285223.
• Junker M., Schuster C., McDonnell, A.V., Sorg K.E., Finn M.C., Berger B. & Clark P.L.* (2006) Pertactin bhelix folding mechanism suggests common themes for secretion and folding of autotransporter proteins. Proceedings of the National Academy of Sciences USA 103, 4918-4923.
               • Highlighted in Faculty of 1000; evaluated by Doug Barrick
• Evans M.S., Ugrinov, K.G., Frese M.A. & Clark P.L.* (2005) Production of a homogeneous pool of stalled ribosome nascent chain complexes in vivo or in vitro. Nature Methods 2, 757-762.
• Jain M., Evans M.S., King J. & Clark P.L.* (2005) Monoclonal antibody epitope mapping describes tailspike b-helix refolding and aggregation intermediates. Journal of Biological Chemistry 280, 23032-23040.
• Evans M.S., Clarke T.F. IV & Clark P.L.* (2005) Conformations of co-translational folding intermediates. Protein and Peptide Letters 12, 189-195.
• Clark P.L.* (2004) Protein folding in the cell: Reshaping the folding funnel. Trends in Biochemical Sciences 29, 527-534.
• Benton C.B., King J. & Clark P.L.* (2002) Characterization of the protrimer intermediate in the folding pathway of the interdigitated b-helix tailspike protein. Biochemistry 41, 5093-5103.
• Clark P.L * & King J. (2001) A newly synthesized, ribosome-bound polypeptide chain adopts conformations dissimilar from early in vitro refolding intermediates. Journal of Biological Chemistry 276, 25411-25420.
• Raso S.W., Clark P.L., Haase-Pettingell C., King J. & Thomas G.J.* (2001) Distinct cysteine sulfhydryl environments detected by analysis of Raman S-H markers of CysàSer mutant proteins. Journal of Molecular Biology 307, 899-911.
• Clark P.L., Weston B.F. & Gierasch L.M.* (1998) Probing the folding of a b-clam protein using singletryptophan constructs. Folding & Design 3, 401-412.
• Clark P.L., Liu Z.P., Rizo J. & Gierasch L.M.* (1997) Cavity formation before stable hydrogen bonding in the folding of a b-clam protein. Nature Structural Biology 4, 883-886.
• Clark P.L., Liu Z.P., Zhang J. & Gierasch L.M.* (1996) Intrinsic tryptophans of CRABPI as probes of structure and folding. Protein Science 5, 1108-1117.

Non-Referreed Publications

Review Articles, Perspectives, Editorials & Book Chapters

• Clark PL (2019) Proteins in the cell. Protein Science 28, 1175-1176.
• Riback J.A., Bowman M.A., Zmyslowski A., Knoverek C.R., Jumper J., Hinshaw J., Kaye E.B., Freed K.F., Clark P.L.* & Sosnick T.R.* (2018) Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”. Science 361, doi:10.1126/science.aar7949.
• Wilson D.N.* & Clark P.L.* (2016) Climbing to the peak of nascent chain knowledge. Nature Structural & Molecular Biology 23, 949-951.
• Clark P.L.* & Elcock A.H. (2016) Molecular chaperones: Providing a safe place to weather a mid-life protein-folding crisis. Nature Structural & Molecular Biology 23, 621-623.
• Clark P.L.* (2016) How to build a complex, functional propeller protein, from parts. Trends in Biochemical Sciences 41, 290-292.
• Brodsky J.L.* & Clark P.L.* (2014) Protein folding in the cell, from atom to organism. FASEB Journal 28, 5034-5038.
• Renn J. & Clark P.L.* (2011) Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo. Methods in Enzymology 492, 233-251.
• Clark P.L.* (2011) Adding protease digestion to the membrane protein toolbox. Journal of Molecular Biology 406, 543-544.
• Clark P.L.* & Ugrinov K.G. (2009) Measuring co-translational conformations of nascent polypeptide chains. Methods in Enzymology 466, 565-588.

Other Publications

• Clark P.L. “Ask Professor Sarah Bellum” a career development column published in the Biophysical Society Newsletter, BPS Bulletin (2002-2005; 2011-2013).
• Gao B., Clark P.L., Finn M.C. & Lieberman M.* (2004) Attachment of Salmonella phage tailspike protein to chemically modified silicon [100]. TMS Letters 1, 123-124.
• Clark P.L.* (2003) “Chaperones” in Genetics. 1st Ed, Macmillan USA, Farmington Hills, MI. readership: an edited encyclopedia geared toward high school students and entry level undergraduates not majoring in the natural sciences
• Clark P.L., Liu Z.-P., Rizo J., Sukumar M., Rotondi K.S. & Gierasch L.M.* (1999) Folding of a predominantly b-sheet protein with a central cavity, in Peptides: Frontiers of Peptide Science, J.P. Tam and P.T.P. Kaumaya, Eds., Kluwer/ESCOM, pp. 349-351.

Career Development Articles

Patricia Clark has authored numerous advice columns on the often uncharted waters of early-career development.

• Authorship and Collaboration (2002) [PDF, 73k]
• Female Mentors (2002) [PDF, 27k]
• Working Hours in Graduate School (2002) [PDF, 66k]
• Lab Moving and Transitions (2002) [PDF, 67k]