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Items: 1 to 50 of 80

1.

Proteins in the cell.

Clark PL.

Protein Sci. 2019 Jul;28(7):1175-1176. doi: 10.1002/pro.3665. No abstract available.

PMID:
31152461
2.

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.

Riback JA, Bowman MA, Zmyslowski AM, Plaxco KW, Clark PL, Sosnick TR.

Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):8889-8894. doi: 10.1073/pnas.1813038116. Epub 2019 Apr 16.

PMID:
30992378
3.

Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Riback JA, Bowman MA, Zmyslowski A, Knoverek CR, Jumper J, Kaye EB, Freed KF, Clark PL, Sosnick TR.

Science. 2018 Aug 31;361(6405). pii: eaar7949. doi: 10.1126/science.aar7949.

PMID:
30166460
4.

Collateral Damage: Insulin-Dependent Diabetes Induced With Checkpoint Inhibitors.

Stamatouli AM, Quandt Z, Perdigoto AL, Clark PL, Kluger H, Weiss SA, Gettinger S, Sznol M, Young A, Rushakoff R, Lee J, Bluestone JA, Anderson M, Herold KC.

Diabetes. 2018 Aug;67(8):1471-1480. doi: 10.2337/dbi18-0002. Epub 2018 Jun 24. Review.

5.

Non-fluorescent mutant of green fluorescent protein sheds light on the mechanism of chromophore formation.

Bartkiewicz M, Kazazić S, Krasowska J, Clark PL, Wielgus-Kutrowska B, Bzowska A.

FEBS Lett. 2018 May;592(9):1516-1523. doi: 10.1002/1873-3468.13051. Epub 2018 Apr 20.

6.

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.

Faisal FE, Newaz K, Chaney JL, Li J, Emrich SJ, Clark PL, Milenković T.

Sci Rep. 2017 Nov 2;7(1):14890. doi: 10.1038/s41598-017-14411-y.

7.

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.

Rodriguez A, Wright G, Emrich S, Clark PL.

Protein Sci. 2018 Jan;27(1):356-362. doi: 10.1002/pro.3336. Epub 2017 Nov 21.

8.

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

Riback JA, Bowman MA, Zmyslowski AM, Knoverek CR, Jumper JM, Hinshaw JR, Kaye EB, Freed KF, Clark PL, Sosnick TR.

Science. 2017 Oct 13;358(6360):238-241. doi: 10.1126/science.aan5774.

9.

Widespread position-specific conservation of synonymous rare codons within coding sequences.

Chaney JL, Steele A, Carmichael R, Rodriguez A, Specht AT, Ngo K, Li J, Emrich S, Clark PL.

PLoS Comput Biol. 2017 May 5;13(5):e1005531. doi: 10.1371/journal.pcbi.1005531. eCollection 2017 May.

10.

Climbing to the peak of nascent-chain knowledge.

Wilson DN, Clark PL.

Nat Struct Mol Biol. 2016 Nov 4;23(11):949-951. doi: 10.1038/nsmb.3314. No abstract available.

PMID:
27814347
11.

DegP Chaperone Suppresses Toxic Inner Membrane Translocation Intermediates.

Braselmann E, Chaney JL, Champion MM, Clark PL.

PLoS One. 2016 Sep 14;11(9):e0162922. doi: 10.1371/journal.pone.0162922. eCollection 2016.

12.

Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis.

Clark PL, Elcock AH.

Nat Struct Mol Biol. 2016 Jul 6;23(7):621-3. doi: 10.1038/nsmb.3255. No abstract available.

PMID:
27384188
13.

Quality over quantity: optimizing co-translational protein folding with non-'optimal' synonymous codons.

Jacobson GN, Clark PL.

Curr Opin Struct Biol. 2016 Jun;38:102-10. doi: 10.1016/j.sbi.2016.06.002. Epub 2016 Jun 16. Review.

14.

How to Build a Complex, Functional Propeller Protein, From Parts.

Clark PL.

Trends Biochem Sci. 2016 Apr;41(4):290-292. doi: 10.1016/j.tibs.2016.02.010. Epub 2016 Mar 9.

15.

Methylation of insulin DNA in response to proinflammatory cytokines during the progression of autoimmune diabetes in NOD mice.

Rui J, Deng S, Lebastchi J, Clark PL, Usmani-Brown S, Herold KC.

Diabetologia. 2016 May;59(5):1021-9. doi: 10.1007/s00125-016-3897-4. Epub 2016 Feb 24.

16.

Extracellular protease digestion to evaluate membrane protein cell surface localization.

Besingi RN, Clark PL.

Nat Protoc. 2015 Dec;10(12):2074-80. doi: 10.1038/nprot.2015.131. Epub 2015 Nov 19.

17.

Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore.

Cressiot B, Braselmann E, Oukhaled A, Elcock AH, Pelta J, Clark PL.

ACS Nano. 2015 Sep 22;9(9):9050-61. doi: 10.1021/acsnano.5b03053. Epub 2015 Aug 28.

18.

Characterization of the ecological interactions of Roundup Ready 2 Yield® soybean, MON 89788, for use in ecological risk assessment.

Horak MJ, Rosenbaum EW, Phillips SL, Kendrick DL, Carson D, Clark PL, Nickson TE.

GM Crops Food. 2015;6(3):167-82. doi: 10.1080/21645698.2015.1067365.

19.

Roles for Synonymous Codon Usage in Protein Biogenesis.

Chaney JL, Clark PL.

Annu Rev Biophys. 2015;44:143-66. doi: 10.1146/annurev-biophys-060414-034333. Epub 2015 Feb 26. Review.

PMID:
25747594
20.

Multiple driving forces required for efficient secretion of autotransporter virulence proteins.

Drobnak I, Braselmann E, Clark PL.

J Biol Chem. 2015 Apr 17;290(16):10104-16. doi: 10.1074/jbc.M114.629170. Epub 2015 Feb 10.

21.

Protein folding in the cell, from atom to organism.

Brodsky JL, Clark PL.

FASEB J. 2014 Dec;28(12):5034-8. doi: 10.1096/fj.14-1202ufm. No abstract available.

22.

Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion.

Drobnak I, Braselmann E, Chaney JL, Leyton DL, Bernstein HD, Lithgow T, Luirink J, Nataro JP, Clark PL.

Mol Microbiol. 2015 Jan;95(1):1-16. doi: 10.1111/mmi.12838. Epub 2014 Nov 24. Review.

23.

Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design.

Sander IM, Chaney JL, Clark PL.

J Am Chem Soc. 2014 Jan 22;136(3):858-61. doi: 10.1021/ja411302m. Epub 2014 Jan 13.

24.

An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C-terminal stable core.

Besingi RN, Chaney JL, Clark PL.

Mol Microbiol. 2013 Dec;90(5):1028-45. doi: 10.1111/mmi.12414. Epub 2013 Oct 20.

25.

Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis.

Querol L, Clark PL, Bailey MA, Cotsapas C, Cross AH, Hafler DA, Kleinstein SH, Lee JY, Yaari G, Willis SN, O'Connor KC.

Neurology. 2013 Sep 10;81(11):956-63. doi: 10.1212/WNL.0b013e3182a43b48. Epub 2013 Aug 6.

26.

Folding the proteome.

Braselmann E, Chaney JL, Clark PL.

Trends Biochem Sci. 2013 Jul;38(7):337-44. doi: 10.1016/j.tibs.2013.05.001. Epub 2013 Jun 11. Review.

27.
28.

ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein.

Renn JP, Junker M, Besingi RN, Braselmann E, Clark PL.

Chem Biol. 2012 Feb 24;19(2):287-96. doi: 10.1016/j.chembiol.2011.11.009. Epub 2011 Dec 29.

29.

Structure-based prediction reveals capping motifs that inhibit β-helix aggregation.

Bryan AW Jr, Starner-Kreinbrink JL, Hosur R, Clark PL, Berger B.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11099-104. doi: 10.1073/pnas.1017504108. Epub 2011 Jun 17.

30.

Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo.

Renn JP, Clark PL.

Methods Enzymol. 2011;492:233-51. doi: 10.1016/B978-0-12-381268-1.00030-6.

PMID:
21333794
31.

Adding protease digestion to the membrane protein toolbox.

Clark PL.

J Mol Biol. 2011 Mar 4;406(4):543-4. doi: 10.1016/j.jmb.2011.01.023. Epub 2011 Jan 13. No abstract available.

PMID:
21238458
32.

Cotranslational folding increases GFP folding yield.

Ugrinov KG, Clark PL.

Biophys J. 2010 Apr 7;98(7):1312-20. doi: 10.1016/j.bpj.2009.12.4291.

33.

Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function.

Clarke TF 4th, Clark PL.

BMC Genomics. 2010 Feb 18;11:118. doi: 10.1186/1471-2164-11-118.

34.

Slow formation of aggregation-resistant beta-sheet folding intermediates.

Junker M, Clark PL.

Proteins. 2010 Mar;78(4):812-24. doi: 10.1002/prot.22609.

PMID:
19847915
35.

Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion.

Junker M, Besingi RN, Clark PL.

Mol Microbiol. 2009 Mar;71(5):1323-32. doi: 10.1111/j.1365-2958.2009.06607.x. Epub 2009 Jan 26.

36.

Measuring cotranslational folding of nascent polypeptide chains on ribosomes.

Clark PL, Ugrinov KG.

Methods Enzymol. 2009;466:567-90. doi: 10.1016/S0076-6879(09)66024-9. Epub 2009 Nov 13.

PMID:
21609877
37.

Rare codons cluster.

Clarke TF 4th, Clark PL.

PLoS One. 2008;3(10):e3412. doi: 10.1371/journal.pone.0003412. Epub 2008 Oct 15.

38.

Cotranslational folding promotes beta-helix formation and avoids aggregation in vivo.

Evans MS, Sander IM, Clark PL.

J Mol Biol. 2008 Nov 14;383(3):683-92. doi: 10.1016/j.jmb.2008.07.035. Epub 2008 Jul 22.

39.

A conserved stable core structure in the passenger domain beta-helix of autotransporter virulence proteins.

Renn JP, Clark PL.

Biopolymers. 2008 May;89(5):420-7. doi: 10.1002/bip.20924.

PMID:
18189304
40.

Genetic variability of the european corn borer, Ostrinia nubilalis, suggests gene flow between populations in the Midwestern United States.

Krumm JT, Hunt TE, Skoda SR, Hein GL, Lee DJ, Clark PL, Foster JE.

J Insect Sci. 2008;8:1-12. doi: 10.1673/031.008.7201.

41.

Enrolling subjects by exception from consent versus proxy consent in trauma care research.

Wright DW, Clark PL, Pentz RD, Hertzberg V, Kellermann AL.

Ann Emerg Med. 2008 Apr;51(4):355-60, 360.e1-3. Epub 2007 Oct 15.

PMID:
17933428
42.

Folding and unfolding of a non-fluorescent mutant of green fluorescent protein.

Kutrowska BW, Narczyk M, Buszko A, Bzowska A, Clark PL.

J Phys Condens Matter. 2007 Jul 18;(28):285223.

43.

Genetic structure and molecular variability of Spodoptera frugiperda (Lepidoptera: Noctuidae) collected in maize and cotton fields in Brazil.

Martinelli S, Clark PL, Zucchi MI, Silva-Filho MC, Foster JE, Omoto C.

Bull Entomol Res. 2007 Jun;97(3):225-31.

PMID:
17524154
44.

Population variation of the fall armyworm, Spodoptera frugiperda, in the Western Hemisphere.

Clark PL, Molina-Ochoa J, Martinelli S, Skoda SR, Isenhour DJ, Lee DJ, Krumm JT, Foster JE.

J Insect Sci. 2007;7:5. doi: 10.1673/031.007.0501.

45.

ProTECT: a randomized clinical trial of progesterone for acute traumatic brain injury.

Wright DW, Kellermann AL, Hertzberg VS, Clark PL, Frankel M, Goldstein FC, Salomone JP, Dent LL, Harris OA, Ander DS, Lowery DW, Patel MM, Denson DD, Gordon AB, Wald MM, Gupta S, Hoffman SW, Stein DG.

Ann Emerg Med. 2007 Apr;49(4):391-402, 402.e1-2. Epub 2006 Sep 29.

PMID:
17011666
46.

Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) larval feeding behavior on transgenic maize (MON 863) and its isoline.

Clark PL, Vaughn TT, Meinke LJ, Molina-Ochoa J, Foster JE.

J Econ Entomol. 2006 Jun;99(3):722-7.

PMID:
16813304
47.

Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins.

Junker M, Schuster CC, McDonnell AV, Sorg KA, Finn MC, Berger B, Clark PL.

Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4918-23. Epub 2006 Mar 20.

48.

Life-threatening maternal and fetal macrocytic anemia from antiretroviral therapy.

Myers SA, Torrente S, Hinthorn D, Clark PL.

Obstet Gynecol. 2005 Nov;106(5 Pt 2):1189-91.

PMID:
16260567
49.

Homogeneous stalled ribosome nascent chain complexes produced in vivo or in vitro.

Evans MS, Ugrinov KG, Frese MA, Clark PL.

Nat Methods. 2005 Oct;2(10):757-62.

PMID:
16179922
50.

Monoclonal antibody epitope mapping describes tailspike beta-helix folding and aggregation intermediates.

Jain M, Evans MS, King J, Clark PL.

J Biol Chem. 2005 Jun 17;280(24):23032-40. Epub 2005 Apr 14.

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