BIOLOGICAL CHEMISTRY Protein-Mediated Molecular Recognition	UNC Chemistry

Updated November 2009 (PubMed links are underlined.)

Li C, Wang G-F, Wang Y, Creager-Allen R, Lutz E A, Scronce,H, Slade K M. Ruf RA, Mehl RA Pielak, G. J. 2009. Protein ¹⁹F NMR in Escherichia coli. Journal of the American Chemical Society: in press.

Sharaf NG, Barnes CO, Charlton LM, Young GB, Pielak GJ. 2009. A bioreactor for in-cell protein NMR. Journal of Magnetic Resonance: in press.

Miklos AC, Li C, Pielak GJ. 2009. Using NMR-detected backbone amide ¹H exchange to assess macromolecular crowding effects on globular-protein stability. Methods in Enzymology: 466: 1-18.

Li C, Wang Y, Pielak GJ. 2009. Translational and rotational diffusion of a small globular protein under crowded conditions. Journal of Physical Chemistry B: 113: 13390–13392.

Li C, Lutz EA, Slade KM, Ruf RA, Wang G, Pielak GJ. 2009. ¹⁹F-NMR studies of α-synuclein conformation and fibrillation. Biochemistry 48: 8578–8584.

Slade KM, Baker R, Chua M, Thompson NL, Pielak GJ. 2009. Effects of recombinant protein expression on green fluorescent protein diffusion in Escherichia coli. Biochemistry, 48: 5083–5089.

Slade KM, Steele BL, Pielak GJ, Thompson NL. 2009. Quantifying GFP diffusion in Escherichia coli by using continuous photobleaching with evanescent illumination. Journal of Physical Chemistry B: 113, 4837-4845.

Li C, Pielak G J 2009. Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions, Journal of the American Chemical Society 131, 1368-1369.

Pielak GJ, Li C, Miklos AC, Schlesinger AP, Slade, K M, Wang G., Zigoneanu IG. 2009. Protein NMR under physiological conditions, Biochemistry 48, 226–234.

Ruf RA, Lutz EA, Zigoneanu IG, Pielak G J. 2008. α-Synuclein conformation affects its tyrosine-dependant oxidative aggregation. Biochemistry 47: 13604-13609.

Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, Young GB, Macdonald JM, Pielak GJ. 2008. Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR. Journal of the American Chemical Society 130: 6310-6311.

Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ. 2008. Residue-level interrogation of macromolecular crowding effects on protein stability. Journal of the American Chemical Society 130: 6826-6830.

Pielak GJ, Patel CN, Winzor DJ. 2007. Reconsideration of sedimentation equilibrium distributions reflecting the effects of small inert cosolutes on the dimerization of alpha-chymotrypsin. Biophysical Chemistry 130: 89-92.

Charlton, LM, Pielak, GJ 2006. Peeking into living eukaryotic cells with high-resolution NMR, Proceedings of the National Academy of Sciences of the United States of America 103: 11817-11818.

Bryant, JE, Lecomte, JTJ, Lee, AL, Young, GB,Pielak, GJ 2006. Cytosol has a small effect on protein backbone dynamics, Biochemistry, 45: 10085-10091. Retracted: ibid. 2007. Biochemistry 46: 8206.

McCall, S J, Nassar, R, Malouf, NN, Saunders, AJ, Oakeley, AE, Henderson, PM, Solaro, RJ, Pielak, GJ, Alexander, KA, and Anderson, PAW 2006. Development and cardiac contractility: cardiac troponin T isoforms and cytosolic calcium. Pediatric Research, 60: 276-281.

Pielak, GJ 2006. Woes of proline: a cautionary kinetic tale. Protein Science, 15: 393-394.

McNulty, BC, Young, GB, Pielak, GJ 2006. Macromolecular crowding in the Escherichia coli periplasm maintains α-synuclein disorder. Journal of Molecular Biology, 355: 893-897.

McNulty, BC, Tripathy, A, Young, GB, Orans, J, Pielak, GJ 2006. Temperature-induced reversible conformational change in the first 100 residues of α-synuclein. Protein Science, 15: 602-608.

Barrett, DG, Minder, CM, Mian, MU, Whittington, SJ, Cooper, J, Fuchs, KM, Tripathy, A, Waters, ML, Creamer, TP, Pielak, GJ 2005. Pressure perturbation calorimetry of helical peptides. Proteins: Structure Function and Bioinformatics, 63: 322-326.

Bryant, JE, Lecomte, JT, Lee, AL, Young, GB, Pielak, GJ 2005. Protein dynamics in living cells. Biochemistry 44: 9275 - 9279. Retracted: ibid. 2007. Biochemistry 46: 8206.

Pielak, GJ 2005 A model of cellular organization. Proceedings of the National Academy of Sciences of the United States of America 102: 5901-5902.

Yi, F, Sims, D, Pielak, GJ, Edgell, MH 2005. Impact of robotics and instrument automation on protein stability measurements. Journal of the Association for Laboratory Automation 10: 98-101.

Olteanu A, Pielak, GJ 2004. Peroxidative aggregation of α-synuclein requires tyrosines. Protein Science 13: 2852-2856.

Daughghdrill GW, Pielak GJ, Uversky VN, Cortese MS, Dunker AK. 2005. Natively Disordered Proteins. In Handbook of Protein Folding, ed. J Buchner, T Kiefhaber. Weinheim: Wiley-VCH, pp. 275-357.

Batchelor, J D, Olteanu, A, Tripathy, A, Pielak, GJ (2004). Impact of protein denaturants and stabilizers on water structure. Journal of the American Chemical Society, 126: 1958-1961.

Olteanu, A, Patel, C N, Dedmon, M M, Kennedy, S, Linhoff, M W, Minder, C M, Potts, PR, Deshmukh, M, & Pielak, G J (2003). Stability and apoptotic activity of recombinant human cytochrome c. Biochemical and Biophysical Research Communications 312/3: 733-740.

Yi, F, Sims, DA, Pielak, GJ, Edgell, MH 2003. Testing hypotheses about determinants of protein structure with high-precision, high-throughput stability measurements and statistical modeling. Biochemistry 42: 7594-7603.

Engstrom, G, Rajagukguk, R, Saunders, AJ, Patel, CN, Rajagukguk, S, Merbitz-Zahradnik, T, Xiao, K, Pielak, GJ, Trumpower, B, Yu, C-A, Yu, L, Durham, B, Millett, F 2003. Design of a ruthenium-labeled cytochrome c derivative to study electron transfer with the cytochrome bc1 complex. Biochemistry 42: 2816-2824.

Dedmon, MM, Patel, CN, Young, GB, Pielak GJ. 2002. FlgM gains structure in living cells. Proceedings of the National Academy of Sciences of the United States of America 99: 12861-12864.

Beasley, JR, Doyle DF, Chen L, Cohen DS, Fine BR, Pielak GJ. 2002. Searching for quantitative entropy-enthalpy compensation among protein variants. Proteins: Structure, Function, and Genetics 49: 398-402.

Patel, CN, Noble, S., Weatherly, GT, Tripathy, A, Winzor, DJ, Pielak, GJ. 2002. Effects of molecular crowding by saccharides on alpha-chymotrypsin dimerization. Protein Science 11: 997-1003.

Morar, AS, Pielak GJ. 2002. Crowding by trisaccharides and the 2:1 cytochrome c/cytochrome c peroxidase complex. Biochemistry 41: 547-551.

Morar, AS, Olteanu A, Young GB, Pielak GJ. 2001. Solvent-induced collapse of alpha-synuclein and acid denatured cytochrome c. Protein Science 10: 195-199.

Patel, C, Lind, M, Pielak, GJ. 2001. Characterization of horse cytochrome c expressed in Escherichia coli. Protein Expression and Purification: 22: 220-224.

Davis-Searles, PR, Saunders, AJ, Erie, DA, Winzor, DJ, Pielak, GJ. 2001. Interpreting the effects of small uncharged solutes on protein-folding equilibria. Annual Review of Biophysics and Bioengineering 30: 271-306.

Morar, AS, Wang, X, Pielak, GJ. 2001. Effects of crowding by mono-, di-, and tetrasaccharides on cytochrome c / cytochrome c peroxidase binding: comparing theory to experiment. Biochemistry 40: 281-285.

Pielak, GJ, Wang, X. 2001. Interactions between yeast iso-1-cytochrome c and its peroxidase. Biochemistry 40: 422-428.

Weatherly, GT, Pielak, GJ. 2001. Second virial coefficients as a measure of protein-osmolyte interactions. Protein Science 10: 12-16.

Saunders, AJ, Davis-Searles, PR, Allen, DL, Pielak, GJ, Erie, DA. 2000. Osmolyte-induced changes in protein conformational equilibria. Biopolymers 53: 293-307.

Boyd, J, Dobson, CM, Morar, AS, Williams, RJP, Pielak, GJ. 1999. ¹H and ¹⁵N hyperfine shifts of cytochrome c. Journal of the American Chemical Society121: 9247-9248.

Chen, L, Pielak, GJ, Thompson, NL. 1999. The cytoplasmic region of Fc( g)RIIb1, but not Fc( g)RIIb2, binds phospholipids membranes. Biochemistry 38: 2102-2109.

Hostetter, DR, Weatherly, GT, Beasley, JR, Bortone, K, Cohen, DS, Finger, SA, Hardwidge, P, Kakouras, D, Saunders, AJ, Trojak, SK, Waldner, JL, Pielak, GJ. 1999. Partially formed native tertiary interactions in the A-state of cytochrome c. Journal of Molecular Biology 289: 639-644.

Lahr, SJ, Broadwater, A, Carter, CW, Jr., Collier, ML, Hensley, L, Waldner, JL, Pielak, GJ, Edgell, MH. 1999. Patterned library analysis: a method for the quantitative assessment of hypotheses concerning the determinants of protein structure. Proceedings of the National Academy of Sciences of the United States of America 96 : 14860-14865.

Mei, H, Wang, K, Peffer, N, Weatherly, GT, Cohen, DS, Pielak, GJ, Durham, B, Millett, F. 1999. Role of configurational gating in intramolecular electron transfer from cytochrome c to the radical cation in cytochrome c peroxidase. Biochemistry 39: 6846-6854.

Morar, AS, Kakouras, D, Young, GB, Boyd, J, Pielak, GJ. 1999. Expression of ¹⁵ N-labeled eukaryotic cytochrome c in Escherichia coli. Journal of Biological Inorganic Chemistry 4: 220-222.

Waldner, JL, Lahr, SJ, Edgell, MH, Pielak, GJ. 1999. Nonideality and protein thermal denaturation. Biopolymers 49: 471-479.

Wang, X, Pielak, GJ. 1999. Equilibrium thermodynamics of a physiologically-relevant heme-protein complex. Biochemistry 38: 16876-16881.

Allen, DL, Pielak, GJ. 1998. Baseline length and automated fitting of denaturation data. Protein Science 7: 1262-1263.

Davis-Searles, PR, Morar, AS, Saunders, AJ, Erie, DA, Pielak, GJ. 1998. Sugar-induced molten-globule model. Biochemistry: 17048-17053.

Fairris JL, Wang K, Geren L, Pielak GJ, Durham B, Millett F. 1998. Intramolecular electron transfer in yeast cytochrome c covalently bonded to ruthenium(II) polypyridine complexes at cys39. In: Photochemistry and Radiation Chemistry: American Chemical Society Advances in Chemistry Series 254. American Chemical Society: Washington, D.C. pp. 99-110.

Marmorino, JL, Lehti, M, Pielak, GJ. 1998. Native tertiary structure in an A-state. Journal of Molecular Biology 275: 379-388.

Waldner, JL, Lahr, SJ, Edgell, MH, Pielak, GJ. 1998. Effects of a polyhistidine terminal extension on eglin c stability. Analytical Biochemistry 263: 116-118.

Wrobel, JA, Chao, S-F, Conrad, MJ, Merker, JD, Swanstrom, R, Pielak, GJ, Hutchison, CA, III. 1998. A genetic approach for identifying critical residues in the fingers and palm subdomains of HIV-1 reverse transcriptase. Proceedings of the National Academy of Sciences of the United States of America 95: 638-645.

Chen, L, Thompson, NL, Pielak, GJ. 1997. Design, synthesis, and characterization of the genes for mouse Fc g RIIb1 and Fc g RIIb2 cytoplasmic regions. Protein Science 6: 1038-1046.

Pielak, GJ. 1997. Review of "Circular dichroism and the conformational analysis of biomolecules." Fasman, G.D., Ed., Plenum, NY (1997). American Scientist 85 : 391-392.

Beasley, JR, Pielak, GJ. 1996. Requirements for perpendicular helix pairing. Proteins: Structure Function And Genetics 26 : 95-107.

Betz, SF, Marmorino, JL, Saunders, AJ, Doyle, DF, Young, GB, Pielak, GJ. 1996. Unusual effects of an engineered disulfide on global and local protein stability. Biochemistry 35: 7422-7428.

Doyle, DF, Waldner, JL, Parikh, S, Alcazar-Roman, L, Pielak, GJ. 1996. Changing the transition state for protein (un)folding. Biochemistry 35: 7403-7411.

Mei, H, Wang, K, McKee, S, Wang, X, Waldner, JL, Pielak, GJ, Durham, B, Millett, F. 1996. Control of formation and dissociation of the high-affinity complex between cytochrome c and cytochrome c peroxidase by ionic strength and the low-affinity binding site. Biochemistry 35: 15800-15806.

Miller, MA, Geren, L, Han, GW, Saunders, A, Beasley, J, Pielak, GJ, Durham, B, Millett, F, Kraut, J. 1996. Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering. Biochemistry35 : 667-673.

Pappa, HS, Tajbaksh, S, Saunders, AJ, Pielak, GJ, Poulos, TL. 1996. Probing the cytochrome c peroxidase-cytochrome c electron transfer reaction using site specific crosslinking. Biochemistry35 : 4837-4845.

Pielak GJ, Auld DS, Betz SF, Hilgen-Willis SE, Garcia LL. 1996. Nuclear magnetic resonance studies of class I cytochromes c. In: Scott RA, Mauk AG, eds. Cytochromes c: A Multidisciplinary Approach. Sausalito: University Science Books. pp. 203-284.

Wang, K, Mei, H, Geren, L, Miller, MA, Saunders, A, Wang, X, Waldner, JL, Pielak, GJ, Durham, B, Millett, F. 1996. Design of a ruthenium-cytochrome c derivative to measure electron transfer to the radical cation and oxyferryl heme in cytochrome c peroxidase. Biochemistry 35: 15107-15119.

Cohen, DS, Pielak, GJ. 1995. Entropic stabilization of cytochrome c upon reduction. Journal of the American Chemical Society 117 : 1675-1677.

Geren, LM, Beasley, JR, Fine, BR, Saunders, AJ, Hibdon, S, Pielak, GJ, Durham, B, Millett, F. 1995. Design of a ruthenium-cytochrome c derivative to measure electron transfer to the initial acceptor in cytochrome c oxidase. Journal of Biological Chemistry 270 : 2466-2472.

Marmorino, JL, Pielak, GJ. 1995. A native tertiary interaction stabilizes the A state of cytochrome c. Biochemistry 34: 3140-3143.

Pielak, GJ, Auld, DS, Beasley, JR, Betz, SF, Cohen, DS, Doyle, DF, Finger, SA, Fredericks, ZL, Hilgen-Willis, S, Saunders, AJ, Trojak, SK. 1995. Protein thermal denaturation, side-chain models, and evolution: amino acid substitutions at a conserved helix-helix interface. Biochemistry 34 : 3268-3276.

Cohen, DS, Pielak, GJ. 1994. The stability of yeast iso-1-cytochrome c as a function of pH and temperature. Protein Science 3 : 1253-1260.

Auld, DS, Young, GB, Saunders, AJ, Doyle, DF, Pielak, GJ. 1993. Probing weakly-polar interactions in cytochrome c. Protein Science 2 : 2187-2197.

Fredericks, ZL, Pielak, GJ. 1993. Exploring the interface between the N- and C-terminal helices of cytochrome c by random mutagenesis within the C-terminal helix. Biochemistry 32: 929-936.

Hilgen-Willis, S, Bowden, EF, Pielak, GJ. 1993. Dramatic stabilization of ferricytochrome c upon reduction. Journal of Inorganic Biochemistry 51: 649-653.

Marmorino, JL, Auld, DS, Betz, SF, Doyle, DF, Young, GB, Pielak, GJ. 1993. Amide proton exchange rates of oxidized and reduced Saccharomyces cerevisiae iso-1-cytochrome c. Protein Science 2 : 1966-1974.

Saunders, AJ, Young, GB, Pielak, GJ. 1993. Polarity of disulfide bonds. Protein Science 2: 1183-1184.

Greene, RM, Betz, SF, Hilgen-Willis, S, Auld, DS, Fencl, JB, Pielak, GJ. 1993. Changes in global stability and local structure of cytochrome c upon substituting phenylalanine-82 with tyrosine. Journal of Inorganic Biochemistry 51: 663-676.

Willie, A, McLean, M, Liu, R-Q, Hilgen-Willis, S, Saunders, AJ, Pielak, GJ, Sligar, SG, Durham, B, Millett, F. 1993. Intracomplex electron transfer between ruthenium-65-cytochrome b₅ and position-82 variants of yeast iso-1-cytochrome c. Biochemistry32: 7519-7525.

Betz, SF, Pielak, GJ. 1992. Introduction of a disulfide bind into cytochrome c stabilizes a compact denatured state. Biochemistry 31: 12337-12344.

Gao, Y, McLendon, G, Pielak, GJ, Williams, RJP. 1992. Electron-proton coupling in cytochrome c studied using protein variants. European Journal of Biochemistry204: 337-352.

Auld, DS, Pielak, GJ. 1991. Constraints on amino acid substitutions in the N-terminal helix of cytochrome c explored by random mutagenesis. Biochemistry 30: 8684-8690.

Concar, DW, Whitford, D, Pielak, GJ, Williams, RJP. 1991. The role of phenylalanine-82 in electron-exchange reactions of eukaryotic cytochromes c. Journal of the American Chemical Society 113: 2401-2406.

Gao, Y, Boyd, J, Pielak, GJ, Williams, RJP. 1991. Proton nuclear magnetic resonance as a probe of differences in structure between the C102T and F82S;C102T variants of iso-1- cytochrome c from the yeast Saccharomyces cerevisiae. Biochemistry 30: 7033-7040.

Gao, Y, Boyd, J, Pielak, GJ, Williams, RJP. 1991. Comparison of reduced and oxidized yeast iso-1-cytochrome c using proton paramagnetic shifts. Biochemistry 30 : 1928-1934.

Hilgen, SE, Pielak, GJ. 1991. The function of the Saccharomyces cerevisiae iso-1-cytochrome c gene is independent of the codon at invariant residue phe82 when the gene is present on a low copy number vector. Protein Engineering 4: 575-578.

Thurgood, AGP, Pielak, GJ, Cutler, RL, Davies, AM, Greenwood, C, Mauk, AG, Smith, M, Williamson, DJ, Moore, GR. 1991. Change in charge of an unvaried heme contact residue does not cause a major change of conformation in cytochrome c. Federation of European Biochemical Societies Letters 284: 173-177.

Wang, X, Pielak, GJ. 1991. Temperature-sensitive variants of Saccharomyces cerevisiae iso-1- cytochrome c produced by random mutagenesis of codons 43 to 54. Journal of Molecular Biology 221 : 97-105.

Gao, Y, Boyd, J, Williams, RJ, Pielak, GJ. 1990. Assignment of proton resonances, identification of secondary structural elements, and analysis of backbone chemical shifts for the C102T variant of yeast iso-1-cytochrome c and horse cytochrome c. Biochemistry 29: 6994-7003.

Liang, N, Mauk, AG, Pielak, GJ, Johnson, JA, Smith, M, Hoffman, BM. 1988. Regulation of interprotein electron transfer by residue 82 of yeast cytochrome c. Science240 : 311-313.

Pielak, GJ, Atkinson, RA, Boyd, J, Williams, RJP. 1988. Two-dimensional NMR as a probe of structural similarity applied to mutants of cytochrome c. European Journal of Biochemistry177: 179-185.

Pielak, GJ, Boyd, J, Moore, GR, Williams, RJP. 1988. Proton NMR studies show that the THR 102 mutant of yeast iso-1-cytochrome c is a typical member of the cytochrome c family. European Journal of Biochemistry 177 : 167-177.

Cutler, RL, Pielak, GJ, Mauk, AG, Smith, M. 1987. Replacement of cysteine-107 of Saccharomyces cerevisiae iso-1- cytochrome c with threonine: improved stability of the mutant protein. Protein Engineering 1 : 95-99.

Liang, N, Pielak, GJ, Mauk, AG, Smith, M, Hoffman, BM. 1987. Yeast cytochrome c with phenylalanine or tyrosine at position 87 transfers electrons to (zinc cytochrome c peroxidase)+ at a rate ten thousand times that of serine-87 or glycine-87 variants. Proceedings of the National Academy of Sciences of the United States of America 84: 1249-1252.

Pielak, GJ, Concar, DW, Moore, GR, Williams, RJP. 1987. The structure of cytochrome c and its relation to recent studies of long-range electron transfer. Protein Engineering 1 : 83-88.

Pielak, GJ, Oikawa, K, Mauk, AG, Smith, M, Kay, CM. 1986. Elimination of the negative Soret Cotton effect of eukaryotic cytochromes c by replacement of an invariant phenylalanine residue by site-directed mutagenesis. Journal of the American Chemical Society 108 : 2724-2727.

Pielak, GJ, Gurusiddiwiah, S, Legg, JI. 1986. Quantification of azo-coupled lysine in azo proteins by amino acid analysis. Analytical Biochemistry 56 : 403-405.

Pielak, GJ, Mauk, AG, Smith, M. 1985. Site-directed mutagenesis of cytochrome c shows that an invariant phe is not essential for function. Nature 313: 152-154.

Pielak, GJ, Urdea, MS, Legg, JI. 1984. Preparation and characterization of arsanilazo and sulfanilazo proteins. Biochemistry 23 : 596-603.

Pielak, GJ, Urdea, MS, Igi, K, Legg, JI. 1984. Azo protein analogs: synthesis and characterization of arsanilazo and sulfanilazo derivatives of tyrosine and histidine. Biochemistry 23: 589-596.

Legg JI, Igi K, Pielak GJ, Warner BD, Urdea MS. 1980. Circular dichroism as a probe of metal Ion interactions with azo proteins. In: Douglas BE, Yoshihiko S, eds. Stereochemistry of Optically Active Transition Metal Compounds. Washington, D.C.: American Chemical Society. pp. 195-205.

Gary J. Pielak, CB# 3290, Venable and Kenan Laboratories, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, 919-966-3671