Publications


Goldenberg, D. P. & Argyle, B. (2014). Minimal effects of macromolecular crowding on an intrinsically disordered protein: A small-angle neutron scattering study. Biophys. J., 106, 905–914.
http://dx.doi.org/10.1016/j.bpj.2013.12.003

Goldenberg, D. P. & Argyle, B. (2014). Self crowding of globular proteins studied by small-angle X-ray scattering. Biophys. J., 106, 895–904.
http://dx.doi.org/10.1016/j.bpj.2013.12.004

Goldenberg, D. P. (2013). Protein folding and assembly. In Encyclopedia of Biological Chemistry (Lennarz, W. J. & Lane, M., eds.), volume 3, pp. 625–631. Academic Press, Waltham, MA, 2nd edition.
http://dx.doi.org/10.1016/B978-0-12-378630-2.00064-5

Johansen, D., Jeffries, C. M. J., Hammouda, B., Trewhella, J. & Goldenberg, D. P. (2013). Correction. Biophys. J., 105, 1285–1286.
http://dx.doi.org/10.1016/j.bpj.2013.08.014

Johansen, D., Jeffries, C. M. J., Hammouda, B., Trewhella, J. & Goldenberg, D. P. (2011). Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching. Biophys. J., 100, 1120–1128.
http://dx.doi.org/10.1016/j.bpj.2011.01.020

Narajan, S., Amir, D., Grupi, A., Goldenberg, D. P., Minton, A. P. & Haas, E. (2011). Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion. Biophys. J., 100, 2991–2999.
http://dx.doi.org/10.1016/j.bpj.2011.03.065

Johansen, D., Trewhella, J. & Goldenberg, D. P. (2011). Fractal dimension of an intrinsically disordered protein: Small-angle X-ray scattering and computational study of the bacteriophage λ-protein. Protein Sci., 20, 1955–1970.
http://dx.doi.org/10.1002/pro.739

Thorpe, I. F., Goldenberg, D. P. & Voth, G. A. (2011). An exploration of transferability in multiscale course-grained peptide models. J. Phys. Chem. B, 115, 11911–11926.
http://dx.doi.org/10.1021/jp204455g

Goldenberg, D. P. (2010). The product operator formalism: A physical and graphical interpretation. Concepts Magn. Reson. Part A., 36A, 49–83.
http://dx.doi.org/10.1002/cmr.a.20156

Zakharova, E., Horvath, M. P. & Goldenberg, D. P. (2009). Structure of a serine protease poised to resynthesize a peptide bond. Proc. Natl. Acad. Sci., USA, 106, 11034–11039.
http://dx.doi.org/10.1073/pnas.0902463106

Wang, Y., Trewhella, J. & Goldenberg, D. P. (2008). Small-angle x-ray scattering of reduced ribonuclease A: Effects of solution conditions and comparisons with a computational model of unfolded proteins. J. Mol. Biol., 377, 1576–1592.
http://dx.doi.org/10.1016/j.jmb.2008.02.009

Zakharova, E., Horvath, M. P. & Goldenberg, D. P. (2008). Functional and structural roles of the Cys14-Cys38 Disulfide of Bovine Pancreatic Trypsin Inhibitor. J. Mol. Biol., 382, 998–1013.
http://dx.doi.org/10.1016/j.jmb.2008.07.063

Hanson, W. M., Domek, G. J., Horvath, M. P. & Goldenberg, D. P. (2007). Rigidification of a flexible protease inhibitor variant upon binding to trypsin. J. Mol. Biol., 366, 230–243.
http://dx.doi.org/10.1016/j.jmb.2006.11.003

Bulaj, G., Koehn, R. E. & Goldenberg, D. P. (2004). Alteration of the disulfide-coupled folding pathway of BPTI by circular permutation. Protein Sci., 13, 1182–1196.
http://dx.doi.org/10.1110/ps.03563704

Goldenberg, D. P. (2004). Protein folding and assembly. In Encyclopedia of Biological Chemistry (Lennarz, W. J. & Lane, M., eds.), volume 3, pp. 493–499. Academic Press/Elsevier Science, San Diego.
http://dx.doi.org/10.1016/B0-12-443710-9/00541-X

Goldenberg, D. P. (2003). Computational simulation of the statistical properties of unfolded proteins. J. Mol. Biol., 326, 1615–1633.
http://dx.doi.org/10.1016/S0022-2836(03)00033-0

Hanson, W. M., Beeser, S. A., Oas, T. G. & Goldenberg, D. P. (2003). Identification of a residue critical for maintaining the functional conformation of BPTI. J. Mol. Biol., 333, 425–441.
http://dx.doi.org/10.1016/j.jmb.2003.08.023

van Horn, J. D., Bulaj, G., Goldenberg, D. P. & Burrows, C. J. (2003). The Cys-Xaa-His metal-binding motif. N versus S coordination and nickel-mediated formation of cysteinyl sulfinic acid. J. Biol. Inorg. Chem., 8, 601–610.
http://dx.doi.org/10.1007/s00775-003-0454-7

Price-Carter, M., Bulaj, G. & Goldenberg, D. P. (2002). Initial disulfide formation steps in the folding of an ω-conotoxin. Biochemistry, 41, 3507–3519.
http://dx.doi.org/10.1021/bi012033c

Bulaj, G. & Goldenberg, D. P. (2001). Mutational analysis of hydrogen bonding residues in the BPTI folding pathway. J. Mol. Biol., 313, 639–656.
http://dx.doi.org/10.1006/jmbi.2001.5046

Goldenberg, D. P., Koehn, R. E., Gilbert, D. E. & Wagner, G. (2001). Solution structure and backbone dynamics of an ω-conotoxin precursor. Protein Sci., 10, 538–550.
http://www.proteinscience.org/cgi/content/abstract/10/3/538

Bulaj, G. & Goldenberg, D. P. (2001). ϕ-Values for BPTI folding intermediates and implications for transition states. Nature Struct. Biol., 8, 326–330.
http://dx.doi.org/10.1038/86200

Favre, I., Moss, G. W. J., Goldenberg, D. P., Otlewski, E. & Moczydlowski, E. (2000). Structure-Activity Relationships for the Interaction of Bovine Pancreatic Trypsin Inhibitor with an Intracellular Site on a Large Conductance Ca2+-Activated K+ Channel. Biochemistry, 39, 2001–2012.
http://dx.doi.org/10.1021/bi992140v

Bulaj, G. & Goldenberg, D. P. (1999). Early events in the disulfide-coupled folding of BPTI. Protein Sci., 8, 1825–1842.
http://www.proteinscience.org/cgi/content/abstract/8/9/1825

Goldenberg, D. P. (1999). Finding the right fold. Nature Struct. Biol., 6, 987–990.
http://dx.doi.org/10.1038/14866

Sreerama, N., Manning, M. C., Powers, M. E., Zhang, J.-X., Goldenberg, D. P. & Woody, R. W. (1999). Tyrosine, phenylalanine and disulfide contributions to the circular dichroism of proteins: CD spectra of wild-type and mutant bovine pancreatic trypsin inhibitor. Biochemistry, 38, 10814 –10822.
http://dx.doi.org/10.1021/bi990516z

Beeser, S. A., Oas, T. G. & Goldenberg, D. P. (1998). Determinants of backbone dynamics in native BPTI: Cooperative influence of the 14-38 disulfide and the Tyr 35 side chain. J. Mol. Biol., 284, 1581–1596.
http://dx.doi.org/10.1006/jmbi.1998.2240

Bulaj, G., Kortemme, T. & Goldenberg, D. P. (1998). Ionization-reactivity relationships for cysteine thiols in polypeptides. Biochemistry, 37, 8965–8972.
http://dx.doi.org/10.1021/bi973101r

Poulter, D. & Goldenberg, D. (1998). Structure: Organic biological molecules. In Principles of Chemistry in Biology (Theil, E., ed.), pp. 1–49. Am. Chem. Soc., Washington, DC.

Price-Carter, M., Hull, M. S. & Goldenberg, D. P. (1998). Roles of individual disulfide bonds in the stability and folding of an ω-conotoxin. Biochemistry, 37, 9851–9861.
http://dx.doi.org/10.1021/bi9803978

Beeser, S. A., Goldenberg, D. P. & Oas, T. G. (1997). Enhanced protein flexibility caused by a destabilizing amino acid replacement in BPTI. J. Mol. Biol., 269, 154–164.
http://dx.doi.org/10.1006/jmbi.1997.1031

Goldenberg, D. P. (1997). Analysis of protein conformation by gel electrophoresis. In Protein Structure: A Practical Approach (Creighton, T., ed.), pp. 187–218. IRL Press, Oxford, 2nd edition.

Zhang, J.-X. & Goldenberg, D. P. (1997). Mutational analysis of the BPTI folding pathway: I. Effects of aromatic Leu substitutions on the distribution of folding intermediates. Protein Sci., 6, 1549–1562.
http://dx.doi.org/10.1002/pro.5560060719

Zhang, J.-X. & Goldenberg, D. P. (1997). Mutational analysis of the BPTI folding pathway: II. Effects of aromatic Leu substitutions on folding kinetics and thermodynamics. Protein Sci., 6, 1563–1576.
http://dx.doi.org/10.1002/pro.5560060719

Goldenberg, D. P. (1996). Transverse urea-gradient gel electrophoresis. In Current Protocols in Protein Science (Coligan, J., Dunn, B., Ploegh, H., Speicher, D. & Wingfield, P., eds.), pp. 7.4.1 – 7.4.13. Wiley, New York.
http://dx.doi.org/10.1002/0471140864.ps0704s03

Goldenberg, D. P. (1996). How to go from U to N (book review). Nature Struct. Biol., 3, 314–316.
http://dx.doi.org/10.1038/nsb0496-314

Price-Carter, M., Gray, W. R. & Goldenberg, D. P. (1996). Folding of ω-conotoxins. 1. Efficient disulfide-coupled folding of mature sequences in vitro. Biochemistry, 35, 15537–15546.
http://dx.doi.org/10.1021/bi961574c

Price-Carter, M., Gray, W. R. & Goldenberg, D. P. (1996). Folding of ω-conotoxins. 2. Influence of precursor sequences and protein disulfide isomerase. Biochemistry, 35, 15547–15557.
http://dx.doi.org/10.1021/bi9615755

Goldenberg, D. P., Mendoza, J. A. & Zhang, J.-X. (1995). Mutational analysis of the BPTI folding pathway. In Methods in Protein Structure Analysis (Appella, M. A. . E., ed.), pp. 483–492. Plenum, New York.

Goldenberg, D. P. & Creighton, T. E. (1994). A fishy tale of protein folding (commentary). Curr. Biol., 4, 1026–1029.
http://dx.doi.org/10.1016/S0960-9822(00)00234-7

Mendoza, J. A., Jarstfer, M. B. & Goldenberg, D. P. (1994). Effects of amino acid replacements on the reductive unfolding kinetics of pancreatic trypsin inhibitor. Biochemistry, 33, 1143–1148.
http://dx.doi.org/10.1021/bi00171a013

Goldenberg, D. P. & Zhang, J. X. (1993). Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor. Proteins: Struct. Funct. Gen., 15, 322–329.
http://dx.doi.org/10.1002/prot.340150309

Zhang, J.-X. & Goldenberg, D. P. (1993). Amino acid replacement that eliminates kinetic traps in the BPTI folding pathway. Biochemistry, 32, 14075–14081.
http://dx.doi.org/10.1021/bi00214a001

Goldenberg, D. P., Bekeart, L. S., Laheru, D. A. & Zhou, J. D. (1993). Probing the determinants of disulfide stability in native pancreatic trypsin inhibitor. Biochemistry, 32, 2835–44.
http://dx.doi.org/10.1021/bi00062a015

Goldenberg, D. P. (1992). Mutational analysis of protein folding and stability. In Protein Folding (Creighton, T., ed.), pp. 353–403. W.H. Freeman, New York.

Goldenberg, D. P. (1992). Native and non-native intermediates in the BPTI folding pathway. Trends Biochem. Sci., 17, 257–261.
http://dx.doi.org/10.1016/0968-0004(92)90405-X

Goldenberg, D. P., Berger, J. M., Laheru, D. A., Wooden, S. & Zhang, J.-X. (1992). Genetic dissection of pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci., USA, 89, 5083–5087.
http://dx.doi.org/10.1073/pnas.89.11.5083

Jascur, T., Goldenberg, D. P., Vestweber, D. & Schatz, G. (1992). Sequential translocation of an artificial precursor protein across the two mitochondrial membranes. J. Biol. Chem., 267, 13636–13641.
http://www.jbc.org/content/267/19/13636.abstract

Klemm, J. D., Wozniak, J. A., Alber, T. & Goldenberg, D. P. (1991). Correlation between mutational destabilization of phage T4 lysozyme and increased unfolding rates. Biochemistry, 30, 589–594.
http://dx.doi.org/10.1021/bi00216a038

Coplen, L. J., Frieden, R. W. & Goldenberg, D. P. (1990). A genetic screen to identify variants of bovine pancreatic trypsin inhibitor with altered folding energetics. Proteins, 7, 16–31.
http://dx.doi.org/10.1002/prot.340070103

Goldenberg, D. P. (1989). Analysis of protein conformation by gel electrophoresis. In Protein Structure: A practical approach (Creighton, T., ed.), pp. 225–250. IRL Press, Oxford.

Goldenberg, D. P. (1989). Circularly permuted proteins (Commentary). Prot. Eng., 2, 493–495.
http://dx.doi.org/10.1093/protein/2.7.493

Goldenberg, D. P., Frieden, R. W., Haack, J. A. & Morrison, T. B. (1989). Mutational analysis of a protein folding pathway. Nature, 338, 127–132.
http:/dx.doi.org/10.1038/338127a0

Rote, K. V., Hough, R., Goldenberg, D. & Rechsteiner, M. C. (1989). Circular pancreatic trypsin inhibitor: a novel substrate for studies on intracellular proteolysis. J. Biol. Chem., 264, 1156–1162.
http://www.jbc.org/content/264/2/1156.abstract

Goldenberg, D. P. (1988). Genetic studies of protein stability and mechanisms of folding. Annu. Rev. Biophys. Biophys. Chem., 17, 481–507.
http://dx.doi.org/10.1146/annurev.bb.17.060188.002405

Goldenberg, D. P. (1988). Kinetic analysis of the folding and unfolding of a mutant form of bovine pancreatic trypsin inhibitor lacking the cysteine-14 and -38 thiols. Biochemistry, 27, 2481–2489.
http://dx.doi.org/10.1021/bi00407a034

Goldenberg, D. P. & Creighton, T. E. (1985). The energetics of protein structure and folding. Biopolymers, 24, 167–182.
http://dx.doi.org/10.1002/bip.360240114

Chazin, W. J., Goldenberg, D. P., Creighton, T. E. & Wüthrich, K. (1985). Comparative studies of conformation and internal mobility in native and circular basic pancreatic trypsin inhibitor by 1H nuclear magnetic resonance in solution. Eur. J. Biochem., 152, 429–437.
http://dx.doi.org/10.1111/j.1432-1033.1985.tb09215.x

Goldenberg, D. P. (1985). Dissecting the roles of individual interactions in protein stability: Lessons from a circularized protein. J. Cell. Biochem., 29, 321–335.
http://dx.doi.org/10.1002/jcb.240290406

Goldenberg, D. P. & Creighton, T. E. (1984). Gel Electrophoresis in Studies of Protein Conformation and Folding. Anal. Biochem., 138, 1–18.
http://dx.doi.org/10.1016/0003-2697%2884%2990761-9

Smith, D. H., Goldenberg, D. P. & King, J. (1984). Use of temperature sensitive mutations to dissect pathways of protein folding and subunit interaction. In The Protein Folding Problem, Am. Assoc. Adv. Sci. Symposium Vol. 89 (Wetlaufer, D., ed.), pp. 115–143. Westview Press, Boulder.

Creighton, T. E. & Goldenberg, D. P. (1984). Kinetic role of a meta-stable native-like two-disulphide species in the folding transition of bovine pancreatic trypsin inhibitor. J. Mol. Biol., 179, 497–526.
http://dx.doi.org/10.1016/0022-2836(84)90077-9

Goldenberg, D. P. & Creighton, T. E. (1984). Folding pathway of a circular form of bovine pancreatic trypsin inhibitor. J. Mol. Biol., 179, 527–545.
http://dx.doi.org/10.1016/0022-2836(84)90078-0

Goldenberg, D. P., Smith, D. H. & King, J. (1983). Genetic analysis of the folding pathway for the tail spike protein of phage P22. Proc. Natl. Acad. Sci., USA, 80, 7060–7064.
http://dx.doi.org/10.1073/pnas.80.3.760

Goldenberg, D. P., Smith, D. H. & King, J. (1983). Genetic and biochemical analysis of in vivo protein folding and subunit assembly. Biopolymers, 22, 125–129.
http://dx.doi.org/10.1002/bip.360220120

Goldenberg, D. P. & Creighton, T. E. (1983). Circular and circularly permuted forms of bovine pancreatic trypsin inhibitor. J. Mol. Biol., 165, 407–413.
http://dx.doi.org/10.1016/S0022-2836(83)80265-4

Goldenberg, D. P., Berget, P. B. & King, J. (1982). Maturation of the tail spike endorhamnosidase of Salmonella phage P22. J. Biol. Chem., 257, 7864–7871.
http://www.jbc.org/cgi/content/abstract/257/13/7864

Goldenberg, D. & King, J. (1982). Trimeric intermediate in the in vivo folding and subunit assembly of the tail spike endorhamnosidase of bacteriophage P22. Proc. Natl. Acad. Sci., USA, 79, 3403–3407.
http://dx.doi.org/10.1073/pnas.79.11.3403

Goldenberg, D. P. & King, J. (1981). Temperature-sensitive mutants blocked in the folding or subunit assembly of the bacteriophage P22 tail spike protein. II. Active mutant protein matured at 30 degrees C. J. Mol. Biol., 145, 633–651.
http://dx.doi.org/10.1016/0022-2836(81)90307-7