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. & W&uum;lthrich, 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