Supporting Information
Burial of Nonpolar Surface Area and Thermodynamic
Stabilization of Globins as a Function
of Chain Elongation
Theodore S. Jennaro, Matthew R. Beaty, Neșe Kurt-Yilmaz#, Benjamin L. Luskin, Silvia
Cavagnero*
Department of Chemistry, University of Wisconsin-Madison
Madison, WI, 53706
Running title: Role of Chain Elongation in Protein Folding
Key words: protein folding, hydrophobic effect, folding entropy, free energy, protein
biosynthesis
#
Present Address: Department of Biochemistry and Molecular Pharmacology,
University of Massachusetts Medical School, 364 Plantation Street, Worcester MA, 01605-2324
* Correspondence to: Silvia Cavagnero, Department of Chemistry, University of WisconsinMadison, 1101 University Avenue, Madison, Wisconsin 53706, USA, Phone: 608-262-5430,
Fax: 608-262-991 8, Email: cavagnero@chem.wisc.edu
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SUPPORTING TABLES
Table S1. List of the 22 globins studied in this work, including protein name, source organism,
PDB code and pertinent references.
Protein
Leghemoglobin A
Organism
Glycine max
PDB Id
Reference
Globin Type
1BIN
(Hargrove, 1997)46
3-3 Globin
(soybean)
Cyano-Met Myoglobin
Elephas maximus
1EMY
(Bisig, 1995)45
3-3 Globin
Flavohemoglobin
Escherichia coli
1GVH
(Ilari, 2002)49
3-3 Globin
Trematode Hemoglobin
Paramphistomum
1H97
(Pesce, 2001)43
3-3 Globin
epiclitum
Cyano-Met Myoglobin
Caretta caretta
1LHT
(Nardini, 1995)42
3-3 Globin
Myoglobin
Aplysia limacine
1MBA
(Scouloudi,
3-3 Globin
1978)41
Myoglobin
Phoca vitulina
1MBS
(Scouloudi,
3-3 Globin
1978)41
Myoglobin
Sus scrofa
1MWD
(Krzywda, 1998)40
3-3 Globin
1MYT
(Birnbaum,
3-3 Globin
(pig)
Myoglobin
Thunnus albacores
1994)39
(albacore tuna)
Myoglobin
Physeter catodon
1VXF
(Yang, 1996)38
3-3 Globin
1YMB
(Evans, 1990)37
3-3 Globin
2GDM
(Harutyunyan,
3-3 Globin
(sperm whale)
Metmyoglobin
Equus caballus
(horse)
Leghemoglobin
Lupinus luteus
1995)36
Myoglobin
Thunnus atlanticus
2NRL
(Schreiter, 2007)35
3-3 Globin
2WY4
(Shepherd, 2010)34
3-3 Globin
(atlantic tuna)
Single Domain
Campylobacter jejuni
Haemoglobin
2
Neuroglobin
Mus musculus
3GKT
(Moschetti,
3-3 Globin
2009)33
Hemoglobin
Paramecium caudatum
1DLW
(Pesce, 2000)32
2-2 Globin
Hemoglobin
Chlamydomonas
1DLY
(Pesce, 2000)32
2-2 Globin
1S69
(Trent, 2004)30
2-2 Globin
2IG3
(Nardini, 2006)31
2-2 Globin
1UVX
(Milani, 2004)29
2-2 Globin
1UX8
(Giangiacomo,
2-2 Globin
moewusii
Cyanoglobin
Synechocystis sp PCC
6803
Group III Truncated
Campylobacter jejuni
Hemoglobin
Group I Truncated
Chlamydomonas
Hemoglobin
moewusii
Haemglobin
Bacillus subtilis
2005)28
Protoglobin
Methanosarcina
2VEB
acetivorans
(Nardini, 2008)27
Archaeal
Globin
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SUPPORTING FIGURE LEGENDS
Figure S1. Fraction of nonpolar solvent-accessible surface area (fNSASA) as a function of percent
chain length of the individual globins examined in this work. The data pertain to both fully
extended and native-like conformations of (A) fifteen 3-3 globins, (B) six 2-2 globins and (C) the
archaeal globin from Methanosarcina acetivorans.
Figure S2. Graphical representation of the nonpolar character of the globins studied in this
work: (A) fifteen 3-3 globins, (B) six 2-2 globins and (C) the archaeal globin from
Methanosarcina acetivorans. The plots illustrate the mean buried area upon folding according to
Rose et al.1 for each residue along the sequence. This parameter is defined as the difference
between the solvent accessible surface area of the unfolded amino acid (within a model
tripeptide) and the average solvent-accessible surface area of the same amino acid within a set of
reference folded proteins. Mean buried areas upon folding are reported as averages over a fiveresidue sliding window. The residues comprising the native helices of three representative
proteins (derived from the corresponding PDB files) are mapped above the plots.
Figure S3. Graphical representation of the nonpolar character of the globins studied in this
work: (A) fifteen 3-3 globins, (B) six 2-2 globins and (C) the archaeal globin from
Methanosarcina acetivorans. The plots illustrate the fractional mean buried area upon folding
according to Rose et al.1 for each residue along the sequence. This parameter is defined as the
normalized difference between the solvent accessible surface area of the unfolded amino acid
(within a model tripeptide) and the average solvent-accessible surface area of the same amino
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acid within a set of reference folded proteins. Normalization is achieved by dividing the above
difference by the solvent-accessible surface area in the unfolded residues (within a model
tripeptide). Fractional mean buried areas upon folding are reported as averages over a fiveresidue sliding window. The residues comprising the native helices of three representative
proteins (derived from the corresponding PDB files) are mapped above the plots.
Figure S4. Relative difference in fNSASA, defined as in the Methods section, for each of the
globin helices of the individual globins examined in this work. Values are provided for both the
fully extended and native-like conformations of (A) fifteen 3-3 globins, (B) six 2-2 globins and
(C) the archaeal globin from Methanosarcina acetivorans.
Figure S5. Standard-state folding entropy as a function of percent chain length of the individual
globins examined in this work. All values were determined at 298 K. The panels illustrate
folding entropies of (A) fifteen 3-3 globins, (B) six 2-2 globins and (C) the archaeal globin from
Methanosarcina acetivorans.
Figure S6. Representative three-dimensional structures of a 3-3, a 2-2 and an archaeal globin
studied in this work: A) 1H97 from Paramphistomum epiclitum. B) 1S69 from Synechocystis sp
PCC 6803. C) 2VEB from Methanosarcina acetivorans. All structures were generated with
PyMOL (version 1.2r2, Schrödinger, LLC). The images were created by Wade Hanson, a Native
American high-school student, as part of his summer research experience at UW-Madison within
the Madison Pre-College Enrichment Opportunity Program for Learning Excellence (PEOPLE)
program. The colors he chose denote key aspects of his cultural heritage and personal
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experience. In image A: red and white denote the UW-Madison signature colors. In image B: the
structure is reminiscent of the Ojibwe Native Americans’ Medicine Wheel, with white
representing the north and winter, yellow representing the east, spring and rising sun; and green
denoting the south, summer and the growth and warmth it brings; and blue representing the west,
fall and the waters of Lake Superior. In image C: the structure is reminiscent of the Native
American Medicine Wheel, a wheel that all tribes share. Each color denotes the four main
human races, with the blending tones implying peaceful coexistence.
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SUPPORTING FIGURES
Figure S1
7
Figure S2
8
Figure S3
9
Figure S4
10
Figure S5
11
Figure S6
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