-
Notifications
You must be signed in to change notification settings - Fork 0
/
chapter3.aux
145 lines (145 loc) · 8.35 KB
/
chapter3.aux
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
\relax
\@writefile{toc}{\contentsline {chapter}{\numberline {III.}\uppercase {Multiple Evolutionary Origins of Ubiquitous Cu2+\newline and Zn2+ Binding in the S100 Protein Family}}{28}}
\@writefile{toc}{\contentsline {section}{ Author Contributions}{28}}
\@writefile{toc}{\contentsline {section}{ Abstract}{28}}
\citation{donato_functions_2013,zimmer_evolution_2013}
\citation{wolf_chemotactic_2008,leclerc_binding_2009,sorci_danger_2011}
\citation{shaw_s100b-rage-mediated_2003,klingelhofer_epidermal_2009,wang_s100a14_2015}
\citation{yang_s100a12_2007,damo_molecular_2013,zackular_nutritional_2015}
\citation{marenholz_s100_2004,sedaghat_s100_2008,donato_rage:_2007,west_s100a7_2010,averill_s100a9_2011,riuzzi_s100b_2011,boye_s100a4_2010,yamaoka_gene_2013,gross_joining_2013,bresnick_s100_2015}
\citation{zimmer_evolution_2013,marenholz_s100_2004}
\citation{bertini_solution_2012,santamaria-kisiel_calcium-dependent_2006,rustandi_ca2+-dependent_1998}
\citation{zimmer_molecular_2003,zimmer_calcium-dependent_2010}
\citation{moroz_role_2010,gilston_binding_2016}
\citation{sivaraja_copper_2006}
\citation{heierhorst_interaction_1997}
\citation{damo_molecular_2013}
\citation{ohalloran_metallochaperones_2000,maret_zinc_2013}
\citation{moroz_role_2010,gilston_binding_2016}
\citation{moroz_role_2010,gilston_binding_2016}
\@writefile{toc}{\contentsline {section}{ Introduction}{29}}
\citation{arnesano_structural_2005,koch_implications_2007}
\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Transition metal binding occurs at a common site in diverse S100s}}{30}}
\newlabel{samplefigure}{{4}{30}}
\citation{zimmer_evolution_2013,marenholz_s100_2004,ravasi_probing_2004,kraemer_structural_2008,shang_chromosomal_2008}
\citation{kraemer_structural_2008}
\citation{hedges_molecular_2006}
\citation{zimmer_evolution_2013,marenholz_s100_2004,kraemer_structural_2008,shang_chromosomal_2008}
\@writefile{toc}{\contentsline {section}{ Results}{32}}
\@writefile{toc}{\contentsline {subsection}{ The S100 family arose in the ancestor of Olfactores}{32}}
\@writefile{toc}{\contentsline {subsection}{ Model-based phylogenetic approaches reveal well-supported clades}{32}}
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces Model-based phylogenetics reveal several S100 subfamilies}}{35}}
\newlabel{samplefigure}{{5}{35}}
\citation{alexander_pyron_large-scale_2011,chiari_phylogenomic_2012,faircloth_phylogenomic_2013,green_three_2014,satoh_chordate_2014,gallus_disentangling_2015,prum_comprehensive_2015,diaz-jaimes_complete_2016,tarver_interrelationships_2016}
\citation{marenholz_s100_2004,shang_chromosomal_2008,dorin_related_1990}
\citation{shang_chromosomal_2008}
\@writefile{toc}{\contentsline {subsection}{ Synteny and taxonomic distribution further support relationships among S100 proteins}{36}}
\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Phylogeny, synteny, and taxonomic distribution provide a picture of S100 evolution}}{37}}
\newlabel{samplefigure}{{6}{37}}
\citation{shang_chromosomal_2008}
\citation{moroz_role_2010,gilston_binding_2016}
\citation{koch_implications_2007,tsvetkov_thermodynamics_2010}
\@writefile{toc}{\contentsline {subsection}{ Transition metal binding is nearly universal across the family}{39}}
\citation{damo_molecular_2013,koch_implications_2007,vorum_expression_1996,kordowska_ca2+_1998,fritz_crystal_2002,schafer_brain_2000,baudier_ions_1986}
\citation{gilston_binding_2016,vorum_expression_1996,schafer_brain_2000,moroz_both_2009}
\citation{wilcox_isothermal_2008}
\citation{koch_implications_2007,vorum_expression_1996,schafer_brain_2000,sturchler_s100a16_2006,becker_s100p_1992,rety_crystal_1999,wilder_location_2003,wright_three-dimensional_2005,garrett_biosensor_2008,murray_structural_2012,babini_structural_2011}
\@writefile{lof}{\contentsline {figure}{\numberline {7}{\ignorespaces Transition metal binding is conserved in the S100 family}}{41}}
\newlabel{samplefigure}{{7}{41}}
\citation{koch_implications_2007,bertini_solution_2009,mani_circular_1983,schafer_s100_1996}
\citation{hernandez_determining_2007}
\citation{streicher_modulation_2010}
\@writefile{toc}{\contentsline {subsection}{ Early-diverging tunicate S100s bind transition metals}{43}}
\@writefile{lof}{\contentsline {figure}{\numberline {8}{\ignorespaces Early-branching tunicate S100 binds transition metals at a non-canonical site}}{44}}
\newlabel{samplefigure}{{8}{44}}
\@writefile{lof}{\contentsline {figure}{\numberline {9}{\ignorespaces Human S100A5 does not bind transition metals at the same site as B and the calgranulins}}{46}}
\newlabel{samplefigure}{{9}{46}}
\@writefile{toc}{\contentsline {subsection}{ Transition metal binding occurs at independently evolved binding sites}{46}}
\citation{moroz_role_2010,koch_implications_2007,kordowska_ca2+_1998}
\citation{schafer_brain_2000}
\citation{koch_implications_2007}
\citation{arnesano_structural_2005}
\citation{yamashita_where_1990,babor_prediction_2008,rubino_coordination_2012}
\citation{holt_global_2009}
\citation{gribenko_oligomerization_1998}
\citation{arnesano_structural_2005,mills_metal_1985,grabarek_insights_2011,chung_ef-hand_2016}
\@writefile{toc}{\contentsline {section}{ Discussion}{49}}
\@writefile{toc}{\contentsline {subsection}{ Transition metal binding occurs at independently evolved binding sites}{49}}
\citation{sivaraja_copper_2006}
\citation{bjork_identification_2009}
\citation{kerkhoff_zinc_1999}
\citation{damo_molecular_2013,gagnon_manganese_2015}
\citation{damo_molecular_2013}
\citation{donato_intracellular_2003}
\citation{hopt_methods_2003,hyun_zinc_2004}
\citation{moroz_role_2010,gilston_binding_2016}
\citation{kraemer_structural_2008}
\citation{zimmer_evolution_2013,marenholz_s100_2004,shang_chromosomal_2008}
\citation{zimmer_evolution_2013,marenholz_s100_2004,shang_chromosomal_2008}
\citation{zimmer_evolution_2013}
\@writefile{toc}{\contentsline {subsection}{ Expansion of the family}{51}}
\citation{kraemer_structural_2008}
\citation{kraemer_structural_2008}
\citation{marenholz_s100_2004,bertini_solution_2009,h_differential_1987,zimmer_tissue_1987,kuznicki_tissue_1989,zimmer_s100_1995,gribenko_molecular_2001}
\citation{moroz_role_2010,gilston_binding_2016}
\citation{zimmer_evolution_2013,marenholz_s100_2004,kraemer_structural_2008}
\citation{altschul_basic_1990}
\citation{leinonen_sequence_2011}
\citation{grabherr_trinity:_2011}
\@writefile{toc}{\contentsline {section}{ Conclusion}{53}}
\citation{li_clustering_2001}
\citation{liu_msaprobs:_2010}
\citation{larsson_aliview:_2014}
\citation{guindon_new_2010}
\citation{le_improved_2008}
\citation{anisimova_survey_2011}
\@writefile{toc}{\contentsline {section}{ Materials and Methods}{54}}
\@writefile{toc}{\contentsline {subsection}{ Sequence Set}{54}}
\citation{aberer_exabayes:_2014}
\citation{jones_rapid_1992}
\@writefile{toc}{\contentsline {subsection}{ Phylogenetic Trees}{55}}
\@writefile{toc}{\contentsline {subsection}{ Molecular cloning and Protein Expression/Purification}{55}}
\citation{gill_calculation_1989,walker_proteomics_2005}
\citation{birdsall_correction_1983}
\@writefile{toc}{\contentsline {subsection}{ Protein characterization}{57}}
\@writefile{toc}{\contentsline {subsection}{ Native electrospray ionization time-of-flight mass spectrometry (nano ESI-MS)}{59}}
\citation{schuck_size-distribution_2000,brown_macromolecular_2006}
\citation{webb_comparative_2002}
\@writefile{toc}{\contentsline {subsection}{ Sedimentation velocity analytical ultracentrifugation}{61}}
\@writefile{toc}{\contentsline {subsection}{ Homology model}{61}}
\@writefile{toc}{\contentsline {section}{ Bridge to Chapter IV}{62}}
\@setckpt{chapter3}{
\setcounter{page}{64}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
\setcounter{enumiii}{0}
\setcounter{enumiv}{0}
\setcounter{footnote}{0}
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{chapter}{3}
\setcounter{section}{8}
\setcounter{subsection}{0}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
\setcounter{figure}{9}
\setcounter{table}{0}
\setcounter{float@type}{4}
\setcounter{ContinuedFloat}{0}
\setcounter{KVtest}{0}
\setcounter{subfigure}{0}
\setcounter{subfigure@save}{0}
\setcounter{lofdepth}{1}
\setcounter{subtable}{0}
\setcounter{subtable@save}{0}
\setcounter{lotdepth}{1}
\setcounter{linenumber}{0}
\setcounter{LN@truepage}{80}
\setcounter{@todonotes@numberoftodonotes}{0}
\setcounter{NAT@ctr}{0}
\setcounter{citation}{0}
\setcounter{@shownumdepth}{0}
\setcounter{parentequation}{0}
}