Elucidating Collagen Degradation Synergy between Col G and Col H from Hathewaya (Clostridium) histolytica and Identifying novel structural features in HPT and REC domains from VarS histidine kinase in V. alginolyticus

Perry Caviness
University of Arkansas PhD thesis 28030553 (2020 Jul)

URL: https://www.proquest.com/openview/69a7776e338c00e51bf030fa88a6dfde/

Submitted to SASBDB: 2020 Aug 12 Published in SASBDB: 2020 Aug 20

SASDJQ6 – Full-length Collagenase H containing N-terminal Catalytic domain and C-terminal Non-Catalytic domains Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen Binding Domain (CBD) Sample: Collagenase ColH (Full-length) monomer, 112 kDa Hathewaya histolytica protein Buffer: 10 mM HEPES, 100 mM NaCl, 0.4 mM EGTA, 2.4 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Dec 12 RgGuinier 4.1 nm Dmax 14.0 nm VolumePorod 198 nm3

SASDJR6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) Sample: Collagenase ColH (Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD)) monomer, 23 kDa Hathewaya histolytica protein Buffer: 10 mM HEPES, 100 mM NaCl, 0.4 mM EGTA, 2.4 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Sep 25 RgGuinier 2.6 nm Dmax 8.7 nm VolumePorod 29 nm3

SASDJS6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) bound to triple helical collagen like-peptide [(POG)10]3 Sample: Collagenous Peptide model [(PPG)10] trimer, 9 kDa synthetic construct protein Collagenase ColH (Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD)) monomer, 23 kDa Hathewaya histolytica protein Buffer: 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Dec 12 RgGuinier 3.5 nm Dmax 14.5 nm VolumePorod 41 nm3

SASDJT6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1, Polycystic Kidney disease domain 2 and Collagen binding domain (CBD) with Y689S, F712S, Y780S, H782S, Y796S and Y801S bound to collagen like-peptide Sample: Collagen like-peptide [GPRG(POG)13] trimer, 11 kDa protein Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser, Phe712Ser, Tyr780Ser, His782Ser, Tyr796Ser and Tyr801) monomer, 33 kDa Hathewaya histolytica protein Buffer: 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 4.0 nm Dmax 22.0 nm VolumePorod 61 nm3

SASDJU6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser, Phe712Ser, Tyr780Ser, His782Ser, Tyr796Ser and Tyr801Ser Sample: Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser, Phe712Ser, Tyr780Ser, His782Ser, Tyr796Ser and Tyr801) monomer, 33 kDa Hathewaya histolytica protein Buffer: 50 mM Tris, 1 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 3.3 nm Dmax 11.0 nm VolumePorod 34 nm3

SASDJV6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser bound to triple helical collagen like-peptide Sample: Collagen like-peptide [GPRG(POG)13] trimer, 11 kDa protein Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) monomer, 33 kDa Hathewaya histolytica protein Buffer: 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Dec 12 RgGuinier 4.4 nm Dmax 21.0 nm VolumePorod 79 nm3

SASDJW6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser Sample: Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr689Ser and Phe712Ser) monomer, 33 kDa Hathewaya histolytica protein Buffer: 50 mM Tris, 1 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 3.7 nm Dmax 11.5 nm VolumePorod 38 nm3

SASDJX6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease 1 (PKD1) domain, Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) bound to triple helical collagen like-peptide Sample: Collagen like-peptide [GPRG(POG)13] trimer, 11 kDa protein Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD)) monomer, 34 kDa Hathewaya histolytica protein Buffer: 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 4.0 nm Dmax 22.0 nm VolumePorod 63 nm3

SASDJY6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 1 (PKD1), Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) Sample: Collagenase ColH (Polycystic kidney disease 1 (PKD1), Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD)) monomer, 34 kDa Hathewaya histolytica protein Buffer: 10 mM HEPES, 100 mM NaCl, 0.4 mM EGTA, 2.4 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 3.4 nm Dmax 11.0 nm VolumePorod 32 nm3

SASDJZ6 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr780Ser, His782Ser, Tyr796Ser, Tyr801Ser Sample: Collagenase ColH (Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr780Ser, His782Ser, Tyr796Ser and Tyr801Ser) monomer, 23 kDa Hathewaya histolytica protein Buffer: 50 mM Tris, 1 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 2.5 nm Dmax 9.0 nm VolumePorod 20 nm3

SASDJ27 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr780Ser, His782Ser, Tyr796Ser and Tyr801Ser bound to triple helical collagen like-peptide Sample: Collagen like-peptide [GPRG(POG)13] trimer, 11 kDa protein Collagenase ColH (Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) with Tyr780Ser, His782Ser, Tyr796Ser and Tyr801Ser) monomer, 23 kDa Hathewaya histolytica protein Buffer: 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 3.2 nm Dmax 18.0 nm VolumePorod 34 nm3

SASDJ37 – Collagenase H C-terminal non-catalytic segments Polycystic Kidney disease domain 2 (PKD2) and Collagen binding domain (CBD) bound to triple helical collagen like-peptide Sample: Collagenase ColH (Polycystic kidney disease domain 2 (PKD2) and Collagen binding domain (CBD)) monomer, 23 kDa Hathewaya histolytica protein Collagen like-peptide [GPRG(POG)13] trimer, 11 kDa protein Buffer: 50 mM HEPES, 100 mM NaCl, 5 mM CaCl2, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 5 RgGuinier 3.3 nm Dmax 18.0 nm VolumePorod 35 nm3