The strength of interfacial proteins

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Citation for published version (APA):

Oude Vrielink, A. S. (2017). The strength of interfacial proteins. Technische Universiteit Eindhoven.

Document status and date: Published: 05/07/2017

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Chapter 1 ... 1

Chapter 2 ... 29

Chapter 3 ... 45

Chapter 4 ... 69

Chapter 5 ... 103

Summary ... 121

Samenvatting ...124

Curriculum Vitae ... 127

List of publications ...128

Dankwoord ... 129

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1

General introduction

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1.1 Ice-binding and ice nucleating proteins

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Figure 1.1

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Chapter 1 I General introduction

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Figure 1.3

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1.4 Activity assays of ice-binding proteins

∆𝑇_𝐹 = 𝐾_𝐹∙ 𝑏 ∙ 𝑖 ∆𝑇_𝐹 𝐾_𝐹

𝑏 𝑖

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Figure 1.5

● ○

▼ ● ○

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Chapter 1 I General introduction Figure 1.8 𝑟3 𝑐𝑖 𝑟 𝑟3

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𝑘 𝑐_𝑖 𝑘 𝑐_𝑖 𝑎1 𝑎2 𝑎3 𝑐 𝑎₁ 𝑎₂ 𝑎₃ 𝑐 𝑐

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Figure 1.9

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Figure 1.11

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Figure 1.12

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Figure 1.13

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Figure 1.14

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2

Suspended crystalline films of protein hydrophobin I

(HFBI)

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Chapter 2 I Suspended crystalline protein films of hydrophobin I (HFBI)

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𝑎 =

2.2 Results and discussion

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𝑞 = 𝑞 = 𝐼 = 𝐴𝑞𝐵_{+ 𝐶} _{𝑞 −} 0.5 · 𝑐₀= 𝑎₀= 𝑞 = 𝑞 =

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Figure 2.2

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Figure 2.3 𝑞 = 𝑞 = 𝑎 = 𝑎 = 𝑎 = 𝑏 𝛾 = 𝑑₁₀−1 _{𝑎 = 2𝑑} 10/√3 𝑎 = 𝑎 =

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Chapter 2 I Suspended crystalline protein films of hydrophobin I (HFBI) 𝑑₁₁−1 √3 · 𝑑10−1 𝑑20−1 2 · 𝑑10−1 Table 2.1 d₁₀−1 _d 20 −1

2.3 Conclusion

𝑎 =

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0.5 · 𝑐0= 𝑎0=

Figure 2.4

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3

Analysis of ice recrystallization inhibition activity of

wild-type ocean pout ice-binding protein QAE and its

T18N mutant

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3.1 Introduction

∆𝑇 = 𝑇∞− 𝑇(𝑟) = _𝜌∆𝐻2𝜎𝑇∞ 𝑓𝑟 ∆𝑇 𝑇_∞ 𝑟 𝜎 𝜌 ∆𝐻𝑓 〈𝑅𝑛〉 〈𝑅𝑛〉 = 〈𝑅𝑛,0〉 + 𝑘𝑑𝑡1/𝑚 𝑘_𝑑 𝑚 𝑚 𝑘_𝑑

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Chapter 3 I Analysis of IRI activity of QAE WT and QAE T18N lim_{𝑄→ 0}𝑘_𝑑=8𝜎𝛺2𝐷𝑤𝑐𝑤,𝑒𝑞 9𝑅𝑇 𝑄 𝜎 𝛺 𝐷_𝑤 𝑐_{𝑤,𝑒𝑞} 𝑅 𝑇

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Chapter 3 I Analysis of IRI activity of QAE WT and QAE T18N

3.2 Results and discussion

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Figure 3.2

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〈𝑅_𝑛〉3

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𝑘_𝑑 〈𝑅𝑛〉3

Figure 3.4 〈𝑅𝑛〉3

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𝑘𝑑 𝑘𝑑 (𝑐) = 𝑘𝑑0− 𝑘𝑑0 1+exp ((𝑐_𝑖−𝑐)/𝑠) 𝑐𝑖 𝑘_𝑑(𝑐) = 𝑘𝑑0−_{1+exp ((𝑐}𝑘𝑑0 𝑖−𝑐)/𝑠) 𝑐 𝑘_𝑑0 𝑐 𝑐_𝑖 𝑐𝑖 𝑐𝑖 𝑘𝑑 𝑘_𝑑

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Figure 3.5

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Figure 3.6

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𝑐𝑖 𝑐𝑖

Figure 3.8

𝑐𝑖

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3.4 Material and methods

∼

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Chapter 3 I Analysis of IRI activity of QAE WT and QAE T18N 〈𝑅𝑛〉 𝑘𝑑 〈𝑅𝑛〉3 𝑐𝑖 𝑘𝑑 (𝑐) = 𝑘𝑑0−_{1+exp ((𝑐}𝑘𝑑0 𝑖−𝑐)/𝑠) 𝑐 𝑘𝑑0 𝑐 𝑐𝑖 TH = 𝑇𝑓− 𝑇𝑚

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4

Unusually high mechanical stability of bacterial

adhesin extender domains having calcium clamps

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Chapter 4 I Unusually high mechanical stability of bacterial adhesin extender domains

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Figure 4.1 ∆𝐿_𝑐 𝐿_𝑝 ∆𝐿_𝑐 𝐿_𝑝 ∆𝐿_𝑐 𝐿𝑝 𝐿𝑎𝑎 𝑁𝑎𝑎 𝐿 ∆𝐿_𝑐 𝑑_N;C

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Chapter 4 I Unusually high mechanical stability of bacterial adhesin extender domains 𝐿_𝑎𝑎=∆𝐿𝑐+𝑑N;C 𝑁𝑎𝑎 𝑑_N;C 𝑁𝑎𝑎 𝐿𝑎𝑎 𝐿_𝑎𝑎 Figure 4.2 Table 4.1 𝑑_N;C 𝐿𝑎𝑎

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Figure 4.4

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Chapter 4 I Unusually high mechanical stability of bacterial adhesin extender domains 𝑐𝑣= 𝜎_µ 𝜎 µ 𝑐̅_𝑣 𝑐̅𝑣 𝑐̅𝑣 Table 4.3.

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𝑘_𝑢 𝐹 𝑘_𝑢0 _𝜈 𝜅 ∆𝐺 𝑥_𝑢 𝑘_𝐵 𝑇 𝑥_𝑢 𝑘_𝑢0 _𝐹 𝑘_𝑐𝑣 𝐹 (𝑘_𝑐𝑣) =𝑘𝐵𝑇 𝑥𝑢 ln ( 𝑘𝑐𝑣𝑥𝑢 𝑘𝐵𝑇𝑘𝑢0). 𝑥𝑢 𝑥𝑢 𝑘𝑢0 𝑥_𝑢 𝑥_𝑢 Figure 4.7

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𝑥𝑢 𝑘𝑢0

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Figure 4.11

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Chapter 4 I Unusually high mechanical stability of bacterial adhesin extender domains 𝐴(𝑣) = 𝐴0+ 𝐴𝐷𝐶· 𝑣0 2 √(𝑣₀2_−𝑣2)+𝑣02𝑣2 𝑄2 𝐴(𝑣) 𝑣 𝐴0 𝐴𝐷𝐶 𝑣0 𝑄 𝑃 𝑘 𝑘 =𝑘𝐵𝑇 〈𝑧2〉= 𝑘_𝐵𝑇 𝑃 𝑘𝐵 𝑇 〈𝑧2〉   ∆𝐿 ∆𝐿𝑐 𝐿𝑝 𝐹(𝑥) = (𝑘𝐵𝑇 𝐿𝑝) [ 1 4(1−𝑥 𝐿𝑐) 2− 1 4+ 𝑥 𝐿𝑐] 𝐹(𝑥) 𝐿𝑐 𝐿𝑝 𝑘𝐵 𝑇 𝑥

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Amino acid sequence of MpAFP RII8-GFP. MASSHHHHHHSSGLVPRGSHMTEATAGTVTVNAITSDDVINASEAAGTVAVSGTATGGDIAEGDTVTLEINGETY TTTVDANGEWSVDVAGSDLAADTAFDAVVTSSDAAGNTVDTTGSSTHTVDTEATAGTVTVNAITSDDVINASEAA GTVAVSGTATGGDIAEGDTVTLEINGETYTTTVDANGEWSVDVAGSDLAADTAFDAVVTSSDAAGNTVDTTGSST HTVDTEATAGTVTVNAITSDDVINASEAAGTVAVSGTATGGDIAEGDTVTLEINGETYTTTVDANGEWSVDVAGS DLAADTAFDAVVTSSDAAGNTVDTTGSSTHTVDTEATAGTVTVNAITSDDVINASEAAGTVAVSGTATGGDIAEG DTVTLEINGETYTTTVDANGEWSVDVAGSDLAADTAFDAVVTSSDAAGNTVDTTGSSTHTVDKLMVSKGEELFTG VVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFK SAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNG IKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDE LYKKLTEATAGTVTVNAITSDDVINASEAAGTVAVSGTATGGDIAEGDTVTLEINGETYTTTVDANGEWSVDVAG SDLAADTAFDAVVTSSDAAGNTVDTTGSSTHTVDTEATAGTVTVNAITSDDVINASEAAGTVAVSGTATGGDIAE GDTVTLEINGETYTTTVDANGEWSVDVAGSDLAADTAFDAVVTSSDAAGNTVDTTGSSTHTVDTEATAGTVTVNA ITSDDVINASEAAGTVAVSGTATGGDIAEGDTVTLEINGETYTTTVDANGEWSVDVAGSDLAADTAFDAVVTSSD AAGNTVDTTGSSTHTVDTEATAGTVTVNAITSDDVINASEAAGTVAVSGTATGGDIAEGDTVTLEINGETYTTTV DANGEWSVDVAGSDLAADTAFDAVVTSSDAAGNTVDTTGSSTHTVDCC

Amino acid sequence of I27RS8.

MGSSHHHHHHSSGLVPRGSHMLIEVEKPLYGVEVFVGETAHFEIELSEPDVHGQWKLKGQPLTASPDCEIIEDGK KHILILHNCQLGMTGEVSFQAANAKSAANLKVKELRSLIEVEKPLYGVEVFVGETAHFEIELSEPDVHGQWKLKG QPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQAANAKSAANLKVKELRSLIEVEKPLYGVEVFVGETAHFE IELSEPDVHGQWKLKGQPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQAANAKSAANLKVKELRSLIEVEK PLYGVEVFVGETAHFEIELSEPDVHGQWKLKGQPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQAANAKSA ANLKVKELRSLIEVEKPLYGVEVFVGETAHFEIELSEPDVHGQWKLKGQPLTASPDCEIIEDGKKHILILHNCQL GMTGEVSFQAANAKSAANLKVKELRSLIEVEKPLYGVEVFVGETAHFEIELSEPDVHGQWKLKGQPLTASPDCEI IEDGKKHILILHNCQLGMTGEVSFQAANAKSAANLKVKELRSLIEVEKPLYGVEVFVGETAHFEIELSEPDVHGQ WKLKGQPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQAANAKSAANLKVKELRSLIEVEKPLYGVEVFVGE TAHFEIELSEPDVHGQWKLKGQPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQAANAKSAANLKVKELRSC C

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Amino acid sequence of MhLap RII8.

MASSHHHHHHSSGLVPRGSHMSFDATAGALTVSLDTVDNTAQTANLSGTTTDVAPNEQVAITITDSAGNIVNAIA TVGADGSYSLTGVDISSLVDGSLTVEASAQDRNGNALTDSANGALDATAGDLTVSVGTIDNTAQTVNLSGTTTDV APNGQVAITMTDSAGNIVNATATVGADGSYSLTGVDISSLVDGDLTVEASAQDRNGNAVSDSANGTFDATAGDLT VSVDTVDSTAQTANLSGTTTDVALNSQVDLTVTDSAGNVVTATTTVGADGSYSLTGVDISSLVDGNLTVEATAQD RNGNAVSDSAAGSLDATTGALTVSLDTVDNAAQTVDLSGTTADVAPNSQVNVTITDSTGNVVNAITTVGADGSYS LTGVDISSLVDGDLTVEASAQGRNGNALTDSANGALKLDATAGDLTVSIATIDNGNQTINLSGTTTDVAPNSQVE VTITDSAGNVVNATATVGANGSYFLTGVDISRLVDGSLTVEALAQDRNGNAVSDSANGTFDATAGDLTVSVDTVD NTAQTVNLSGTTTDVAPNGQIAITITDSAGNAVNATTTVDADGAYTLTGVDISRLVDGNLTIEATAQDRNGNAVS DSAAGSLDATTGDLTVAIANVDNGNQTADLSGSTTDVAPNSQVNVTITDSAGSTVTATAIVGADGSYTLSGVDIS SLVDGDLTAEASAQDRNGNHVSDSVTGSFDATAGDLAVTISNVDNGAQTIDLSGTTTDVAPNSEVEVTITDSAGN VVNTTATVDADGSYTLTGVDIASLVDGNLTVEATAQDRNGNAVSDSANGTFDATCC

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𝐿𝑝 𝐹(𝑥) = (𝑘𝐵𝑇 𝐿𝑝) [ 1 4(1−𝑥 𝐿𝑐) 2− 1 4+ 𝑥 𝐿𝑐] 𝐹(𝑥) 𝐿𝑐 𝐿𝑝 𝑘𝐵 𝑇 𝑥 Table A1. Table A2.

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Chapter 4 I Unusually high mechanical stability of bacterial adhesin extender domains Table A3. Table A4. 𝑛 𝜎𝑛= √𝜎1 2_+𝜎 22+𝜎32+…+𝜎𝑛2 𝑛

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Figure A2.

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5

Towards investigating the interaction strength

between ice-binding proteins and ice

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Chapter 5 I Towards analysis of the interaction strength between IBPs and ice

5.2 Results and Discussion

Figure 5.1

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Chapter 5 I Towards analysis of the interaction strength between IBPs and ice Figure 5.7 𝐹_𝑧− 𝐹_𝑏 = 𝐹𝑧= 𝑉 · 𝜌 · 𝑔 𝑉 𝜌 𝑔 𝐹_𝑏= 𝑉 · 𝜌 · 𝑔 𝑉 𝜌 𝑔 𝐴 = 2 𝜋 · 𝑟 · ℎ 𝑟 = ℎ =

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Figure 5.8

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Summary

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Samenvatting

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Samenvatting

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The strength of interfacial proteins

Table of Contents

Chapter 1 ... 1

Chapter 2 ... 29

Chapter 3 ... 45

Chapter 4 ... 69

Chapter 5 ... 103

Summary ... 121

Samenvatting ...124

Curriculum Vitae ... 127

List of publications ...128

Dankwoord ... 129

1

General introduction

1.1 Ice-binding and ice nucleating proteins

1.4 Activity assays of ice-binding proteins

2

Suspended crystalline films of protein hydrophobin I

(HFBI)

2.2 Results and discussion

2.3 Conclusion

3

Analysis of ice recrystallization inhibition activity of

wild-type ocean pout ice-binding protein QAE and its

T18N mutant

3.1 Introduction

3.2 Results and discussion

3.4 Material and methods

4

Unusually high mechanical stability of bacterial

adhesin extender domains having calcium clamps

5

Towards investigating the interaction strength

between ice-binding proteins and ice

5.2 Results and Discussion

Summary

Samenvatting