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Fighting microbial infections with force fields: Evaluating conformational ensembles ofintrinsically disordered proteins

Jephthah, Stephanie

2021

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Citation for published version (APA):Jephthah, S. (2021). Fighting microbial infections with force fields: Evaluating conformational ensembles ofintrinsically disordered proteins. Printed in Sweden by Media-Tryck, Lund University.

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Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteinsSTÉPHANIE JEPHTHAH

DIVISION OF THEORETICAL CHEMISTRY | LUND UNIVERSITY

ISBN: 978-91-7422-806-9

Theoretical ChemistryDepartment of Chemistry

Faculty of ScienceLund University 9

789174

228069

NO

RDIC

SW

AN

EC

OLA

BEL

3041

090

3Pr

inte

d by

Med

ia-T

ryck

, Lun

d 20

21

4

3

α

+ −

α

α

C

CH3H

H3N COO+ -

Alanine (Ala, A)

H CH2

CO

NH2

C

H3N COO+ -

Asparagine (Asn, N)

CH2H

CH2

HN

C

H2N

NH2

H2C

+

C

H3N COO+ -

Arginine (Arg, R)

H CH2

CO

O

C

H3N COO+ -

-

Aspartic acid (Asp, D)

H CH2

HS

C

H3N COO+ -

Cysteine (Cys, C)

H CH2

H2C

C O

H2N

C

H3N COO+ -

Glutamine (Gln, Q)

H CH2

H2C

C O

O

C

H3N COO+ -

-

Glutamic acid (Glu, E)

H H

C

H3N COO+ -

Glycine (Gly, G)

H CH2

C

NHN

HC

HC

C

H3N COO+ -

Histidine (His, H)

H CH

CH3

H2C CH3

C

H3N COO+ -

Isoleucine (Ile, I)

H CH2

HC

CH3H3C

C

H3N COO+ -

Leucine (Leu, L)

CH2H

CH2

H2C

H2C

NH3

C

H3N COO+ -

+

Lysine (Lys, K)

CH2H

S

H2C

H3C

C

H3N COO+ -

Methionine (Met, M)

H CH2

CHC

CHHC

CHHC

C

H3N COO+ -

Phenylalanine (Phe, F)

H2C

CH2

C

H2N COO

CH2

+ -

Proline (Pro, P)

H CH2

HO

C

H3N COO+ -

Serine (Ser, S)

H CH

OHH3C

C

H3N COO+ -

Threonine (Thr, T)

H CH2

C

HNC

C

HCHC

CH

CH

HC

C

H3N COO+ -

Tryptophan (Trp, W)

H CH2

CHC

CHHC

CHC

HO

C

H3N COO+ -

Tyrosine (Tyr, Y)

CH3

H CH

H3C

C

H3N COO+ -

Valine (Val, V)

+−

(φ, ψ) αβ

C

RH

+H3N COO

(a)

C

R H

NH3+OOC

(b)

(c)

C

R1H

+H3N C

R2 H

COO

C

O

N

H O

C C

R3H

H

N C

O

C

R4 H

N

H

C

O

N

H

C

O

N

HO

C

H

N

α β

(φ, ψ) = (− ◦,+ ◦) . .

FCR = + + −,

NCPR = | + − −|,+ −

0.0

0.2

0.4

0.6

0.8

1.0

0.0 0.2 0.4 0.6 0.8 1.0

R1

R2

R3

R4

R4

Frac

tion

of n

egat

ivel

y ch

arge

d re

sidu

es

Fraction of positively charged residues

< <− ≤

> ≤> >

Function

Antiviral

Antibacterial

Antifungal

Bu ering

Digestion

Mineralization

Lubrication &visoelasticity

Tissuecoating

Carbonic anhydrasesHistatins

Histatins

AmylasesMucins

StatherinMucins

HistatinsCystatins

PRPsStatherin

AmylasesCystatinsMucinsPRPsStatherin

Histatins

Peroxidases

AmylasesCystatins

Mucins

LactoferrinLysozyme

LactoferrinMucinsPeroxidases

Cystatins

+ ∼

+

+

+

+

α β

( )ρ

( ) → → ( ) →→ ∞

( )

( ) = +

∫ ∞ρ( ( )− )

sin( ),

rdr

0

1g(r)

r

( )

( ) =ε ε

.

ε ε

( ) =

∫ ∞− ( ) =

ε ε=

ε ε.

( ) = − cos θ

ε ε,

=θ

( ) = − ( )

( ε ε )

(α +

),

α

/

( ) = −[ + + ]

= −[( α + α ) + +

α α ν ν

(ν + ν )

]/( ε ) ,

ν

O

H H

O

H H

C

R2H

C

R1 H

C

O

N

H

C

Rn-1H

C

Rn H

COO

C

O

N

H

(a) (b)

NH3+

= + -

= + + + + + .

=∑

( − ) ,

=∑

θ(θ − θ ) ,

θ θ θ

φ

φ

=∑

φ[ + cos( φ − φ )],

φ

ξ

=∑

ξ(ξ − ξ ) ,

ξ

r0

i j i

j

k0

i

j k

l

i

j k

l

=∑<

ε

((σ)

−(σ) )

,

ε σ

=∑<

ε ε.

N

C

− +

= + -

= + + + .

=

−∑=

( , + − ) ,

, +

=∑<

( ),

( )

( ) =

{, ≥ + ,

∞, < + ,

=∑<

( ) =∑<

ε ε

exp[−κ( − ( + ))]

( + κ )( + κ ),

κ

= −∑<

ε,

ε

Fr

F = −∂∂r

.

F = · a = · ∂ r

∂,

v

v(

+)= v

(−

)+ F ( ),

r ( + ) = r ( ) + · v(

+).

r0

t0

r1 r2v1/2 v3/2 v5/2

t1 t2

t

(a) (b) (c) (d) (e)

=−τ

,

τ

( )

( )

( ) ≤ ( )

( ) > ( ) ∈ [ , ]

< −[ ( )− ( )]/

(a)

(b)

(c)

Rg

t

(a) Globular

Rg

t

(b) Flexible

( )

( ) = 〈 ( ′ + ) ( )〉.

=( )

τ

τ =

∫ ∞( ) ,

= /τ

ε( )

ε( ) =

√√√√( − )

∑=

( − 〈 〉) ,

〈 〉

. ..

−0.6

−0.4

−0.2

0.0

0.2

0.4

0.6

0.8

1.0

C(t)

Time, t

(a) ACF

Sim 1Sim 2Sim 3

0.00

0.01

0.02

0.03

0.04

ε(n)

Block size, n

(b) BSE

=

√∑= ‖r ‖∑

=

,

r

=√

‖r − r ‖ .

α

−

α β β

( ) =

⟨ ∣∣∣∣∣∑=

exp( q · r )∣∣∣∣∣⟩.

( ) =

⟨( ) /

[∑=

exp( q · r )][∑

=

exp(− q · r )]⟩

,

( ) =∑=

∑=

( ) /

( ) .

qk ks

k0 2

ksq=ks-k0 q

θ|k | = |ks| = /λ

λ

= | | = sin (θ)

λ.

( )

( ) = ( ) ( ),

( ) ( )

0.01

0.10

1.00

0.0 0.1 0.2 0.3 0.4

I(q)/I

(0)

q (Å)

(a) Form factor

0.0

0.5

1.0

1.5

2.0

2.5

0 1 2 3 4

(qR

g)2 I(q

)/I0

qRg

(b) Kratky plot

0.00

0.02

0.04

0.06

0.08

0 20 40 60 80 100

P(r)

r (Å)

(c) Pair distance distribution

( )( ) ( )

( )

( ) =

∫ ∞( )

sin ( ).

=

∫( )∫( )

,

( ) =

∫( ) .

=

( ) = ( ) exp

(−

),

ln(( ))= ln

(( ))− .

< .

< .

−2.5

−1.5

−0.5

0.5

1.5

0 5 10 15 20

ln(I(

q))

q2 (nm−2)

< .

θθ = . ·

→ ∗→ ∗

α

β

-20

-10

0

10

20

180 195 210 225 240Δ

(M-1

cm-1

)

(nm)

-helix-sheet

Random coilPPII

αβ

= − ,

[θ] λ

[θ] =· θλ

· · ,

θλ λ

ε

ε = · .

ε

[θ] = · ε

++ +

FCR = . NCPR = .

FCR = . NCPR = .

..

(b)

0.0

0.4

0.8

1.2

1.6

2.0

5.0 10.0 15.0 20.0 25.0

p(Rg)

Rg (Å)

Hst5_HIEHst5_HIP

(a)

β

α

βα

>< ≤ ≤

◦ ◦ ◦ ◦◦

◦

◦

.

∼ . ± .

〈 〉

8 9

10 11 12 13 14 15 16 17

0 10 20 30 40 50 60

Rg

(Å)

T (°C)

NMRSAXS

MD(A3)MD(A4)

MD(C3)MC(IW)

〈 〉

−16000

−12000

−8000

−4000

0

4000

185 200 215 230 245 260

[θ] (

deg

cm2 d

mol−1

)

λ (nm)

10 °C20 °C37 °C50 °C

+ . +

β

0.02

0.04

0.06

0.08

0.10

0.12

0.14

0.16

1 2 3 4 5 6 7 8

Clu

ster

pop

ulat

ion

Cluster number

AB

CD

< .

0

20

40

60

80

100

3 5 7 9 11 13

PPII

cont

ent (

%)

# of proline residues

ABCD

.

/

+ . .+ . .+ . .+ . .

−

+− +

0.01

0.10

1.00

0 1 2 3 4

I(q)/I

(0)

q (nm−1)

ExpNSpdCSpd

( )

0.0

1.0

2.0

3.0

4.0

5.0

0.6 0.9 1.2 1.5 1.8

p(R

g)

Rg (nm)

NSpdLNSpdSNSpdL*NSpdS*CSpdLCSpdSCSpdL*CSpdS*

P−113

0.0

0.5

1.0

1.5

2.0

2.5

0 1 2 3 4

(qR

g)2 I(q

)/I0

qRg

ExpNSpdCSpd

(a)

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0 1 2 3 4 5

P(r)

r (nm)

ExpNSpdCSpd

(b)

α

−15

−10

−5

0

5

10

200 210 220 230 240 250

[θ] (

mde

g)

λ (nm)

Hst5NSpdCSpd

0.01

0.10

1.00

0 1 2 3 4

I(q)/I

0

q (nm−1)

ExpEOM

MD

(a) Form factor

0.00

0.50

1.00

1.50

2.00

2.50

3.00

0 1 2 3 4

(qR

g)2 I(q

)/I0

qRg

(b) Kratky plot

β

α

β α

α

α

α β

α

·

80

81

82