Investigating Hydrophilic Pores in Model Lipid Bilayers Using

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Invited Feature Article

Investigating Hydrophilic Pores in Model Lipid Bilayers using Molecular Simulations: Correlating Bilayer Properties with Pore Formation Thermodynamics Yuan Hu, Sudipta Kumar Sinha, and Sandeep Patel Langmuir, Just Accepted Manuscript • Publication Date (Web): 23 Jan 2015 Downloaded from http://pubs.acs.org on January 26, 2015

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

Langmuir is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

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ΔG(r) = 2πrΓl − πr 2 Γs ( )

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r r ∗ = Γl /Γs

r ∗ ΔG(r ∗ ) = πΓl 2 /Γs

+


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, - .

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7

$ . ' 8" '

" $ . ' F


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=A ==

0.D = ! $ . ( $ 0.D 3

=A =

!- '1 !+A!6" r I $ . ( += H τT I = 7 E 7 0 4 τP I =

+=× =−4 −1

-5 ! . ( , . ( ( % / .

7

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2

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Γ − Γξ=0 Γξ=1 − Γξ=0

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& ξ *0 Γ Γξ=0 Γξ=1 ) ' " 4 E

Γ=

2 2 tanh α · |Δr(i) | = tanh α · Δx(i) + Δy(i)

'+"

(i) | Δx(i) |Δr Δy(i) ! tanh(3.0) ≈ 1

α $ ( A


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4 α = 3.0/R Γξ=1 , *0 ξ ξ ref

Ubias = 1/2kΔξ 2 = 1/2k(ξ − ξ ref )2

'6"

Ubias k i E

F (r(i) ) = −

∂Ubias ∂Ubias ∂ξ ∂ξ =− = −kΔξ ∂ r(i) ∂ξ ∂ r(i) ∂ r(i)

& r(i) i

'"

F (ri ) E

1 − tanh2 α · Δx(i) 2 + Δy(i) 2 Δx F (x(i) ) = −α · kΔξ · (Γξ=1 − Γξ=0 ) Δx(i) 2 + Δy(i) 2 1 − tanh2 α · Δx(i) 2 + Δy(i) 2 Δy F (y(i) ) = −α · kΔξ · (Γξ=1 − Γξ=0 ) Δx(i) 2 + Δy(i) 2

'F"

F (z(i) ) = 0

(Fi ·ri)

9 '9!" : 0.1 ' B" 09.D@ = *0 ' *0 " *0 ( ) + Γξ=0 Γξ=1

8 B

$

$ += 7 %

=


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Γξ=0 == ) #

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( '*0I==" == >??2 ) == >??2 # *0 - ( '*0I =" === >??2

. .@ ( *0 4

2 )

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7

7 $


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*0 F == F= = *0 7 +=== >??2 (

7

3 $ 7 +== ( = ) =

< *0 % *0 # 9! ' @00

1 ! ! !-"

'7&,." B . @ 'B.@"

$

$

!" # 7

ξ @00

7 == ξ 1


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*0 ξ 3

*

'! . . !-" $ *0 ξ ) ρ(r, z) *0 ξ ' 1 " 7 ( = ) ' ( 6 E 5 + 0*6 8 8" ' : E ,

+,

6,

= + =6; 2 1 ! !- ( (

7 2 +


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!( < ξ >I=6 7 < ξ >I=6; 7

=6 =6; < ξ > < ξ > =6 =6; *0 * < ξ > 1

1

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3

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1 +, 7

1 +, 1 + 6== >? 1 0.1 ) ξ I=+ ! 0.1 * 0. 1

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( ) . ( 3

!- '1 !+;" 7

6


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Rnet 9

*0 ξ # Rnet = 1 ! π ξ ξ < 0.46

$ , 6 ( + * '50," '5B" ) 3 7

& @00 0. 1

8 @00

50,

9!

) !


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( ' == >?"

.@ *0 ξ ' " - ) ( ( 9! # ξ ref = 1.00 @00

9! 9! +== 0.1 1 !+ 0.1 (

8

ξ ref = 1.0 8 @00

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+ 0

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=;6+ nm2 =F++ nm2

@ + '@!0 "

6+ + '@&0 " @&0! '6 " :6×10−20 > @!0! @&0

:A ×10−20 >

7 ) ΔGnucl + ΔG1 7

Rnet ( ' ! + " 7 Rnet ξ !- 1 !6 ( ξ = 0.925 ;


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Page 18 of 62

7 ξ = 0.925 ΔG1 1 ! !- ΔGnucl ΔG1 ,0 7 ΔGnucl ΔG1 =F+ =; nm2 ,0 * (

' 1 +

+@" $

! ) 1 1 ! !- ΔGnucl ΔG1

Kc , Kc

Kc 1

Kc & KC )

:

++ 7 ( , 9 @00

?

7 @00

4 :


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@ 0.1 $ 3 #

1

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+= H . $

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$

$ $ J 0.1 ++ H

0.1 =6

(

' ( 1 " 7

' 1 6," & 0.1 3 & 2 $ A


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7

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' A" > !

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! @00

' "

( ( = ( 1 ' ( 6 E 5 + 0*6 8 8" ' : E ? 0.D #

D

+ 6 F ; : A = + 6 F ; :

@!0 @&0 @0 @*0 @*0D @*08 @*0! 0*0 0*0D 0*08 0*0! @008 @&0! @!0! @0! @00 @00D @00!

,0 =FA =FF+ =F; =;6+ =;=+ =; 6 =; =; 6 =F; =F:6 =FA =F6 =F++ =FF6 =F6+ =F: =F+6 =F6

6+ 6 + 6= 6 6 6= +A 6= +A 6= +; 6 66 += +F +: +:

Kc +A :A :A; =6 ;+ A;: = =;= :+ =FF F= ;: ; :6 =+6 A A:: +66

ΔG1 ΔGnucl 66F: ;A AA: +6 : ;F; 6FA ;; + ==+ 6; =FF 6A ; +:6; F = 6:: ;+ 6F= FF: 66+F F: : 6+ + =A :;= =;+ +6 +A; 6:; ; 6 +: F6

ΔG2 F6 F; F;+ A; FF A A6 F = F


ΔG3 ΔGpore

+: 6;A ;+: FA 6 +F= + + +=A+ +=A+ A A 6= 66: AA A: ;; ;; =F+ =++ = ==: F:F F+ 6A ; 6+ =F == ;;= ;+ AF; AA

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Page 56 of 62

+E D)

3 D

+ 6 F ; : A = + 6 F ; :

@!0 @&0 @0 @*0 @*0D @*08 @*0! 0*0 0*0D 0*08 0*0! @008 @&0! @!0! @0! @00 @00D @00!

,0 =F:; =F: =FFA =;6= =;= =;== =;=+ =; =F;= =FFA =F; =FA =F= =F6+ =F A =F;A =F+ =F+

6+ + 6= 6 6 6= +: 6= 6= 6= +: 6 66 + +F +A +:

Kc +F F=A :F+ = ; ; ;F : =+; : F :=: :A A6 A6 ;A : F = == =A

ΔG1 ΔGnucl 6+; :F =F+ +6 +6 :+= 6+ A ;; A6 6 + A 6A6 + +AF6 6:6 6: : + A =6 ;F 6A6: F: ==+ ; A6 ++F +6 AFA +6A6 +66 6A+6 == 6;A ;=;

F

ΔG2 +: A 6=A :+ 6= + +=F += +=A


ΔG3 ΔGpore :F + ;A: ; 6F +; F FA A : A : + + 6;A 6;A +F6 +: ;66 :A :; +=6 +;6 +; += + ; === A; := ;A6 6 + == A; F+6 F; +6 ++

Page 57 of 62

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6E )

4 D

+ 6 F ; :

@&0 @0 @00 @!0 @&0! @0! @00! @!0!

,0 =FF+ =F; =F: =FA =F++ =F6+ =F6 =FF6

6 + +F 6+ 6 += +: 66

Kc :A :A; A +A ; =+6 +66 :6

ΔG1 ΔGnucl AA: +6 : ;F; +6 +A; 66F: ;A : 6+ :;= =;+ 6 +: F6 + =A

;

ΔG2 ΔG3 ΔGpore ;+: FA 6 +F= =F == +: 6;A A F:F F+ F = ; 6+ F AF; AA A6 6A


Langmuir

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E )

4 D

+ 6 F ; : A =

@00 0*0 @*0 @00D 0*0D @*0D @008 0*08 @*08 @00! 0*0! @*0!

,0 =F: =; 6 =;6+ =F+6 =F; =;=+ =F6 =F:6 =; 6 =F6 =FA =;

+F +A 6= +: 6= 6 +; +A 6 +: 6= 6=

Kc A =;= =6 A:: :+ ;+ ;: =FF A;: +66 F= =

ΔG1 ΔGnucl +6 +A; +:6; 6FA ;; 6:; ; F = + ==+ 66+F F: 6:: ;+ 6; =FF 6 +: F6 6F= FF: 6A ;

:

ΔG2 FF F;+ F6 F A; F;


ΔG3 ΔGpore

=F == 6= 66: + + ;;= ;+ AA A: +=A+ +=A+ = ==: ;; ;; A A AF; AA =F+ =++

Page 59 of 62

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FE )

+ 4 D

+ 6 F ; : A =

@00D @008 @00! @00 0*0D 0*08 0*0! 0*0 @*0D @*08 @*0! @*0

,0 =F+6 =F6 =F6 =F: =F; =F:6 =FA =; 6 =;=+ =; 6 =; =;6+

+: +; +: +F 6= +A 6= +A 6 6 6= 6=

Kc A:: ;: +66 A :+ =FF F= =;= ;+ A;: = =6

ΔG1 ΔGnucl 6:; ; 66+F F: 6 +: F6 +6 +A; F = 6:: ;+ 6F= FF: +:6; + ==+ 6; =FF 6A ; 6FA ;;

A

ΔG2 FF F F;+ A; F6 F;


ΔG3 ΔGpore

;;= ;+ = ==: AF; AA =F == AA A: ;; ;; =F+ =++ 6= 66: +=A+ +=A+ A A + +

Langmuir

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!" #

F=


Page 60 of 62

Page 61 of 62

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Langmuir

Yuan Hu received his B.S. degree in chemistry in 2008 and earned his M.S. degree in organic chemistry in 2010, from Wuhan University, China. Subsequently, he decided to continue his research interest from experiment to the deep mechanistic understanding by means of computational biophysics and chemistry. He is currently a Ph.D. candidate in University of Delaware. The main focus of his research is using state-‐of-‐art multi-‐ scale free energy simulation methods to explore mechanisms and underlying thermodynamic determinants of cellular uptake of cell penetrating peptides into model biological membranes, a challenging problem which continues to attract significant attention. Sudipta Kumar Sinha obtained his M.Sc.(2005) degree in physical chemistry from the University of Calcutta, Kolkata and Ph.D. (2011) degree in computational biophysical chemistry from Indian Institute of Technology Kharagpur. After a short stay in the Department of Biomedical Engineering at University of California, Davis, he arrived as a postdoctoral fellow at the Department of Chemistry and Biochemistry at University of Delaware. He is currently working on several aspects of membrane biophysics and developing polarizable and charge transfer force fields.


Langmuir

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Sandeep Patel is currently Associate Professor in the Department of Chemistry and Biochemistry at the University of Delaware, USA. He attended Drexel University for his Baccalaureate training in Chemical Engineering, and then headed to the Massachusetts Institute of Technology for his Doctoral work in Chemical Engineering. He obtained his Post-‐Doctoral training in the lab of Professor Charles L. Brooks III while at the Scripps Research Institute in La Jolla, California. Research areas of focus include force field development (particularly polarizable force fields for a variety of biomolecular systems), ion solvation and interfacial behaviors, and membrane biophysics with focus on cell-‐penetrating peptides and underlying thermodynamic and structural mechanisms of translocation.


Investigating Hydrophilic Pores in Model Lipid Bilayers Using

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