Investigating Hydrophilic Pores in Model Lipid Bilayers Using

Yuan Hu received his B.S degree in chemistry in 2008 and earned his M.S. .... fields: Fundamental principles of the membrane response and its biomedic...
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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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       r           r ∗ = Γl /Γs     

       r ∗      ΔG(r ∗ ) = πΓl 2 /Γs              

+

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           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

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  Ubias         k                 i  E

F (r(i) ) = −

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                ! (                        < ξ >I=6                     7                         < ξ >I=6; 7           

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

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   (                '   == >?"     

       

              

                 

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7                         )             ΔGnucl           +              ΔG1  7         

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

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

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      !            @00

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

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 @!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 

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  +: 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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  +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

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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 ++

                       

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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 

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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;

ACS Paragon Plus Environment

ΔG3 ΔGpore

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

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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; 

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ΔG3 ΔGpore

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

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   !" #

F=

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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.                  

     

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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.  

 

 

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