Thermodynamic  and  Kine/c  Characteriza/on   of  Folding  Mechanisms  of  CheY  Circular   Permutants   Tyler  Ogden   Brooks  Group   Hampshire  College  

Sequence-­‐dependent  folding  behavior   Free  Energy  Landscape   Theory  

•  Folding  characterized  by  free   energy  minima   •  Analyze  at  Tf  to  see  basins  of   unfolded  and  na/ve  state  

CheY  protein  

•  (αβ)5   •  How  do  cuts  between  secondary   structures  affect  folding?     •  Inform  protein  engineering   Hills  and  Brooks.  JMB  (2008)  382,  485-­‐495  

Three  Circular  Permutant  Systems   CpB2:  Cut  between  residues   35-­‐36   • End  of  β2  in  N-­‐terminal   CpB3:  cut  between  residues   62-­‐63   • In  turn  between  β3α3;   splits  C-­‐terminal  and  N-­‐ terminal   CpB4:  cut  between  residues   77-­‐78   • In  turn  between  α3β4  in  C-­‐ terminal  

The  Go-­‐Model   •  Residues  as  Cα  ‘beads’   •  Na/ve  contacts:   –  Side-­‐chain  side-­‐chain  interac/ons   –  Backbone  H-­‐bonds   •  Lennard-­‐Jones  poten/al  for  i  -­‐  j  >  2  

σij 12 σij 10 σij 6 Vij = �ij [13( ) − 18( ) + 4( ) ] rij rij rij •  Non-­‐na/ve  repulsion  

σij 12 Vij = �ij [13( ) ] rij •  This  simple  model  has  been  successfully  applied  to  inves/gate   folding  mechanisms  of  several  proteins  in  the  past   Karanicolas  and  Brooks.  Prot  Sci  (2002)  11:2351  

Simula/on  Details   •  Thermodynamic    -­‐  Replica  Exchange  

–  10,000  exchange  cycles  (exchange  every  20,000  steps)   –  4  temperature  windows  (.87  Tf,  .97  Tf,  1.08  Tf,  1.20  Tf)     –  Umbrella  bias:  8  rgyr  biases  spanning  1.0  Rg0    to  2.0  Rg0   –  Using  gorex.pl  from  the  MRMTSB  toolset     –  Unbiased  data  using  WHAM   0 g

•  Kine/c    

–  48  independent  unbiased  MD  simula/ons  at  .87  Tf  for  2  x   108  /me  steps   –  Unfolded  state  obtained  from  hea/ng  to  1.5  Tf   –  Time  step  is  22fs     –  Langevin  Dynamics  

Folding  of  CheY1  

1Hills  and  Brooks.  JMB  (2008)  382,  485-­‐495  

 

•  N-­‐terminus  nuclea/on   •  Frustra/on  in  α2β3α3β4   tetrad   •  C-­‐terminus  folding  is   accompanied  by  loosening  of   en/re  structure   •  Non-­‐obligate  intermediate   –  Structured  N-­‐terminus   –  Unstructured  C-­‐terminus   •  Agrees  with  experimental   results2   2Kathuria,  Day,  Wallace  &  Majhews.  JMB    

(2008)  382,  467-­‐484  

Qtotal  

Change  in  Tf   Na/ve  State  Stability   • Tf  at  peak   Tf  CpB2  =  280  K       Tf    CpB3  =  285  K   Tf  CpB4  =  287  K  

CpB2-­‐Energy  Landscape  and   Folding   1 1

0.6

0.8 0.6





0.8

C-term N-term Helices 2&3 Helix 3&4 Strands 3&4 Strands 4&5

0.4

0.4

0.2 0 0

N-term CpB2 C-term CpB2 N-term WT C-term WT

0.2

0.2

0.4 0.6 Qtotal

0.8

1

0 0

1000 500 1500 Time (arbitrary units)

2000

CpB4-­‐Energy  Landscape  and   Folding  

CpB3  –  Energy  Landscape  and   Folding  (Major  Error  in  Kine/cs)  

Conclusions   •  Simula/ons  predict  cut-­‐dependent  folding  for   a  constant  amino  acid  sequence   •  Cuts  change  stability  of  na/ve  state   •  Loca/on  of  intermediate  on  folding  pathway   may  vary  (CpB3)   •  Suggests  possibility  of  tuning  protein  folding   pathways    

Acknowledgements   •  •  •  •  •  • 

Karunesh  Arora  (UMICH)   Charlie  (UMICH)   David  Braun  (UMICH)   Ron  Hills  (UNE)   John  Karanicolas  (KU)   Bob  Majhews    (UMASS  Medical  School)  

Thermodynamic and Kine

tetrad. • C-‐terminus folding is accompanied by loosening of enstructure. • Non-‐obligate intermediate. – Structured N-‐terminus. – Unstructured C-‐terminus.

3MB Sizes 2 Downloads 48 Views

Recommend Documents

pdf-1833\hawaiis-da-kine-kookbook-by-harvey-s-okumura.pdf
pdf-1833\hawaiis-da-kine-kookbook-by-harvey-s-okumura.pdf. pdf-1833\hawaiis-da-kine-kookbook-by-harvey-s-okumura.pdf. Open. Extract. Open with. Sign In.

thermodynamic-aspects-of-cycles-with-supercritical-fluids.pdf ...
thermodynamic-aspects-of-cycles-with-supercritical-fluids.pdf. thermodynamic-aspects-of-cycles-with-supercritical-fluids.pdf. Open. Extract. Open with. Sign In.

A computational interface for thermodynamic ...
processes, the kinetics of the system, e.g. the microstructure as a function of time, ... Calc and MATLAB [6] by the MEX (MATLAB Executable) file .... however, from release R14SP2, LOADLIBRARY is supported on both Windows and Linux. 5.

[PDF] Thermodynamic and Transport Properties of Fluids
Book sinopsis. Contains various tables including: Data of Refrigerant 134a (tetrafluoroethane - CH2F-CF3) and the table of R12. Relatet.

STANDARD THERMODYNAMIC PROPERTIES OF ...
A., and Syverud, A. N., JANAF Thermochemical Tables, Third Edi- .... As2. Diarsenic. 222.2. 171.9. 239.4. 35.0. As2O5. Arsenic(V) oxide. -924.9. -782.3. 105.4.

THERMODYNAMIC APPROACH TO STUDY PHOSPHATE ...
There was a problem previewing this document. Retrying... Download. Connect more apps... Try one of the apps below to open or edit this item.

Effect of thermodynamic history on secondary ...
Oct 4, 2007 - +39 050 2214322; fax: +39 050 2214333. E-mail address: [email protected] (S. Sharifi). ... Available online at www.sciencedirect.com. Journal of ..... we speculate that this interpretation can account for the presented results.

A Thermodynamic Perspective on the Interaction of Radio Frequency ...
Apr 1, 2012 - would reach the same extreme temperature of millions of degrees. ... possibly carcinogenic to humans by the world health organization (WHO).