SMD of TFIIB

From: jonas condes (jonamdtf_at_yahoo.com.mx)
Date: Fri Aug 18 2006 - 14:40:46 CDT

Hi, all. Well, I`m performing an SMD of the protein TFIIB. What I did at first is a search for a hinge region by using the program Dyndom. In this case my output are the values of the dihedral angles within the hinge region that are necessary in order to pass from one conformation to the other (open-closen or reverse). The protein consists of two cyclin subdomains and I want to see if I can pass from one conformation to the other. The problem now is that I don`t know how to input this information in any NAMD conf. file given that the only parameters I can state are the constant force: k and the constant velocity pulling: v, in order to direct my run in the direction of the dihedrals displacements! How can I do this?
  Thanks
   
  * the outputs from my dyndom run are also attached in the message

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DynDom - Protein Domain Motions
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(All numbering and residues are taken from first PDB file)

DynDom run details

  Property   Value
  Name
  Conformer 1
(PDB) 		1C9.pdb (E)
  Conformer 2
(PDB) 		1TFBmod14_autopsf.pdb (X)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 101 3.96   113 - 207   210 - 215
2 97 3.24   208 - 209   216 - 310

Sequence


                            __________________________________________________ 
 1C9.pdb(E)               : DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIA 
                          :                                                    
 1TFBmod14_autopsf.pdb(X) : SRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIA 
                            __________________________________________________ 

                            _________________________________________204______ 
 1C9.pdb(E)               : SACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLIT 
                          :                                                    
 1TFBmod14_autopsf.pdb(X) : SACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLIT 
                            _________________________________________204______ 

                            __________________________________________________ 
 1C9.pdb(E)               : TGDFMSRFCSNLCLPKQVQMAATXiARKAVELDLVPGRSPISVAAAAIYM 
                          :                                                    
 1TFBmod14_autopsf.pdb(X) : TGDFMSRFCSNLCLPKQVQMAATXiARKAVELDLVPGRSPISVAAAAIYM 
                            __________________________________________________ 

                            __________________________________________________ 
 1C9.pdb(E)               : ASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPV 
                          :                                                    
 1TFBmod14_autopsf.pdb(X) : ASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPV 
                            __________________________________________________ 

                            ______                                             
 1C9.pdb(E)               : DKLPQL                                             
                          :                                                    
 1TFBmod14_autopsf.pdb(X) : DKLPQL                                             
                            ______                                             

Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		106.8
Translation
(A) 		5.0
Closure
(%) 		97.1
Bending Residues
( green ) 		  204 - 219
Bending Region Analysis
Downloading Image
lines cross at centre of rotation
(Move mouse over image to change conformation)

RASMOL Script

Download RASMOL script file and run with command
"rasmol -script <script-filename>" 		Download

For further details email : sjh@cmp.uea.ac.uk

DynDom Copyright © 2003

DynDom - Protein Domain Motions
Home
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Search Protein Families
Browse Non-Redundant Movemnets
Search Non-Redundant Movements

(All numbering and residues are taken from first PDB file)

Bending Residue Dihedral Analysis

Residue
i		 Residue
i+1		 Distance of hinge axis to residue i in conformer 1
(A) 		Distance of hinge axis to residue i in conformer 2
(A) 		Change in psi (i)
(deg) 		Change in phi (i+1)
(deg) 		Angle of psi(i) axis to hinge axis conformer 1
(deg) 		Angle of psi(i) axis to hinge axis conformer 2
(deg) 		Percentage Progress
(deg)
 GLU-203   THR-204  26.0 20.3 -144.4 -50.8 48.9 47.2 -108.2
 THR-204   SER-205  23.7 19.4 129.0 -142.7 82.9 60.6 1.1
 SER-205   VAL-206  20.0 18.4 -124.4 45.6 22.3 52.4 57.5
 VAL-206   ASP-207  17.6 16.9 -153.4 18.3 100.1 112.4 -36.9
 ASP-207   LEU-208  14.7 14.2 -36.1 -109.6 78.9 97.9 -59.4
 LEU-208   ILE-209  11.5 15.9 -124.1 -76.3 19.4 61.8 139.8
 ILE-209   THR-210  10.0 13.7 131.5 -176.9 89.5 70.5 -10.7
 THR-210   THR-211  7.0 9.9 -147.9 -67.3 36.1 82.3 -87.9
 THR-211   GLY-212  4.1 11.2 11.8 -24.8 146.7 169.0 12.9
 GLY-212   ASP-213  6.4 11.5 70.5 -60.7 112.9 110.7 -10.1
 ASP-213   PHE-214  8.9 7.7 -16.9 61.0 45.4 81.9 -19.0
 PHE-214   MET-215  7.1 8.2 2.7 -26.0 136.0 158.5 16.1
 MET-215   SER-216  4.4 9.6 -2.6 104.2 19.1 53.4 -71.9
 SER-216   ARG-217  6.9 6.2 94.0 -40.8 120.0 159.3 268.2
 ARG-217   PHE-218  8.3 8.3 28.3 -44.7 97.7 125.4 -7.5
 PHE-218   CYS-219  6.1 8.5 46.9 3.8 138.0 87.6 -8.3
 CYS-219   SER-220  3.1 5.4 13.5 -44.8 156.3 155.7 30.8

Downloading Image

Graph shows rotational transition at bending residues and can be used to identify hinge bending residues.
Probably only informative for interdomain rotations greater than 20 degrees

For further details email : sjh@cmp.uea.ac.uk

DynDom Copyright © 2003

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