Molecular

 Systems:  Size  and  Complexity  

Protein  A  

Ribosome  

Camphor  

Diazepam  (Valium)   2  
 From  2D  to  3D  
A  Simple  Case:  C6H12  
 
z  

x  

y  
9  
                             ATOM          2  C          HEX      1        0.974            0.314            0.529  
Internal  Coordinates:  Z-­‐Matrix  Format  

•   distances  
•   angles  
113.1°   •   dihedral  (or  torsion)  angles  

1.4  Å  
178.0°  

10  
 Internal  Coordinates:  Z-­‐Matrix  Format  
Methane  xyz  coordinates:  
!
C 0.000000 0.000000 0.000000!
H 0.000000 0.000000 1.089000!
H 1.026719 0.000000 -0.363000!
H -0.513360 -0.889165 -0.363000!
H -0.513360 0.889165 -0.363000 !
 
Methane  z-­‐matrix  format:  
C!
H 1 1.089000 !
H 1 1.089000 2 109.4710 !
H 1 1.089000 2 109.4710 3 120.0000 !
H 1 1.089000 2 109.4710 3 -120.0000 !

11  
 Biomolecular  Structure  InformaVon:  
Ordered  Secondary  Structures  
helices  

27.7  Å  
12  
 Biomolecular  Structure  InformaVon:  
Ordered  Secondary  Structures  
sheets  

13  
 Biomolecular  Structure  InformaVon:  
Disordered  Secondary  Structures  
Loops  and  random  coils  

hgp://atlas.physbio.mssm.edu/~mezei/proj/mod_loop/   14  
 Molecular  Structure  Sources  
•  Molecular  Builders:  
Ideal  soluVon  for  small  systems  with  simple  and  defined  structure.  

C6H6  
15  
A  Bit  More  “Complex”  to  Build…  
 

Hydrolase  (OGlcNAc-­‐ase)  
2VVS  (PDBID)  
Heavy  atoms:  4753  
Weight:  84  kDa  

16  
 Molecular  Structure  Sources  
•  Online  Databases  
 Ideal  for  small  molecules  with  complex  structure  and  for  large  molecular  
systems  such  as  proteins,  nucleic  acids,  or  biomolecular  complexes.  
 
 Cambridge  Structural  Database  (CSD)  
 hgp://www.ccdc.cam.ac.uk/     Small  
 Inorganic  Crystal  Structure  Database  (ICSD)   Molecules  
   hgp://www.fiz-­‐karlsruhe.de/icsd_home.html  
   
 Protein  Databank  (PDB)  
 hgp://www.pdb.org/pdb/home/home.do   Large  
 Nucleic  Acids  Database  (NDB)   Biomolecules  
 hgp://ndbserver.rutgers.edu/index.html    
   

17  
18  
 X-­‐Ray  Crystallography  
1  

Single  crystal  X-­‐Ray  diffractometer.  

2  

3  
Electron  density  map  
hgp://biop.ox.ac.uk/www/lab_journal_1998/Endicog.html  

DiffracVon  pagern  
hgp://news.chess.cornell.edu/archive/highlights/dnsmtrls.htm  
 X-­‐Ray  Crystallography  
The  Unit  Cell  

Asymmetric  Unit  

Space  groups  describe  the  

symmetry  of  a  unit  cell  (230  
variaVons).  
 
Asymmetric  unit  is  the  repeat  
unit  within  the  unit  cell.  
20  
 Small  Molecules  vs.  Large  
Biomolecular  Systems  
Small-­‐molecule  Crystallography   Macromolecule  Crystallography  

•   Molecules  with  fewer  than  100  atoms   •   Systems  with  >10000  atoms  
•   Generally  easy  to  crystallize   •   Difficult  to  crystallize  (unfolding)  
•   MonocromaVc  X-­‐ray  source   •   Synchrotron  light  source  
(diffractometer)   •   Lower  resoluVon    
•   High  resoluVon   •   Refinement  steps  required  
(computaVonal  methods)  
21  
 Protein  Crystallography:    
Synchrotron  Light  Source  
European  Synchrotron  Radia&on  Facility  (ESRF),  Grenoble,  France    

22  
 Nuclear  MagneVc  Resonance  (NMR)  
Signal  intensiVes  in  the  2D  NOESY,  3D  15N-­‐NOESY-­‐HSQC  and  3D  13C-­‐NOESY-­‐HSQC  spectra  

NOEij ≈ 1 6
r ij

A  NOESY  NMR  spectrum  (

hgp://www.pnas.org/content/104/48/18941/F3.expansion.html)    
23  
 Cryo-­‐Electron  Microscopy  (cryo-­‐EM)  

15  Å  resoluVon  cryo-­‐EM  structure  of  the  core  complex  of  a  Type  IV  
secreVon  systems  (T4SSs)  (see  Fronzes  et  al.,  Science  (2009),  323,  
hgp://www.lps.u-­‐psud.fr/CollecVf/GDRcryo/materiel.html     266-­‐268)   24