Protein Binding Ligands, Affinity and Specificity

Protein  Binding: Ligands,  Affinity  and  Specificity Key  terms   • Ligand   • Affinity   • Specificity   Proteins  don’t  act  alone   • Myglobin  binds  Heme  and  O2   • Hemoglobin?   • Proteins  act  on  things     – transport  and  catalysis   • Or  work  together  to  make  things   – Structural  proteins  like  microtubules  and  collagen   What  can  be  a  protein’s  ligand?   • Small  molecules   – For  example  O2  in  Hb  and  Mb   • Larger  molecules   – Complex  sugar   • Other  proteins  or  even  more  copies  of  itself   What  governs  protein-­‐ligand   interacSon?   • What  types  of  bonds  determine  the  final   structure  of  a  protein?   • These  same  interacSons  determine  how   strongly  a  protein  can  hold  onto  its  ligand.   • The  number  and  specific  locaSon  of   interacSons   Mb  and  Hb   • Affinity:  Kd   – Low  Kd,  high  affinity   – High  Kd,  low  affinity   Y = fractional binding • Ligand:  02   1.0 0.5 0 0 10 20 O2 30 40 • Specificity:  The  distal  hisSdine  helps  select  for   O2  over  CO   Strong  binding  when…   • The  protein  and  ligand  fit  together     • The  chemical  contacts  are  right   Good contacts high affinity “Fits” but poor contacts: low affinity High selectivity! Covalent  vs  Noncovalent  bonds   Can you draw an example of each of these? Can you easily recognize them in a figure? Binding  affinity  vs  specificity   • The  strength  of  each  bond  adds  to  the  binding   affinity   – Many  noncovalent  bonds  can  result  in  “Sght   binding”   • The  more  bonds  formed  the  more  specific  the   protein  is  to  for  ligand   – Especially  true  for  ionic  interacSons   Visualizing  specificity   Specificity  and  FuncSon   What  you  already  know,  and  why.   • Each  protein  can  bind  more  than  one  different   ligand  at  a  Sme   • Binding  of  a  ligand  can  change  protein   structure   • A  change  in  protein  structure  can  be  passed   along  by  non-­‐covalent  bonds   What  would  happen?   • If  a  lysozyme  increased  sugar  affinity  at  the   cost  of  specificity?   – Lysozyme  breaks  down  complex  sugars  that  make   up  bacterial  cell  walls.   A  fun  example   • Microtubules   • Part  of  the  cytoskeletal  network   • Divide  chromosomes  during  mitosis   • Large  fibers  made  up  of  dimers  of  two  related   proteins   A  fun  example   α + β Kd ~ 1 nM + Kd is very high + γ lowers the Kd γ + γ γ Kd still low Gartner and Hiatt, 1994 γ Dynamic  Instability   • Tubulin  monomers  have  a  ligand   – GTP   • Over  Sme,  Tubulin  in  the  microtubules   hydrolyze  GTP   – GTP      H2PO4    +   • This  causes  a  structural  rearrangement  that   lowers  the  stability  of  dimer-­‐dimer  contacts   What  happens?   • To  the  board.   • Inner  Life  of  the  Cell   – Worth  watching  in  total,  but  just  a  quick  clip  of   microtubule  polymerizaSon  and  depolymerizaSon   for  now   Summary   • Proteins  interact  with  many  things   • Which  protein  interacts  with  what?   – The  shape  and  chemical  nature  of  each  protein’s   surface  determines  specificity   • A  protein’s  affinity  for  a  ligand  is  based  on  the   summaSon  of  non-­‐covalent  bonds   – Low  Kd,  High  affinity