Please enable JavaScript.
Coggle requires JavaScript to display documents.
Protein conformations - Coggle Diagram
Protein conformations
forces
covalent bonding
backbone bonds
planar (straight), partial double bond that doesn't allow free rotation
can flip between conformations if given energy
trans conformation
- common
- lower energy
cis conformation
-
Ramachandran plot
- based on the idea 2 atoms due to steric collisions/overlapping van der Waals
- coloured regions indicate where the atoms can be arranged
-
hydrogen bonding
- weak bond between H and an electro-ve atom (attracts a shared pair of electrons
- causes polarity due to partial charge differences
- between the carbonyl O2 and the amino group H
entropic/hydrophobic
- proteins hydrophobic regions are in the core as they would decrease entropy (molecular disorder) if exposed
- aromatic rings are stacked as it causes cation-pi electrons which stabilises the arrangement
-
native state refers to when a protein is folded in such a way that it is 3-D and functional
- incorrect formation: modified activity, harmful or inactive
-
assembly:
- involves quaternary structure
- can be simultaneously folding followed assembly or assembling pre-folded proteins
histones: H3 and H4 are not stabile as their hphobic regions are expose
- they can bond to each repeatedly to stabilise each other
- further stabilised by DNA
GCN4 is a yeast transcription activator
- homodimer
- DNA specificity mediated by polar and water molecules
- held together by leucine zipper a parallel alpha coil
- polar asparagine on each side of zipper to form a H bond so the helices don't slide
- salt bridges to strengthen the end of the coil due to 2 opposingly charged amino acids
methods of study
-
simulation based on molecular dynamic but:
- accuracy is unclear
- time needed to observe is unknown