Transcript Protein structure

Protein structure
Marlou Snelleman
2012
Overview

Sequence to structure

Hydrogen bonds
 Helices
 Sheets
 Turns

Hydrophobicity
 Helices
 Sheets

Structure and function
 Active sites
 DNA binding
 Transmembrane

PDB
Sequence to structure
 Sequences do not exist
 Structures do!
DVTVSDNGTS
ITITSGRLEA
TDKVVALEDG
ASLYIAKP
Amino acids – Hydrogen bonds
 The amino acids can make hydrogen bonds
 with their backbone,
 and some with their side chain
 A hydrogen bond needs
 a donor: donates a hydrogen (N-H or O-H)
 an acceptor: accepts the donated hydrogen (N or O)
Example
Hydrogen bonds - Helices
 Amino acids in a helix make hydrogen bonds
 with their backbone
 from O of residue 1
 to the N-H of residue 5
 Etc.
Hydrogen bonds - Sheets
 Parallel
 Anti-parallel
Hydrogen bonds - Turns
2
3
1
4
Hydrophobicity
Hydrophobicity – Protein structure
 Secondary structure elements tend to have
 one side turned to the surface (hydrophilic)
 one side turned to the core (hydrophobic)
Hydrophobicity – Helices
 Most helices have one side hydrophobic and one
side hydrophilic
 Pattern:
 XOOOXOOXOOOX
hydrophobic:O
hydrophilic: X
 Approximately!
Hydrophilic
Hydrophobic
Hydrophobicity – Sheets
 Pattern: OXOXOXOX (hydrophobic:O, hydrophilic: X)
Hydrophobic
Hydrophilic
Structure and function
 The structure of the protein relates to the function
 Sometimes the protein needs other subunits to be
functional
 For example: Hemoglobin
Structure and function – Active sites
 Active site: amino acids in this site have an
active function
 For example:
 Cleaving a peptide bond (Trypsin)
 Binding a ligand (GTPases)
 Catalyze a reaction (Amylase)
 Active and/or binding sites are often in a
cavity in the protein
Structure and function – Active sites
Structure and function – Active sites
Structure and function – DNA binding
Structure and function – Transmembrane
 Transmembrane proteins
are ‘inside-out’ proteins
 situated in the hydrophobic
membrane
 Protein surface hydrophobic
 Protein core hydrophilic
 Function at the inside of the
protein
 For example: proton or ion
channels
PDB – Database of protein structures
 Structures can be solved by crystallography or
NMR
 Protein
 DNA and RNA
 Complexes
 Data of these experiments is in PDB-files
 One file contains the coordinates of each atom
of the protein
 Yasara can make a 3D picture out of these
complicated files