Marlou Snelleman 2012 Protein structure

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

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! HydrophobicHydrophilic

Hydrophobicity – Sheets Hydrophilic Hydrophobic Pattern: OXOXOXOX (hydrophobic:O, hydrophilic: X)

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 – 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