Can also be used to help align sequences (e.g.Can be used as information to predict function.Fold prediction by comparing to database of known structures.Framework model of protein folding, collapse secondary structures.SS Information can be used for downstream analysis:.Reminder- secondary structure is usually divided into three categories: Anything else – turn/loop Alpha helix Beta strand (sheet).
If >threshold predict this is an alpha helix/beta sheet otherwise this is coil TGTAGPOLKCHIQWMLPLKK.Most alpha helices are ~12 residues longMost beta strands are ~6 residues long.Long-range interactions are not included.Accuracy of prediction seems to hit a ceiling of 70-80% accuracy.Smarter machine learning algorithms (e.g.Exploiting stereochemistry, residue contact patterns, information theory, preference calculation, etc.The method is strict but consistent (as opposed to expert assignments in PDBĪ more challenging task:Predicting secondary structure from primary sequence alone DSSP (Dictionary of Secondary Structure of a Protein) – assignssecondary structure to proteins which have a crystal (x-ray) or NMR (Nuclear Magnetic Resonance) structure H = alpha helix B = beta bridge (isolated residue) E = extended beta strand G = 3-turn (3/10) helix I = 5-turn () helix T = hydrogen bonded turn S = bend DSSP uses hydrogen-bonding structure to assign Secondary Structure Elements (SSEs).An easier question – what is the secondary structure when the 3D structure is known?.Protein secondary structure Alpha-helix Beta strands/sheet SARS Protein From Staphylococcus Aureus 1 MKYNNHDKIR DFIIIEAYMF RFKKKVKPEV DMTIKEFILL TYLFHQQENT SHHH HHHHHHHHHH HHHHHHTTT SS HHHHHHH HHHHS S SE 51 LPFKKIVSDL CYKQSDLVQH IKVLVKHSYI SKVRSKIDER NTYISISEEQ EEHHHHHHHS SS GGGTHHH HHHHHHTTS EEEE SSSTT EEEE HHH 101 REKIAERVTL FDQIIKQFNL ADQSESQMIP KDSKEFLNLM MYTMYFKNII HHHHHHHHHH HHHHHHHHHH HTT SS S SHHHHHHHH HHHHHHHHHH 151 KKHLTLSFVE FTILAIITSQ NKNIVLLKDL IETIHHKYPQ TVRALNNLKK HHH SS HHH HHHHHHHHTT TT EEHHHH HHHSSS HHH HHHHHHHHHH 201 QGYLIKERST EDERKILIHM DDAQQDHAEQ LLAQVNQLLA DKDHLHLVFE HTSSEEEE S SSTT EEEE HHHHHHHHH HHHHHHHHTS SS TT SS Protein primary structure 20 amino acid types A generic residue Peptide bond SARS Protein From Staphylococcus Aureus 1MKYNNHDKIR DFIIIEAYMF RFKKKVKPEV 31 DMTIKEFILL TYLFHQQENTLPFKKIVSDL 61 CYKQSDLVQH IKVLVKHSYI SKVRSKIDER 91 NTYISISEEQ REKIAERVTL FDQIIKQFNL 121 ADQSESQMIP KDSKEFLNLM MYTMYFKNII 151 KKHLTLSFVE FTILAIITSQ NKNIVLLKDL 181 IETIHHKYPQ TVRALNNLKKQGYLIKERST 211 EDERKILIHM DDAQQDHAEQ LLAQVNQLLA 241 DKDHLHLVFE C E N T E R F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U Master CourseDNA/Protein Structure-functionAnalysis and PredictionLecture 7Protein Secondary Structure Prediction
0 kommentar(er)
