From amino acids to proteins

From amino acids to proteins Peptide bond Energetics of folding Backbone conformation The peptide bond • Forward reaction is a dehydration, backward reaction is an hydrolysis • Note energetics • Two amino acids combine to form a dipeptide, three to form a tripeptide, several to form an oligopeptide, many to form a protein Protein sequence • >sp|P54209|ATC1_DUNBI CATION-TRANSPORTING ATPASE CA1 (EC 3.6.1.-) Dunaliella bioculata. • MVSHASSGRPSSRDTGMVYLGLGMQDAYSSEVQEVAAFYHVDLDRGLSDRDVQQARIKYGRNQMEAE QSTPLWKLILKQFDDLLVKILLGAAIVDFIIAISEGESIQSGLIEPMVILLILVANATVGVVTERNAEKAIEQLKS YEADDATVLRNGQLQLIPSADIVPGDIVELAVGNKVPADTRVSHIYTTSLKIDQSLLTGESQAVEKHTEVVH NEQAVYQDKLNMLFSGTLVVAGRARGIVVGTGSNTAIGKIRDAMGVEEDVVTPLKAKLDEFGALLSKVIA GICVLVWVVNINRFNDPALGGWFQGAIHYFKIAVALAVAAIPEGLPAVVTTCLALGTRKMARHNAIVRTLP SVETLGCTTVICSDKTGTLTTNQMSVIKVAAVQSSSSQLAEFDVTGTTFSPEGMVLGPGGVVLRQPADTP CLAHAAQCAALCNDSQVFVAQKTGTLQRIGESTEIALRVFAEKIGLPSSIRPDRPISRSQFGTNNFWQEDV ERLALLEFSRDRKMMSVLVKGSDRQHNIWSKGAPEFVLRKCSHVLANNGEGAVPLTDNMRQAILSDMQ AFGSRQALRCLALAFKSVPTTTTKLDYSDESGLTFIGLLGMHDPPRPECRSALSTCHNAGIKVIMVTGDNK GTAEAVARQVGALSPSTALAGSDDEDNLGISYTGREFEEMGALGQAAATRNLVVLSRVEPMHKLRLVEL LKAQGHVVAMTGDGVNDAPALLRADIGIAMGSGTAVAKHAADMVLGDDNFATIVFAVAEGRVIFNNTKQF IRYMISSNIGEVVAIFLAALLGLPEVLTPVQLLWVNLVTDGLPATALGFNRADKDMMARGPRRVDDPIVNG WLFLRYLIIGMYVGIVTVYGFIWWYISFPEGGNMTWSQLTHFQACASQPGGAKDCEVFHSKHPTTISMSV LVVVEMFNALNNLSEDSSLLRIPPWDNKWLVGAIATSMALHFGILYTGASAMFGVTGLSFAEWTMVIKLSA PVILVDEIMKAWSRRRQRHPASSRGGPVSLMEIQVPLTSSSRDEAALKLK • • FASTA format for presentation of amino acid sequence of a protein Different proteins with different sequence, related proteins with related sequence No obvious pattern • Protein sequences fold • Such sequences may fold to an organized structure – Not necessarily a simple linear collapse • http://www.youtube.com/watch?v=swEc_sUVz5I – Folding occurs by formation of intermediate domains • http://www.youtube.com/watch?v=AlfvWESPyZY&feature=related • What structure actually forms depends on sequence • Driving force for collapse = hydrophobicity • Controlling force for specific structure = stronger interactions, or loss thereof Getting along with your neighbors • • • • Bond Energy Example Covalent bonds 100-600 KJ/mole -S-S- Ionic bonds 15 KJ/mole COO- - NH3+ Hydrogen bonds 5 KJ/mole Van der Waals 4 KJ/mole -O-H …. O=C- -C-H … H-C- Amino acids capable of all of these interactions Covalent bonds: too strong to break or rearrange, so all folding depends on weak interactions BUT – the energies of weak interactions enter in, not as positive contributors, but as costs… …incurred in transition from unfolded to folded forms Collapse to a folded structure Energetics • Van der Waals interactions always available • VdW sufficient to replace hydrogen bonds • In water, hydrocarbons replace hydrogen bonds between water molecules with van der Waals interactions – a small, but cumulative cost. • Clustering hydrocarbons together retains their van der Waals interactions, and regenerates water H-bonds Ending up at a specific structure Avoiding energy costs • Ionic interactions/hydrogen bonds: abundantly available in unfolded state (with water and dissolved salts) – Little gain from forming those interactions in folded state – Very high cost if folded state does not permit these interactions The Peptide Bond Six atoms, (Ca1, C, O, N, H, Ca2) all lie in a plane. The reason for the planarity The peptide bond is rigid and planar because Atoms involved in double bonds distribute the bonds in a plane The double bond character of the C puts Ca1, C, O, and N in a plane The double bond character of the N puts C, N, H, and Ca2 in (the same) plane Details • Barrier to Rotation about C-N bond is 60 kJ/mole • Peptide bond is planar with Cα groups typically trans to the peptide bond (better accommodate R groups) • Cα groups are still sp3 hybridized, still have 109.5 bond angles and can rotate around the single bond linking them to the atoms of the peptide bond • The latter rotations allow side chains to move in three dimensions • Not all conformations are possible A different view of the protein backbone • • • • • Succession of units extending from one Cα carbon to the next Each unit consists of atoms in a single plane Each unit can rotate around the bond connecting it to the Cα carbon The two rotational angles at each carbon are, in principle, independent. In fact, they are not independent Phi and Psi angles • Note in this diagram which is Nterminal direction, which is Cterminal • Phi angle is with the phormer amino acid (n-1) • Psi angle is with the Psubsequent amino acid (n+1) • For each Cα carbon, can measure and plot phi, psi • = Ramachandran plot Measured, theoretical phi, psi angles • Relatively restricted range of possibilities because of steric interactions between side chain and backbone atoms And those are sweet spots… • Look in detail at amino acid configurations – Amine/Amide orientations in Asn/Gln/His – Similar considerations for vals (see fig ->) – Ramachandran angles • Resulting adjustments – 99% of amino acid side chains in relaxed (trans) configuration – >98% Ramachandran angles favorable