Class Note for BIOC 460 at UA 2
Class Note for BIOC 460 at UA 2
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Date Created: 02/06/15
BIOC 460 Spring 2008 LEC 5 Lecture 5 Protein Secondary Structure Reading Berg Tymoczko amp Stryer 6th ed Chapter 2 pp 3745 Problems in textbook chapter 2 pp 6364 159 Directory of Jmol structures of proteins httpwwbiochemarizonaeduclassesbioutG2462amolroutinesroutineshtml Basic Jmol structure of the x helix MWW Jmol routine showing lots ofviews ofcx helix amp 2 other kinds of helices Jmol structures ofp barrel and 3 clam proteins httr WWW biochem ariznna edu la ri ABZABZaimoibeta domainbeta domain htmi Key Concepts Proteins secondary structure major types of secondary structure found in many proteins a helix B conformation 5 turns surface loops not really secondary structure because not regular repetitive Unusual secondary structures examples collagen helix found in collagen not covered in this course other kinds of helices eg pi helix and 3m helix not covered in this course Secondary structures are stabilized by all kinds of noncovalent bonds but especially by hydrogen bonds Learning Objectives Define secondary structure of a protein List examples of categories of secondary structure that occur in proteins Describe the ahelix including what groups serve as hydrogen bond donors and acceptors chirality of most cc helices in proteins right or lefthandedness number of residues per turn orientation of R groups relative to axis of the helix the helix dipole which end is 6 which is 6 and packing density of atoms Describe conformation including which groups serve as hydrogen bond donors and acceptors and orientation of R groups in a B pleated sheet Explain parallel and antiparallel 3 conformation Learning Objectives continued Identify the most important noncovalent interactions stabilizing the ahelix and Bconformations Explain what a Bturn is where Bturns are often found in proteins and what types of amino acid residues are often found in Bturns Be able to identify ahelices and strands or sheets consisting of 2 or more Bstrands on a ribbon depiction of a protein structure Protein Secondary Structure Local regularrecognizable conformations observed for parts of the peptide backbone of a protein Examples a helix B conformation 3 turns collagen helix Properties of peptide bond amp hydrogen bonds gt 2 structures aw planarity adjacent planes related in space by set of 2 dihedral angles for each amino acid residue hydrogen bonds Strongest are linear Protein functional groups capable of Hbonding tend to do so to maximum possible extent protein backbone amide groups amide C0 H N Review 4 successive planar peptide groups bounded by the a C s of 5 successive amino acid residues 4 Carboxyl i l r i LL i39l terminus ismWk V 39 L 505 J31 Amino terminus LLJLI NECrv CurC CEN 6 coplanar atoms of1 peptide bond Can CO NH Can1 from u C of one residue to a C of next residue Jmo structure planar peptide group Secondary structures stabilized mainly by hydrogen bonds between backbone amide N H groups and carbonyl O s Protein Secondary Structure BIOC 460 Spring 2008 a helix backbone coiled spiral conformation rodlike structure 039 hellx Usually righthanded in proteins Basic Jmol structgre of the or helix R groups radiate outward from helical cylinder Jmol routine showin cc helix amp 2 other kinds of helices 39 BaCKbone quot regu39ari repeat39ng r tat39 ni res39due by res39dua Hydrogen bonding pattern for or helix H bonds almost parallel to Each residue has close to the same 11 15 coordinates A a T c 9 helix axis from carbonyl O of residue n to H N group of residue n4 36 residues per 360 turn of or helix Whole a helix a dipole 36 Nterm end 5 N Cterm end 6 I 0 C N5 Berg et al Fig 2 29 Ramachandran Plotplot of W51 coordinates of Ramachandran Plot WAD angles for a helix each amino acid residue Every amino acid residue has its own set of dull angles de ning direction 39 For regwari repeat39ng local StrUCtlres ke 0 hellxi eaCh res39due has the from which rest of chain comes into that residue s Cor atom rotation around same 431 angles 5 COHfOFmathh has a differsif set 0f 431 values N Cabond and angle at which rest of chain goes out from that Co atom 39 3980 rotation around Ca Ccammy bond 0 Ramachandran Plot 80 120 139 vs 1 for a large number of nonglycine 12 60 amino acid residues in a A protein pyruvate kinase 3 6 e 0 Blueshaded areas are 3 o Ill Lefthanded sterically allowed no 60 helix very rare steric clashes for these quot 3960 combinations of angles for 120 Righthanded residues with side chains 39110 helix common largerthan Gly 48 73980 1 i y 180 0 130 7180 7120 760 0 50 120 480 Nelson amp Cox Lehninger Principles of 39 39 4th ed Fig 49b 0 degrees Berg et al Fig 231 l 39 Proteins with a lot of the polypeptide chain in Coiled coils of a helices in some proteins a helical conformation 2 righthanded cc helices coiled around each other in lefthanded direction Jmo39 Struotures 0f some u39hEI39cal prete39ns Supercoiled structure has great tensile strength like a rope with twisted hh n39li hinrhem zri ma 4 39 we 4 39 39 39 L domain html Strands Berg at 339quot F39g39 23933 insoluble mammalian hair quills claws horns Some globular proteins compact 3D structure examples Some transcriptional regulator proteins leucine zipperquot motif Myosin muscle Examples Examples Ferm39n an quot390quot StOrage pr te39n stkeratin a brous protein elongated 3dimensional structure water Myoglobin Ozbinding protein especially rich in muscle cells A W Berg et al Fig 2 43 V L lt spacefilling I atoms all nonH atoms shown Ribbon rendition shows only the polypeptide backbone f39 3 I B tracing in space rg quot 39139 i mamp 7 11 11h1 quot i r Nelson amp Cox Lehninger Principles ofk quot w l e Biochemistry 4th ed Fig 416 0 LEC 5 Protein Secondary Structure BIOC 460 Spring 2008 LEC 5 5 conformation Backbone nearly fully extended not coiled All residues in 5 sheet have the same 1151 angles Distance between adjacent AA residues 3 5 A further apart more stretched out than in ii helix Side chains R groups point in alternateopposite directions for adjacent residues in chain NH group and 00 group of peptide bond point in opposite directions away from average direction of extended backbone of chain 9 9 i 399 A a 0 0quot of a aquot 0 g i cr Berg et al 0 Fig 2 35 or 0 3 0 a x o 5 conformation Backbone amide NH and 00 groups again almost fully hydrogenbonded but hydrogen bonds can be between different sections of the backbone OR between sections of backbone on different polypep ide chains No predictable relationship in the amino acid sequence for what sections are hydrogen bonded to each other Hydrogen bonds more or less at right angles to direction of backbone of chain Antiparallel 5 conformation 1 strands run in opposite 39 directions i tug0 Berg et al i Fig 2 36 39 5 conformation Parallel conformation strands run in same direction Berg et al Fig 2 37 Mixed 5 conformation mixture of parallel and antiparallel strands Berg et al Fig 2 38 Ramachandran Plot 1 ltIgt angles for i conformation For regular repeating local structures like or helix or for 5 conformation each residue has the same ltIgt1 angles 5 conformation has its own set oflt1gt1 values different from or helix l80 120 Beta strands Le hand d 60 i alpha heli l o 760 Righthanded 39120 alpha helix 3980 77 r L i 1 mo lZO 60 O 60 IZO l80 Berg et al Fig 2 34 pleated sheets 4stranded antiparallel B pleated sheet planes of peptide bonds quotpleatsquot indicated R groups yellow alternately extending above and below sheet Garrett amp Grisham Biochemistry 3rd ed Fig 510 Protein Secondary Structure 5 pleated sheets 3stranded antiparallel B pleated sheet planes of peptide bonds quotpleatsquot indicated R groups purple alternately extending above and below sheet Side View s 39 7 Nelson amp Cox Lehninger Principles of Biochemistry 3rd ed Fig 47a BIOC 460 Spring 2008 3 pleated sheets 3stranded parallel 3 pleated sheet planes of peptide bonds quotpleatsquot indicated R groups purple alternately extending above and below sheet b Parallel if S39de V39ew Nelson amp Cox Lehninger Principles of Biochemistry 3rd ed Fig 47b Examples of p conformation in proteins Jmol structures of 5 barrel and 5 clam proteins htt lvMvaiochemarizonaeduclasseslbioc462462al39mollbeta domainbeta domainhtm twisted 3 sheet A ball amp stick B ribbon model C ribbon model from quotsidequot to show quottwistquot Berg et al Fig 2 39 Berg et al Fig 2 39 Examples of 3 conformation in proteins Fatty acid binding protein mostly 5 conformation 5 sheet in a clam motif Berg et al Fig 2 40 5 turns reverse turns 3 hairpins 3 bends Abrupt change in direction of polypeptide backbone at surface of protein Stabilized by hydrogen bond across stem of hairpin Snarp turn in space gt steric problems with larger amino acid side c ains often involve Gly Asn Ser small hydrophilic residues or Pro has builtin elbowbend in backbone to help startturn 6 19 32K 7 0 A 399 3 739 quotquotquotquot a Berg et al Fig 241 0 Loops not really secondary structure No regular recognizable or periodic structures Longer excursions of backbone than simple reverse turns Usually at surface of protein Often mediate interactions with other molecules Example loops in antibodies Figure shows structure of one domain of an antibody polypeptide red loops involved in binding antigen flexible structures in loops interact with antigen Berg et al Fig 2 42 LEC 5 Protein Secondary Structure Up next Tertiary structure 3dimensional conformation of whole polypeptide in its folded state Quaternary structure 3dimensional relationship ofthe different polypeptide chains subunits in a multimeric protein the way the subunits fit toge her and their symmetry relationships Only in proteins with more than one polypep ide chain Proteins with only one chain have no quaternary structure
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