Macromolecular Structure BCH 701
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This 23 page Class Notes was uploaded by Kian Berge on Thursday October 15, 2015. The Class Notes belongs to BCH 701 at North Carolina State University taught by John Cavanagh in Fall. Since its upload, it has received 33 views. For similar materials see /class/223860/bch-701-north-carolina-state-university in Biochemistry at North Carolina State University.
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Date Created: 10/15/15
3 Sheets Basic unit is a B strand The polypeptide chain is almost fully extended when connected to form a sheet Bstrands aren t stable on their own like to hook up Usually from 510 residues d and LI is allowed in upper left quadrant of the Ramachandran plot a Bstrand Not stable by itself Bsneet Usually not very long about 510 residues 2 n c o H n a N Hlillllll OC n n c Ollllllli HN I l 2 90 pr 2 n Rn H E o H n l 1 N Hlmmi O c n C Ommn H N T T nn 9 o H l I 2 an n N H IIIIII lIOC Agtnn 7 p 2 C N N Hnum 2 Z OC n p N HH 5 C Omlul i O H 0 ll 2 n n z a z gn n x n 0 mm 0 C H l 9 a l E 3 H F K quot Qn 2 no n p 3 z l o T H l m an Z nnz H r o S H n 2 n H O l I Z Antiparallel Bsheet Most run N9 C Most stable NH of 1 strand hooks up with CO of next strand Hbond run at right angles to plane of sheet Pleat is not completely flat even through strand extended C atoms successively above and below the plane side chains alternately point up and down too Parallel 3 sheet All strands go in same direction Hbonds not completely at right angles Side chains go up and down Pleat rolls a little bit more m N N N N 2 2c 2 C C O c o c i N 7H N H N H C Ca Ca cm O C 00 C oww CO 20 HN mH N 1 7Nlt mHiN Cu cu c cl oc woc oc 0c N H N H N H NH Cu Ca Ca ca C C c O O W 0 C H N N HN H N Cr C Cu cu OC C c C N N N H N H Ci CEx C x CEI c c c 39c Antiparallel is more common and more stable Each has a distinctive Hbond pattern Parallel has a higher energy conformation therefore it is less stable Sometimes parallel and antiparallel can mix 20 of the time Ni 19 N N N cu c C C a Ca OC N HlllllllOC C C N H ummo C N N H Ca Ca Ca C C u cOummHN co O C 0000 C 0 H N CZOHIIHHH N HN H N Ca c C C u 1 a Cu OC N Himmoc O a N 0 C N Hmiim0c N N N H C c q a C CK Cu COllllllllH N c I C c 0 H N C OummH N 4 N 0404 N Ca Cu Cu C 1 Ca 02C N HHIImOC C OC N HmumoC N N w N H C AC C Ca C c N t C it As they occur in known structure almost all B sheets have twisted strands The twist always has the same handedness which is defined as right handedness twist Can rotate on themselves So we have dhelices and Bstrands all linking up These are connected by loop regions of various lengths and shapes Loop regions exposed to solvent are rich in charged and polar hydrophilic residues Loop is most important part of 20 structure About 13 of proteins are loops Loops that connect 2 adjacent antiparallel Bstrands are called hairpins Short hairpins are called reverse turns Loops are short about 24 residues Usually has a glycine at position 2 Hairpin laoy Hairpin Imp Tyne II leap strand 1 strand 2 20 Number g mhumhvir 7 l DW quotWHH ofloop 6 4 V ni regions 12 3 Strand 1 f l3 strand 2 391 7 L 9 8 V w 3 7 Bstmnd 1 l4 B strand 2 4 i r quotquotquotnrnmu quotWin 0 4 8 l2 I6 20 24 Number of residues in loan region Gamma turns Only 1 residue in an antiparallel Bsheet not involved in the Hbonding pattern Not very favorable Tightly compact Classical 7 turn Inverse 7 turn Bturns 24 residues in turn 2 residues not in Hbonds of Bsheet The 2 residues on either side ofthe non Hbonded residues are included in the Bturn therefore 4 residues i9 i 3 TYPE gt Type II by factor 23 Primes indicate mirror images Need some kind of flexibility so glycine and proline in turns The conformations of short loops depends on positions of certain residues in the loop usually Gly Asn or Pro due to cistrans isomerization Type I can have any amino acid at i 9 i 3 except for Pro at i 2 Gly dominates at i 3 and Pro at i 1 of both and II turns Asp Asn Ser and Cys frequently occur at i where their side chains often hydrogen bond to the NH or i 2 Gly Asn occur mainly at i 2 or type II turns Asn Gly occur a lot at i 2 of type II turns because they adopt the required backbone angles most easily Bigger turns are seen but not as frequently and have less defined conformations Enthalpy forming breaking bonds Entropy gt entropy the more favorable depending on which one drives determines where or if bonds broken or formed stopping entropy motion Certain entropic effects hep molecules recognize target molecules Drug design messing with entropic motion of the surface of proteins Stopping entropy at 1 spot causes entropy to distribute through other parts of the proteins surface Different ways of highlighting 2 structure We like Topology Diagrams Simple connectivity pictures Used mainly to compare Bstructures twist not seen 4 antiparallel Flavodoxin A miX NO I 5 strands 5 parallel BStrands AntiparalleI barrel IS sheet Notice ordering laStOC anln 28 are adjacent don t form sheet 3 hairpin a simple motif 2 adjacent antiparallel strands joined by a short loop 25 residues The Greek Motif 4 adjacent antiparallel Bstrands connected by loops Greek keys seem to form one long antiparallel structure with loops in the middle of both B strands as shown below By structural changes in the loop regions between B strands 1 and 2 and between B strands 3 and 4 the top part folds down so that B strand 2 associates with B strand 1 E Bstrands 1 and 2 then form hydrogen bonds and the Greek key is formed BdB motif Parallel The hairpin connects 2 antiparallel Bstrands so what connects 2 parallel strands If 2 adjacent strands are consecutive in the amino acid sequence the two ends that are to be connected are at opposite edges of the Bsheet The polypeptide chain must cross the Bsheet from one edge to the other and connect the next B strand close to the point where the 1St Bstrand started Such crossovers are often made by dhelices Bstrand loop ahelix Bstrand Domains are built from structural motifs So if we look at a big protein we may see very familiar domains that al fit together to make something unique a If N c a M i N c 5 ii iiii MN vi vii C N y C M c N viii 0 Figure 221 Two sequentially adjacent hairpin motifs can be arranged in 24 different ways into a 3 sheet of four strands a Topology diagrams for those arrangements that were found in a survey of all known structures in 1991 The Greek key motifs in i and v occurred 74 times whereas the arrangement shown in viii occurred only once b Topology diagrams for those 16 arrangements that did not occur in any structure known at that time Most of these arrangements contain a pair of adjacent parallel 3 strands omomomo p c U813 7 N rj 0mm General conclusions up to now 1 Interiors of proteins contain mainly hydrophobic side chains Ile Leu Val 2 The main chain in the interior is arranged in 2 structure to neutralize its polar atoms through Hbonds Core forms 1st then 2 structure 3 2 main types of 2 structure OLhelices and Bstrandssheets 3 sheets can have their strand antiparallel parallel or mixed sheets usually inside with hydrophobic facing into 4 The interior is connected to the surface by loops 5 Well known motifs helix loop helix and hairpin B Ot B B IOOIO B Structure Non superimposable 3D arrangements that are interconvertible without breaking covalent bonds 9 CONFORMATIONS Primary Sewndnry Tertiary Quaternary 20 amino acids differing in SIDE CHAINS these side chains must confer 3D structure otherwise all would look the same All amino acids except glycine are chiral they can exist in mirror image forms All backbones are the same LorD L form Dform TheLform reads CORN in clockwise direction The translational machinery for protein synthesis has evolved only to use Lforms Angles and rotations between adjacent residues N dC OLC C39LIJ O C Nw amp Angle of rotation the only degrees of freedom are around the OLC atomsbonds Each amino acid residue is associated with 2 conformational angles 4 and LI Structurally we like to define I and LI very accurately CD and LI are called dihedral or torsion angles peptide band A polypeptide chain consists of multiple peptide units represented by gray boxes Each subunit is rigid and planar The peptide units can rotate around the Ca along the LI and b angles So can d and LI have any value NO Most combinations of LI and d for an amino acid are not allowed because of steric collisions between the side chains and main chain Theoretically if the torsion angles all are 180 we have a purely trans system N COL C if the torsion angles are all 0 we have the purely cis arrangement Which is preferred For the peptide bond on Ci Ni1 The trans is preferred 100021
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