Observation of glycine zipper and unanticipated occurrence of ambidextrous helices in the crystal structure of a chiral undecapeptide

BMC Structural Biology

Volumn 7, Issue , 2007, Pages

  Acharya, Rudresh ^a   Gupta, Madhvi ^b   Ramakumar, Suryanarayanarao ^a   Ramagopal, Udupi A ^c   Chauhan, Virander S ^b  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLGLYCYLALANYLPHENYLLEUCYLGLYCYLPHENYLLEUCYLGLYCYLPHENYLALANYLGLYCINAMIDE; AMINO ACID DERIVATIVE; GLYCINE; PEPTIDE; PHENYLALANINE DERIVATIVE; UNCLASSIFIED DRUG; AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; CHIRALITY; CIRCULAR DICHROISM; CRYSTAL STRUCTURE; HYDROGEN BOND; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; X RAY DIFFRACTION; CHEMISTRY; X RAY CRYSTALLOGRAPHY;

AMINO ACID MOTIFS; AMINO ACIDS; CIRCULAR DICHROISM; CRYSTALLOGRAPHY, X-RAY; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 35548998221     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-7-51     Document Type: Article

References (33)

1. De novo design and structural characterization of proteins and metalloproteins. WF DeGrado CM Summa V Pavone F Nastri A Lombardi, Annu Rev Biochem 1999 68 779 819 10.1146/annurev.biochem.68.1.779 10872466
2. Design of a 20-amino acid, three stranded beta-sheet protein. T Kortemme M Ramirez-Alvarado L Serrano, Science 1998 281 253 256 10.1126/science.281.5374. 253 9657719
3. Designing a 20-residue protein. JW Neidigh RM Fesinmeyer NH Andersen, Nat Struct Biol 2002 9 425 430 10.1038/nsb798 11979279
4. Tryptophan zippers: stable, monomeric beta-hairpins. AG Cochran NJ Skelton MA Starovasnik, Proc Natl Acad Sci USA 2001 98 5578 5583 11331745 10.1073/pnas.091100898
5. De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: compaction mediated by weak interactions. UA Ramagopal S Ramakumar D Sahal VS Chauhan, Proc Natl Acad Sci USA 2001 98 870 874 11158562 10.1073/pnas.98.3.870
6. De novo design: backbone conformational constraints in nucleating helices and beta-hairpins. P Balaram, J Pept Res 1999 54 195 199 10.1034/j.1399-3011. 1999.00119.x 10517156
7. Conformational characteristics of peptides containing alpha, beta-dehydroamino acid residues. RM Jain VS Chauhan, Biopolymers 1996 40 105 119 10.1002/(SICI)1097-0282(1996)40:1<105::AID-BIP5>3.0.CO;2-# 8541443
8. Stereochemical criteria for peptides and proteins V. Conformation of a system of three linked peptide units. CM Venkatachalam, Biopolymers 1968 6 1425 1436 10.1002/bip.1968.360061006 5685102
9. On the conformational flexibility of model compounds of β-substituted α, β-unsaturated peptides. D Ajo M Casarin G Granozzi, J Mol Struct 1982 86 297 300
10. α, β-Dehydroamino acid residues in the design of peptide structures. Molecular and crystal structures of two folded dehydropeptides. V Busetti M Crisma C Toniolo S Salvadori G Balboni, Int J Biol Macromol 1992 14 23 28 10.1016/S0141-8130(05)80015-7 1596468
11. Dehydrophenylalanine can occur at various reverse turn sites: Conformational analysis of ΔPhe containing model peptides. AC Bach II LM Gierasch, Biopolymers 1986 25 S175 S191 3779025
12. 3. VS Chauhan KK Bhandary, Int J Peptide Protein Res 1992 39 223 228
13. Solution structure of peptides containing two dehydrophenylalanine residues: A CD investigation. O Pieroni A Fissi C Pratesi PA Temussi F Ciardelli, Biopolymers 1993 33 1 10 10.1002/bip.360330102 8427926
14. 10 helical nonapeptides. KR Rajashankar S Ramakumar VS Chauhan, J Am Chem Soc 1992 114 9225 9226 10.1021/ja00049a086
15. Crystal and molecular structure of the dehydropeptide Ac-ΔPhe-Val-ΔPhe-NHMe. MR Ciajolo A Tuzi CR Pratesi A Fissi O Pieroni, Int J Peptide Protein Res 1991 38 539 544
16. First observation of a α-helix in α, β- dehydrooligopeptides: Crystal structure of Boc-Val-ΔPhe-Ala-Leu-Gly-OMe. KR Rajashankar S Ramakumar RM Jain VS Chauhan, J Am Chem Soc 1995 117 10129 10130 10.1021/ja00145a031
17. Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions. UA Ramagopal S Ramakumar P Mathur R Joshi VS Chauhan, Protein Eng 2002 15 331 335 10.1093/protein/15.4.331 11983934
18. The C-H.O hydrogen bond: structural implications and supramolecular design. GR Desiraju, Acc Chem Res 1996 29 441 449 10.1021/ar950135n
19. The enzyme stability of dehydropeptides. ML English CH Stammer, Biochem Biophys Res Comm 1978 83 1464 1467 10.1016/0006-291X(78)91385-2 697874
20. De novo design and characterization of a helical hairpin eicosapeptides: Emergence of an anion receptor in the linker region. Rudresh S Ramakumar UA Ramagopal Y Inai S Goel D Sahal VS Chauhan, Structure 2004 12 1 20 10.1016/j.str.2004.02.014 14725756
21. Rendezvous in a membrane: close packing, hydrogen bonding, and the formation of transmembrane helix oligomers. D Schneider, FEBS Lett 2004 577 5 8 10.1016/j.febslet.2004.10.029 15527753
22. The Cα - -H⋯O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions. A Senes I Ubarretxena-Belandia DM Engelman, Proc Natl Acad Sci USA 2001 98 9056 9061 11481472 10.1073/pnas.161280798
23. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. A Senes DE Engel WF DeGrado, Curr Opin Struct Biol 2004 14 465 479 10.1016/j.sbi.2004.07.007 15313242
24. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighbouring positions. A Senes M Gerstein DM Engelman, J Mol Biol 2000 296 921 936 10.1006/jmbi.1999.3488 10677292
25. Genomic analysis of membrane protein families: abundance and conserved motifs. Y Liu DM Engelman M Gerstein, Genome Biol 2002 3 research0054 12372142
26. Folding, aggregation and molecular recognition in peptides. IL Karle, Acta Crystallogr B 1992 48 341 356 10.1107/S0108768192000673 1418817
27. +-selectivity filter. FI Valiyaveetil M Sekedat R Mackinnon TW Muir, Proc Natl Acad Sci USA 2004 101 17045 17049 15563591 10.1073/pnas.0407820101
28. zPhe side chains. Y Inai T Ito T Hirabayashi K Yokoto, Biopolymers 1993 33 1173 1184 10.1002/bip.360330804 8364153
29. Mechanism of helix induction by trifluoroethanol: A framework for extrapolating the helix-forming propensities of peptides form trifluoroethanol/water mixtures back to water. P Luo RL Baldwin, Biochemistry 1997 36 8413 8421 10.1021/bi9707133 9204889
30. Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins. M Buck, Q Rev Biophys 1998 31 297 355 10.1017/S003358359800345X 10384688
31. Effect of trifluoroethanol on protein secondary structure: an NMR and CD study using a synthetic actin peptide. FD Sonnichen JE Van Eyk RS Hodges BD Sykes, Biochemistry 1992 31 8790 8798 10.1021/bi00152a015 1390666
32. Solution conformation and synthesis of a linear heptapeptide containing two dehydrophenylalanine residues separated by three L-amino acids. A Gupta A Bhardwaj VS Chauhan, J Chem Soc Perkin Trans 1990 2 1911 1916
33. A program for automatic solution and refinement of crystal structures. GM Sheldrick, University of Gottingen, Gottingen, Germany