Variation of the intercalating proline in artificial peptides mimicking the DNA binding and bending IHF protein

Amino Acids

Volumn 43, Issue 1, 2012, Pages 289-298

  Scholz, S ^a   Liebler, E K ^a   Eickmann, B ^a   Fritz, H J ^a   Diederichsen, U ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Amino acids; Conformation; DNA binding and bending; IHF protein; Peptides

Indexed keywords

1,2,3,4 TETRAHYDROISOQUINOLINE 3 CARBOXYLIC ACID; 3,4 DEHYDROPROLINE; ALPHA METHYLPROLINE; CURVED DNA; CYCLOPEPTIDE; DENDRIMER; DOUBLE STRANDED DNA; FLUOROPROLINE; INTEGRATION HOST FACTOR; LYSINE; PEPTIDE DERIVATIVE; PHENYLALANINE; PROLINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; BINDING SITE; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; DNA STRUCTURE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GEL ELECTROPHORESIS; MOLECULAR RECOGNITION; MOLECULAR SIZE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

BINDING SITES; DNA; DNA-BINDING PROTEINS; INTEGRATION HOST FACTORS; MOLECULAR MIMICRY; NUCLEIC ACID CONFORMATION; PEPTIDES, CYCLIC; PROLINE;

EID: 84862764680     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-011-1073-1     Document Type: Article

References (34)

1. Albericio F (2002) Methoden der organischen Chemie (Houben Weyl) In Büchel KH (ed) Georg Thieme Verlag, Stuttgart, vol E 22a, pp 58-61
2. D Barth AG Milbradt C Renner L Moroder 2004 A (4R)- or a (4S)-fluoroproline residue in position Xaa of the (Xaa-Yaa-Gly) collagen repeat severely affects triple-helix formation Chembiochem 5 79 86 14695516 10.1002/cbic.200300702 1:CAS:528:DC%2BD2cXlvVKksg%3D%3D (Pubitemid 38095024)
3. E Benedetti B Di Blasio V Pavone C Pedone A Felix M Goodman 1981 Conformational studies of peptides: crystal and molecular structures of L-3,4-dehydroproline and its t-butoxycarbonyl and acetyl amide derivatives Biopolymers 20 283 302 10.1002/bip.1981.360200204 1:CAS:528:DyaL3MXkvFyhtLc%3D
4. L Benoiton 1964 Amino acids and peptides; II. synthesis of ε-N-methyl-l-lysine and related compounds Can J Chem 42 2043 2047 10.1139/v64-301 1:CAS:528:DyaF2cXks1WqsLk%3D
5. CA Bewley AM Gronenborn GM Clore 1998 Minor groove-binding architectural proteins: structure, function, and DNA recognition Annu Rev Biophys Biomol Struct 27 105 131 9646864 10.1146/annurev.biophys.27.1.105 1:CAS:528: DyaK1cXktVSlt7c%3D (Pubitemid 28286011)
6. R Bollhagen M Schmiedberger K Barlos E Grell 1994 A new reagent for the cleavage of fully protected peptides synthesised on 2-chlorotrityl chloride resin J Chem Soc Chem Commun 22 2260 2559
7. K Drlica J Rouviere-Yaniv 1987 Histonelike proteins of bacteria Microbiol Rev 51 301 319 3118156 1:CAS:528:DyaL2sXmtlaltbk%3D
8. RS Erdmann M Kümin H Wennemers 2009 (4R)- and (4S)-Azidoprolines- conformation directing amino acids and sites for functionalization Chimia 63 197 200 10.2533/chimia.2009.197 1:CAS:528:DC%2BD1MXmtVals7Y%3D
9. D Fernandez-Forner G Gasals E Navarro H Ryder F Albericio 2001 Solid-phase synthesis of 4-aminopiperidine analogues using the Alloc protecting group: an investigation of Alloc removal from secondary amines Tetrahedron Lett 42 4471 4474 10.1016/S0040-4039(01)00755-9 1:CAS:528:DC%2BD3MXksFOjt7w%3D (Pubitemid 32537722)
10. M Filutowicz K Appelt 1988 The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K γ origin and is essential for replication Nucl Acids Res 16 3829 3843 2967465 10.1093/nar/16.9.3829 1:CAS:528:DyaL1cXktFOrsrk%3D
11. GH Fisher DI Marlborough JW Ryan AM Felix 1978 L-3,4-Dehydroproline analogs of bradykinin Arch Biochem Biophys 189 81 85 708052 10.1016/0003- 9861(78)90116-9 1:CAS:528:DyaE1cXlsVSrsL0%3D
12. DI Friedman 1988 Integration host factor: a protein for all reasons Cell 55 545 554 2972385 10.1016/0092-8674(88)90213-9 1:CAS:528:DyaL1MXjsFeruw%3D%3D
13. A Grove TC Saavedra 2002 The role of surface-exposed lysines in wrapping about the bacterial histone-like protein HU Biochemistry 41 7597 7603 12056890 10.1021/bi016095e 1:CAS:528:DC%2BD38Xjs12htLk%3D (Pubitemid 34627786)
14. MG Hinds JH Welsh DM Brennand M Fisher MJ Glennie NGJ Richards DL Turner JA Robinson 1991 Synthesis, conformational properties, and antibody recognition of peptides containing β-turn mimetics based on α-alkylproline derivatives J Med Chem 34 1777 1789 2061921 10.1021/jm00110a005 1:CAS:528:DyaK3MXkvFarur0%3D
15. JA Hodges RT Raines 2003 Stereoelectronic effects on collagen stability: the dichotomy of 4-fluoroproline diastereomers J Am Chem Soc 125 9262 9263 12889933 10.1021/ja035881z 1:CAS:528:DC%2BD3sXltlCksbo%3D (Pubitemid 36936025)
16. JC Horng RT Raines 2006 Stereoelectronic effects on polyproline conformation Protein Sci 15 74 83 16373476 10.1110/ps.051779806 1:CAS:528:DC%2BD28XktlSrtw%3D%3D (Pubitemid 43004235)
17. RM Hughes ML Benshoff ML Waters 2007 Effects of chain length and N-methylation on a cation-π interaction in a β-hairpin peptide Chem Eur J 13 5753 5764 17431866 10.1002/chem.200601753 1:CAS:528:DC%2BD2sXotVaktb0%3D (Pubitemid 47117397)
18. W Kim KI Hardcastle VP Conticello 2006 Fluroproline flip-flop: regiochemical reversal of a stereoelectronic effect on peptide and protein structures Angew Chem 118 8321 8325 10.1002/ange.200603227
19. A Lesarri EJ Cocinero JC López JL Alonso 2005 Shape of (4S)- and (4R)-hydroxyproline in gas phase J Am Chem Soc 127 2572 2579 15725012 10.1021/ja045955m 1:CAS:528:DC%2BD2MXptlSnsA%3D%3D (Pubitemid 40330928)
20. EK Liebler U Diederichsen 2004 From IHF protein to design and synthesis of a sequence-specific DNA bending peptide Org Lett 6 2893 2896 15330641 10.1021/ol049016a 1:CAS:528:DC%2BD2cXlvVartbk%3D (Pubitemid 39178034)
21. M Lorenz A Hillisch SD Goodman S Diekman 1999 Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer Nucl Acids Res 27 4619 4625 10556318 10.1093/nar/27.23.4619 1:CAS:528:DyaK1MXnvVanu78%3D
22. L Moitoso de Vargas S Kim A Landy 1989 DNA looping generated by two bending protein IHF and two domains of lambda integrase Science 244 1457 1461 2544029 10.1126/science.2544029 1:CAS:528:DyaL1MXksFars7o%3D (Pubitemid 19171678)
23. D Naduthambi NJ Zondlo 2006 Stereoelectronic tuning of the structure and stability of the Trp cage miniprotein J Am Chem Soc 128 12430 12431 16984189 10.1021/ja0648458 1:CAS:528:DC%2BD28XptFaiurk%3D (Pubitemid 44476629)
24. DE Pettijohn 1988 Histone-like proteins and bacterial chromosome structure J Biol Chem 263 12793 12796 3047111 1:CAS:528:DyaL1cXmtVKku7s%3D
25. C Renner S Alefelder JH Bae N Budisa R Huber L Moroder 2001 Fluoroprolines as tools for protein design and engineering Angew Chem Int Ed 40 923 925 10.1002/1521-3773(20010302)40:5<923::AID-ANIE923>3.0.CO;2-# 1:CAS:528:DC%2BD3MXitFWgu74%3D (Pubitemid 32225503)
26. PA Rice 1997 Making DNA do a U-turn: IHF and related proteins Curr Opin Struct Biol 7 86 93 9032059 10.1016/S0959-440X(97)80011-5 1:CAS:528: DyaK2sXhtleqtrk%3D (Pubitemid 27092383)
27. PA Rice S Yang K Mizuuchi HA Nash 1996 Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn Cell 87 1295 1306 8980235 10.1016/S0092-8674(00)81824-3 1:CAS:528:DyaK2sXit12jtg%3D%3D (Pubitemid 27010112)
28. F Ruan Y Chen K Itoh T Sasaki PB Hopkins 1991 Synthesis of peptides containing unnatural, metal-ligating residues: aminodiacetic acid as a peptide side chain J Org Chem 56 4347 4354 10.1021/jo00014a006 1:CAS:528: DyaK3MXksFShtLo%3D
29. MD Shoulders JA Hodges RT Raines 2006 Reciprocity of steric and stereoelectronic effects in the collagen triple helix J Am Chem Soc 128 8112 8113 16787056 10.1021/ja061793d 1:CAS:528:DC%2BD28XltlSns74%3D (Pubitemid 43967736)
30. LS Sonntag S Schweizer C Ochsenfeld H Wennemers 2006 The "Azido Gauche Effect"-implications for the conformation of Azidoprolines J Am Chem Soc 128 14697 14703 17090057 10.1021/ja0654938 1:CAS:528:DC%2BD28XhtFWju7vM (Pubitemid 44749873)
31. KK Swinger PA Rice 2004 IHF and HU: flexible architects of bent DNA Curr Opin Struct Biol 14 28 35 15102446 10.1016/j.sbi.2003.12.003 1:CAS:528:DC%2BD2cXhsFWru7k%3D (Pubitemid 38249589)
32. D Ussery TS Larsen KT Wilkes C Friis P Worning A Krogh S Brunak 2001 Genome organisation and chromatin structure in Escherichia coli Biochimie 83 201 212 11278070 10.1016/S0300-9084(00)01225-6 1:CAS:528:DC%2BD3MXitlWjtrk%3D (Pubitemid 32243565)
33. JH Welsh O Zerbe W von Philipsborn JA Robinson 1992 β-Turns induced in bradykinin by (S)-α-methylproline FEBS Lett 297 216 220 1544400 10.1016/0014-5793(92)80541-N 1:CAS:528:DyaK38XhvVyiurs%3D
34. HM Wu DM Crothers 1984 The locus of sequence-directed and protein-induced DNA bending Nature 308 509 513 6323997 10.1038/308509a0 1:CAS:528: DyaL2cXhvVKmtLk%3D (Pubitemid 14130840)