Exploiting diverse stereochemistry of b-amino acids: Toward a rational design of sheet-forming b-peptide systems

Amino Acids

Volumn 43, Issue 2, 2012, Pages 735-749

  Pohl, Gabor ^a   Beke Somfai, Tamas ^a   Csizmadia, Imre G ^a,b   Perczel, András ^a,c  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b UNIVERSITY OF TORONTO   (Canada)

^c Open Laboratory of Protein Science   (Hungary)

Author keywords

B amino acid; B peptide; Chirality; Computational chemistry; Foldamer; Sheet structures

Indexed keywords

3 AMINO 2,3 DIMETHYLPROPANOIC ACID; 3 AMINOPROPANOIC ACID; BETA AMINO ACID; BETA PEPTIDE; CARBENE; METHYL GROUP; PEPTIDE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BETA SHEET; CHIRALITY; COMPUTER ANALYSIS; CONTROLLED STUDY; ENANTIOMER; HYDROGEN BOND; INTERMETHOD COMPARISON; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; STEREOCHEMISTRY; THERMODYNAMICS; VALIDATION STUDY;

BETA-ALANINE; COMPUTER SIMULATION; HEPTANES; HYDROGEN BONDING; MODELS, MOLECULAR; OLIGOPEPTIDES; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; SOLVENTS; STEREOISOMERISM; THERMODYNAMICS; WATER;

PANDANUS TECTORIUS;

EID: 84864760631     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-011-1124-7     Document Type: Article

References (25)

1. Beke T, Csizmadia IG, Perczel A (2004) Toward a rational design of beta-peptide structures. J Comp Chem 25:285-307
2. Beke T, Somlai C, Perczel A (2006a) Theoretical study on tertiary structural elements of beta-peptides: Nanotubes formed from parallel-sheet- derived assemblies of beta-peptides. J Comp Chem 27:20-38
3. Beke T, Csizmadia IG, Perczel A (2006b) On the flexibility of betapeptides. J Am Chem Soc 128:5158-5167
4. Chung YJ, Huck BR, Christianson LA, Stanger HE, Krauthauser S, Powell DR, Gellman SH (2000) Stereochemical control of hairpin formation in beta-peptides containing dinipecotic acid reverse turn segments. J Am Chem Soc 122:3995-4004
5. Daura X, Gademann K, Schafer H, Jaun B, Seebach D, van Gunsteren WF (2001) The beta-peptide hairpin in solution: Conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation. J Am Chem Soc 123:2393-2404
6. Durani S (2008) Protein Design with L-and D-alpha-Amino Acid Structures as the Alphabet. Acc Chem Res 41:1301-1308
7. Frackenpohl J, Arvidsson PI, Schreiber JV, Seebach D (2001) The outstanding biological stability of beta-and gamma-peptides toward proteolytic enzymes: An in vitro investigation with fifteen peptidases. Chem Bio Chem 2:445-455
8. Gaussian 03, Revision C.02, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian, Inc., Wallingford CT
9. Günther R, Hofmann H-J (2002) Theoretical prediction of substituent effects on the intrinsic folding properties of beta-peptides. Helv Chim Acta 85:2149-2168
10. Günther R, Hofmann H-J, Kuczera K (2001) Searching for periodic structures in beta-peptides. J Phys Chem B 105:5559-5567
11. Karle I, Gopi HN, Balaram P (2002) Infinite pleated beta-sheet formed by the beta-hairpin Boc-beta-Phe-beta-Phe-D-Pro-Glybeta-Phe-beta-Phe-OMe PNAS. Proc Natl Acad Sci USA 99:5160-5164
12. Krauthauser S, Christianson LA, Powell DR, Gellman SH (1997) Antiparallel sheet formation in beta-peptide foldamers: Effects of beta-amino acid substitution on conformational preference. J Am Chem Soc 119:11719-11720
13. Lin J-Q, Luo S-W, Wu Y-D (2002) Theoretical study of sheets formed by beta-Peptides. J Comput Chem 23:1551-1558
14. Mandity IM, Weber E, Martinek TA, Olajos G, Tóth GK, Vass E, Fülöp F (2009) Design of Peptidic Foldamer Helices: A Stereochemical Patterning Approach. Angew Chem Int Ed 48:2171-2175
15. Martinek TA, Fülöp F (2003) Side-chain control of beta-peptide secondary structures-Design principles. Eur J Biochem 270: 3657-3666
16. Martinek TA, Tóth GK, Vass E, Hollósi M, Fülöp F (2002) cis-2-aminocyclopentanecarboxylic acid oligomers adopt a sheetlike structure: Switch from helix to nonpolar strand. Angew Chem Int Ed 41:1718
17. Möhle K, Günther R, Thormann M, Sewald N, Hofmann H-J (1999) Basic conformers in beta-peptides. Biopolymers 50:167-184
18. Pohl G, Beke T, Csizmadia IG, Perczel A (2010) Extended Apolar beta-Peptide Foldamers: The Role of Axis Chirality on beta-Peptide Sheet Stability. J Phys Chem B 114:9338-9348
19. Seebach D (2004) The world of beta-and gamma-peptides comprised of homologated proteinogenic amino acids and other components. Chem Biodivers 1:1111-1239
20. Seebach D, Abele S, Gademann K, Jaun B (1999) Pleated sheets and turns of beta-peptides with proteinogenic side chains. Angew Chem Int Ed 38:1595-1597
21. Sharma GVM, Reddy KR, Krishna PR, Sankar AR, Narsimulu K, Kumar SK, Jayaprakash P, Jagannadh B, Kunwar AC (2003) Robust mixed 10/12 helices promoted by alternating chirality in a new family of C-linked carbo-beta-peptide. J Am Chem Soc 125:13670-13671
22. Sharma GVM, Chandramouli N, Choudhary M, Nagendar P, Ramakrishna KVS, Kunwar AC, Schramm P, Hofmann H-JJ (2009) Hybrid Helices: Motifs for Secondary Structure Scaffolds in Foldamers. Am Chem Soc 131:17335-17344
23. Stenberg P, Luthman K, Artirsson P (1999) Prediction of membrane permeability to peptides from calculated dynamic molecular surface properties. Pharm Res 16:205-212
24. Tomasi J, Persico M (1994) Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent. Chem Rev 94:2027-2094
25. Wu Y-D, Wang D-P (1998) Theoretical studies of beta-peptide models. J Am Chem Soc 120:13485-13493