Basic conformers in ?-peptides

Möhle, Kerstin; Günther, Robert; Thormann, Michael; Sewald, Norbert; Hofmann, Hans‐Jörg

doi:10.1002/(sici)1097-0282(199908)50:2<167::aid-bip6>3.0.co;2-m

Biopolymers

1999

DOI: 10.1002/(sici)1097-0282(199908)50:2<167::aid-bip6>3.0.co;2-m

|View full text |Cite

Basic conformers in ?-peptides

Kerstin Möhle

Robert Günther²,

Michael Thormann³

et al.

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...

Citation Types

Supporting

Mentioning

Contrasting

Year Published

2000

2004

Publication Types

Select...

Article5

Relationship

Self Cite0

Independent5

Authors

Journals

Cited by 136 publications

(36 citation statements)

References 62 publications

(76 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1). Moreover, these data support considerably the results from previous studies showing that substitutions at C(b) have a higher impact on the backbone flexibility than substitutions at C(a) [70]. Due to the geminal disubstitution with the same substituents in aA and bB, each minimum conformation of these compounds has an energetically equivalent mirror-image conformer, whose torsion angles differ only by sign.…”

supporting

confidence: 88%

“…Possibly, a greater influence on structuring could be expected from substituents at C(b) affecting f, than from substituents at C(a) influencing y. This conclusion is clearly confirmed by the torsion-angle data for the conformers of the monosubstituted b-amino acid model compounds A and B presented in our preceding paper ( [70], cf. also [71] [72]).…”

supporting

confidence: 61%

“…5. As already pointed out in our previous study on the U, A, and B monomers [70], oligomers of the various C 6 conformations could easily be thought of, since Hbonding occurs within the same b-amino acid unit (1 3 1 interaction, nomenclature according to [92]). Periodic structures of C 6 conformers could formally be described as H 6 helices, although they are more sheet-or ladder-like.…”

mentioning

confidence: 87%

“…Although the H-bonded pseudocycle involves three residues (1 2 3 interaction), nonperiodic and periodic oligomers can be constructed from all C 8 conformers in any combination. A periodic secondary structure consisting of four C I 8 units (H 8 ) of the C(b)-monosubstituted b-amino acid B was predicted by ab initio calculations to be of comparable stability to the experimentally determined H 14 and H 12 helices [70]. Oligomerization of C II 8 conformers such as aA2 leads to a twisted sheet-like structure, which formally could also be considered as an H 8 helix.…”

mentioning

confidence: 91%

“…± To examine the influence of disubstitution, systematic conformational analyses on the blocked b-amino acid monomers aA, bB, aB, and AB were performed in analogy to the procedure previously described in the investigations of the unsubstituted compound U and the monosubstituted derivatives A and B [70]. In our notation, the small letters a and b designate Me substituents in (R)-configuration at the C(a) and C(b) backbone atoms, respectively, and the capital letters A and B Me substituents in the corresponding (S)-configurations (cf.…”

mentioning

confidence: 99%

See 4 more Smart Citations

Theoretical Prediction of Substituent Effects on the Intrinsic Folding Properties of β-Peptides

Günther

Hofmann

2002

HCA

View full text Add to dashboard Cite

Dedicated to Prof. Dr. Peter Welzel on the occasion of his 65th birthday A systematic conformational analysis on blocked b-amino acids as constituents of b-peptides by ab initio MO theory reveals that the conformer pool of b-peptide monomers is essentially determined by the conformation of simple submonomer fragments. The influence of single and multiple substitutions at the C(a) and C(b) backbone atoms on the intrinsic folding properties of the monomers was estimated both in the singlemolecule approximation and in a polar solvent continuum, applying a quantum-chemical SCRF model. Substitution at C(b) has a higher impact on the b-amino acid conformation than a substitution at C(a). It can be shown that the conformations of important periodic secondary structures in b-peptides belong to the conformer pool of the monomers, even for those secondary-structure elements where H-bond formation appears only in longer sequences. Rules for design of special secondary-structure types by selection of an actual substituent pattern in the b-amino acid constituents have been derived within the monomer approach.1. Introduction. ± In recent years, oligomers of b-amino acids, called b-peptides, have gained much attraction because of their ability to form well-ordered secondary structures [1 ± 6], e.g., b-strand-like conformers [7 ± 9], reverse turns [10 ± 14], and, in particular, helices with differing H-bonding patterns [15 ± 34]. Some representatives are stable against proteases [35 ± 37] and can be translocated across the cell membrane [38] [39], which makes b-peptides possible candidates for pharmacological applications [40 ± 49]. In comparison to a-amino acid constituents, b-amino acids offer a much greater number of different substituent patterns, which should influence the secondarystructure formation in peptide sequences. Therefore, it might be useful to look for the intrinsic folding properties in b-peptide models with substituents in various positions.It is a tempting approach to derive the characteristic secondary structures in peptide sequences from the conformational properties of the monomer constituents (monomer approach). Numerous systematic conformational analyses on blocked a-amino acids and unnatural amino acids have been reported [50 ± 74]. These theoretical studies, employing molecular-orbital (MO) theory and empirical force fields, indicate that most of the typical secondary structures found in peptides and proteins already belong to the conformer pool of the monomers. This concerns even those secondary-structure elements that are characterized by H-bond formation between amino acid residues that are more or less distant in the sequence. Obviously, H-bonds may significantly influence the stability relationships between competing folding alternatives, but they are not the driving force for the formation of the corresponding conformers themselves.

show abstract

supporting

confidence: 88%

supporting

confidence: 61%

mentioning

confidence: 87%

mentioning

confidence: 91%

mentioning

confidence: 99%

See 3 more Smart Citations

Theoretical Prediction of Substituent Effects on the Intrinsic Folding Properties of β-Peptides

Günther

Hofmann

2002

HCA

View full text Add to dashboard Cite

show abstract

Improved treatment of cyclic ?-amino acids and successful prediction of ?-peptide secondary structure using a modified force field: AMBER*C

et al. 2000

View full text Add to dashboard Cite

We added parameters to the AMBER* force field to model cyclic β‐amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon–carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of trans‐2‐aminocyclohexanecarboxylic acid (trans‐ACHC) and trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen‐bonding tendencies of simple diamide derivatives of trans‐ACHC and trans‐ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by β‐amino acid homo‐oligomers. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 763–773, 2000

show abstract

Reversible peptide folding: Dependence on molecular force field used

Damm¹,

Gunsteren²

2000

J. Comput. Chem.

View full text Add to dashboard Cite

Temperature‐dependent nuclear magnetic resonance (NMR) and CD spectra of methanol solutions of a β‐heptapeptide have been interpreted in such a way that the secondary structure, a 314‐helix, is assumed to be stable in a temperature range of between 298 and 393 K. This is in contrast to the results of a 50‐ns molecular dynamics simulation using the GROMOS96 force field, which found a melting temperature of about 340 K. This discrepancy is addressed by further computational studies using the OPLS‐AA force field. The conformational energetics of N‐formyl‐3‐aminobutanamide in vacuo are obtained using ab initio and density functional quantum‐mechanical calculations at the HF/6‐31G*, B3LYP/6‐31G*, and B3LYP/6‐311+G* levels of theory. The results permit development of torsional parameters for the OPLS‐AA force field that reproduce the conformational energetics of the monomer. By varying the development procedure, three parameter sets are obtained that focus on reproducing either low‐energy or high‐energy conformations. These parameter sets are tested by simulating the reversible folding of the β‐heptapeptide in methanol. The melting temperature of the helix formed (>360 K) is found to be higher than the one obtained from simulations using the GROMOS96 force field (∼340 K). Differences in the potential energy functions of the latter two force fields are evaluated and point to the origins of the difference in stability. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 774–787, 2000

show abstract

scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.

Contact Info

customersupport@researchsolutions.com

10624 S. Eastern Ave., Ste. A-614

Henderson, NV 89052, USA

Blog Terms and Conditions API Terms Privacy Policy Contact Cookie Preferences Do Not Sell or Share My Personal Information

Made with 💙 for researchers

Part of the Research Solutions Family.

Basic conformers in ?-peptides

Cited by 136 publications

References 62 publications

Theoretical Prediction of Substituent Effects on the Intrinsic Folding Properties of β-Peptides

Theoretical Prediction of Substituent Effects on the Intrinsic Folding Properties of β-Peptides

Improved treatment of cyclic ?-amino acids and successful prediction of ?-peptide secondary structure using a modified force field: AMBER*C

Reversible peptide folding: Dependence on molecular force field used

Contact Info

Product

Resources

About