Publication

Molecular modeling and design of regioselectively addressable functionalized templates with rigidified three-dimensional structures

1999
Journal Articles

Abstract

Extensive conformational analysis of a series of beta-alkyl substituted cyclopeptides-cyclo(Pro(1)-Xaa(2)-Nle(3)-Ala(4)-Nle(5)-Pro(6) Xaa(7)-Nle(8)-Ala(9)-Nle(10)) and cyclo[Pro(1)-Xaa(2)-Nle(3)-(Cys(4)-Nle(5)-Pro(6)-Xaa(7)-Nle(8)-Cys(9))-N le(10)] as well as their corresponding unsubstituted core structures cyclo(Pro(1)-Xaa(2)-Ala(3)-Cys(4)-Ala(5)-Pro(6)-Xaa(7)-Ala(8)-Ala(9)-Ala (10)) and cyclo(Pro(1)-Xaa(2)-Ala(3)-Cys(4)-Ala(5)-Pro(6)-Xaa(7)-Ala(8)-Cys(9)-Ala (10)) has been performed employing both the ECEPP/2 and the MAB force fields (Xaa = Gly, L-Ala, D-Ala, Aib, and D-Pro). Results show that (a) possible three-dimensional structures of the cyclo(Pro(1)-Gly(2)-Lys(3)-Ala(4)-Lys(5)-Pro(6)-Gly(7)-Lys(8)-Ala(9)-Lys (10)) molecule are nor limited to a single extended "rectangular" conformation with all Lys side chains oriented at the same side of the molecule; (b) conformational equilibrium in monocyclic analogues obtained by replacements of conformationally flexible Gly residues for L-Ala, D-Ala, Aib, or D-Pro is not significantly shifted towards the target "rectangular" conformational type; and (c) introduction of disulfide bridges between positions 4 and 9 is a very powerful way to stabilize the target conformations in the resulting bicyclic molecules. These findings form the basis for further design of rigidified regioselectively addressable functionalized templates with many application areas ranging from biostructural to diagnostic purposes. (C) 1999 John Wiley & Sons, Inc.

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https://infoscience.epfl.ch/entities/publication/35e7a325-16f1-4b90-85a0-4dfc08c0ace7

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1999
Journal Articles

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/35e7a325-16f1-4b90-85a0-4dfc08c0ace7

About this result

Related concepts (30)

Protein structure

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.

Protein dynamics

Proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.

Cyclic compound

A cyclic compound (or ring compound) is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where all the atoms are carbon (i.e., are carbocycles), none of the atoms are carbon (inorganic cyclic compounds), or where both carbon and non-carbon atoms are present (heterocyclic compounds with rings containing both carbon and non-carbon).

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Molecular modeling and design of regioselectively addressable functionalized templates with rigidified three-dimensional structures

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