Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• between domains in the form of an α-helical coiled coil structure. The common motif has heptad repeats in the format (abcdefg)n, where the ‘a’ and ‘d’ positions are hydrophobic residues (with leucine being in the d position most of the times). These residues interact to form the coiled coil structure

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• shown as blue arrows. B) sMTL-13 (aa28-155), encoded by Rv1419, showed with 100% confidence sequence similarity to a ricin B-like lectin of Streptomyces olivaceoviridis, the sequence identity was 22%. C) Known domain structure of HBHA (Rv0475): Transmembrane domain (TM), coiled coil domain, and heparin

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• sequences preferentially. Moreno et al. reported a coiled-coil structure formed by the complex of the DNA duplex with pentamidine. The authors showed that the central part of the pentamidine binds to the minor groove, whereas the charged terminal amidine groups interact electrostatically with negatively

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• coiled-coil motifs as in Figure 6. If every a and d position of each individual helix is occupied by a hydrophobic amino acid, the helices can intertwine and bury their hydrophobic side groups into each other. This hydrophobic interaction that drives the formation of coiled-coil motifs can be further

• enhanced by electrostatic interactions between amino acids residing on the c and g positions of the α-helices. Ghadiri et al. showed that such coiled-coil peptides are capable of self-replication [35]. As depicted in Figure 7, helical polypeptides can act as a template for shorter peptide fragments by

• means of molecular recognition. The peptide building blocks again are ligated, resulting in the formation of a template duplex with a coiled-coil motif. When separated from the original template, a copy of the template is obtained. Initially these replicating systems were reported to show only parabolic

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• group. We explored a 26-residue coiled-coil peptide which undergoes a conformational transition to amyloid fibrils in 24 hours under physiological conditions [41], but remains random coil if one of three serine residues carries a phosphate group [27]. The aggregation process could be restored by

• Peptide model Peptide KFM6 follows a typical coiled-coil heptad repeat sequence and it includes five amino acids (-R-R-A-S-L-) in positions 20–24, in proximity to the C-terminus, that serve as the recognition motif for PKA. The crucial role of this recognition motif for efficient phosphorylation has long

• structure of KFM6. The nonpolar leucine residues at positions a and d contribute to thermal stability by hydrophobic core packing of the leucine zipper motif (“knobs-into-holes principle”). Charged amino acids at positions e, g, b, and c stabilize the coiled-coil by intramolecular electrostatic attractions

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• Strategies to achieve controlled nanoparticle aggregation have gained much interest, due to the versatility of such systems and their applications in materials science and medicine. In this article we demonstrate that coiled-coil peptide-induced aggregation based on electrostatic interactions is highly

• macrostructures. Keywords: coiled-coil peptides; α-helical fibrils; controlled aggregation; gold nanoparticles; multivalency; Introduction In the past few decades metal and semiconductor nanoparticles, including gold nanoparticles, have gained much interest due to their desirable optical, magnetic, and

• assembly [9]. Peptide-based nanoparticle aggregation was demonstrated first by Woolfson and coworkers by means of coiled-coil peptides that were immobilized on the nanoparticle surface [26]. Reversibility of the assembly formation, a key feature of a switchable system, has thus far been explored only for a

Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine

• Holger Erdbrink,
• Elisabeth K. Nyakatura,
• Susanne Huhmann,
• Ulla I. M. Gerling,
• Dieter Lentz,
• Beate Koksch and
• Constantin Czekelius

Beilstein J. Org. Chem. 2013, 9, 2009–2014, doi:10.3762/bjoc.9.236

• in solution, they are often stabilized in proteins by being wound around each other in a superhelix, a so-called coiled-coil arrangement, where hydrophobic side chain interactions are maximized within a helical interface. Coiled-coil structures are based on a (pseudo-) repetitive sequence (abcdefg)n

• [14][15]. Therefore, the preparation of enantiomerically pure fluorinated isoleucine analogues with retained α-helix propensity is of general interest for site-specific modification of coiled-coil positions in parallel packing arrangements, especially when solid phase peptide synthesis is employed

Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

• Raheleh Rezaei Araghi,
• Carsten C. Mahrenholz,
• Rudolf Volkmer and
• Beate Koksch

Beilstein J. Org. Chem. 2012, 8, 640–649, doi:10.3762/bjoc.8.71

• denaturation. Keywords: β- and γ-amino acids; coiled coil; foldamer; screening libraries; SPOT technique; Introduction Coiled-coil domains, which consist of two or more α-helices, are the most common representatives of α-helix-mediated protein–protein interactions, which regulate many important biological

• the concept of rational drug design based on coiled-coil proteins [6]. In this context, the use of unnatural amino acids in peptidomimetics is advisable, to enhance enzymatic stability, limit conformational flexibility, and improve pharmacodynamics and bioavailability [7]. In order to manipulate helix

• with α-peptides [11]. Therefore, elucidating the side-chain compositions responsible for selective intermolecular interactions in an otherwise natural coiled-coil assembly should facilitate the design of helix–helix interaction motifs. We broadly surveyed interaction properties in order to improve the

Chemical aminoacylation of tRNAs with fluorinated amino acids for in vitro protein mutagenesis

• Shijie Ye,
• Allison Ann Berger,
• Dominique Petzold,
• Oliver Reimann,
• Benjamin Matt and
• Beate Koksch

Beilstein J. Org. Chem. 2010, 6, No. 40, doi:10.3762/bjoc.6.40

• , enabling better diffusion across the membranes [16]. Koksch and co-workers have developed a model peptide system based on the coiled-coil folding motif. They used it to show that the impact of fluorine substitution on structure and stability is strongly dependent on the position and the number of fluorine