scholarly journals From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach

Soft Matter ◽  
2016 ◽  
Vol 12 (21) ◽  
pp. 4783-4793 ◽  
Author(s):  
Tatjana Škrbić ◽  
Artem Badasyan ◽  
Trinh Xuan Hoang ◽  
Rudolf Podgornik ◽  
Achille Giacometti
Keyword(s):  
Secondary Structures ◽  
Broken Symmetry ◽  
Side Chains ◽  
P Protein

Protein-like systems are studied using models of increasing complexity starting from a tangent-beads chain and gradually adding the possibility of overlapping for consecutive beads, as well the presence of additional smaller beads mimicking side chains, using Wang–Landau techniques.

In-Peptide Synthesis of Imidazolidin-2-one Scaffolds, Equippable with Proteinogenic or Taggable/Linkable Side Chains, General Promoters of Unusual Secondary Structures

2019 ◽  
Vol 84 (9) ◽  
pp. 4992-5004 ◽  
Author(s):  
Rossella De Marco ◽  
Junwei Zhao ◽  
Arianna Greco ◽  
Simone Ioannone ◽  
Luca Gentilucci
Keyword(s):  
Peptide Synthesis ◽  
Secondary Structures ◽  
Side Chains

scholarly journals Changes in Secondary Structures and Acidic Side Chains of Melibiose Permease upon Cosubstrates Binding

2006 ◽  
Vol 91 (12) ◽  
pp. 4440-4449 ◽  
Author(s):  
Xavier León ◽  
Raymonde Lemonnier ◽  
Gérard Leblanc ◽  
Esteve Padrós
Keyword(s):  
Secondary Structures ◽  
Side Chains

scholarly journals Two-dimensional infrared correlation spectroscopy studies on secondary structures and hydrogen bondings of side chains of proteins

2003 ◽  
Vol 17 (2-3) ◽  
pp. 79-100 ◽  
Author(s):  
Yukihiro Ozaki ◽  
Koichi Murayama ◽  
Yuqing Wu ◽  
Boguslawa Czarnik-Matusewicz
Keyword(s):  
Secondary Structures ◽  
Correlation Spectroscopy ◽  
Side Chains ◽  
Two Dimensional ◽  
2D Ir ◽  
Intensity Changes ◽  
Specific Order ◽  
Spectroscopy Studies ◽  
2D Correlation Spectroscopy ◽  
Hydrogen Bondings

This review paper reports usefulness of two-dimensional (2D) correlation spectroscopy in analyzing infrared (IR) spectra of proteins in aqueous solutions. In the 2D approach, spectral peaks are spread over the second dimension, thereby simplifying the visualization of complex spectra consisting of many overlapped bands, and enhancing spectral resolution. 2D correlation spectroscopy has a powerful deconvolution ability for highly overlapped amide I, amide II, and amide III bands of proteins, enabling these bands to be assigned to various secondary structures. It also provides the specific order of the spectral intensity changes taking place during the measurement on the value of controlling variable affecting the spectra. Therefore, one can monitor the order of secondary structure variations in proteins by using 2D IR correlation spectroscopy. 2D correlation spectroscopy also provides new insight into the hydrogen bondings of side chains of proteins. In this review the principles and advantages of 2D correlation spectroscopy are outlined first and then three examples of the applications of 2D IR spectroscopy to protein research are presented.

Synthesis, and Helix or Hairpin-Turn Secondary Structures of “Mixed” α/β-Peptides Consisting of Residues with Proteinogenic Side Chains and of 2-Amino-2-methylpropanoic Acid (Aib).

ChemInform ◽  
2006 ◽  
Vol 37 (49) ◽  
Author(s):  
Dieter Seebach ◽  
Bernhard Jaun ◽  
Radovan Sebesta ◽  
Raveendra I. Mathad ◽  
Oliver Floegel ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Side Chains

scholarly journals Structural Diversity of Peptoids: Tube-Like Structures of Macrocycles

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 150
Author(s):  
Claudine Nicole Herlan ◽  
Katharina Sommer ◽  
Patrick Weis ◽  
Martin Nieger ◽  
Stefan Bräse
Keyword(s):  
Structural Diversity ◽  
Secondary Structures ◽  
Side Chains ◽  
Guest Chemistry

Peptoids, or poly-N-substituted glycines, are characterised by broad structural diversity. Compared to peptides, they are less restricted in rotation and lack backbone-derived H bonding. Nevertheless, certain side chains force the peptoid backbone into distinct conformations. Designable secondary structures like helices or nanosheets arise from this knowledge. Herein, we report the copper-catalysed alkyne-azide cycloaddition (CuAAC) of macrocycles to form innovative tube-like tricyclic peptoids, giving access to host–guest chemistry or storage applications. Different linker systems make the single tubes tuneable in size and enable modifications within the gap. An azobenzene linker, which is reversibly switchable in conformation, was successfully incorporated and allowed for light-triggered changes of the entire tricyclic structure.

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