The Promiscuity of β-Strand Pairing Allows for Rational Design of β-Sheet Face Inversion

2008 ◽  
Vol 130 (44) ◽  
pp. 14370-14371 ◽  
Author(s):  
Koki Makabe ◽  
Shohei Koide
Keyword(s):  
Rational Design ◽  
Face Inversion ◽  
Sheet Face ◽  
Β Sheet

scholarly journals An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour

2016 ◽  
Vol 473 (19) ◽  
pp. 3269-3290 ◽  
Author(s):  
Neda Motamedi-Shad ◽  
Alistair M. Jagger ◽  
Maximilian Liedtke ◽  
Sarah V. Faull ◽  
Arjun Scott Nanda ◽  
...  
Keyword(s):  
Rational Design ◽  
Conformational Transition ◽  
Structural Basis ◽  
Linear Polymers ◽  
Single Chain ◽  
Opposite Face ◽  
Induced Changes ◽  
Β Sheet ◽  
Chain Form ◽  
Antiprotease Activity

Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A — on the opposite face of the molecule — more liable to adopt an ‘open’ state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin–enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the ‘open’ state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation.

Controlling the Morphology of Cross β-Sheet Assemblies by Rational Design

2005 ◽  
Vol 127 (23) ◽  
pp. 8562-8570 ◽  
Author(s):  
Songpon Deechongkit ◽  
Evan T. Powers ◽  
Shu-Li You ◽  
Jeffery W. Kelly
Keyword(s):  
Rational Design ◽  
Β Sheet

The fabrication of self-assembling peptides into nanofiber scaffolds through molecular self-assembly

2004 ◽  
Vol 820 ◽  
Author(s):  
Xiaojun Zhao ◽  
Jessica Dai ◽  
Shuguang Zhang
Keyword(s):  
Cell Cultures ◽  
Self Assembly ◽  
Rational Design ◽  
Biophysical Properties ◽  
Ph Values ◽  
Nanofiber Scaffold ◽  
Self Assembling ◽  
Nanofiber Scaffolds ◽  
D Cell ◽  
Β Sheet

AbstractWe designed and fabricated a class of self-assembling peptides into nanofiber scaffolds. KLDL-12 has been shown to be a permissible nanofiber scaffold for chondrocytes in cartilage 3-D cell cultures. However, the biochemical, structural, and biophysical properties of KLDL- 12 remain unclear. We show that KLDL-12 peptides form stable β-sheet structures at different pH values and that KLDL-12 and RIDI-12 self-assemble into nanofibers. The nanofiber length, though, is sensitive to pH changes. These results not only suggest the importance of electrostatic attraction or repulsion affecting the fiber lengths but also provide us with useful information for rational design and fabrication of peptide scaffolds.

scholarly journals A rational design to create hybrid β-sheet breaker peptides to inhibit aggregation and toxicity of amyloid-β

MedChemComm ◽  
2011 ◽  
Vol 2 (1) ◽  
pp. 60-64 ◽  
Author(s):  
Ilona B. Bruinsma ◽  
Anna Karawajczyk ◽  
Gijs Schaftenaar ◽  
Robert M. W. de Waal ◽  
Marcel M. Verbeek ◽  
...  
Keyword(s):  
Rational Design ◽  
Amyloid Β ◽  
Β Sheet

The fabrication of self-assembling peptides into nanofiber scaffolds through molecular self-assembly

2004 ◽  
Vol 823 ◽  
Author(s):  
Xiaojun Zhao ◽  
Jessica Dai ◽  
Shuguang Zhang
Keyword(s):  
Cell Cultures ◽  
Self Assembly ◽  
Rational Design ◽  
Biophysical Properties ◽  
Ph Values ◽  
Nanofiber Scaffold ◽  
Self Assembling ◽  
Nanofiber Scaffolds ◽  
D Cell ◽  
Β Sheet

AbstractWe designed and fabricated a class of self-assembling peptides into nanofiber scaffolds. KLDL-12 has been shown to be a permissible nanofiber scaffold for chondrocytes in cartilage 3-D cell cultures. However, the biochemical, structural, and biophysical properties of KLDL-12 remain unclear. We show that KLDL-12 peptides form stable β-sheet structures at different pH values and that KLDL-12 and RIDI-12 self-assemble into nanofibers. The nanofiber length, though, is sensitive to pH changes. These results not only suggest the importance of electrostatic attraction or repulsion affecting the fiber lengths but also provide us with useful information for rational design and fabrication of peptide scaffolds.

Rational Design of β-Sheet Ligands Against Aβ42-Induced Toxicity

2011 ◽  
Vol 133 (12) ◽  
pp. 4348-4358 ◽  
Author(s):  
Katrin Hochdörffer ◽  
Julia März-Berberich ◽  
Luitgard Nagel-Steger ◽  
Matthias Epple ◽  
Wolfgang Meyer-Zaika ◽  
...  
Keyword(s):  
Rational Design ◽  
Β Sheet

scholarly journals De novo rational design of a freestanding, supercharged polypeptide, proton-conducting membrane

2020 ◽  
Vol 6 (29) ◽  
pp. eabc0810 ◽  
Author(s):  
Chao Ma ◽  
Jingjin Dong ◽  
Marco Viviani ◽  
Isotta Tulini ◽  
Nicola Pontillo ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Rational Design ◽  
De Novo ◽  
Proton Translocation ◽  
Proton Conduction ◽  
Device Fabrication ◽  
Proton Conducting ◽  
Intrinsically Disordered ◽  
Design Paradigm ◽  
Β Sheet

Proton translocation enables important processes in nature and man-made technologies. However, controlling proton conduction and fabrication of devices exploiting biomaterials remains a challenge. Even more difficult is the design of protein-based bulk materials without any functional starting scaffold for further optimization. Here, we show the rational design of proton-conducting, protein materials exceeding reported proteinaceous systems. The carboxylic acid–rich structures were evolved step by step by exploring various sequences from intrinsically disordered coils over supercharged nanobarrels to hierarchically spider β sheet containing protein-supercharged polypeptide chimeras. The latter material is characterized by interconnected β sheet nanodomains decorated on their surface by carboxylic acid groups, forming self-supportive membranes and allowing for proton conduction in the hydrated state. The membranes showed an extraordinary proton conductivity of 18.5 ± 5 mS/cm at RH = 90%, one magnitude higher than other protein devices. This design paradigm offers great potential for bioprotonic device fabrication interfacing artificial and biological systems.

Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey
Keyword(s):  
Nucleic Acid ◽  
Boron Nitride ◽  
Nucleic Acids ◽  
Dynamic Stability ◽  
Peptide Nucleic Acid ◽  
Rational Design ◽  
Peptide Nucleic Acids ◽  
Boron Nitride Nanotubes ◽  
Molecular Hybrids ◽  
Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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