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
2016 ◽  
Vol 473 (19) ◽  
pp. 3269-3290 ◽  
Author(s):  
Neda Motamedi-Shad ◽  
Alistair M. Jagger ◽  
Maximilian Liedtke ◽  
Sarah V. Faull ◽  
Arjun Scott Nanda ◽  
...  

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.


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

2004 ◽  
Vol 820 ◽  
Author(s):  
Xiaojun Zhao ◽  
Jessica Dai ◽  
Shuguang Zhang

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.


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):  

2004 ◽  
Vol 823 ◽  
Author(s):  
Xiaojun Zhao ◽  
Jessica Dai ◽  
Shuguang Zhang

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.


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

2020 ◽  
Vol 6 (29) ◽  
pp. eabc0810 ◽  
Author(s):  
Chao Ma ◽  
Jingjin Dong ◽  
Marco Viviani ◽  
Isotta Tulini ◽  
Nicola Pontillo ◽  
...  

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.


2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey

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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