iPEP: peptides designed and selected for interfering with protein interaction and function

2008 ◽  
Vol 36 (6) ◽  
pp. 1442-1447 ◽  
Author(s):  
Jody M. Mason ◽  
Kristian M. Müller ◽  
Katja M. Arndt
Keyword(s):  
Protein Interaction ◽  
Electrostatic Interactions ◽  
Rational Design ◽  
Protein Fragment ◽  
Hydrophobic Collapse ◽  
Helix Formation ◽  
Protein Fragment Complementation ◽  
Folding Pathways ◽  
Library Screen ◽  
And Function

Semi-rational design is combined with PCAs (protein-fragment complementation assays) and phage-display screening techniques to generate a range of iPEPs (interfering peptides) that target therapeutically relevant proteins with much higher interaction stability than their native complexes. PCA selection has been improved to impose a competitive and negative design initiative on the library screen, thus simultaneously improving the specificity of assay ‘winners’. The folding pathways of designed pairs imply that early events are dominated by hydrophobic collapse and helix formation, whereas later events account for the consolidation of more intricate intermolecular electrostatic interactions.

scholarly journals Correction: Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor

2021 ◽  
Author(s):  
Kaho Suzuki ◽  
Yousuke Takaoka ◽  
Minoru Ueda
Keyword(s):  
Transcription Factor ◽  
Protein Interaction ◽  
Rational Design ◽  
Protein Protein Interaction ◽  
Inhibiting Protein

Correction for ‘Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor’ by Kaho Suzuki et al., RSC Chem. Biol., 2021, DOI: 10.1039/d0cb00204f.

scholarly journals Tunable assembly of amyloid-forming peptides into nanosheets as a retrovirus carrier

2015 ◽  
Vol 112 (10) ◽  
pp. 2996-3001 ◽  
Author(s):  
Bin Dai ◽  
Dan Li ◽  
Wenhui Xi ◽  
Fang Luo ◽  
Xiang Zhang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Rational Design ◽  
Structural Model ◽  
Amyloid Fibril ◽  
Computational Approaches ◽  
Retroviral Transduction ◽  
And Function

Using and engineering amyloid as nanomaterials are blossoming trends in bionanotechnology. Here, we show our discovery of an amyloid structure, termed “amyloid-like nanosheet,” formed by a key amyloid-forming segment of Alzheimer’s Aβ. Combining multiple biophysical and computational approaches, we proposed a structural model for the nanosheet that is formed by stacking the amyloid fibril spines perpendicular to the fibril axis. We further used the nanosheet for laboratorial retroviral transduction enhancement and directly visualized the presence of virus on the nanosheet surface by electron microscopy. Furthermore, based on our structural model, we designed nanosheet-forming peptides with different functionalities, elucidating the potential of rational design for amyloid-based materials with novel architecture and function.

Models of cooperativity in protein folding

1995 ◽  
Vol 348 (1323) ◽  
pp. 61-70 ◽  
Keyword(s):  
Protein Folding ◽  
Molten Globule ◽  
Core Collapse ◽  
Hydrophobic Core ◽  
Model Studies ◽  
Helix Formation ◽  
Collapse Model ◽  
Folding Pathways ◽  
State Behaviour ◽  
Denatured States

What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In ‘helix-coil’ theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the folding pathways. 2. In the ‘sidechain packing’ model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the ‘hydrophobic core collapse’ model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.

scholarly journals Rational design of a stapled JAZ9 peptide inhibiting protein–protein interaction of a plant transcription factor

2021 ◽  
Author(s):  
Kaho Suzuki ◽  
Yousuke Takaoka ◽  
Minoru Ueda
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Protein Interaction ◽  
Rational Design ◽  
Master Regulators ◽  
Jasmonate Signaling ◽  
Protein Protein Interaction ◽  
Inhibiting Protein

A rationally designed stapled JAZ peptide selectively inhibited MYCs, master-regulators of the jasmonate signaling in Arabidopsis thaliana. It is proposed as a novel chemical tool for the analysis of MYC related jasmonate signaling.

Rational Design of Organic Electro-Optic Materials

2001 ◽  
Vol 708 ◽  
Author(s):  
Alex Jen ◽  
Robert Neilsen ◽  
Bruce Robinson ◽  
William H. Steier ◽  
Larry Dalton
Keyword(s):  
Wavelength Division Multiplexing ◽  
Material Properties ◽  
Electrostatic Interactions ◽  
Rational Design ◽  
Elevated Temperatures ◽  
Optical Loss ◽  
Quality Factors ◽  
Electro Optic ◽  
Lattice Hardening

ABSTRACTA number of material properties must be optimized before organic electro-optic materials can be used for practical device applications. These include electro-optic activity, optical transparency, and stability including both thermal and photochemical stability. Exploiting an improved understanding of the structure/function relationships, we have recently prepared materials exhibiting electro-optic coefficients of greater than 50 pm/V and optical loss values of less than 0.7 dB/cm at the telecommunication wavelengths of 1.3 and 1.55 microns. When oxygen is excluded to a reasonable extent, long-term photostability to optical power levels of 20 mW has been observed. Photostability is further improved by addition of scavengers and by lattice hardening. Long-term (greater than 1000 hours) thermal stability of poling-induced electro-optic activity is also observed at elevated temperatures (greater than 80°C) when appropriate lattice hardening is used. The successful improvement of organic electro-optic materials rests upon (1) attention to the design of chromophore structure including design to inhibit unwanted intermolecular electrostatic interactions and to improve chromophore instability and (2) attention to processing conditions including those involved in spin casting, electric field poling, and lattice hardening. A particularly attractive new direction has been the exploitation of dendrimer structures and particularly of multi-chromophore containing dendrimer structures. This approach has permitted the simultaneous improvement of all material properties. Development of new materials has facilitated the fabrication of a number of prototype devices and most recently has permitted investigation of the incorporation of electro-optic materials into photonic bandgap and microresonator structures. The latter are relevant to active wavelength division multiplexing (WDM). Significant quality factors (greater than 10,000) have been realized for such devices permitting wavelength discrimination at telecommunication wavelengths of 0.01 nm.

Universal strategies in research and drug discovery based on protein-fragment complementation assays

2007 ◽  
Vol 6 (7) ◽  
pp. 569-582 ◽  
Author(s):  
Stephen W. Michnick ◽  
Po Hien Ear ◽  
Emily N. Manderson ◽  
Ingrid Remy ◽  
Eduard Stefan
Keyword(s):  
Drug Discovery ◽  
Protein Fragment ◽  
Protein Fragment Complementation ◽  
Fragment Complementation
Sign in / Sign up

Export Citation Format

Share Document