Elastic Effects behind Cooperative Bonding in β-Sheets

2004 ◽  
Vol 126 (40) ◽  
pp. 13140-13143 ◽  
Author(s):  
Jan Rossmeisl ◽  
Jens K. Nørskov ◽  
Karsten W. Jacobsen
Keyword(s):  
Β Sheets ◽  
Cooperative Bonding

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

Charge-Separated Fmoc-Peptide β-Sheets: Sequence-Secondary Structure Relationship for Arranging Charged Side Chains on Both Sides

2014 ◽  
Vol 3 (11) ◽  
pp. 1182-1188 ◽  
Author(s):  
Toru Nakayama ◽  
Taro Sakuraba ◽  
Shunsuke Tomita ◽  
Akira Kaneko ◽  
Eisuke Takai ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Side Chains ◽  
Structure Relationship ◽  
Β Sheets

scholarly journals Implementing Zn2+ ion and pH-value control into artificial mussel glue proteins by abstracting a His-rich domain from preCollagen

Soft Matter ◽  
2021 ◽  
Author(s):  
Sandra Arias ◽  
Shahrouz Amini ◽  
Jana M. Krüger ◽  
Lukas D. Bangert ◽  
Hans G. Börner
Keyword(s):  
Ph Value ◽  
Control Mechanisms ◽  
Rich Domain ◽  
Glue Proteins ◽  
Β Sheets ◽  
Mussel Adhesive

A chemically activated mussel-inspired polymerization of a His-rich peptide, yielded artificial mussel glue proteins, where β-sheets can be triggered to mimic both adhesive motifs and cohesion control mechanisms of the mussel adhesive apparatus.

scholarly journals The Budapest Amyloid Predictor and Its Applications

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 500
Author(s):  
László Keresztes ◽  
Evelin Szögi ◽  
Bálint Varga ◽  
Viktor Farkas ◽  
András Perczel ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Support Vector ◽  
User Needs ◽  
Computational Technique ◽  
Linear Support Vector Machine ◽  
Β Sheets ◽  
Artificial Neural ◽  
Amorphous Aggregation

The amyloid state of proteins is widely studied with relevance to neurology, biochemistry, and biotechnology. In contrast with nearly amorphous aggregation, the amyloid state has a well-defined structure, consisting of parallel and antiparallel β-sheets in a periodically repeated formation. The understanding of the amyloid state is growing with the development of novel molecular imaging tools, like cryogenic electron microscopy. Sequence-based amyloid predictors were developed, mainly using artificial neural networks (ANNs) as the underlying computational technique. From a good neural-network-based predictor, it is a very difficult task to identify the attributes of the input amino acid sequence, which imply the decision of the network. Here, we present a linear Support Vector Machine (SVM)-based predictor for hexapeptides with correctness higher than 84%, i.e., it is at least as good as the best published ANN-based tools. Unlike artificial neural networks, the decisions of the linear SVMs are much easier to analyze and, from a good predictor, we can infer rich biochemical knowledge. In the Budapest Amyloid Predictor webserver the user needs to input a hexapeptide, and the server outputs a prediction for the input plus the 6 × 19 = 114 distance-1 neighbors of the input hexapeptide.

scholarly journals Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial

2004 ◽  
Vol 13 (4) ◽  
pp. 1134-1147 ◽  
Author(s):  
Clara M. Santiveri ◽  
Jorge Santoro ◽  
Manuel Rico ◽  
M. Angeles Jiménez
Keyword(s):  
Hydrophobic Surface ◽  
Β Sheets ◽  
The Stability ◽  
Β Sheet

scholarly journals Structural Mechanism for Regulation of Bcl-2 protein Noxa by phosphorylation

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Christine B. Karim ◽  
L. Michel Espinoza-Fonseca ◽  
Zachary M. James ◽  
Eric A. Hanse ◽  
Jeffrey S. Gaynes ◽  
...  
Keyword(s):  
Md Simulations ◽  
Salt Bridges ◽  
Binding Assays ◽  
Peptide Backbone ◽  
Structural Mechanism ◽  
Binding Partner ◽  
Flexible Loop ◽  
Bh3 Domain ◽  
N Terminus ◽  
Β Sheets

Abstract We showed previously that phosphorylation of Noxa, a 54-residue Bcl-2 protein, at serine 13 (Ser13) inhibited its ability to promote apoptosis through interactions with canonical binding partner, Mcl-1. Using EPR spectroscopy, molecular dynamics (MD) simulations and binding assays, we offer evidence that a structural alteration caused by phosphorylation partially masks Noxa’s BH3 domain, inhibiting the Noxa-Mcl-1 interaction. EPR of unphosphorylated Noxa, with spin-labeled amino acid TOAC incorporated within the BH3 domain, revealed equilibrium between ordered and dynamically disordered states. Mcl-1 further restricted the ordered component for non-phosphorylated Noxa, but left the pSer13 Noxa profile unchanged. Microsecond MD simulations indicated that the BH3 domain of unphosphorylated Noxa is housed within a flexible loop connecting two antiparallel β-sheets, flanked by disordered N- and C-termini and Ser13 phosphorylation creates a network of salt-bridges that facilitate the interaction between the N-terminus and the BH3 domain. EPR showed that a spin label inserted near the N-terminus was weakly immobilized in unphosphorylated Noxa, consistent with a solvent-exposed helix/loop, but strongly constrained in pSer13 Noxa, indicating a more ordered peptide backbone, as predicted by MD simulations. Together these studies reveal a novel mechanism by which phosphorylation of a distal serine inhibits a pro-apoptotic BH3 domain and promotes cell survival.

scholarly journals Correlated motions are a fundamental property of β-sheets

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
R. Bryn Fenwick ◽  
Laura Orellana ◽  
Santi Esteban-Martín ◽  
Modesto Orozco ◽  
Xavier Salvatella
Keyword(s):  
Fundamental Property ◽  
Correlated Motions ◽  
Β Sheets

scholarly journals Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy

2017 ◽  
Vol 121 (38) ◽  
pp. 8935-8945 ◽  
Author(s):  
Justin P. Lomont ◽  
Joshua S. Ostrander ◽  
Jia-Jung Ho ◽  
Megan K. Petti ◽  
Martin T. Zanni
Keyword(s):  
Ir Spectroscopy ◽  
Infrared Spectra ◽  
Transition Dipole ◽  
2D Ir ◽  
Β Sheets
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