scholarly journals An Ornithine-Free Gramicidin S Analogue Using Norleucine, Cyclo(Val–Nle–Leu–D-Phe–Pro)2, Forms Helically Aligned β-Sheets

2021 ◽  
Vol 69 (11) ◽  
pp. 1097-1103
Author(s):  
Akiko Asano ◽  
Chisato Minami ◽  
Shiori Matsuoka ◽  
Takuma Kato ◽  
Mitsunobu Doi
Keyword(s):  
Gramicidin S ◽  
Β Sheets

Antiparallel Pleated β-Sheets Observed in Crystal Structures of N,N-Bis(trichloroacetyl) and N,N-Bis(m-bromobenzoyl) Gramicidin S

2001 ◽  
Vol 395 (1) ◽  
pp. 85-93 ◽  
Author(s):  
Mitsunobu Doi ◽  
Saori Fujita ◽  
Yoshio Katsuya ◽  
Masahiro Sasaki ◽  
Taizo Taniguchi ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Gramicidin S ◽  
Β Sheets

[Leu2]Gramicidin S preserves the structural properties of its parent peptide and forms helically aligned β-sheets

2019 ◽  
Vol 75 (10) ◽  
pp. 1336-1343
Author(s):  
Akiko Asano ◽  
Shiori Matsuoka ◽  
Chisato Minami ◽  
Takuma Kato ◽  
Mitsinobu Doi
Keyword(s):  
Structural Properties ◽  
Chemical Shifts ◽  
Structural Characteristics ◽  
Crystallographic Analysis ◽  
Coupling Constants ◽  
Side Chains ◽  
Gramicidin S ◽  
Β Sheets ◽  
Solvent Molecules ◽  
Novel Scaffold

For crystallographic analysis, Leu was substituted for Orn in Gramicidin S (LGS) to suppress interactions with hydrophilic solvent molecules, which increased the flexibility of the Orn side chains, leading to disorder within the crystals. The asymmetric unit (C62H94N10O10·1.296C3H8O·1.403H2O) contains three LGS molecules (A, B and C) forming β-turn and intramolecular β-sheet structures. With the exception of one motif in molecule C, D-Phe-Pro turn motifs (Phe is phenylalanine and Pro is proline) were classed as type II′ β-turns. The peptide backbones twist slightly to the right along the long axis of the molecule. The puckering of Pro is in a Cγ-endo or twisted Cγ-endo–Cβ-exo form. Flanking molecules are arranged such that the angles (A...B = 104°, B...C = 139° and C...A = 117°) form helical β-sheets. Solvent molecules interact with the peptide backbones supporting the β-sheets. The forms of the replacement Leu side chains are consistent with the e-form of the Orn side chain in GS analogues. No hydrophilic region composed of solvent molecules, such as that observed in Gramicidin S hydrochloride (GS·HCl) crystals, was found. The perturbation of αH chemical shifts and coupling constants of CONH showed that the structural properties of GS·HCl and LGS are similar to each other in solution. CD spectra also supported the structural similarity. With the sequence cyclo(–Val–Leu–Leu–D-Phe–Pro–)2 (Val is valine and Leu is leucine), LGS lacks the amphiphilicity and antimicrobial activity of parental Gramicidin S (GS). However, the structure of LGS reflects the structural characteristics of GS and no disordering inconvenient for structural analysis was found. Thus, LGS could be a novel scaffold useful for studying β-turn and sheet structures.

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>

Both D-phenylalanine and Proline Keep the Type II' β-turn During Thermocyclization of Linear Gramicidin S Precursor Analogues

2014 ◽  
Vol 11 (4) ◽  
pp. 313-316
Author(s):  
Hai-Qiang Wu ◽  
Xiao-Ru Zhang ◽  
Xiao-Bing Li ◽  
Lian-Quan Gu ◽  
Lin-Kun An
Keyword(s):  
Type Ii ◽  
Gramicidin S

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
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