scholarly journals Comparison of α-Helix and β-Sheet Structure Adaptation to a Quantum Dot Geometry: Toward the Identification of an Optimal Motif for a Protein Nanoparticle Cover

ACS Omega ◽  
2019 ◽  
Vol 4 (8) ◽  
pp. 13086-13099 ◽  
Author(s):  
Katarzyna Kopeć ◽  
Marta Pędziwiatr ◽  
Dominik Gront ◽  
Olga Sztatelman ◽  
Jakub Sławski ◽  
...  
Keyword(s):  
Quantum Dot ◽  
Sheet Structure ◽  
Structure Adaptation ◽  
Α Helix ◽  
Β Sheet

The optical properties of α2-macroglobulin from normal and from cystic fibrosis plasma

1981 ◽  
Vol 59 (7) ◽  
pp. 519-523 ◽  
Author(s):  
Janice B. Y. Richman ◽  
Jacob A. Verpoorte
Keyword(s):  
Cystic Fibrosis ◽  
Optical Properties ◽  
Fluorescence Spectra ◽  
Molar Ratios ◽  
Normal Individuals ◽  
Α2 Macroglobulin ◽  
Tryptophan Residues ◽  
Sheet Structure ◽  
Α Helix ◽  
Β Sheet

The α2-macroglobulin (α2-M) was purified from the plasma of normal individuals and from that of cystic fibrosis patients. The proteins exhibited identical optical properties. Both proteins have an absorbance coefficient of A = 1060 g∙cm−2 at 280 nm. The circular dichroism spectra are identical and indicate about 45% β-sheet structure and almost no α-helix. The spectra of solutions at pH 8.0 do not change when trypsin is added.The fluorescence spectra of the α2-M measured at pH 8.0 have contributions by tyrosine and tryptophan residues. The fluorescence intensities are identical and are enhanced about 30% when trypsin is added in 2:1 molar ratios.

Post-assembly α-helix to β-sheet structural transformation within SAF-p1/p2a peptide nanofibers

Soft Matter ◽  
2018 ◽  
Vol 14 (44) ◽  
pp. 8986-8996 ◽  
Author(s):  
Evan K. Roberts ◽  
Kong M. Wong ◽  
Elizabeth J. Lee ◽  
Melina M. Le ◽  
Dipam M. Patel ◽  
...  
Keyword(s):  
Structural Transformation ◽  
Coiled Coils ◽  
Peptide Nanofibers ◽  
Sheet Structure ◽  
Peptide System ◽  
Α Helix ◽  
Β Sheet

The SAF-p1/p2a binary peptide system co-assembles in water into α-helical coiled coils, but can convert post-assembly into a β-sheet structure.

13C CP/MAS NMR Spectroscopic Characterization of Native Silk Fibers

2011 ◽  
Vol 175-176 ◽  
pp. 328-332 ◽  
Author(s):  
Wei Zhang ◽  
Jian Xin He ◽  
Yan Wang
Keyword(s):  
13C Nmr Spectroscopy ◽  
Spectroscopic Characterization ◽  
Random Coil ◽  
Silk Fibers ◽  
Significant Difference ◽  
Sheet Structure ◽  
Α Helix ◽  
Cp Mas Nmr ◽  
Β Sheet

Differences in secondary structure among Bombyx mori (B. mori) silk and two wild silks of Antheraea yamamai (A. yamamai) and Antheraea pernyi (A. pernyi) were investigated by CP/MAS 13C NMR Spectroscopy. The β-sheet structure was primary in three silk, and B. mori silk had the highest β-sheet structure. Although amino acid compositions are very similar for two wild silk, their secondary structures had significant difference. A. yamamai silk contained more α-helix structure, whereas more β-turn and random coil structures formed in A. pernyi silk. B. mori silk was mainly composed of anti-parallel β-sheet structure, however, the parallel β-sheet structure was advantage in the two wild silks, and A. yamamai silk contained more anti-parallel β-sheet conformation than A. pernyi silk.

Effects of Cosolvents and Macromolecular Crowding on the Phase Transitions and Temperature-Pressure Stability of Chiral and Racemic Poly-Lysine

2018 ◽  
Vol 232 (7-8) ◽  
pp. 1111-1125 ◽  
Author(s):  
Jim-Marcel Knop ◽  
Roland Winter
Keyword(s):  
Macromolecular Crowding ◽  
Helical Structure ◽  
Racemic Mixture ◽  
Sheet Structure ◽  
Different Types ◽  
Pressure Stability ◽  
Temperature And Pressure ◽  
Α Helix ◽  
Β Sheet ◽  
Volume Decrease

Abstract FTIR spectroscopy has been used to reveal the effects of different types of cosolvents (TMAO, urea) as well as macromolecular crowding (using the crowding agent Ficoll) on the temperature and pressure dependent structure of poly-L-lysine, poly-D-lysine and their racemic mixture. Compared to the effects of cosolvents on the unfolding transition of proteins, their effects on the α-helix to aggregated β-sheet transition of polylysine are quite small. High hydrostatic pressure has been found to favor the α-helical state over the aggregated β-sheet structure which is reflected in a volume decrease of ΔV=−32 mL mol−1, indicating that the packing mode is more efficient in the α-helical structure. Both, addition of urea and TMAO lead to a decrease in pressure stability of the aggregated β-sheet structure, which is accompanied by a three-fold decrease in ΔV, whereas the macromolecular crowder has little effect on the β-to-α transition. The more than 3 kbar higher β-to-α transition pressure of the racemic mixture compared with PLL confirms the drastic stabilization of β-sheet aggregates if the stereoisomers PLL and PDL are combined. Changes in hydration and packing of the polypeptide occurs upon interaction and fine packing of the polypeptide’s chains of opposed chirality, which are slightly modulated by the properties of cosolute and crowding, only. The underlying solvational and packing mechanisms observed here may be decisive factors responsible for the spontaneous protein aggregation in general and, as such, may shed additional light on the molecular basis of amyloid-associated diseases.

Scorpion toxin-potassium channel interaction law and its applications.

2020 ◽  
Vol 01 ◽  
Author(s):  
Zheng Zuo ◽  
Zongyun Chen ◽  
Zhijian Cao ◽  
Wenxin Li ◽  
Yingliang Wu
Keyword(s):  
Potassium Channel ◽  
Scorpion Toxin ◽  
Scorpion Toxins ◽  
Toxin Binding ◽  
Channel Interaction ◽  
Binding Interface ◽  
Α Helix ◽  
Interaction Law ◽  
Binding Interfaces ◽  
Β Sheet

: The scorpion toxins are the largest potassium channel-blocking peptide family. The understanding of toxin binding interfaces is usually restricted by two classical binding interfaces: one is the toxin α-helix motif, the other is the antiparallel β-sheet motif. In this review, such traditional knowledge was updated by another two different binding interfaces: one is BmKTX toxin using the turn motif between the α-helix and antiparallel β-sheet domains as the binding interface, the other is Ts toxin using turn motif between the β-sheet in the N-terminal and α-helix domains as the binding interface. Their interaction analysis indicated that the scarce negatively charged residues in the scorpion toxins played a critical role in orientating the toxin binding interface. In view of the toxin negatively charged amino acids as “binding interface regulator”, the law of scorpion toxin-potassium channel interaction was proposed, that is, the polymorphism of negatively charged residue distribution determines the diversity of toxin binding interfaces. Such law was used to develop scorpion toxin-potassium channel recognition control technique. According to this technique, three Kv1.3 channel-targeted peptides, using BmKTX as the template, were designed with the distinct binding interfaces from that of BmKTX through modulating the distribution of toxin negatively charged residues. In view of the potassium channel as the common targets of different animal toxins, the proposed law was also shown to helpfully orientate the binding interfaces of other animal toxins. Clearly, the toxin-potassium channel interaction law would strongly accelerate the research and development of different potassium channelblocking animal toxins in the future.

scholarly journals Nanostructure of bioactive glass affects bone cell attachment via protein restructuring upon adsorption

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ukrit Thamma ◽  
Tia J. Kowal ◽  
Matthias M. Falk ◽  
Himanshu Jain
Keyword(s):  
Bioactive Glass ◽  
Cell Response ◽  
Interfacial Layer ◽  
Cell Attachment ◽  
Bone Cell ◽  
Nano Structure ◽  
Rgd Sequence ◽  
Engineered Tissue ◽  
Α Helix ◽  
Β Sheet

AbstractThe nanostructure of engineered bioscaffolds has a profound impact on cell response, yet its understanding remains incomplete as cells interact with a highly complex interfacial layer rather than the material itself. For bioactive glass scaffolds, this layer comprises of silica gel, hydroxyapatite (HA)/carbonated hydroxyapatite (CHA), and absorbed proteins—all in varying micro/nano structure, composition, and concentration. Here, we examined the response of MC3T3-E1 pre-osteoblast cells to 30 mol% CaO–70 mol% SiO2 porous bioactive glass monoliths that differed only in nanopore size (6–44 nm) yet resulted in the formation of HA/CHA layers with significantly different microstructures. We report that cell response, as quantified by cell attachment and morphology, does not correlate with nanopore size, nor HA/CHO layer micro/nano morphology, or absorbed protein amount (bovine serum albumin, BSA), but with BSA’s secondary conformation as indicated by its β-sheet/α-helix ratio. Our results suggest that the β-sheet structure in BSA interacts electrostatically with the HA/CHA interfacial layer and activates the RGD sequence of absorbed adhesion proteins, such as fibronectin and vitronectin, thus significantly enhancing the attachment of cells. These findings provide new insight into the interaction of cells with the scaffolds’ interfacial layer, which is vital for the continued development of engineered tissue scaffolds.

scholarly journals Structural and Technological Approach to Reveal the Role of the Lipid Phase in the Formation of Soy Emulsion Gels with Chia Oil

Gels ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 48
Author(s):  
Ana M. Herrero ◽  
Claudia Ruiz-Capillas
Keyword(s):  
Raman Spectroscopy ◽  
Structural Properties ◽  
Structural Changes ◽  
Protein Secondary Structure ◽  
Lipid Phase ◽  
Α Helix ◽  
Β Sheet ◽  
Shed Light ◽  
Chia Oil

Considerable attention has been paid to emulsion gels (EGs) in recent years due to their interesting applications in food. The aim of this work is to shed light on the role played by chia oil in the technological and structural properties of EGs made from soy protein isolates (SPI) and alginate. Two systems were studied: oil-free SPI gels (SPI/G) and the corresponding SPI EGs (SPI/EG) that contain chia oil. The proximate composition, technological properties (syneresis, pH, color and texture) and structural properties using Raman spectroscopy were determined for SPI/G and SPI/EG. No noticeable (p > 0.05) syneresis was observed in either sample. The pH values were similar (p > 0.05) for SPI/G and SPI/EG, but their texture and color differed significantly depending on the presence of chia oil. SPI/EG featured significantly lower redness and more lightness and yellowness and exhibited greater puncture and gel strengths than SPI/G. Raman spectroscopy revealed significant changes in the protein secondary structure, i.e., higher (p < 0.05) α-helix and lower (p < 0.05) β-sheet, turn and unordered structures, after the incorporation of chia oil to form the corresponding SPI/EG. Apparently, there is a correlation between these structural changes and the textural modifications observed.

scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Amyloid Β ◽  
Density Functional Theory Calculations ◽  
Tau Proteins ◽  
Functional Theory ◽  
Energy Profiles ◽  
Α Helix ◽  
Semi Empirical ◽  
Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

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