scholarly journals Dual-Crystallizable Silk Fibroin/Poly(L-lactic Acid) Biocomposite Films: Effect of Polymer Phases on Protein Structures in Protein-Polymer Blends

2021 ◽  
Vol 22 (4) ◽  
pp. 1871
Author(s):  
Fang Wang ◽  
Yingying Li ◽  
Christopher R. Gough ◽  
Qichun Liu ◽  
Xiao Hu
Keyword(s):  
Thermal Stability ◽  
Lactic Acid ◽  
Silk Fibroin ◽  
Hydrophobic Interactions ◽  
Protein Structures ◽  
Secondary Structures ◽  
Synthetic Polymer ◽  
Protein Secondary Structures ◽  
Blending Method ◽  
Rigid Amorphous

Biopolymer composites based on silk fibroin have shown widespread potential due to their brilliant applications in tissue engineering, medicine and bioelectronics. In our present work, biocomposite nanofilms with different special topologies were obtained through blending silk fibroin with crystallizable poly(L-lactic acid) (PLLA) at various mixture rates using a stirring-reflux condensation blending method. The microstructure, phase components, and miscibility of the blended films were studied through thermal analysis in combination with Fourier-transform infrared spectroscopy and Raman analysis. X-ray diffraction and scanning electron microscope were also used for advanced structural analysis. Furthermore, their conformation transition, interaction mechanism, and thermal stability were also discussed. The results showed that the hydrogen bonds and hydrophobic interactions existed between silk fibroin (SF) and PLLA polymer chains in the blended films. The secondary structures of silk fibroin and phase components of PLLA in composites vary at different ratios of silk to PLLA. The β-sheet content increased with the increase of the silk fibroin content, while the glass transition temperature was raised mainly due to the rigid amorphous phase presence in the blended system. This results in an increase in thermal stability in blended films compared to the pure silk fibroin films. This study provided detailed insights into the influence of synthetic polymer phases (crystalline, rigid amorphous, and mobile amorphous) on protein secondary structures through blending, which has direct applications on the design and fabrication of novel protein–synthetic polymer composites for the biomedical and green chemistry fields.

scholarly journals Multi-task deep learning for concurrent prediction of protein structural properties

2021 ◽  
Author(s):  
Buzhong Zhang ◽  
Jinyan Li ◽  
Lijun Quan ◽  
Qiang Lyu
Keyword(s):  
Deep Learning ◽  
Structural Properties ◽  
Solvent Accessibility ◽  
Close Association ◽  
Protein Structures ◽  
Secondary Structures ◽  
Structural Features ◽  
New Method ◽  
Machine Learning Techniques ◽  
Protein Secondary Structures

AbstractProtein structural properties are diverse and have the characteristics of spatial hierarchy, such as secondary structures, solvent accessibility and backbone angles. Protein tertiary structures are formed in close association with these features. Separate prediction of these structural properties has been improved with the increasing number of samples of protein structures and with advances in machine learning techniques, but concurrent prediction of these tightly related structural features is more useful to understand the overall protein structure and functions. We introduce a multi-task deep learning method for concurrent prediction of protein secondary structures, solvent accessibility and backbone angles (ϕ, ψ). The new method has main two deep network modules: the first one is designed as a DenseNet architecture a using bidirectional simplified GRU (GRU2) network, and the second module is designed as an updated Google Inception network. The new method is named CRRNN2.CRRNN2 is trained on 14,100 protein sequences and its prediction performance is evaluated by testing on public benchmark datasets: CB513, CASP10, CASP11, CASP12 and TS1199. Compared with state-of-the-art methods, CRRNN2 achieves similar, or better performance on the prediction of 3- and 8-state secondary structures, solvent accessibility and backbone angles (ϕ, ψ). Online CRRN-N2 applications, datasets and standalone software are available at http://qianglab.scst.suda.edu.cn/crrnn2/.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

2021 ◽  
Author(s):  
Rakesh Vaiwala ◽  
K. Ganapathy Ayappa
Keyword(s):  
Phase Space ◽  
Force Field ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Secondary Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Radius Of Gyration ◽  
Protein Secondary Structures

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by mapping the bonds and angles for 20 amino acids onto target distributions obtained from fully atomistic simulations in explicit solvent. A dual-basin potential is introduced for stabilizing backbone angles, to cover a wide spectrum of protein secondary structures. The backbone dihedral potential enables folding of the protein from an unfolded initial state to the folded native structure. The proposed force field is validated by evaluating structural properties of several model peptides and proteins including the SARS-CoV-2 fusion peptide, consisting of α-helices, β-sheets, loops and turns. Detailed comparisons with fully atomistic simulations are carried out to assess the ability of the proposed force field to stabilize the different secondary structures present in proteins. The compact conformations of the native states were evident from the radius of gyration as well as the high intensity peaks of the root mean square deviation histograms, which were found to lie below 0.4 nm. The Ramachandran-like energy landscape on the phase space of backbone angles (θ) and dihedrals (ϕ) effectively captured the conformational phase space of α-helices at ~(ϕ=50°, θ=90°) and β-strands at ~(ϕ=±180°, θ=90°-120°). Furthermore, the residue-residue native contacts are also well reproduced by the proposed DPD model. The applicability of the model to multidomain complexes is assessed using lysozyme as well as a large α helical bacterial pore-forming toxin, cytolysin A. Our studies illustrate that the proposed force field is generic, and can potentially be extended for efficient in-silico investigations of membrane bound polypeptides and proteins using DPD simulations.

scholarly journals Constrained Peptides as Miniature Protein Structures

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Hang Yin
Keyword(s):  
Protein Engineering ◽  
Protein Interactions ◽  
Protein Structures ◽  
Secondary Structures ◽  
Biological Functions ◽  
Protein Protein Interactions ◽  
Protein Secondary Structures ◽  
Recent Developments ◽  
Noncovalent Bonds ◽  
Constrained Peptides

This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.

scholarly journals Plasticized and Nanofilled Poly(Lactic Acid) Nanocomposites: Mechanical, Thermal and Morphology Properties

2016 ◽  
Vol 846 ◽  
pp. 429-433 ◽  
Author(s):  
Buong Woei Chieng ◽  
Ibrahim Nor Azowa ◽  
Yoon Yee Then ◽  
Yuet Ying Loo
Keyword(s):  
Thermal Stability ◽  
Plastic Deformation ◽  
Tensile Strength ◽  
Lactic Acid ◽  
Poly Lactic Acid ◽  
Melt Blending ◽  
Elongation At Break ◽  
Epoxidized Palm Oil ◽  
Blending Method ◽  
Polymeric Chains

Poly(lactic acid) (PLA)-based nanocomposites filled with graphene nanoplatelets (xGnP) and containing epoxidized palm oil (EPO) as plasticizer were prepared by melt blending method. PLA was first plasticized by EPO to improve its flexibility and thereby overcome its problem of brittleness. Then, xGnP was incoporated into plasticized PLA to enhance its mechanical properteis. Plasticized and naonofilled PLA nanocomposites (PLA/EPO/xGnP) showed improvement in the elongation at break by 61% compared with plasticized PLA (PLA/EPO). The use of EPO and xGnP increases the mobility of the polymeric chains, thereby improving the flexibility and plastic deformation of PLA. The nanocomposites also resulted in an increase of up to 26.5% in the tensile strength compared with PLA/EPO blend. PLA/EPO reinforced with xGnP shows that increasing the xGnP content triggers a substantial increase in thermal stability. The TEM image of PLA/EPO/xGnP shows that the xGnP was uniformly dispersed in the PLA matrix and no obvious aggregation is observed.

scholarly journals 2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content

2019 ◽  
Vol 47 (W1) ◽  
pp. W477-W481 ◽  
Author(s):  
Elliot D Drew ◽  
Robert W Janes
Keyword(s):  
Secondary Structure ◽  
Protein Structures ◽  
Secondary Structures ◽  
Residue Level ◽  
Side Chain ◽  
Related Protein ◽  
Tertiary Structures ◽  
Secondary Structure Content ◽  
Protein Secondary Structures

Abstract 2StrucCompare is a webserver whose primary aim is to visualize subtle but functionally important differences between two related protein structures, either of the same protein or related homologues, with similar or functionally different tertiary structures. At the heart of the package is identifying and visualizing differences between conformations at the secondary structure and at the residue level, such as contact differences or side chain conformational differences found between two protein chains. The protein secondary structures are determined according to four established methods (DSSP, STRIDE, P-SEA and STICKS), and as each employs different assignment strategies, small conformational differences between the two structures can give rise to paired residues being denoted as having different secondary structure features with the different methods. 2StrucCompare captures both the large and more subtle differences found between structures, enabling visualization of these differences that could be key to an understanding of a proteins’ function. 2StrucCompare is freely accessible at http://2struccompare.cryst.bbk.ac.uk/index.php

Searching techniques for databases of protein secondary structures

1989 ◽  
Vol 15 (4-5) ◽  
pp. 287-298 ◽  
Author(s):  
Peter J. Artymiuk ◽  
David W. Rice ◽  
Eleanor M. Mitchell ◽  
Peter Willett
Keyword(s):  
Secondary Structure ◽  
Protein Data Bank ◽  
Protein Structures ◽  
Three Dimensional ◽  
Data Bank ◽  
Secondary Structures ◽  
British Library ◽  
Geometric Information ◽  
Protein Secondary Structures ◽  
Funded Research Project

This paper summarizes the findings of a recent, British Library-funded research project into computer techniques for searching the three-dimensional protein structures that occur in the Protein Data Bank. The work focuses on the secondary structures of proteins and utilizes both angular and distance geometric information. Algorithms are presented for the auto matic identification of secondary structure elements, of sec ondary structure motifs and of proteins with similar secondary structures.

Thermal degradation kinetics of Opuntia Ficus Indica flour and talc-filled poly (lactic acid) hybrid biocomposites by TGA analysis

2021 ◽  
pp. 002199832110082
Author(s):  
Azzeddine Gharsallah ◽  
Abdelheq Layachi ◽  
Ali Louaer ◽  
Hamid Satha
Keyword(s):  
Thermal Stability ◽  
Lactic Acid ◽  
Thermal Degradation ◽  
Degradation Kinetics ◽  
Degradation Mechanism ◽  
Melt Processing ◽  
Thermal Degradation Kinetics ◽  
Poly Lactic Acid ◽  
Opuntia Ficus Indica ◽  
Model Free

This paper reports the effect of lignocellulosic flour and talc powder on the thermal degradation behavior of poly (lactic acid) (PLA) by thermogravimetric analysis (TGA). Lignocellulosic flour was obtained by grinding Opuntia Ficus Indica cladodes. PLA/talc/ Opuntia Ficus Indica flour (OFI-F) biocomposites were prepared by melt processing and characterized using Wide-angle X-ray scattering (WAXS) and Scanning Electron Microscope (SEM). The thermal degradation of neat PLA and its biocomposites can be identified quantitatively by solid-state kinetics models. Thermal degradation results on biocomposites compared to neat PLA show that talc particles at 10 wt % into the PLA matrix have a minor impact on the thermal stability of biocomposites. Loading OFI-F and Talc/OFI-F mixture into the PLA matrix results in a decrease in the maximum degradation temperature, which means that the biocomposites have lower thermal stability. The activation energies (Ea) calculated by the Flynn Wall Ozawa (FWO) and Kissinger Akahira Sunose (KAS) model-free approaches and by model-fitting (Kissinger method and Coats-Redfern method) are in good agreement with one another. In addition, in this work, the degradation mechanism of biocomposites is proposed using Coats-Redfern and Criado methods.

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