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Surface Decoration of Selenium Nanoparticles by Proteins from the Culinary-Medicinal Shiitake Mushroom, Lentinus edodes (Agaricomycetes), for Enhanced Fibrinolytic Activity

Ali SM, Raman J, Lakshmanan H, Ling TC, Phan CW, Tan YS, et al.

Int J Med Mushrooms, 2018;20(11):1021-1030.
PMID: 30806227 DOI: 10.1615/IntJMedMushrooms.2018028307

Lentinus edodes (shiitake mushroom) has exhibited fibrinolytic activity. We synthesized and characterized selenium nanoparticles (SeNPs) using protein precipitated from the mushroom. We also investigated the fibrinolytic activity of the SeNPs. The proteins from a crude extract of L. edodes were recovered through the use of aqueous 2-phase separation, and these we used as the capping agent in SeNP biosynthesis. We characterized the SeNPs using UV-visible spectrophotometry, field emission scanning electron microscopy (FESEM), energy dispersive X-ray (EDX), transmission electron microscopy (TEM), particle size distribution analysis, and Fourier transform infrared spectroscopy (FT-IR). The fibrinolytic capability of the SeNPs was tested through an in vitro fibrin plate assay. The UV-visible spectra showed maximal absorbance at 220 nm. FESEM images showed that the SeNPs were dispersed and did not clump. The TEM images revealed a spherical shape and average size of the SeNPs. The particle size distribution analysis confirmed the mean size of the SeNPs at 64.53 nm. A strong signal for the presence of selenium was observed in the EDX analysis. The FT-IR spectrum revealed the involvement of protein functional groups in the reduction of sel-enite. Overall, the SeNPs capped with protein from shiitake mushroom were effective as an in vitro fibrinolytic agent.

Matched MeSH terms: Fungal Proteins/chemistry
Structural and rheological changes of texturized mung bean protein induced by feed moisture during extrusion

Hossain Brishti F, Chay SY, Muhammad K, Rashedi Ismail-Fitry M, Zarei M, Karthikeyan S, et al.

Food Chem, 2021 May 15;344:128643.
PMID: 33246681 DOI: 10.1016/j.foodchem.2020.128643

Mung bean protein isolate was texturized at different feed moisture contents (30.0, 49.3, and 60.0%) at a constant temperature (144.57 °C) to evaluate the changes in protein profile, solubility, thermal, structural (at secondary and tertiary levels) and rheological properties. SDS-PAGE, surface hydrophobicity, circular dichroism, FTIR spectroscopy, and fluorescence analyses revealed protein unfolding, aggregation, and structural rearrangement as a function of feed moisture content. Extrusion at 49.3% feed moisture produced texturized mung bean protein (TMBP) with favourable partial denaturation, the formation of small aggregates, improved solubility, and digestibility with strong gel forming behaviour, whereas 30.0 and 60.0% moisture content resulted in complete protein denaturation, the undesirable formation of large aggregates and weak gels. In conclusion, protein denaturation and formation of aggregates can be controlled by manipulating feed moisture content during extrusion, with 49.3% feed moisture prompting favourable partial denaturation to produce TMBP with desirable qualities for use as a vegetarian-based meat extender.

Matched MeSH terms: Plant Proteins/chemistry*
A novel sponge-derived protein thrombocorticin is a new agonist for thrombopoietin receptor

Watari H, Nakajima H, Atsuumi W, Nakamura T, Nanya T, Ise Y, et al.

Comp Biochem Physiol C Toxicol Pharmacol, 2019 Jul;221:82-88.
PMID: 30978513 DOI: 10.1016/j.cbpc.2019.04.003

We screened 868 marine extracts in search of hematopoietic molecules resulted in findings of several extracts that proliferated Ba/F3-HuMpl cells but not the cells expressed with other hematopoietic cytokine receptors, EPO and G-CSF. Separation of the most potent extract of a Micronesian sponge Corticium sp., guided by the cell proliferation assay using Ba/F3-HuMpl cells resulted in an isolation of thrombocorticin (ThC), a novel 14 kDa protein as an active principal. ThC displayed concentration-dependent proliferation of Ba/F3-HuMpl cells, and had a stronger activity than that of eltrombopag, a small molecule drug used to treat thrombocytopenia. ThC induced phosphorylation of STAT5, suggesting that it activates Jak/STAT pathway as in the case of TPO. These results together indicated that ThC is a specific agonist for c-Mpl, although the size and shape differs largely from TPO. Here we present isolation, characterization and biological activity of ThC.

Matched MeSH terms: Proteins/chemistry
Molecular evolutionary and 3D protein structural analyses of Lactobacillus fermentum elongation factor Tu, a novel brain health promoting factor

Ong JS, Liu YW, Liong MT, Choi SB, Tsai YC, Low WY

Genomics, 2020 11;112(6):3915-3924.
PMID: 32629096 DOI: 10.1016/j.ygeno.2020.06.052

The role of microbiota in gut-brain communication has led to the development of probiotics promoting brain health. Here we report a genomic study of a Lactobacillus fermentum PS150 and its patented bioactive protein, elongation factor Tu (EF-Tu), which is associated with cognitive improvement in rats. The L. fermentum PS150 circular chromosome is 2,238,401 bp and it consists of 2281 genes. Chromosome comparisons with other L. fermentum strains highlighted a cluster of glycosyltransferases as potential candidate probiotic factors besides EF-Tu. Molecular evolutionary analyses on EF-Tu genes (tuf) in 235 bacteria species revealed one to three copies of the gene per genome. Seven tuf pseudogenes were found and three species only possessed pseudogenes, which is an unprecedented finding. Protein variability analysis of EF-Tu showed five highly variable residues (40 K, 41G, 42 L, 44 K, and 46E) on the protein surface, which warrant further investigation regarding their potential roles as binding sites.

Matched MeSH terms: Proteins/chemistry*
Fulltext Subcritical Water Technology for Enhanced Extraction of Biochemical Compounds from Chlorella vulgaris

Awaluddin SA, Thiruvenkadam S, Izhar S, Hiroyuki Y, Danquah MK, Harun R

Biomed Res Int, 2016;2016:5816974.
PMID: 27366748 DOI: 10.1155/2016/5816974

Subcritical water extraction (SWE) technology has been used for the extraction of active compounds from different biomass materials with low process cost, mild operating conditions, short process times, and environmental sustainability. With the limited application of the technology to microalgal biomass, this work investigates parametrically the potential of subcritical water for high-yield extraction of biochemicals such as carbohydrates and proteins from microalgal biomass. The SWE process was optimized using central composite design (CCD) under varying process conditions of temperature (180-374°C), extraction time (1-20 min), biomass particulate size (38-250 μm), and microalgal biomass loading (5-40 wt.%). Chlorella vulgaris used in this study shows high volatile matter (83.5 wt.%) and carbon content (47.11 wt.%), giving advantage as a feedstock for biofuel production. The results showed maximum total carbohydrate content and protein yields of 14.2 g/100 g and 31.2 g/100 g, respectively, achieved under the process conditions of 277°C, 5% of microalgal biomass loading, and 5 min extraction time. Statistical analysis revealed that, of all the parameters investigated, temperature is the most critical during SWE of microalgal biomass for protein and carbohydrate production.

Matched MeSH terms: Proteins/chemistry
Fulltext AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

Wisitponchai T, Shoombuatong W, Lee VS, Kitidee K, Tayapiwatana C

BMC Bioinformatics, 2017 Apr 19;18(1):220.
PMID: 28424069 DOI: 10.1186/s12859-017-1628-6

BACKGROUND: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet.
RESULTS: In this study, we established an ensemble computational model for discriminating the near-native docking pose of APKs named "AnkPlex". A dataset of APKs was generated from seven X-ray APKs, which consisted of 3 internal domains, using the reliable docking tool ZDOCK. The dataset was composed of 669 and 44,334 near-native and non-near-native poses, respectively, and it was used to generate eleven informative features. Subsequently, a re-scoring rank was generated by AnkPlex using a combination of a decision tree algorithm and logistic regression. AnkPlex achieved superior efficiency with ≥1 near-native complexes in the 10 top-rankings for nine X-ray complexes compared to ZDOCK, which only obtained six X-ray complexes. In addition, feature analysis demonstrated that the van der Waals feature was the dominant near-native pose out of the potential ankyrin-protein docking poses.
CONCLUSION: The AnkPlex model achieved a success at predicting near-native docking poses and led to the discovery of informative characteristics that could further improve our understanding of the ankyrin-protein complex. Our computational study could be useful for predicting the near-native poses of binding proteins and desired targets, especially for ankyrin-protein complexes. The AnkPlex web server is freely accessible at http://ankplex.ams.cmu.ac.th .

Matched MeSH terms: Proteins/chemistry
ENRI: A tool for selecting structure-based virtual screening target conformations

Akbar R, Jusoh SA, Amaro RE, Helms V

Chem Biol Drug Des, 2017 May;89(5):762-771.
PMID: 27995760 DOI: 10.1111/cbdd.12900

Finding pharmaceutically relevant target conformations from an arbitrary set of protein conformations remains a challenge in structure-based virtual screening (SBVS). The growth in the number of available conformations, either experimentally determined or computationally derived, obscures the situation further. While the inflated conformation space potentially contains viable druggable targets, the increase of conformational complexity, as a consequence, poses a selection problem. To address this challenge, we took advantage of machine learning methods, namely an over-sampling and a binary classification procedure, and present a novel method to select druggable receptor conformations. Specifically, we trained a binary classifier on a set of nuclear receptor conformations, wherein each conformation was labeled with an enrichment measure for a corresponding SBVS. The classifier enabled us to formulate suggestions and identify enriching SBVS targets for six of seven nuclear receptors. Further, the classifier can be extended to other proteins of interest simply by feeding new training data sets to the classifier. Our work, thus, provides a methodology to identify pharmaceutically interesting receptor conformations for nuclear receptors and other drug targets.

Matched MeSH terms: Proteins/chemistry*
Samira-VP: A simple protein alignment method with rechecking the alphabet vector positions

Fotoohifiroozabadi S, Mohamad MS, Deris S

J Bioinform Comput Biol, 2017 Apr;15(2):1750004.
PMID: 28274174 DOI: 10.1142/S0219720017500044

Protein structure alignment and comparisons that are based on an alphabetical demonstration of protein structure are more simple to run with faster evaluation processes; thus, their accuracy is not as reliable as three-dimension (3D)-based tools. As a 1D method candidate, TS-AMIR used the alphabetic demonstration of secondary-structure elements (SSE) of proteins and compared the assigned letters to each SSE using the [Formula: see text]-gram method. Although the results were comparable to those obtained via geometrical methods, the SSE length and accuracy of adjacency between SSEs were not considered in the comparison process. Therefore, to obtain further information on accuracy of adjacency between SSE vectors, the new approach of assigning text to vectors was adopted according to the spherical coordinate system in the present study. Moreover, dynamic programming was applied in order to account for the length of SSE vectors. Five common datasets were selected for method evaluation. The first three datasets were small, but difficult to align, and the remaining two datasets were used to compare the capability of the proposed method with that of other methods on a large protein dataset. The results showed that the proposed method, as a text-based alignment approach, obtained results comparable to both 1D and 3D methods. It outperformed 1D methods in terms of accuracy and 3D methods in terms of runtime.

Matched MeSH terms: Proteins/chemistry*
Molecular Modeling and Simulation of Transketolase from Orthosiphon stamineus

Ng ML, Rahmat ZB, Bin Omar MSS

Curr Comput Aided Drug Des, 2019;15(4):308-317.
PMID: 30345923 DOI: 10.2174/1573409914666181022141753

BACKGROUND: Orthosiphon stamineus is a traditional medicinal plant in Southeast Asia countries with various well-known pharmacological activities such as antidiabetic, diuretics and antitumor activities. Transketolase is one of the proteins identified in the leaves of the plant and transketolase is believed able to lower blood sugar level in human through non-pancreatic mechanism. In order to understand the protein behavioral properties, 3D model of transketolase and analysis of protein structure are of obvious interest.
METHODS: In the present study, 3D model of transketolase was constructed and its atomic characteristics revealed. Besides, molecular dynamic simulation of the protein at 310 K and 368 K deciphered transketolase may be a thermophilic protein as the structure does not distort even at elevated temperature. This study also used the protein at 310 K and 368 K resimulated back at 310 K environment.
RESULTS: The results revealed that the protein is stable at all condition which suggest that it has high capacity to adapt at different environment not only at high temperature but also from high temperature condition to low temperature where the structure remains unchanged while retaining protein function.
CONCLUSION: The thermostability properties of transketolase is beneficial for pharmaceutical industries as most of the drug making processes are at high temperature condition.

Matched MeSH terms: Plant Proteins/chemistry*
Investigations on the interactions of proteins with nanocellulose produced via sulphuric acid hydrolysis

Gunathilake TMSU, Ching YC, Uyama H, Nguyen DH, Chuah CH

Int J Biol Macromol, 2021 Dec 15;193(Pt B):1522-1531.
PMID: 34740692 DOI: 10.1016/j.ijbiomac.2021.10.215

The investigation of protein-nanoparticle interactions contributes to the understanding of nanoparticle bio-reactivity and creates a database of nanoparticles for use in nanomedicine, nanodiagnosis, and nanotherapy. In this study, hen's egg white was used as the protein source to study the interaction of proteins with sulphuric acid hydrolysed nanocellulose (CNC). Several techniques such as FTIR, zeta potential measurement, UV-vis spectroscopy, compressive strength, TGA, contact angle and FESEM provide valuable information in the protein-CNC interaction study. The presence of a broader peak in the 1600-1050 cm-1 range of CNC/egg white protein FTIR spectrum compared to the 1600-1050 cm-1 range of CNC sample indicated the binding of egg white protein to CNC surface. The contact angle with the glass surface decreased with the addition of CNC to egg white protein. The FESEM EDX spectra showed a higher amount of N and Na on the surface of CNC. It indicates the density of protein molecules higher around CNC. The zeta potential of CNC changed from -26.7 ± 0.46 to -21.7 ± 0.2 with the introduction of egg white protein due to the hydrogen bonding, polar bonds and electrostatic interaction between surface CNC and protein. The compressive strength of the egg white protein films increased from 0.064 ± 0.01 to 0.36 ± 0.02 MPa with increasing the CNC concentration from 0 to 4.73% (w/v). The thermal decomposition temperature of CNC/egg white protein decreased compared to egg white protein thermal decomposition temperature. According to UV-Vis spectroscopy, the far-UV light (207-222nm) absorption peak slightly changed in the CNC/egg white protein spectrum compared to the egg white protein spectrum. Based on the results, the observations of protein nanoparticle interactions provide an additional understanding, besides the theoretical simulations from previous studies. Also, the results indicate to aim CNC for the application of nanomedicine and nanotherapy. A new insight given by us in this research assumes a reasonable solution to these crucial applications.

Matched MeSH terms: Proteins/chemistry*
TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

Cao H, Ng MCK, Jusoh SA, Tai HK, Siu SWI

J Comput Aided Mol Des, 2017 Sep;31(9):855-865.
PMID: 28864946 DOI: 10.1007/s10822-017-0047-0

[Formula: see text]-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM . Website is implemented in PHP, MySQL and Apache, with all major browsers supported.

Matched MeSH terms: Membrane Proteins/chemistry*
Fulltext Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure

Ishak SNH, Aris SNAM, Halim KBA, Ali MSM, Leow TC, Kamarudin NHA, et al.

Molecules, 2017 Sep 25;22(10).
PMID: 28946656 DOI: 10.3390/molecules22101574

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacilluszalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Matched MeSH terms: Bacterial Proteins/chemistry
Fulltext The Effect of N-Terminal Domain Removal towards the Biochemical and Structural Features of a Thermotolerant Lipase from an Antarctic Pseudomonas sp. Strain AMS3

Latip W, Raja Abd Rahman RNZ, Leow ATC, Mohd Shariff F, Kamarudin NHA, Mohamad Ali MS

Int J Mol Sci, 2018 Feb 13;19(2).
PMID: 29438291 DOI: 10.3390/ijms19020560

Lipase plays an important role in industrial and biotechnological applications. Lipases have been subject to modification at the N and C terminals, allowing better understanding of lipase stability and the discovery of novel properties. A thermotolerant lipase has been isolated from Antarctic Pseudomonas sp. The purified Antarctic AMS3 lipase (native) was found to be stable across a broad range of temperatures and pH levels. The lipase has a partial Glutathione-S-transferase type C (GST-C) domain at the N-terminal not found in other lipases. To understand the influence of N-terminal GST-C domain on the biochemical and structural features of the native lipase, the deletion of the GST-C domain was carried out. The truncated protein was successfully expressed in E. coli BL21(DE3). The molecular weight of truncated AMS3 lipase was approximately ~45 kDa. The number of truncated AMS3 lipase purification folds was higher than native lipase. Various mono and divalent metal ions increased the activity of the AMS3 lipase. The truncated AMS3 lipase demonstrated a similarly broad temperature range, with the pH profile exhibiting higher activity under alkaline conditions. The purified lipase showed a substrate preference for a long carbon chain substrate. In addition, the enzyme activity in organic solvents was enhanced, especially for toluene, Dimethylsulfoxide (DMSO), chloroform and xylene. Molecular simulation revealed that the truncated lipase had increased structural compactness and rigidity as compared to native lipase. Removal of the N terminal GST-C generally improved the lipase biochemical characteristics. This enzyme may be utilized for industrial purposes.

Matched MeSH terms: Bacterial Proteins/chemistry*
Fulltext Analysis of viral diversity for vaccine target discovery

Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS, et al.

BMC Med Genomics, 2017 12 21;10(Suppl 4):78.
PMID: 29322922 DOI: 10.1186/s12920-017-0301-2

BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets.
RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis.
CONCLUSION: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

Matched MeSH terms: Viral Proteins/chemistry
Intensification of Inclusion Body Processing via Temperature-Based Refolding

Wong RS, Alias NNM, Ong EBB, Liew MWO

Methods Mol Biol, 2023;2617:189-200.
PMID: 36656525 DOI: 10.1007/978-1-0716-2930-7_13

Inclusion bodies (IB) are dense insoluble aggregates of mostly misfolded polypeptides that usually result from recombinant protein overexpression. IB formation has been observed in protein expression systems such as E. coli, yeast, and higher eukaryotes. To recover soluble recombinant proteins in their native state, IB are commonly first solubilized with a high concentration of denaturant. This is followed by concurrent denaturant removal or reduction and a transition into a refolding-favorable chemical environment to facilitate the refolding of solubilized protein to its native state. Due to the high concentration of denaturant used, conventional refolding approaches can result in dilute products and are buffer inefficient. To circumvent the limitations of conventional refolding approaches, a temperature-based refolding approach which combines a low concentration of denaturant (0.5 M guanidine hydrochloride, GdnHCl) with a high temperature (95 °C) during solubilization was proposed. In this chapter, we describe a temperature-based refolding approach for the recovery of core streptavidin (cSAV) from IB. Through the temperature-based approach, intensification was achieved through the elimination of a concentration step which would be required by a dilution approach and through a reduction in buffer volumes required for dilution or denaturant removal. High-temperature treatment during solubilization may have also resulted in the denaturation and aggregation of undesired host-cell proteins, which could then be removed through a centrifugation step resulting in refolded cSAV of high purity without the need for column purification. Refolded cSAV was characterized by biotin-binding assay and SDS-PAGE, while purity was determined by RP-HPLC.

Matched MeSH terms: Recombinant Proteins/chemistry
Molecular Modeling and Dynamic Simulation of Arabidopsis Thaliana Carotenoid Cleavage Dioxygenase Gene: A Comparison with Bixa orellana and Crocus Sativus

Priya R, Sneha P, Rivera Madrid R, Doss CGP, Singh P, Siva R

J Cell Biochem, 2017 09;118(9):2712-2721.
PMID: 28145590 DOI: 10.1002/jcb.25919

Carotenoid cleavage dioxygenase (CCD) gene, ubiquitously found in numerous types of plants, are eminent in synthesizing the various volatile compounds (β-ionone, C13-norisoprenoid, geranylacetone) known as apocarotenoids. These apocarotenoids have various biological functions such as volatile signals, allelopathic interaction and plant defense. In Arabidopsis genome sequence, four potential CCD genes have been identified namely CCD1, CCD4, CCD7, and CCD8. These four genes give rise to diverse biological functions with almost similar sequence identity. In this investigation, an in silico analysis was proposed to study CCD proteins in Arabidopsis thaliana, aiming at constructing three-dimensional (3D) structure for CCD1 proteins of Bixa orellana and Crocus sativus to observe the structural difference among AtCCD (A. thaliana CCD) proteins. The quality of modeled structures was evaluated using RAMPAGE, PSVS protein validation server and Q Mean server. Finally, we utilised molecular dynamics simulation to identify the stability of the predicted CCD protein structures. The molecular dynamic simulation also revealed that AtCCD4 protein showed lesser stability when compared to other CCD proteins. Overall results from molecular dynamics analysis predicted that BoCCD1, CsCCD1, and AtCCD1 show similar structural characteristics. J. Cell. Biochem. 118: 2712-2721, 2017. © 2017 Wiley Periodicals, Inc.

Matched MeSH terms: Arabidopsis Proteins/chemistry*
Fulltext NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning

Høie MH, Kiehl EN, Petersen B, Nielsen M, Winther O, Nielsen H, et al.

Nucleic Acids Res, 2022 Jul 05;50(W1):W510-W515.
PMID: 35648435 DOI: 10.1093/nar/gkac439

Recent advances in machine learning and natural language processing have made it possible to profoundly advance our ability to accurately predict protein structures and their functions. While such improvements are significantly impacting the fields of biology and biotechnology at large, such methods have the downside of high demands in terms of computing power and runtime, hampering their applicability to large datasets. Here, we present NetSurfP-3.0, a tool for predicting solvent accessibility, secondary structure, structural disorder and backbone dihedral angles for each residue of an amino acid sequence. This NetSurfP update exploits recent advances in pre-trained protein language models to drastically improve the runtime of its predecessor by two orders of magnitude, while displaying similar prediction performance. We assessed the accuracy of NetSurfP-3.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features, with a runtime that is up to to 600 times faster than the most commonly available methods performing the same tasks. The tool is freely available as a web server with a user-friendly interface to navigate the results, as well as a standalone downloadable package.

Matched MeSH terms: Proteins/chemistry
Fulltext Immobilization of α-Amylase from Anoxybacillus sp. SK3-4 on ReliZyme and Immobead Supports

Kahar UM, Sani MH, Chan KG, Goh KM

Molecules, 2016 Sep 09;21(9).
PMID: 27618002 DOI: 10.3390/molecules21091196

α-Amylase from Anoxybacillus sp. SK3-4 (ASKA) is a thermostable enzyme that produces a high level of maltose from starches. A truncated ASKA (TASKA) variant with improved expression and purification efficiency was characterized in an earlier study. In this work, TASKA was purified and immobilized through covalent attachment on three epoxide (ReliZyme EP403/M, Immobead IB-150P, and Immobead IB-150A) and an amino-epoxide (ReliZyme HFA403/M) activated supports. Several parameters affecting immobilization were analyzed, including the pH, temperature, and quantity (mg) of enzyme added per gram of support. The influence of the carrier surface properties, pore sizes, and lengths of spacer arms (functional groups) on biocatalyst performances were studied. Free and immobilized TASKAs were stable at pH 6.0-9.0 and active at pH 8.0. The enzyme showed optimal activity and considerable stability at 60 °C. Immobilized TASKA retained 50% of its initial activity after 5-12 cycles of reuse. Upon degradation of starches and amylose, only immobilized TASKA on ReliZyme HFA403/M has comparable hydrolytic ability with the free enzyme. To the best of our knowledge, this is the first report of an immobilization study of an α-amylase from Anoxybacillus spp. and the first report of α-amylase immobilization using ReliZyme and Immobeads as supports.

Matched MeSH terms: Bacterial Proteins/chemistry*
Fulltext Implications of partial conjugation of whey protein isolate to durian seed gum through Maillard reactions: foaming properties, water holding capacity and interfacial activity

Amid BT, Mirhosseini H, Poorazarang H, Mortazavi SA

Molecules, 2013 Dec 06;18(12):15110-25.
PMID: 24322494 DOI: 10.3390/molecules181215110

This paper deals with the conjugation of durian seed gum (DSG) with whey protein isolate (WPI) through Maillard reactions. Subsequently, the functional properties of durian seed gum in the non-conjugated (control sample) and conjugated forms were compared with several commercial gums (i.e., Arabic gum, sodium alginate, kappa carrageenan, guar gum, and pectin). The current study revealed that the conjugation of durian seed gum with whey protein isolate significantly (p < 0.05) improved its foaming properties. In this study, the conjugated durian seed gum produced the most stable foam among all samples. On the other hand, the emulsion stabilized with the conjugated durian seed gum also showed more uniform particles with a larger specific surface area than the emulsion containing the non-conjugated durian seed gum. The conjugated durian seed gum showed significant different foaming properties, specific surface area, particle uniformity and water holding capacity (WHC) as compared to the target polysaccharide gums. The conjugated durian seed gum showed more similar functional properties to Arabic gum rather than other studied gums.

Matched MeSH terms: Milk Proteins/chemistry*
Crystallization and X-ray analysis of the T = 4 particle of hepatitis B capsid protein with an N-terminal extension

Tan WS, McNae IW, Ho KL, Walkinshaw MD

Acta Crystallogr Sect F Struct Biol Cryst Commun, 2007 Aug 01;63(Pt 8):642-7.
PMID: 17671358

Hepatitis B core (HBc) particles have been extensively exploited as carriers for foreign immunological epitopes in the development of multicomponent vaccines and diagnostic reagents. Crystals of the T = 4 HBc particle were grown in PEG 20,000, ammonium sulfate and various types of alcohols. A temperature jump from 277 or 283 to 290 K was found to enhance crystal growth. A crystal grown using MPD as a cryoprotectant diffracted X-rays to 7.7 A resolution and data were collected to 99.6% completeness at 8.9 A. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 352.3, b = 465.5, c = 645.0 A. The electron-density map reveals a protrusion that is consistent with the N-terminus extending out from the surface of the capsid. The structure presented here supports the idea that N-terminal insertions can be exploited in the development of diagnostic reagents, multicomponent vaccines and delivery vehicles into mammalian cells.

Matched MeSH terms: Nucleocapsid Proteins/chemistry*

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