Displaying publications 1 - 20 of 578 in total

  1. Iqbal MJ, Faye I, Samir BB, Said AM
    ScientificWorldJournal, 2014;2014:173869.
    PMID: 25045727 DOI: 10.1155/2014/173869
    Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth.
    Matched MeSH terms: Proteins/chemistry*
  2. Krishnan H, Gopinath SCB
    Int J Biol Macromol, 2023 Aug 30;247:125740.
    PMID: 37423441 DOI: 10.1016/j.ijbiomac.2023.125740
    Anticoagulant therapies are crucial in the management of surgical complications as well as the prophylaxis of thrombosis. Many studies are being conducted on the Habu snake-venom anticoagulant, FIX-binding protein (FIX-Bp), for its greater potency and strong affinity to FIX clotting factor. On the other hand, the capacity to promptly reverse such acute anticoagulation is equally important. Combining a reversible anticoagulant with FIX-Bp may be advantageous in maintaining the balance between adequate anticoagulation and repealing when necessary. In this study, authors integrated FIX-Bp and RNA aptamer-based anticoagulants into a single target, FIX clotting factor, in order to achieve a robust anticoagulant effect. An in-silico and electrochemical approach were used to investigate the combination of FIX-Bp and RNA aptamers as a bivalent anticoagulant and to verify the competing or predominant binding sites of each anticoagulant. The in-silico analysis discovered that both the venom- and aptamer-anticoagulant had a strong affinity for the FIX protein at the Gla-domain and EGF-1 domain by holding 9 conventional hydrogen bonds with the binding energy of -34.859 kcal/mol. The electrochemical technique verified that both anticoagulants had different binding sites. The impedance load upon RNA aptamer binding to FIX protein was 14 %, whereas the addition of FIX-Bp caused a significant impedance rise of 37 %. This indicates that the addition of aptamers prior to FIX-Bp is a promising strategy for the conception of a hybrid anticoagulant.
    Matched MeSH terms: Carrier Proteins/chemistry
  3. Alias FL, Nezhad NG, Normi YM, Ali MSM, Budiman C, Leow TC
    Mol Biotechnol, 2023 Nov;65(11):1737-1749.
    PMID: 36971996 DOI: 10.1007/s12033-023-00725-y
    Heterologous functional expression of the recombinant lipases is typically a bottleneck due to the expression in the insoluble fraction as inclusion bodies (IBs) which are in inactive form. Due to the importance of lipases in various industrial applications, many investigations have been conducted to discover suitable approaches to obtain functional lipase or increase the expressed yield in the soluble fraction. The utilization of the appropriate prokaryotic and eukaryotic expression systems, along with the suitable vectors, promoters, and tags, has been recognized as a practical approach. One of the most powerful strategies to produce bioactive lipases is using the molecular chaperones co-expressed along with the target protein's genes into the expression host to produce the lipase in soluble fraction as a bioactive form. The refolding of expressed lipase from IBs (inactive) is another practical strategy which is usually carried out through chemical and physical methods. Based on recent investigations, the current review simultaneously highlights strategies to express the bioactive lipases and recover the bioactive lipases from the IBs in insoluble form.
    Matched MeSH terms: Recombinant Proteins/chemistry
  4. Barakat A, Ghabbour HA, Al-Majid AM, Soliman SM, Ali M, Mabkhot YN, et al.
    Molecules, 2015;20(7):13240-63.
    PMID: 26197312 DOI: 10.3390/molecules200713240
    The synthesis of 2,6-bis(hydroxy(phenyl)methyl)cyclohexanone 1 is described. The molecular structure of the title compound 1 was confirmed by NMR, FT-IR, MS, CHN microanalysis, and X-ray crystallography. The molecular structure was also investigated by a set of computational studies and found to be in good agreement with the experimental data obtained from the various spectrophotometric techniques. The antimicrobial activity and molecular docking of the synthesized compound was investigated.
    Matched MeSH terms: Bacterial Proteins/chemistry*; Fungal Proteins/chemistry*
  5. Anbu P, Gopinath SCB, Chaulagain BP, Lakshmipriya T
    Biomed Res Int, 2017 03 28;2017:2195808.
    PMID: 28459056 DOI: 10.1155/2017/2195808
    Matched MeSH terms: Bacterial Proteins/chemistry*; Fungal Proteins/chemistry*
  6. Ngo TA, Dinh H, Nguyen TM, Liew FF, Nakata E, Morii T
    Chem Commun (Camb), 2019 Oct 15;55(83):12428-12446.
    PMID: 31576822 DOI: 10.1039/c9cc04661e
    DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.
    Matched MeSH terms: Proteins/chemistry
  7. Low TY, Lee PY
    Methods Mol Biol, 2023;2690:69-80.
    PMID: 37450137 DOI: 10.1007/978-1-0716-3327-4_6
    Proteins often interact with each other to form complexes and play functional roles in almost all cellular processes. The study of protein-protein interactions is therefore critical to understand protein function and biological pathways. Affinity Purification coupled with Mass Spectrometry (AP-MS) is an invaluable technique for identifying the interaction partners in protein complexes. In this approach, the protein of interest is fused to an affinity tag, followed by the expression and purification of the fusion protein. The affinity-purified sample is then analyzed by mass spectrometry to identify the interaction partners of the bait proteins. In this chapter, we detail the protocol for tandem affinity purification (TAP) based on the use of the FLAG (a fusion tag with peptide sequence DYKDDDDK) and hemagglutinin (HA) peptide epitopes. The immunoprecipitation using dual-affinity tags offers the advantage of increasing the specificity of the purification with lower nonspecific-background interactions.
    Matched MeSH terms: Proteins/chemistry
  8. Wijekoon MMJO, Mahmood K, Ariffin F, Mohammadi Nafchi A, Zulkurnain M
    Int J Biol Macromol, 2023 Jun 30;241:124539.
    PMID: 37085081 DOI: 10.1016/j.ijbiomac.2023.124539
    Fat-soluble vitamins (FSVs) offer a range of beneficial properties as important nutrients in human nutrition. However, the high susceptibility to environmental conditions such as high temperature, light, and oxygen leads to the degradation of these compounds. This review highlights the different formulations underlying the encapsulation of FSVs in biopolymer (polysaccharide and protein) and lipid-based micro or nanocarriers for potential applications in food and pharmaceutical industries. In particular, the function of these carrier systems in terms of encapsulation efficiency, stability, bioavailability, and bio-accessibility is critically discussed. Recently, tremendous attention has been paid to encapsulating FSVs in commercial applications. According to the chemical nature of the active compound, the vigilant selection of delivery formulation, method of encapsulation, and final application (type of food) are the key important factors to be considered in the encapsulation of FSVs to ensure a high loading capacity, stability, bioavailability, and bio-accessibility. Future studies are recommended on the effect of different vitamin types and micro and nano encapsulate sizes on bioaccessibility and biocompatibility through in vitro/in vivo studies. Moreover, the toxicity and safety evaluation of encapsulated FSVs in human health should be evaluated before commercial application in food and pharmaceuticals.
    Matched MeSH terms: Proteins/chemistry
  9. Abd Rahim FN, Wan Ibadullah WZ, Saari N, Brishti FH, Mustapha NA, Ahmad N, et al.
    Int J Biol Macromol, 2023 Jul 01;242(Pt 3):124908.
    PMID: 37217045 DOI: 10.1016/j.ijbiomac.2023.124908
    Rice bran protein concentrates (RBPC) were extracted using mild alkaline solvents (pH: 8, 9, 10). The physicochemical, thermal, functional, and structural aspects of freeze-drying (FD) and spray-drying (SD) were compared. FD and SD of RBPC had porous and grooved surfaces, with FD having non-collapsed plates and SD being spherical. Alkaline extraction increases FD's protein concentration and browning, whereas SD inhibits browning. According to amino acid profiling, RBPC-FD9's extraction optimizes and preserves amino acids. A tremendous particle size difference was prominent in FD, thermally stable at a minimal maximum of 92 °C. Increased pH extraction gives FD greater exposal surface hydrophobicity and positively relates to denaturation enthalpy. Mild pH extraction and drying significantly impacted solubility, improved emulsion properties, and foaming properties of RBPC as observed in acidic, neutral, and alkaline environments. RBPC-FD9 and RBPC-SD10 extracts exhibit outstanding foaming and emulsion activity in all pH conditions, respectively. Appropriate drying selection, RBPC-FD or SD potentially employed as foaming/emulsifier agent or meat analog.
    Matched MeSH terms: Plant Proteins/chemistry
  10. Yu H, Zheng Y, Zhou C, Liu L, Wang L, Cao J, et al.
    Carbohydr Polym, 2024 Feb 01;325:121583.
    PMID: 38008470 DOI: 10.1016/j.carbpol.2023.121583
    The potential of ultrasonication-driven molecular self-assembly of whey protein isolate (WPI) with chitosan (CS)/chitooligosaccharide (COS) to stabilize Pickering emulsions was examined, based on CS/COS ligands-induced partial unfolding in remodeling the Pickering particles features. Multi-spectral analysis suggested obvious changes in conformational structures of WPI due to interaction with CS/COS, with significantly higher unfolding degrees of WPI induced by COS. Non-covalent interactions were identified as the major forces for WPI-CS/COS conjugates. Ultrasonication enhanced electrostatic interaction between CS's -NH3 groups and WPI's -COO- groups which improved emulsification activity and storability of WPI-COS stabilized Pickering emulsion. This was attributed to increased surface hydrophobicity and decreased particle size compared to WPI-CS associated with differential unfolding degrees induced by different saccharide ligands. CLSM and SEM consistently observed smaller emulsion droplets in WPI-COS complexes than WPI-CS/COS particles tightly adsorbed at the oil-water interface. The electrostatic self-assembly of WPI with CS/COS greatly enhanced the encapsulation efficiency of quercetin than those stabilized by WPI alone and ultrasound further improved encapsulation efficiency. This corresponded well with the quantitative affinity parameters between quercetin and WPI-CS/COS complexes. This investigation revealed the great potential of glycan ligands-induced conformational transitions of extrinsic physical disruption in tuning Pickering particle features.
    Matched MeSH terms: Whey Proteins/chemistry
  11. Chan YP, Koh CL, Lam SK, Wang LF
    J Gen Virol, 2004 Jun;85(Pt 6):1675-1684.
    PMID: 15166452 DOI: 10.1099/vir.0.19752-0
    Hendra virus (HeV) and Nipah virus (NiV) are members of a new genus, Henipavirus, in the family paramyxoviridae. Each virus encodes a phosphoprotein (P) that is significantly larger than its counterparts in other known paramyxoviruses. The interaction of this unusually large P with its nucleocapsid protein (N) was investigated in this study by using recombinant full-length and truncated proteins expressed in bacteria and a modified protein-blotting protein-overlay assay. Results from our group demonstrated that the N and P of both viruses were able to form not only homologous, but also heterologous, N-P complexes, i.e. HeV N was able to interact with NiV P and vice versa. Deletion analysis of the N and P revealed that there were at least two independent N-binding sites on P and they resided at the N and C termini, respectively. Similarly, more than one P-binding site was present on N and one of these was mapped to a 29 amino acid (aa) C-terminal region, which on its own was sufficient to interact with the extreme C-terminal 165 aa region of P.
    Matched MeSH terms: Recombinant Proteins/chemistry; Viral Proteins/chemistry*; Nucleocapsid Proteins/chemistry*
  12. Yeoh LC, Loh CK, Gooi BH, Singh M, Gam LH
    World J Gastroenterol, 2010 Jun 14;16(22):2754-63.
    PMID: 20533595
    AIM: To identify differentially expressed hydrophobic proteins in colorectal cancer.

    METHODS: Eighteen pairs of colorectal cancerous tissues in addition to tissues from normal mucosa were analysed. Hydrophobic proteins were extracted from the tissues, separated using 2-D gel electrophoresis and analysed using Liquid Chromatography Tandem Mass Spectrometry (LC/MS/MS). Statistical analysis of the proteins was carried out in order to determine the significance of each protein to colorectal cancer (CRC) and also their relation to CRC stages, grades and patients' gender.

    RESULTS: Thirteen differentially expressed proteins which were expressed abundantly in either cancerous or normal tissues were identified. A number of these proteins were found to relate strongly with a particular stage or grade of CRC. In addition, the association of these proteins with patient gender also appeared to be significant.

    CONCLUSION: Stomatin-like protein 2 was found to be a promising biomarker for CRC, especially in female patients. The differentially expressed proteins identified were associated with CRC and may act as drug target candidates.

    Matched MeSH terms: Blood Proteins/chemistry; Membrane Proteins/chemistry; Neoplasm Proteins/chemistry*
  13. Alballa M, Aplop F, Butler G
    PLoS One, 2020;15(1):e0227683.
    PMID: 31935244 DOI: 10.1371/journal.pone.0227683
    Transporters mediate the movement of compounds across the membranes that separate the cell from its environment and across the inner membranes surrounding cellular compartments. It is estimated that one third of a proteome consists of membrane proteins, and many of these are transport proteins. Given the increase in the number of genomes being sequenced, there is a need for computational tools that predict the substrates that are transported by the transmembrane transport proteins. In this paper, we present TranCEP, a predictor of the type of substrate transported by a transmembrane transport protein. TranCEP combines the traditional use of the amino acid composition of the protein, with evolutionary information captured in a multiple sequence alignment (MSA), and restriction to important positions of the alignment that play a role in determining the specificity of the protein. Our experimental results show that TranCEP significantly outperforms the state-of-the-art predictors. The results quantify the contribution made by each type of information used.
    Matched MeSH terms: Carrier Proteins/chemistry; Membrane Proteins/chemistry; Membrane Transport Proteins/chemistry*
  14. Lim CS, Goh SL, Kariapper L, Krishnan G, Lim YY, Ng CC
    Clin Chim Acta, 2015 Aug 25;448:206-10.
    PMID: 26164385 DOI: 10.1016/j.cca.2015.07.008
    Development of indirect enzyme-linked immunosorbent assays (ELISAs) often utilizes synthetic peptides or recombinant proteins from Escherichia coli as immobilized antigens. Because inclusion bodies (IBs) formed during recombinant protein expression in E. coli are commonly thought as misfolded aggregates, only refolded proteins from IBs are used to develop new or in-house diagnostic assays. However, the promising utilities of IBs as nanomaterials and immobilized enzymes as shown in recent studies have led us to explore the potential use of IBs of recombinant Epstein-Barr virus viral capsid antigen p18 (VCA p18) as immobilized antigens in ELISAs for serologic detection of nasopharyngeal carcinoma (NPC).
    Matched MeSH terms: Recombinant Proteins/chemistry; Capsid Proteins/chemistry; Immobilized Proteins/chemistry
  15. Shaibullah S, Mohd-Sharif N, Ho KL, Firdaus-Raih M, Nathan S, Mohamed R, et al.
    Acta Crystallogr F Struct Biol Commun, 2014 Dec 1;70(Pt 12):1697-700.
    PMID: 25484229 DOI: 10.1107/S2053230X14025278
    Melioidosis is an infectious disease caused by the pathogenic bacterium Burkholderia pseudomallei. Whole-genome sequencing revealed that the B. pseudomallei genome includes 5855 coding DNA sequences (CDSs), of which ∼25% encode hypothetical proteins. A pathogen-associated hypothetical protein, BPSL1038, was overexpressed in Escherichia coli, purified and crystallized using vapour-diffusion methods. A BPSL1038 protein crystal that grew using sodium formate as precipitant diffracted to 1.55 Å resolution. It belonged to space group C2221, with unit-cell parameters a = 85.36, b = 115.63, c = 46.73 Å. The calculated Matthews coefficient (VM) suggests that there are two molecules per asymmetric unit, with a solvent content of 48.8%.
    Matched MeSH terms: Bacterial Proteins/chemistry*
  16. Wu T, Wang X, Zhang Z, Gong F, Song T, Chen Z, et al.
    J Bioinform Comput Biol, 2016 06;14(3):1650013.
    PMID: 27225342 DOI: 10.1142/S021972001650013X
    A nuclear export signal (NES) is a protein localization signal, which is involved in binding of cargo proteins to nuclear export receptor, thus contributes to regulate localization of cellular proteins. Consensus sequences of NES have been used to detect NES from protein sequences, but suffer from poor predictive power. Some recent peering works were proposed to use biochemical properties of experimental verified NES to refine NES candidates. Those methods can achieve high prediction rates, but their execution time will become unacceptable for large-scale NES searching if too much properties are involved. In this work, we developed a novel computational approach, named NES-REBS, to search NES from protein sequences, where biochemical properties of experimental verified NES, including secondary structure and surface accessibility, are utilized to refine NES candidates obtained by matching popular consensus sequences. We test our method by searching 262 experimental verified NES from 221 NES-containing protein sequences. It is obtained that NES-REBS runs in 2-3[Formula: see text]mins and performs well by achieving precision rate 47.2% and sensitivity 54.6%.
    Matched MeSH terms: Proteins/chemistry*
  17. Chay SY, Tan WK, Saari N
    J Microencapsul, 2015;32(5):488-95.
    PMID: 26079597 DOI: 10.3109/02652048.2015.1057250
    The aim of this study was to produce and characterise nanosize liposomes containing bioactive peptides with antioxidative and ACE-inhibitory properties, derived from winged bean seeds (WBS) protein. WBS powder was papain-proteolysed, at 70 °C and pH 6.5 for six hours, followed by encapsulation via a solvent-free heating method. The results showed that the WBS proteolysate was successfully incorporated into spherical, unilamellar liposomal particles, with particle diameter, polydispersity index, zeta potential and encapsulation efficiency of 193.3 ± 0.12 nm, 0.4 ± 0.02 (unit less), -70.5 ± 0.30 mV and 27.6 ± 1.17%, respectively. It also demonstrated good storage stability over eight weeks at 4 °C, indicated by slight increment (15.1%) in particle size and a zeta potential only weaker by 17.2% at the end of the study period. These results suggested the feasibility of entrapping water soluble peptides in hydrophobic liposomal system that, upon optimisation, has the potential to act as bioactive food ingredient.
    Matched MeSH terms: Seed Storage Proteins/chemistry*
  18. Gopinath SC, Anbu P, Lakshmipriya T, Tang TH, Chen Y, Hashim U, et al.
    Biomed Res Int, 2015;2015:140726.
    PMID: 26180780 DOI: 10.1155/2015/140726
    Keratinases are proteolytic enzymes predominantly active when keratin substrates are available that attack disulfide bridges in the keratin to convert them from complex to simplified forms. Keratinases are essential in preparation of animal nutrients, protein supplements, leather manufacture, textile processing, detergent formulation, feather meal processing for feed and fertilizer, the pharmaceutical and biomedical industries, and waste management. Accordingly, it is necessary to develop a method for continuous production of keratinase from reliable sources that can be easily managed. Microbial keratinase is less expensive than conventionally produced keratinase and can be obtained from fungi, bacteria, and actinomycetes. In this overview, the expansion of information about microbial keratinases and important considerations in keratinase production are discussed.
    Matched MeSH terms: Bacterial Proteins/chemistry*
  19. Sillitoe I, Andreeva A, Blundell TL, Buchan DWA, Finn RD, Gough J, et al.
    Nucleic Acids Res, 2020 01 08;48(D1):D314-D319.
    PMID: 31733063 DOI: 10.1093/nar/gkz967
    Genome3D (https://www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being 'pushed' to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms.
    Matched MeSH terms: Proteins/chemistry*
  20. Ishak SNH, Kamarudin NHA, Ali MSM, Leow ATC, Rahman RNZRA
    Molecules, 2020 Jul 28;25(15).
    PMID: 32731607 DOI: 10.3390/molecules25153430
    A comparative structure analysis between space- and an Earth-grown T1 recombinant lipase from Geobacillus zalihae had shown changes in the formation of hydrogen bonds and ion-pair interactions. Using the space-grown T1 lipase validated structure having incorporated said interactions, the recombinant T1 lipase was re-engineered to determine the changes brought by these interactions to the structure and stability of lipase. To understand the effects of mutation on T1 recombinant lipase, five mutants were developed from the structure of space-grown T1 lipase and biochemically characterized. The results demonstrate an increase in melting temperature up to 77.4 °C and 76.0 °C in E226D and D43E, respectively. Moreover, the mutated lipases D43E and E226D had additional hydrogen bonds and ion-pair interactions in their structures due to the improvement of stability, as observed in a longer half-life and an increased melting temperature. The biophysical study revealed differences in β-Sheet percentage between less stable (T118N) and other mutants. As a conclusion, the comparative analysis of the tertiary structure and specific residues associated with ion-pair interactions and hydrogen bonds could be significant in revealing the thermostability of an enzyme with industrial importance.
    Matched MeSH terms: Recombinant Proteins/chemistry
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