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Protein and Peptide Letters

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https://www.readbyqxmd.com/read/30207215/amyloid-nano-biofibrils-as-a-new-nano-scaffold-for-lipase-immobilization
#1
Samira Vaziri, Mohammad Fazilati, Amir Arasteh, Habibollah Nazem
Amyloids could be created under destabilizing conditions from various proteins. Having high chemical reactive groups makes the amyloid fibers suitable for enzyme stabilization. Response surface methodology was used in this study to produce the maximum amounts of amyloid fibrils using Design Expert 7 software. Transmission electron microscopy was also employed to confirm the presence of amyloid fibers. The stabilization process was performed by glutaraldehyde mediated covalent cross-links between the enzyme and amyloid fibers...
September 11, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30182833/rwlpap-random-walk-for-lncrna-protein-associations-prediction
#2
Qi Zhao, Dan Liang, Huan Hu, Guofei Ren, Hongsheng Liu
During recent years, many experimental studies have shown that lncRNA-binding proteins play a key role in many biomedical processes. Therefore, it is important to predict the potential lncRNA-protein associations in biomedical researches. Considering the limitations of previous computational methods, we introduce a predictive model called random walk for lncRNA-protein associations prediction (RWLPAP). It belongs to semi-supervised learning algorithms, and thus RWLPAP successfully avoids the difficulty of extracting negative data sets and features...
September 4, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30182832/purification-characterization-of-alkaline-cold-active-lipase-from-acinetobacter-radioresistens-pr8-and-development-of-a-new-zymography-method-for-lipase-detection
#3
Krishna Kant Gupta, Sharmili Jagtap, R Priya, Krishna Ramadas
Lipase zymography methods use costly chromogenic substrates and indicator dyes and are few in numbers. In this present work, an alkalophilic lipase producing bacterium was isolated from soil; screened for extracellular lipase activity and identified to be Acinetobacter radioresistens PR8 by 16S rRNA sequencing (Genbank accession ID: MF073322). Enzyme production kinetics showed maximum production (4.16 U/ml at pH 9) of the enzyme after 72 h. The lipase activity was found to be highest in olive oil (1% v/v; 8...
September 4, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30182831/isolation-purification-and-characterisation-of-a-d-galactose-and-n-acetyl-d-galactosamine-specific-lectin-from-marine-sponge-fasciospongia-cavernosa
#4
Ratheesh Sadanandan, Arun A Rauf
A Lectin from marine sponge Fasciospongia cavernosa named FCL was purified by guar gum affinity chromatography. The molecular mass of the lectin was determined to be 80kDa by SDS-PAGE under reducing and non-reducing conditions. It was found to agglutinate human ABO, rat, rabbit and chicken erythrocytes. The hemagglutinating activity of FCL was reduced by demetallisation with E.D.T.A and regained by the addition of Ca2+, Mg2+,Mn2+,Ba2+ and Fe2+, which shows the metal dependency of the lectin. Mg2+The hemagglutinating activity by the lectin was inhibited by D-galactose and N-acetyl-D-galactosamine...
September 4, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30182830/a-comprehensive-review-of-in-silico-analysis-for-protein-s-sulfenylation-sites
#5
Mehedi Hasan, Shamima Khatun, Hiroyuki Kurata
Cysteine S-sulfenylation is a major type of dynamic post-translational modification of proteins that plays an important role in regulating many biological processes in both of prokaryotic and eukaryotic species. To understand the function of S-sulfenylated proteins, identification of S-sulfenylation sites is an essential step. Due to numerous restrictions of experimental methods, computational prediction of the potential S-sulfenylation sites becomes popular. In this review, we discuss the recent development and challenges in protein S-sulfenylation site prediction from the available datasets, algorithms and, accessible services...
September 4, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30182829/a-brief-review-on-software-tools-in-generating-chou-s-pseudo-factor-representations-for-all-types-of-biological-sequences
#6
Wei Zhao, Likun Wang, Tian-Xiang Zhang, Ze-Ning Zhao, Pu-Feng Du
In the post-genome age, it is more urgent to understand the functions of genes and proteins. Since experimental methods are usually costly and time consuming, computational predictions are recognized as an alternative approach. In developing a predictive method for functional genomics and proteomics, one of the most important steps is to represent biological sequences with a fixed length numerical form, which can be further analyzed using machine learning algorithms. Chou's pseudo-amino acid compositions and the pseudo k-nucleotide compositions are algorithms for this purpose...
September 4, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30152276/hypo-a-database-of-hypothetical-human-proteins
#7
Vijayaraghava Seshadri Sundararajan, Girik Malik, Johny Ijaq, Anuj Kumar, Partha Sarathi Das, P R Shidhi, Achuthsankar S Nair, Prashanth Suravajhala, Pawan K Dhar
All annotated genes were once hypothetical or uncharacterized. Keeping this as an epilogue, we have enhanced our erstwhile database of hypothetical proteins (HP) in human (HypoDB) with added annotation, application programming interfaces and descriptive features. The database hosts 1000+ manually curated records of the known unknown regions in the human genome. The new updated version of HypoDB with functionalities (Blast,Match) is freely accessible at http://www.bioclues.org/hypo2.
August 27, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30129402/deranged-metabolic-profile-and-identification-of-biomarkers-in-the-vitreous-humour-of-patients-with-proliferative-diabetic-retinopathy
#8
Nikhil Shri Sahajpal, Vipan Kumar Vig, Rajbir Singh, Harshinder Singh, Alka Chaubey, Kanwardeep Singh, Rajesh Kumar Goel, Subheet Kumar Jain
Systemic biochemical disarray has been implicated in the pathogenesis and progression of diabetes and its complications. The objective of the present study was to investigate the modifications in the metabolic state of the retina and its microenvironment in response to the systemic metabolic mal-function to understand the different pathways and biomarkers that may be involved in the patho-genesis and progression of proliferative diabetic retinopathy (PDR). The vitreous humour and plas-ma samples from 38 PDR, 7 proliferative vitreo retinopathy (PVR) and 17 control patients undergo-ing pars plana vitrectomy were analysed for sixteen different biomarkers...
August 21, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30129401/evaluation-of-selected-parameters-of-lipid-peroxidation-and-paraoxonase-activity-in-blood-of-patients-with-joint-osteoarthritis
#9
Dorota Olszewska-Slonina, Stanislaw Jung, Krzysztof J Olszewski, Anna Cwynar, Gerard Drewa
INTRODUCTION: Oxidative stress constitutes an important risk factor for tissue/cell damage and is involved in the occurrence and progression of osteoarthritis (OA). The aim of this study was to evaluate the concentration of malondialdehyde (MDA) in synovial fluid (SF) and blood as well as the activity of serum and SF paraoxonase (PON1) of patients with OA. Our study aimed to assess local and systemic responses to oxidative stress. The study included 43 subjects with OA qualified to total joint replacement...
August 21, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30129399/an-overview-of-current-methods-to-confirm-protein-protein-interactions
#10
Kenji Miura
The research field of protein-protein interactions is interdisciplinary and specialized field that spans all aspects of biology, physics and chemistry. In this review, I discuss and compare various methods currently utilized to confirm protein-protein interactions. As a result, it is often necessary to integrate and combine multiple results from different methods to understand protein-protein interactions in detail. It might be desirable for the addition of tags, labeling, and immobilization to solid phases to be unnecessary, and to obtain information on affinity, kinetics, and structure via the analytical method for protein-protein interactions...
August 21, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30129400/bromein-a-bromelain-inhibitor-from-the-pineapple-stem-structural-and-functional-characteristics
#11
Ken-Ichi Hatano, Kenji Takahashi, Masaru Tanokura
Bromelain inhibitor, "bromein", is a proteinase-inhibitor specific to the cysteine proteinase bromelain from the pineapple stem. In the stem, eight bromein isoforms are known to exist and each isoform has a short peptide (light chain) and a long one (heavy chain) with five disulfide bonds. The three-dimensional structure of the sixth isoform (bromein-6) is composed of two domains, inhibitory and stabilizing ones, and each domain contains a three-stranded antiparallel β-sheet. The genomic sequence of a bromein precursor encodes three homologous bromein isoform domains, and each isoform domain has a signal peptide, three interchain peptides between the light chain and heavy chain, two interdomain peptides and a propeptide...
August 20, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30091403/vlp-production-from-recombinant-l1-l2-hpv-16-protein-expressed-in-pichia-pastoris
#12
Alireza Sanchooli, Khosrow Aghayipour, Bahman Abedi Kiasari, Alireza Samarbaf-Zadeh, Ataollah Ghadiri, Manoocher Makvandi
Human papillomavirus 16 is considered a causative agent of genital cancers. Since there is no decisive treatment, the only approach is vaccination of high-risk group. Due to the high cost, the current HPV vaccines are not affordable in developing countries. This study aimed to produce a chimeric L1/L2 protein in Pichia Pastoris system. To develop the VLPs retrieved from chimeric L1/L2 protein HPV-16, first, a cross-neutralizing epitope of HPV-16 L2 gene was inserted into L1 HPV-16 gene. The chimeric L1/L2 HPV-16 was inserted in pPICZA plasmid and expressed in Pichia pastoris (P...
August 9, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30091402/insights-into-the-noncoding-rna-encoded-peptides
#13
Jinchang Pan, Xiaodan Meng, Nan Jiang, Xiaofeng Jin, Chengwei Zhou, Dazhi Xu, Zhaohui Gong
Considerable evidence has indicated that most noncoding RNA (ncRNA) transcripts act directly as functional RNAs rather than as encoded peptides. However, a recent study of ribosome occupancy reported that many large intergenic ncRNAs (lincRNAs) are bound by ribosomes, raising the possibility that they are translated into proteins. These lincRNAs contain either internal ribosomal entry sites (IRES) or short open reading frames (sORFs), and other translation elements, which can be translated into peptides with physiological functions...
August 9, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30081784/adjuvant-activity-of-bursal-pentapeptide-iii-v-in-mice-immunized-with-the-h9n2-avian-influenza-vaccine
#14
Chen Wang, Jiangfei Zhou, Cong Zhang, Zhixin Liu, Yongqing Liu, Kairui Cai, Tengfei Shen, Chengshui Liao
Bursal pentapeptide (BPP)-(III-V) are peptides isolated from the bursa of Fabricius (BF). The peptides' adjuvant activities were evaluated in mice immunized with the H9N2 avian influenza vaccine. The results showed that BPP-IV did not promote humoral or cellular immune responses. BPP-III had no effect on antibody production, but increased populations of CD3+ and CD8+ T cells, CTL levels and proliferation activities of splenic T-lymphocytes. BPP-V increased the level of antibodies (HI, IgG and its subtype IgG1) and the cytokine IL-4, as well as the ratio of CD3+ T cells and its subsets CD4+ and CD8+ T cells, BPP-V also increased CTL level and promoted the proliferation activity of T- and B-lymphocyte...
August 5, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30081783/characterization-of-recombinant-phascolosoma-esculenta-ferritin-as-an-efficient-heavy-metal-scavenger
#15
Hongwei Ding, Jun Zhou, Yu Han, Xiurong Su
With economic development, heavy metal pollution in the environment worsens and causes adverse effects on human health. Ferritin, a special protein with a large hollow space inside, is a major iron storage protein playing an important role in iron metabolism. Here, a recombinant plasmid was constructed by using an open reading frame of Phascolosoma esculenta ferritin. The recombinant ferritin was extracted, purified, and refolded. After treatment with different heavy metals under physiological pH conditions, the aggregation structure, changes in the structure, and heavy metal chelating capacity were examined by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), atomic force microscopy (AFM), and inductively coupled plasma mass spectrometry (ICP-MS)...
August 5, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/30081782/sensitive-and-selective-immunofluorescence-assay-for-ca15-3-detection-using-fluorescein-derivative-a10254
#16
Xiao Ting Huang, Haiyang Liu, Wei Fang, Yan Lin, Ying Tan
The determination of carbohydrate antigen 15-3 (CA15-3), a highly important specific cancer biomarker, in serum is essential for early diagnosis and detection of breast cancer. Herein, a sensitive immunofluorescence assay for CA15-3 detection in serum was developed using the antibody-antigen-antibody sandwich format. A10254, a fluorescein derivative, was used to label the CA15-3 antibody to enhance the assay sensitivity. The obtained fluorescence immunosensor could detect CA15-3 with high sensitivity and favorable specificity...
August 5, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29984641/molecular-aspects-of-the-dengue-virus-infection-process-a-review
#17
Luiz Fernando Da Costa Zonetti, Milena Conceicao Coutinho, Alexandre Suman de Araujo
At the present time, dengue is one of the most important arboviruses affecting man, becoming a serious global public health problem, especially in subtropical and tropical countries, where environmental conditions favor the development and proliferation of the mosquito Aedes aegypti. Dengue is caused by a type of flavivírus, which is an enveloped virus of spherical geometry. Nowadays, it is one of the diseases with the highest incidence in Brazil, reaching the population of all states, regardless of social class...
July 8, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29972101/transglycosylation-activity-of-catalytic-domain-mutant-of-endo-1-3-%C3%AE-glucanase-from-cellulosimicrobium-cellulans
#18
Yoshiji Hantani, Shoko Motoki, Atsushi Miyagawa, Hatsuo Yamamura, Masayuki Oda
A mutation of catalytic residue, Glu119 to Gly, in endo-1,3-β-glucanase from Cellulosimicrobium cellulans DK-1 generates the mutant enzyme (E119G) with decreased hydrolytic activity and which exhibits transglycosylation activity on laminarioligosaccharides. Transglycosylation activity was not observed in the case of laminaribiose as a substrate, probably owing to the lower binding affinity of E119G to laminaribiose than to large laminarioligosaccharides. Notably, the combination of laminaribiose and laminaritriose as a substrate enhanced the transglycosylation activity of E119G...
July 3, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29956608/hyaluronidases-a-therapeutic-enzyme
#19
Naqab Khan, Zahid Rasul Niazi, Fazlur Rehman, Anam Akhtar, Maryam Muhammad Khan, Samiullah Khan, Sheraz Khan
BACKGROUND: Hyaluronidase is the most important enzyme found in the interstitial matrix, effectively degrading the hyaluronic acid. Hyaluronidases are extensively found in the venom of various animals such as snake, scorpion, spider and others. Up till now five venom hyaluronidases are identified with a defined three-dimensional structure. These enzymes are involved in different biochemical, physiological and pathological conditions like degradation of hyaluronic acid, embryogenesis, transmembrane diffusion of drugs and toxins, inflammatory and allergic response to antigens, healing of wounds, bacterial meningitis, bacteremia and pneumonia...
June 29, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29956607/phosphodiesterases-pdes-from-snake-venoms-therapeutic-applications
#20
Bushra Uzair, Barkat Ali Khan, Nourin Sharif, Fouzia Shabbir, Farid Menaa
BACKGROUND: Snake venom, a highly poisonous and active venomous snake's secretion, is a complex mixture of inorganic cations, carbohydrates, lipids, proteins, peptides, toxins and hydrolytic enzymes of importance including Phosphodiesterases (PDEs). These snake venom hydrolytic enzymes interfere in different physiological processes. Snake venom PDEs have several roles to metabolize extracellular nucleotides and to regulate nucleotide based intercellular signalling mechanisms including platelet aggregation, which can lead to death and debilitation in cardiac arrest and strokes in patients having cerebro-vascular and cardiovascular diseases, hypertension and atherosclerosis which is the primary cause of life-threatening diseases such as, stroke and myocardial-infarction...
June 28, 2018: Protein and Peptide Letters
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