8,389 results match your criteria silico functional

Critical assessment of coiled-coil predictions based on protein structure data.

Sci Rep 2021 Jun 14;11(1):12439. Epub 2021 Jun 14.

Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.

Coiled-coil regions were among the first protein motifs described structurally and theoretically. The simplicity of the motif promises that coiled-coil regions can be detected with reasonable accuracy and precision in any protein sequence. Here, we re-evaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Bank, down to each amino acid and its secondary structure. Read More

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Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics.

Sci Rep 2021 Jun 14;11(1):12456. Epub 2021 Jun 14.

Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, Erlangen, Germany.

The family of RNA-binding proteins (RBP) functions as a crucial regulator of multiple biological processes and diseases. However, RBP function in the clinical setting of idiopathic pulmonary fibrosis (IPF) is still unknown. We developed a practical in silico screening approach for the characterization of RBPs using multi-sources data information and comparative molecular network bioinformatics followed by wet-lab validation studies. Read More

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In silico analysis of deleterious SNPs of human MTUS1 gene and their impacts on subsequent protein structure and function.

PLoS One 2021 14;16(6):e0252932. Epub 2021 Jun 14.

Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.

The mitochondrial tumor suppressor 1 (MTUS1) gene acts as a crucial tumor suppressor by inhibiting growth and proliferation of eukaryotic cells including tumor cell lines. Down regulation of MTUS1 gene has been implicated in a wide range of cancers as well as various human diseases. Alteration through nsSNPs can potentially damage the structure and/or function of the protein. Read More

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In Silico Designing of Nanoclusters with a Late Transition Metal for NO Adsorption: An Efficient Approach toward the Development of NO Sensing Materials.

ACS Omega 2021 Jun 21;6(22):14191-14199. Epub 2021 May 21.

Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan.

Gas sensors are widely used for detection of environmental pollution caused by various environmental factors such as road traffic and combustion of fossil fuels. Nitrogen dioxide (NO) is one of the leading pollutants of the present age, which causes a number of serious health issues including acute bronchitis, cough, and phlegm, particularly in children. Nowadays, researchers are focused on designing new sensor materials for detection and removal of NO from the environment. Read More

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FGGA-lnc: automatic gene ontology annotation of lncRNA sequences based on secondary structures.

Interface Focus 2021 Jun 11;11(4):20200064. Epub 2021 Jun 11.

CIFASIS-Conicet-UNR, 27 de Febrero 210 bis, S2000EZP Rosario, Santa Fe, Argentina.

The study of long non-coding RNAs (lncRNAs), greater than 200 nucleotides, is central to understanding the development and progression of many complex diseases. Unlike proteins, the functionality of lncRNAs is only subtly encoded in their primary sequence. Current in-silico lncRNA annotation methods mostly rely on annotations inferred from interaction networks. Read More

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MicroRNA-145-Mediated KDM6A Downregulation Enhances Neural Repair after Spinal Cord Injury the NOTCH2/Abcb1a Axis.

Oxid Med Cell Longev 2021 25;2021:2580619. Epub 2021 May 25.

Department of Spine Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China.

Spinal cord injury (SCI) causes a significant physical, emotional, social, and economic burden to millions of people. MicroRNAs are known players in the regulatory circuitry of the neural repair in SCI. However, most microRNAs remain uncharacterized. Read More

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Heterologous expression of cyanobacterial confers augmented arsenic and cadmium stress tolerance and higher artemisinin in hairy roots.

Plant Biotechnol Rep 2021 Jun 7:1-18. Epub 2021 Jun 7.

Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India.

The present study provides the first report of heterologous expression of phytochelatin synthase from PCC 7120 () into the hairy roots of . Transformed hairy roots of expressing gene showed better tolerance to heavy metals, viz., arsenic (As) and cadmium (Cd) owing to 143 and 191% more As- and Cd-accumulation, respectively, as compared to normal roots with a bioconcentration factor (BCF) of 9. Read More

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Targeting the TLR2 Receptor With a Novel Thymopentin-Derived Peptide Modulates Immune Responses.

Front Immunol 2021 27;12:620494. Epub 2021 May 27.

Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.

The innate and adaptive immune systems act in concert to protect us from infectious agents and other harmful substances. As a state of temporary or permanent immune dysfunction, immunosuppression can make an organism more susceptible to infection, organ injury, and cancer due to damage to the immune system. It takes a long time to develop new immunomodulatory agents to prevent and treat immunosuppressive diseases, with slow progress. Read More

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Structural and functional role of invariant water molecules in matrix metalloproteinases: a data-mining approach.

J Biomol Struct Dyn 2021 Jun 14:1-12. Epub 2021 Jun 14.

Department of Biosciences and Bioengineering,Indian Institute of Technology Guwahati, Guwahati, Assam, India.

Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases known to degrade extracellular matrix (ECM). Being involved in many biological and physiological processes of tissue remodeling, MMPs play a crucial role in many pathological conditions such as arthritis, cancer, cardiovascular diseases, etc. Typically, MMPs possess a propeptide, a zinc-containing catalytic domain, a hinge region and a hemopexin domain. Read More

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B cells acquire a unique and differential transcriptomic profile during pregnancy.

Genomics 2021 Jun 9;113(4):2614-2622. Epub 2021 Jun 9.

Center for Pharmacological and Botanical Studies (CEFYBO-UBA-CONICET), Medical Faculty, Buenos Aires University, Buenos Aires, Argentina; Centro Integrativo de Biología Y Química Aplicada, Universidad Bernardo O'Higgins, 8307993 Santiago, Chile. Electronic address:

Pregnancy alters B cell development and function. B cell activation is initiated by antigens binding to the BCR leading to B cell survival, proliferation, antigen presentation and antibody production. We performed a genome-wide transcriptome profiling of splenic B cells from pregnant (P) and non-pregnant (NP) mice and identified 1136 genes exhibiting differential expression in B cells from P mice (625 up- and 511 down-regulated) compared to NP animals. Read More

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Recent advances in potential drug therapies combating COVID-19 and related coronaviruses-A perspective.

Food Chem Toxicol 2021 Jun 10;154:112333. Epub 2021 Jun 10.

Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China. Electronic address:

Coronaviruses (CoVs) are a large family of viruses responsible for the severe pathophysiological effects on human health. The most severe outbreak includes Severe Acute Respiratory Syndrome (SARS-CoV), Middle East Respiratory Syndrome (MERS-CoV) and Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 poses major challenges to clinical management because no specific FDA-approved therapy yet to be available. Read More

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Mechanism and microstructure based concept to predict skull fracture using a hybrid-experimental-modeling-computational approach.

J Mech Behav Biomed Mater 2021 Jun 1;121:104599. Epub 2021 Jun 1.

SURVICE Engineering Company, 4695 Millennium Dr, Belcamp, MD, 21017, USA.

Cellular and tissue-scale indent/impact thresholds for different mechanisms of functional impairments to the brain would be the preferred method to predict head injuries, but a comprehensive understanding of the dominant possible injury mechanisms under multiaxial stress-states and rates is currently not available. Until then, skull fracture could serve as an indication of head injury. Therefore the ability to predict the initiation of skull fracture through finite element simulation can serve as an in silico tool for assessing the effectiveness of various head protection scenarios. Read More

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In Silico High-Throughput Screening of Ag-Based Electrocatalysts for Anion-Exchange Membrane Fuel Cells.

J Phys Chem Lett 2021 Jun 11:5660-5667. Epub 2021 Jun 11.

Department of Materials Science and Engineering, Korea Advanced Instittue of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.

The alkaline environment in anion-exchange membrane fuel cells allows the use of Pt-free electrocatalysts, thus reducing the system cost. We performed a theoretical high-throughput study of various low-cost Ag-based oxygen reduction reaction anode electrocatalysts and assessed their catalytic performance using density functional theory. From the Materials Project database, a total of 106 binary Ag alloys were investigated by estimating their heat of formation, dissolution potential, and overpotential on low-index surfaces. Read More

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Antineoplastic action of sulforaphane on HeLa cells by modulation of signaling pathways and epigenetic pathways.

Minerva Med 2021 06 11. Epub 2021 Jun 11.

Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia.

Background: Epigenetic modifications alter signaling and molecular pathways and are an important therapeutic target. This study examined the effect of sulforaphane on molecular targets in HeLa cells.

Methods: Quantitative PCR of various molecular targets was performed. Read More

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Anticancer activity of indapamide adsorbed on gold nanoparticles: DFT, in-silico, and in-vitro analysis.

J Mol Recognit 2021 Jun 11:e2920. Epub 2021 Jun 11.

Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, Kerala, 690110, India.

The adsorption properties of the lung cancer agent indapamide (IND) on gold nanoparticles (AuNPs), were studied with the help of surface-enhanced Raman scattering techniques. The structure-activity of the IND and INDA molecule has been studied using DFT/B3LYP methodology. NBO analysis reveals that, both the molecules are stabilized by a C─H O intramolecular hydrogen bonding, apart from the conjugative and intramolecular charge transfer interactions. Read More

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Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity.

Genet Med 2021 Jun 10. Epub 2021 Jun 10.

Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.

Purpose: ADP ribosylation factor guanine nucleotide exchange factors (ARFGEFs) are a family of proteins implicated in cellular trafficking between the Golgi apparatus and the plasma membrane through vesicle formation. Among them is ARFGEF1/BIG1, a protein involved in axon elongation, neurite development, and polarization processes. ARFGEF1 has been previously suggested as a candidate gene for different types of epilepsies, although its implication in human disease has not been well characterized. Read More

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Extracellular vesicle-shuttled miRNAs as a diagnostic and prognostic biomarker and their potential roles in gallbladder cancer patients.

Sci Rep 2021 Jun 10;11(1):12298. Epub 2021 Jun 10.

Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama, Japan.

Circulating microRNAs (miRNAs) in serum extracellular vesicles (EVs) are a promising biomarker in cancer. We aimed to elucidate the serum EVs miRNA biomarkers to identify patients with gallbladder cancer (GBC) and to clarify their potential roles. One hundred nineteen serum EVs from GBC and non-GBC individuals were isolated by pure-EVs-yieldable size-exclusion chromatography, and then were analyzed using a comprehensive miRNAs array and RT-qPCR-based validation. Read More

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Structure-based redesigning of pentoxifylline analogs against selective phosphodiesterases to modulate sperm functional competence for assisted reproductive technologies.

Sci Rep 2021 Jun 10;11(1):12293. Epub 2021 Jun 10.

Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India.

Phosphodiesterase (PDE) inhibitors, such as pentoxifylline (PTX), are used as pharmacological agents to enhance sperm motility in assisted reproductive technology (ART), mainly to aid the selection of viable sperm in asthenozoospermic ejaculates and testicular spermatozoa, prior to intracytoplasmic sperm injection (ICSI). However, PTX is reported to induce premature acrosome reaction (AR) and, exert toxic effects on oocyte function and early embryo development. Additionally, in vitro binding studies as well as computational binding free energy (ΔG) suggest that PTX exhibits weak binding to sperm PDEs, indicating room for improvement. Read More

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NAPG mutation in family members with hereditary hemorrhagic telangiectasia in China.

BMC Pulm Med 2021 Jun 10;21(1):197. Epub 2021 Jun 10.

Department of Pulmonary and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, People's Republic of China.

Background: Hereditary hemorrhagic telangiectasia (HHT) is a disease characterized by arteriovenous malformations in the skin and mucous membranes. We enrolled a large pedigree comprising 32 living members, and screened for mutations responsible for HHT.

Methods: We performed whole-exome sequencing to identify novel mutations in the pedigree after excluding three previously reported HHT-related genes using Sanger sequencing. Read More

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Anti-inflammatory and tight junction protective activity of the herbal preparation STW 5-II on mouse intestinal organoids.

Phytomedicine 2021 Jul 6;88:153589. Epub 2021 May 6.

Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany. Electronic address:

Background: Irritable bowel syndrome (IBS) is a functional bowel disorder, in which recurrent abdominal pain is associated with defecation or a change in bowel habits. STW 5-II is a combination of six medicinal herbs with a clinically proven efficacy in managing IBS.

Aim: This study aims to establish an in vitro IBS model using mouse intestinal organoids and to explore the anti-inflammatory and tight junction protective activities of the multi-herbal preparation STW 5-II. Read More

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Missense RHD single nucleotide variants induce weakened D antigen expression by altering splicing and/or protein expression.

Transfusion 2021 Jun 10. Epub 2021 Jun 10.

Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.

Background: Although D variant phenotype is known to be due to genetic defects, including rare missense single nucleotide variants (SNVs), within the RHD gene, few studies have addressed the molecular and cellular mechanisms driving this altered expression. We and others showed previously that splicing is commonly disrupted by SNVs in constitutive splice sites and their vicinity. We thus sought to investigate whether rare missense SNVs located in "deep" exonic regions could also impair this mechanism. Read More

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Lung MRI with hyperpolarised gases: current & future clinical perspectives.

Br J Radiol 2021 Jun 9:20210207. Epub 2021 Jun 9.

POLARIS, Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, UK.

The use of pulmonary MRI in a clinical setting has historically been limited. Whilst CT remains the gold-standard for lung imaging in many clinical indications, technical developments in ultrashort and zero echo time MRI techniques are beginning to help realise non-ionising imaging in certain lung disorders. In this invited review, we discuss a complementary technique - hyperpolarised (HP) gas MRI with inhaled He and Xe - a method for and imaging of the lung that has great potential as a clinical tool for early detection and improved understanding of pathophysiology in many lung diseases. Read More

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V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity.

J Virol 2021 Jun 2:JVI0061721. Epub 2021 Jun 2.

Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China.

The current pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring RBD mutations during the early transmission phase have altered the receptor binding affinity and infectivity, firstly we analyzed the binding dynamics between SARS-CoV-2 RBD mutants and the human ACE2 receptor. Read More

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Improving the efficacy of exome sequencing at a quaternary care referral centre: novel mutations, clinical presentations and diagnostic challenges in rare neurogenetic diseases.

J Neurol Neurosurg Psychiatry 2021 Jun 8. Epub 2021 Jun 8.

Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

Background: We used a multimodal approach including detailed phenotyping, whole exome sequencing (WES) and candidate gene filters to diagnose rare neurological diseases in individuals referred by tertiary neurology centres.

Methods: WES was performed on 66 individuals with neurogenetic diseases using candidate gene filters and stringent algorithms for assessing sequence variants. Pathogenic or likely pathogenic missense variants were interpreted using in silico prediction tools, family segregation analysis, previous publications of disease association and relevant biological assays. Read More

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De novo and bi-allelic variants in AP1G1 cause neurodevelopmental disorder with developmental delay, intellectual disability, and epilepsy.

Am J Hum Genet 2021 Jun 3. Epub 2021 Jun 3.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.

Adaptor protein (AP) complexes mediate selective intracellular vesicular trafficking and polarized localization of somatodendritic proteins in neurons. Disease-causing alleles of various subunits of AP complexes have been implicated in several heritable human disorders, including intellectual disabilities (IDs). Here, we report two bi-allelic (c. Read More

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Emulsifier peptides derived from seaweed, methanotrophic bacteria, and potato proteins identified by quantitative proteomics and bioinformatics.

Food Chem 2021 May 26;362:130217. Epub 2021 May 26.

National Food Institute, Technical University of Denmark, Denmark; Department of Chemical Engineering, University of Granada, Spain. Electronic address:

Global focus on sustainability has accelerated research into alternative non-animal sources of food protein and functional food ingredients. Amphiphilic peptides represent a class of promising biomolecules to replace chemical emulsifiers in food emulsions. In contrast to traditional trial-and-error enzymatic hydrolysis, this study utilizes a bottom-up approach combining quantitative proteomics, bioinformatics prediction, and functional validation to identify novel emulsifier peptides from seaweed, methanotrophic bacteria, and potatoes. Read More

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Therapeutic Targeting of Repurposed Anticancer Drugs in Alzheimer's Disease: Using the Multiomics Approach.

ACS Omega 2021 Jun 19;6(21):13870-13887. Epub 2021 May 19.

Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University, Shahabad Daulatpur, Bawana Road, Delhi 110042, India.

Aim/hypothesis: The complexity and heterogeneity of multiple pathological features make Alzheimer's disease (AD) a major culprit to global health. Drug repurposing is an inexpensive and reliable approach to redirect the existing drugs for new indications. The current study aims to study the possibility of repurposing approved anticancer drugs for AD treatment. Read More

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Design of New Schiff-Base Copper(II) Complexes: Synthesis, Crystal Structures, DFT Study, and Binding Potency toward Cytochrome P450 3A4.

ACS Omega 2021 Jun 19;6(21):13704-13718. Epub 2021 May 19.

Department of Chemical Sciences, University of Johannesburg, Doornfontein, P.O. Box 17011, Johannesburg 2028, South Africa.

We report the synthesis and crystal structures of three new copper(II) Schiff-base complexes. The complexes have been characterized by elemental analysis and Fourier transform infrared (FT-IR) and UV-visible spectroscopies. The X-ray diffraction (XRD) analysis reveals that complexes and crystallize in a monoclinic space group 2/ and in a triclinic space group 1̅, each adopting a square planar geometry around the metal center. Read More

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Thermal and Acidic Treatments of Gluten Epitopes Affect Their Recognition by HLA-DQ2 .

Front Nutr 2021 19;8:647750. Epub 2021 May 19.

Beijing Key Laboratory of Functional Food From Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.

Celiac disease (CD) is a prevalent disorder with autoimmune features. Dietary exposure of wheat gluten (including gliadins and glutenins) to the small intestine activates the gluten-reactive CD4 T cells and controls the disease development. While the human leukocyte antigen (HLA) is the single most important genetic factor of this polygenic disorder, HLA-DQ2 recognition of gluten is the major biological step among patients with CD. Read More

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Expression Analysis of Long Non-Coding RNAs Related With FOXM1, GATA3, FOXA1 and ESR1 in Breast Tissues.

Front Oncol 2021 19;11:671418. Epub 2021 May 19.

Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Breast cancer is the most common neoplasm among females. Estrogen receptor (ESR) signaling has a prominent impact in the pathogenesis of breast cancer. Among the transcription factors associated with ESR signaling, FOXM1, GATA3, FOXA1 and ESR1 have been suggested as a candidate in the pathogenesis of this neoplasm. Read More

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