11,307 results match your criteria structural classes


A Determinants-of-Fertility Ontology for Detecting Future Signals of Fertility Issues From Social Media Data: Development of an Ontology.

J Med Internet Res 2021 Jun 14;23(6):e25028. Epub 2021 Jun 14.

Department of Health Management, Samyook University, Seoul, Republic of Korea.

Background: South Korea has the lowest fertility rate in the world despite considerable governmental efforts to boost it. Increasing the fertility rate and achieving the desired outcomes of any implemented policies requires reliable data on the ongoing trends in fertility and preparations for the future based on these trends.

Objective: The aims of this study were to (1) develop a determinants-of-fertility ontology with terminology for collecting and analyzing social media data; (2) determine the description logics, content coverage, and structural and representational layers of the ontology; and (3) use the ontology to detect future signals of fertility issues. Read More

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Design Verification as Foundation for Advancing DNA Nanotechnology Applications.

Authors:
Leo Y T Chou

ACS Nano 2021 Jun 14. Epub 2021 Jun 14.

Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada.

Advances in the field of structural DNA nanotechnology have produced a growing number of nanostructures that are now being developed for diverse applications. Often, these nanostructures contain not only nucleic acids but also a myriad of other classes of molecules and materials such as proteins, lipids, sugars, and synthetic polymers. Increasing structural and compositional complexity promises new functional capabilities, but also demands new tools for design verification. Read More

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Driving high quantum yield NIR emission through proquinoidal linkage motifs in conjugated supermolecular arrays.

Chem Sci 2020 Aug 5;11(31):8095-8104. Epub 2020 Aug 5.

Department of Chemistry, French Family Science Center, Duke University 124 Science Drive Durham North Carolina 27708-0346 USA

High quantum yield NIR fluorophores are rare. Factors that drive low emission quantum yields at long wavelength include the facts that radiative rate constants increase proportional to the cube of the emission energy, while nonradiative rate constants increase in an approximately exponentially with decreasing S-S energy gaps (in accordance with the energy gap law). This work demonstrates how the proquinoidal BTD building blocks can be utilized to minimize the extent of excited-state structural relaxation relative to the ground-state conformation in highly conjugated porphyrin oligomers, and shows that 4-ethynylbenzo[][1,2,5]thiadiazole () units that terminate -to- ethyne-bridged (porphinato)zinc () arrays, and 4,7-diethynylbenzo[][1,2,5]thiadiazole () spacers that are integrated into the backbone of these compositions, elucidate new classes of impressive NIR fluorophores. Read More

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Biological Activities and Chemistry of Triterpene Saponins from Species: An Update Review.

Evid Based Complement Alternat Med 2021 26;2021:6617916. Epub 2021 May 26.

College of Agronomy, Jiangxi Agricultural University, Jiangxi Key Laboratory for Post-harvest Technology and Nondestructive Testing of Fruits & Vegetables/Collaborative Innovation Center of Post-harvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang 330045, China.

Plants are known to be a great source of phytochemicals for centuries. , belonging to the Family Fabaceae, is a large and well spread genus comprising about 83 cosmopolitan species, of which one-third are annuals and span diverse ecological niches. species are rich in saponins mainly classified into three classes, namely, steroid alkaloid glycosides, triterpene glycosides, and steroid glycosides. Read More

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Trends in COVID-19 prevalence and mortality: A year in review.

Physica D 2021 Nov 7;425:132968. Epub 2021 Jun 7.

Yau Mathematical Sciences Centre, Tsinghua University, Beijing, China.

This paper introduces new methods to study the changing dynamics of COVID-19 cases and deaths among the 50 worst-affected countries throughout 2020. First, we analyse the trajectories and turning points of rolling mortality rates to understand at which times the disease was most lethal. We demonstrate five characteristic classes of mortality rate trajectories and determine structural similarity in mortality trends over time. Read More

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November 2021

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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Study on bisphenol F, a bisphenol A analogue, at a dairy company: Health hazard and risk assessment.

Food Chem Toxicol 2021 Jun 10;154:112334. Epub 2021 Jun 10.

Department of Veterinary Medicine and Animal Production, University of Naples, Via F. Delpino, 1, 80137, Napoli, Italy. Electronic address:

The occurrence of analogues of bisphenol A (BPA), including bisphenol F(BPF) in milk is still not well known. BPF may enter the milk chain at the farm and during milk processing at the dairy company. This study identified the main BPF contamination pathways using a monitoring model based on the identification of the hazard at three stages along the dairy chain: raw milk from the storage tank, pasteurized milk from the storage tank, and cardboard packaged milk. Read More

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Taming the Antiferromagnetic Beast: Computational Design of Ultrashort Mn-Mn Bonds Stabilized by N-Heterocyclic Carbenes.

Chemistry 2021 Jun 11. Epub 2021 Jun 11.

Universidade Federal do Rio de Janeiro, Instituto de Química, BRAZIL.

The development of complexes featuring low-valent, multiply bonded metal centers is an exciting field with several potential applications. In this work, we describe the design principles and perform an extensive computational investigation of new organometallic platforms featuring the elusive manganese - manganese bond stabilized by experimentally-realized N-heterocyclic carbenes (NHCs). By using DFT computations benchmarked against multireference calculations, as well as MO- and VB-based bonding analyses, we could disentangle the various electronic and structural effects contributing to the thermodynamic and kinetic stability, as well as the experimental feasibility, of the systems. Read More

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New approach methods supporting read-across: Two neurotoxicity AOP-based IATA case studies.

ALTEX 2021 Jun 10. Epub 2021 Jun 10.

Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands.

Read-across approaches are considered key in moving away from in vivo animal testing towards addressing data-gaps using new approach methods (NAMs). Ample successful examples are still required to substantiate this strategy. Here we present and discuss the learnings from two OECD IATA endorsed read-across case studies. Read More

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Stromal Cells Underlining the Paths From Autoimmunity, Inflammation to Cancer With Roles Beyond Structural and Nutritional Support.

Front Cell Dev Biol 2021 25;9:658984. Epub 2021 May 25.

Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States.

Stromal cells provide structural support and nutrients in secondary lymphoid organs and non-lymphoid tissues. However, accumulating evidence suggests that a complex relationship exists between stromal cells and immune cells. Interactions between immune cells and stromal cells have been shown to influence the pathology of both autoimmunity and cancer. Read More

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LigTMap: ligand and structure-based target identification and activity prediction for small molecular compounds.

J Cheminform 2021 Jun 10;13(1):44. Epub 2021 Jun 10.

Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida da Universidade, Taipa, Macau, China.

Target prediction is a crucial step in modern drug discovery. However, existing experimental approaches to target prediction are time-consuming and costly. Here, we introduce LigTMap, an online server with a fully automated workflow that can identify protein targets of chemical compounds among 17 classes of therapeutic proteins extracted from the PDBbind database. Read More

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Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies.

Structure 2021 Jun 1. Epub 2021 Jun 1.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10029, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

Emerging SARS-CoV-2 strains, B.1.1. Read More

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Zero-Shot Learning via Structure-Aligned Generative Adversarial Network.

IEEE Trans Neural Netw Learn Syst 2021 Jun 9;PP. Epub 2021 Jun 9.

In this article, we propose a structure-aligned generative adversarial network framework to improve zero-shot learning (ZSL) by mitigating the semantic gap, domain shift, and hubness problem. The proposed framework contains two parts, i.e. Read More

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Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion.

FEBS J 2021 Jun 8. Epub 2021 Jun 8.

Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan.

Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Read More

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Identification of over 200-fold more hairpin ribozymes than previously known in diverse circular RNAs.

Nucleic Acids Res 2021 Jun 7. Epub 2021 Jun 7.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.

Self-cleaving ribozymes are catalytic RNAs that cut themselves at a specific inter-nucleotide linkage. They serve as a model of RNA catalysis, and as an important tool in biotechnology. For most of the nine known structural classes of self-cleaving ribozymes, at least hundreds of examples are known, and some are present in multiple domains of life. Read More

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The HD-Domain Metalloprotein Superfamily: An Apparent Common Protein Scaffold with Diverse Chemistries.

Catalysts 2020 Oct 15;10(10). Epub 2020 Oct 15.

Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA.

The histidine-aspartate (HD)-domain protein superfamily contains metalloproteins that share common structural features but catalyze vastly different reactions ranging from oxygenation to hydrolysis. This chemical diversion is afforded by (i) their ability to coordinate most biologically relevant transition metals in mono-, di-, and trinuclear configurations, (ii) sequence insertions or the addition of supernumerary ligands to their active sites, (iii) auxiliary substrate specificity residues vicinal to the catalytic site, (iv) additional protein domains that allosterically regulate their activities or have catalytic and sensory roles, and (v) their ability to work with protein partners. More than 500 structures of HD-domain proteins are available to date that lay out unique structural features which may be indicative of function. Read More

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October 2020

Dynamics and mechanism of light harvesting in UV photoreceptor UVR8.

Chem Sci 2020 Oct 28;11(46):12553-12569. Epub 2020 Oct 28.

Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University Columbus OH 43210 USA

Photosynthetic pigments form light-harvesting networks to enable nearly perfect quantum efficiency in photosynthesis excitation energy transfer. However, similar light-harvesting mechanisms have not been reported in light sensing processes in other classes of photoreceptors during light-mediated signaling. Here, based on our earlier report, we mapped out a striking energy-transfer network composed of 26 structural tryptophan residues in the plant UV-B photoreceptor UVR8. Read More

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October 2020

Aperiodic metal-organic frameworks.

Chem Sci 2020 Sep 30;11(41):11094-11103. Epub 2020 Sep 30.

Department of Chemistry, Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA

Metal-organic frameworks (MOFs) represent one of the most diverse structural classes among solid state materials, yet few of them exhibit aperiodicity, or the existence of long-range order in the absence of translational symmetry. From this apparent conflict, a paradox has emerged: even though aperiodicity frequently arises in materials that contain the same bonding motifs as MOFs, aperiodic structures and MOFs appear to be nearly disjoint classes. In this perspective, we highlight a subset of the known aperiodic coordination polymers, including both incommensurate and quasicrystalline structures. Read More

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September 2020

Hemolymph proteins: An overview across marine arthropods and molluscs.

J Proteomics 2021 Jun 4;245:104294. Epub 2021 Jun 4.

Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria. Electronic address:

In this compilation we collect information about the main protein components in hemolymph and stress the continued interest in their study. The reasons for such an attention span several areas of biological, veterinarian and medical applications: from the notions for better dealing with the species - belonging to phylum Arthropoda, subphylum Crustacea, and to phylum Mollusca - of economic interest, to the development of 'marine drugs' from the peptides that, in invertebrates, act as antimicrobial, antifungal, antiprotozoal, and/or antiviral agents. Overall, the topic most often on focus is that of innate immunity operated by classes of pattern-recognition proteins. Read More

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Contributions of secondary alcohol-ketone O-H...O=C and furan-acetate Csp-H...OOC synthons to the supramolecular packings of two bioactive molecules.

Acta Crystallogr C Struct Chem 2021 06 27;77(Pt 6):312-320. Epub 2021 May 27.

Chemistry Department, Faculty of Science, University of Dschang, PO Box 67, Dschang, Cameroon.

The crystal structures of rubescin D (1, CHO) and monadelphin A (2, CHO), bioactive molecules of the vilasinin and gedunin classes of limonoids, respectively, are reported for the first time and the synthons affecting their crystal packings are analyzed on the basis of their occurrences in molecules in the Cambridge Structural Database that share the same moieties. Rubescin D, 1, crystallizes in the space group P2 and its molecular structure consists of three six-membered rings A, C and D having, respectively, envelope, twist-boat and half-chair conformations, and three five-membered rings with half-chair (B and E) and planar conformations (F). Many synthons found in the crystal packing of 1 are in agreement with expectations derived from molecules displaying the same moieties. Read More

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Dietary Phytoestrogens: Neuroprotective Role in Parkinson's Disease.

Curr Neurovasc Res 2021 Jun 4. Epub 2021 Jun 4.

Institute of Pharmaceutical Research, GLA University 17-Km. stone, NH-2 Mathura-Delhi Highway, P.O. Chaumuhan, Mathura-281406 (U.P.), India.

Parkinson's disease (PD) is a neurodegenerative disorder characterized by progressive damage of mesencephalic dopaminergic neurons of the substantia nigra and the striatal projections. Recent studies suggest that estrogen and estrogen-like chemicals have beneficial effects on neurodegenerative diseases, particularly PD. Animal studies demonstrate that estrogen influences dopamine's synthesis, release, and metabolism. Read More

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A structure-kinetic relationship study using matched molecular pair analysis.

RSC Med Chem 2020 Sep 21;11(11):1285-1294. Epub 2020 Sep 21.

Department of Pharmaceutical Chemistry, University of Vienna UZA 2, Althanstrasse 14 1090 Vienna Austria

The lifetime of a binary drug-target complex is increasingly acknowledged as an important parameter for drug efficacy and safety. With a better understanding of binding kinetics and better knowledge about kinetic parameter optimization, intentionally induced prolongation of the drug-target residence time through structural changes of the ligand could become feasible. In this study we assembled datasets from 21 publications and the K4DD (Kinetic for Drug Discovery) database to conduct large scale data analysis. Read More

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September 2020

Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer.

J Am Soc Mass Spectrom 2021 Jun 3. Epub 2021 Jun 3.

Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada.

We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0. Read More

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A Molecular Approach to Quantum Sensing.

ACS Cent Sci 2021 May 20;7(5):712-723. Epub 2021 Apr 20.

Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States.

The second quantum revolution hinges on the creation of materials that unite atomic structural precision with electronic and structural tunability. A molecular approach to quantum information science (QIS) promises to enable the bottom-up creation of quantum systems. Within the broad reach of QIS, which spans fields ranging from quantum computation to quantum communication, we will focus on quantum sensing. Read More

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Marine Sponge is a Promising Natural Source of Anti-SARS-CoV-2 Scaffold.

Front Pharmacol 2021 13;12:666664. Epub 2021 May 13.

Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.

The current pandemic caused by SARS-CoV2 and named COVID-19 urgent the need for novel lead antiviral drugs. Recently, United States Food and Drug Administration (FDA) approved the use of remdesivir as anti-SARS-CoV-2. Remdesivir is a natural product-inspired nucleoside analogue with significant broad-spectrum antiviral activity. Read More

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The missing link: covalent linkages in structural models.

Acta Crystallogr D Struct Biol 2021 Jun 19;77(Pt 6):727-745. Epub 2021 May 19.

Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

Covalent linkages between constituent blocks of macromolecules and ligands have been subject to inconsistent treatment during the model-building, refinement and deposition process. This may stem from a number of sources, including difficulties with initially detecting the covalent linkage, identifying the correct chemistry, obtaining an appropriate restraint dictionary and ensuring its correct application. The analysis presented herein assesses the extent of problems involving covalent linkages in the Protein Data Bank (PDB). Read More

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Developments in Treatment Methodologies Using Dendrimers for Infectious Diseases.

Molecules 2021 May 31;26(11). Epub 2021 May 31.

Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA.

Dendrimers comprise a specific group of macromolecules, which combine structural properties of both single molecules and long expanded polymers. The three-dimensional form of dendrimers and the extensive possibilities for use of additional substrates for their construction creates a multivalent potential and a wide possibility for medical, diagnostic and environmental purposes. Depending on their composition and structure, dendrimers have been of interest in many fields of science, ranging from chemistry, biotechnology to biochemical applications. Read More

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Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae.

Microorganisms 2021 May 19;9(5). Epub 2021 May 19.

Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain.

L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria-nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. Read More

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Chemical Profile, Cytotoxic Activity and Oxidative Stress Reduction of Different L. Extracts.

Molecules 2021 May 22;26(11). Epub 2021 May 22.

Department of Pharmacognosy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 400010 Cluj-Napoca, Romania.

L. (common lilac) is one of the most popular ornamental species, but also a promising not comprehensively studied source of bioactive compounds with important therapeutic potential. Our study was designed to characterize the chemical composition and to assess the antioxidant and cytotoxic properties of ethanolic extracts obtained from L. Read More

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An Analytical Review of the Structural Features of Pentatricopeptide Repeats: Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture.

Authors:
Sailen Barik

Int J Mol Sci 2021 May 20;22(10). Epub 2021 May 20.

EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA.

Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel bihelical structure, so that multiple such units in a polypeptide are arranged in a parallel fashion. The primary structures of the motifs are nonidentical, but amino acids of similar properties occur in strategic positions. Read More

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