Computational evidence for the role of Arabidopsis thaliana UVR8 as UV-B photoreceptor and identification of its chromophore amino acids.

Abstract:

:A homology model of the Arabidopsis thaliana UV resistance locus 8 (UVR8) protein is presented herein, showing a seven-bladed β-propeller conformation similar to the globular structure of RCC1. The UVR8 amino acid sequence contains a very high amount of conserved tryptophans, and the homology model shows that seven of these tryptophans cluster at the 'top surface' of the UVR8 protein where they are intermixed with positive residues (mainly arginines) and a couple of tyrosines. Quantum chemical calculations of excitation spectra of both a large cluster model involving all twelve above-mentioned residues and smaller fragments thereof reveal that absorption maxima appearing in the 280-300 nm range for the full cluster result from interactions between the central tryptophans and surrounding arginines. This observation coincides with the published experimentally measured action spectrum for the UVR8-dependent UV-B stimulation of HY5 transcription in mature A. thaliana leaf tissue. In total these findings suggest that UVR8 has in fact in itself the ability to be an ultraviolet-B photoreceptor in plants.

journal_name

J Chem Inf Model

authors

Wu M,Grahn E,Eriksson LA,Strid A

doi

10.1021/ci200017f

subject

Has Abstract

pub_date

2011-06-27 00:00:00

pages

1287-95

issue

6

eissn

1549-9596

issn

1549-960X

journal_volume

51

pub_type

杂志文章
  • Energetics, Thermodynamics, and Molecular Recognition of Piperine with DNA.

    abstract::Piperine, the bioactive phytochemical from black pepper (Piper nigrum L.), is a nontoxic natural compound exhibiting many physiological and pharmacological properties. They include antioxidant, anti-inflammatory, antimutagenic, antitumor, antiapoptotic, antigenotoxic, antiarthritic, antifungal, antimicrobial, antidepr...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00514

    authors: Haris P,Mary V,Haridas M,Sudarsanakumar C

    更新日期:2015-12-28 00:00:00

  • Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.

    abstract::Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00877

    authors: Wakefield AE,Yueh C,Beglov D,Castilho MS,Kozakov D,Keserű GM,Whitty A,Vajda S

    更新日期:2020-12-28 00:00:00

  • Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles.

    abstract::Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation proc...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00641

    authors: Jafari M,Doustdar F,Mehrnejad F

    更新日期:2019-01-28 00:00:00

  • Multidimensional Drift of Sequence Attributes and Functional Profiles in the Superfamily of the Three-Finger Proteins and Their Structural Homologues.

    abstract::Functional diversity of the three-finger-protein domain (TFPD) had been acquired via hypervariability of some sequence positions and extensive insertion/deletion of short AA-segments that caused multidimensional drift of several sequence attributes such as the overall (HI) and local hydrophobicity levels, the isoelect...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00322

    authors: Galat A

    更新日期:2015-09-28 00:00:00

  • Improved Prediction of Drug-Target Interactions Using Self-Paced Learning with Collaborative Matrix Factorization.

    abstract::Identifying drug-target interactions (DTIs) plays an important role in the field of drug discovery, drug side-effects, and drug repositioning. However, in vivo or biochemical experimental methods for identifying new DTIs are extremely expensive and time-consuming. Recently, in silico or various computational methods h...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00408

    authors: Xia LY,Yang ZY,Zhang H,Liang Y

    更新日期:2019-07-22 00:00:00

  • Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents.

    abstract::Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a co...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00985

    authors: Shahraki A,Işbilir A,Dogan B,Lohse MJ,Durdagi S,Birgul-Iyison N

    更新日期:2021-01-21 00:00:00

  • Interpretation of the binding affinities of PTP1B inhibitors with the MM-GB/SA method and the X-score scoring function.

    abstract::We have studied the binding affinities of a set of 45 small-molecule inhibitors to protein tyrosine phosphatase 1B (PTP1B) through computational approaches. All of these compounds share a common oxalylamino benzoic acid (OBA) moiety. The complex structure of each compound was modeled by using the GOLD program plus the...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci8004429

    authors: Zhang X,Li X,Wang R

    更新日期:2009-04-01 00:00:00

  • Comparative modeling and benchmarking data sets for human histone deacetylases and sirtuin families.

    abstract::Histone deacetylases (HDACs) are an important class of drug targets for the treatment of cancers, neurodegenerative diseases, and other types of diseases. Virtual screening (VS) has become fairly effective approaches for drug discovery of novel and highly selective histone deacetylase inhibitors (HDACIs). To facilitat...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci5005515

    authors: Xia J,Tilahun EL,Kebede EH,Reid TE,Zhang L,Wang XS

    更新日期:2015-02-23 00:00:00

  • Combined 3D-QSAR modeling and molecular docking study on indolinone derivatives as inhibitors of 3-phosphoinositide-dependent protein kinase-1.

    abstract::3-Phosphoinositide-dependent protein kinase-1 (PDK1) is a promising target for developing novel anticancer drugs. In order to understand the structure-activity correlation of indolinone-based PDK1 inhibitors, we have carried out a combined molecular docking and three-dimensional quantitative structure-activity relatio...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800147v

    authors: AbdulHameed MD,Hamza A,Liu J,Zhan CG

    更新日期:2008-09-01 00:00:00

  • Novel inhibitors of human histone deacetylase (HDAC) identified by QSAR modeling of known inhibitors, virtual screening, and experimental validation.

    abstract::Inhibitors of histone deacetylases (HDACIs) have emerged as a new class of drugs for the treatment of human cancers and other diseases because of their effects on cell growth, differentiation, and apoptosis. In this study we have developed several quantitative structure-activity relationship (QSAR) models for 59 chemi...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800366f

    authors: Tang H,Wang XS,Huang XP,Roth BL,Butler KV,Kozikowski AP,Jung M,Tropsha A

    更新日期:2009-02-01 00:00:00

  • Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors.

    abstract::The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silic...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400644r

    authors: Therese PJ,Manvar D,Kondepudi S,Battu MB,Sriram D,Basu A,Yogeeswari P,Kaushik-Basu N

    更新日期:2014-02-24 00:00:00

  • Partitioning of Benzoic Acid into 1,2-Dimyristoyl-sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers.

    abstract::Using an all-atom explicit water model and replica exchange umbrella sampling simulations, we investigated the molecular mechanisms of benzoic acid partitioning into two model lipid bilayers. The first was formed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, whereas the second was composed of an equimo...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00590

    authors: Siwy CM,Delfing BM,Smith AK,Klimov DK

    更新日期:2020-08-24 00:00:00

  • Catalytic Role of Gln202 in the Carboligation Reaction Mechanism of Yeast AHAS: A QM/MM Study.

    abstract::Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate-dependent enzyme involved in the biosynthesis of valine, leucine, isoleucine, and lysine. Experimental evidence has shown that mutation of the Gln202 residue results in a decrease in the enzymatic activity, thus suggesting the main role of the carboligation cat...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00863

    authors: Mendoza F,Medina FE,Jiménez VA,Jaña GA

    更新日期:2020-02-24 00:00:00

  • The valence state combination model: a generic framework for handling tautomers and protonation states.

    abstract::The consistent handling of molecules is probably the most basic and important requirement in the field of cheminformatics. Reliable results can only be obtained if the underlying calculations are independent of the specific way molecules are represented in the input data. However, ensuring consistency is a complex tas...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400724v

    authors: Urbaczek S,Kolodzik A,Rarey M

    更新日期:2014-03-24 00:00:00

  • Structure-Based Discovery of 1H-Indazole-3-carboxamides as a Novel Structural Class of Human GSK-3 Inhibitors.

    abstract::An in silico screening procedure was performed to select new inhibitors of glycogen synthase kinase 3β (GSK-3β), a serine/threonine protein kinase that in the last two decades has emerged as a key target in drug discovery, having been implicated in multiple cellular processes and linked with the pathogenesis of severa...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00486

    authors: Ombrato R,Cazzolla N,Mancini F,Mangano G

    更新日期:2015-12-28 00:00:00

  • Structure-based CoMFA as a predictive model - CYP2C9 inhibitors as a test case.

    abstract::In this study, we tried to establish a general scheme to create a model that could predict the affinity of small compounds to their target proteins. This scheme consists of a search for ligand-binding sites on a protein, a generation of bound conformations (poses) of ligands in each of the sites by docking, identifica...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci800313h

    authors: Yasuo K,Yamaotsu N,Gouda H,Tsujishita H,Hirono S

    更新日期:2009-04-01 00:00:00

  • Searching for recursively defined generic chemical patterns in nonenumerated fragment spaces.

    abstract::Retrieving molecules with specific structural features is a fundamental requirement of today's molecular database technologies. Estimates claim the chemical space relevant for drug discovery to be around 10⁶⁰ molecules. This figure is many orders of magnitude larger than the amount of molecules conventional databases ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400107k

    authors: Ehrlich HC,Henzler AM,Rarey M

    更新日期:2013-07-22 00:00:00

  • AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein-Protein Interaction Interfaces.

    abstract::Inhibition of protein-protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structura...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00103

    authors: Rooklin D,Wang C,Katigbak J,Arora PS,Zhang Y

    更新日期:2015-08-24 00:00:00

  • Comparison Study of Polar and Nonpolar Contributions to Solvation Free Energy.

    abstract::In this study, we compared the contributions of polar and nonpolar interactions to the solvation free energy of a solute in solvent, which is decomposed into four different terms based on the nature of interactions: (i) electrostatic solvation free energy term counting for the work done to move solute charges from fix...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00368

    authors: Izairi R,Kamberaj H

    更新日期:2017-10-23 00:00:00

  • Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries.

    abstract::The community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200078f

    authors: Li L,Wang B,Meroueh SO

    更新日期:2011-09-26 00:00:00

  • Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models.

    abstract::Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL and PubChem. Here, we explore how to use this comprehensive mapping of chemical ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00526

    authors: Zakharov AV,Zhao T,Nguyen DT,Peryea T,Sheils T,Yasgar A,Huang R,Southall N,Simeonov A

    更新日期:2019-11-25 00:00:00

  • Accurate prediction of adsorption energies on graphene, using a dispersion-corrected semiempirical method including solvation.

    abstract::The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can p...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci5003729

    authors: Vincent MA,Hillier IH

    更新日期:2014-08-25 00:00:00

  • What Does the Machine Learn? Knowledge Representations of Chemical Reactivity.

    abstract::In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the fie...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00721

    authors: Kammeraad JA,Goetz J,Walker EA,Tewari A,Zimmerman PM

    更新日期:2020-03-23 00:00:00

  • Relationships between Molecular Complexity, Biological Activity, and Structural Diversity.

    abstract::Following the theoretical model by Hann et al. moderately complex structures are preferable lead compounds since they lead to specific binding events involving the complete ligand molecule. To make this concept usable in practice for library design, we studied several complexity measures on the biological activity of ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0503558

    authors: Schuffenhauer A,Brown N,Selzer P,Ertl P,Jacoby E

    更新日期:2006-03-01 00:00:00

  • Modeling oral rat chronic toxicity.

    abstract::The chronic toxicity is fundamental for toxicological risk assessment, but its correlation with the chemical structures has been studied only little. This is partly due to the complexity of such an experimental test that embraces a plethora of different biological effects and mechanisms of action, making (Q)SAR studie...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci8001974

    authors: Mazzatorta P,Estevez MD,Coulet M,Schilter B

    更新日期:2008-10-01 00:00:00

  • Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures.

    abstract::To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercial...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900068k

    authors: Nichols SE,Domaoal RA,Thakur VV,Tirado-Rives J,Anderson KS,Jorgensen WL

    更新日期:2009-05-01 00:00:00

  • Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields.

    abstract::Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its h...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00287

    authors: Machireddy B,Kalra G,Jonnalagadda S,Ramanujachary K,Wu C

    更新日期:2017-11-27 00:00:00

  • Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs.

    abstract::Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00695

    authors: Burggraaff L,van Veen A,Lam CC,van Vlijmen HWT,IJzerman AP,van Westen GJP

    更新日期:2020-10-26 00:00:00

  • Gas-phase and solution conformations of selected dimeric structural units of heparin.

    abstract::The molecular structure of four dimeric units (D-E, E-F, F-G, and G-H) of the DEFGH structural unit of heparin, their anionic forms, and their sodium salts have been studied using the B3LYP/6-31+G(d) method. The optimized geometries indicate that the most stable structure of these dimeric units in neutral state is sta...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci060060+

    authors: Remko M,von der Lieth CW

    更新日期:2006-07-01 00:00:00

  • Symplectic molecular dynamics simulations on specially designed parallel computers.

    abstract::We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050216q

    authors: Borstnik U,Janezic D

    更新日期:2005-11-01 00:00:00