Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1

[1]  Jiahui Chen,et al.  Improvements to the APBS biomolecular solvation software suite , 2017, Protein science : a publication of the Protein Society.

[2]  Christopher L. McClendon,et al.  Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery. , 2017, Journal of chemical theory and computation.

[3]  G. Groth,et al.  Novel Protein-Protein Inhibitor Based Approach to Control Plant Ethylene Responses: Synthetic Peptides for Ripening Control , 2017, Front. Plant Sci..

[4]  D. Veprintsev,et al.  High-throughput mutagenesis using a two-fragment PCR approach , 2017, Scientific Reports.

[5]  H. Gohlke,et al.  Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase , 2017, Scientific Reports.

[6]  L. Chong,et al.  Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide. , 2016, The journal of physical chemistry letters.

[7]  G. Groth,et al.  Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening , 2016, Scientific Reports.

[8]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[9]  A. Contini,et al.  An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides. , 2016, Journal of chemical theory and computation.

[10]  Anna N. Stepanova,et al.  Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2 , 2015, Cell.

[11]  Mingzhe Li,et al.  EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis , 2015, Cell.

[12]  G. Groth,et al.  Targeting Plant Ethylene Responses by Controlling Essential Protein-Protein Interactions in the Ethylene Pathway. , 2015, Molecular plant.

[13]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[14]  A. Roitberg,et al.  Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. , 2015, Journal of chemical theory and computation.

[15]  H. Mertens,et al.  Structural Model of the Cytosolic Domain of the Plant Ethylene Receptor 1 (ETR1) , 2014, The Journal of Biological Chemistry.

[16]  He Huang,et al.  Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent , 2014, Journal of the American Chemical Society.

[17]  Holger Gohlke,et al.  Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase. , 2014, Journal of molecular biology.

[18]  Dawei Sun,et al.  AAscan, PCRdesign and MutantChecker: A Suite of Programs for Primer Design and Sequence Analysis for High-Throughput Scanning Mutagenesis , 2013, PloS one.

[19]  Holger Gohlke,et al.  Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion , 2013, J. Chem. Inf. Model..

[20]  Daniel R Roe,et al.  PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.

[21]  Holger Gohlke,et al.  Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function , 2013, J. Chem. Inf. Model..

[22]  Carlos Simmerling,et al.  Improved Generalized Born Solvent Model Parameters for Protein Simulations. , 2013, Journal of chemical theory and computation.

[23]  D. Braun,et al.  Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions. , 2013, Methods.

[24]  Matteo Dal Peraro,et al.  Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations , 2013, PLoS Comput. Biol..

[25]  Robert J. Schmitz,et al.  Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas , 2012, Science.

[26]  Hongwei Guo,et al.  Activation of ethylene signaling is mediated by nuclear translocation of the cleaved EIN2 carboxyl terminus , 2012, Cell Research.

[27]  G. Groth,et al.  Cloning, expression and purification of orthologous membrane proteins: a general protocol for preparation of the histidine sensor kinase ETR1 from different species , 2012, Molecular membrane biology.

[28]  Yang Zhang,et al.  Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. , 2011, Biophysical journal.

[29]  Dieter Braun,et al.  Molecular interaction studies using microscale thermophoresis. , 2011, Assay and drug development technologies.

[30]  G. Groth,et al.  New paradigm in ethylene signaling , 2011, Plant signaling & behavior.

[31]  Dieter Braun,et al.  Protein-binding assays in biological liquids using microscale thermophoresis. , 2010, Nature communications.

[32]  G. G. Sanwal,et al.  RIPENING OF CLIMACTERIC FRUITS AND THEIR CONTROL , 2010 .

[33]  José Mario Martínez,et al.  PACKMOL: A package for building initial configurations for molecular dynamics simulations , 2009, J. Comput. Chem..

[34]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[35]  J. Ecker,et al.  Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. , 2009, Genes & development.

[36]  Mazen Ahmad,et al.  Mechanism of fast peptide recognition by SH3 domains. , 2008, Angewandte Chemie.

[37]  Caren Chang,et al.  Heteromeric Interactions among Ethylene Receptors Mediate Signaling in Arabidopsis* , 2008, Journal of Biological Chemistry.

[38]  K. Harter,et al.  Subcellular localization and in vivo interactions of the Arabidopsis thaliana ethylene receptor family members. , 2008, Molecular plant.

[39]  C. Perez-Iratxeta,et al.  K2D2: Estimation of protein secondary structure from circular dichroism spectra , 2008, BMC Structural Biology.

[40]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[41]  B. Bukau,et al.  Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. coli , 2007, BMC biotechnology.

[42]  R. Mannella,et al.  Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms. , 2007, The Journal of chemical physics.

[43]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[44]  Qian Liu,et al.  Receptor Signal Output Mediated by the ETR1 N Terminus Is Primarily Subfamily I Receptor Dependent1[W] , 2006, Plant Physiology.

[45]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[46]  Brad M. Binder,et al.  Short-Term Growth Responses to Ethylene in Arabidopsis Seedlings Are EIN3/EIL1 Independent1 , 2004, Plant Physiology.

[47]  Brad M. Binder,et al.  Arabidopsis Seedling Growth Response and Recovery to Ethylene. A Kinetic Analysis1 , 2004, Plant Physiology.

[48]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[49]  B. Binder,et al.  A Model for Ethylene Receptor Function and 1-Methylcyclopropene Action , 2003 .

[50]  J. Kieber,et al.  Localization of the Raf-like Kinase CTR1 to the Endoplasmic Reticulum of Arabidopsis through Participation in Ethylene Receptor Signaling Complexes* , 2003, Journal of Biological Chemistry.

[51]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

[52]  X. Qu,et al.  Mutational Analysis of the Ethylene Receptor ETR1. Role of the Histidine Kinase Domain in Dominant Ethylene Insensitivity1 , 2002, Plant Physiology.

[53]  Leslie A Kuhn,et al.  Protein unfolding: Rigidity lost , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Y. Gho,et al.  Highly sensitive and fast protein detection with Coomassie brilliant blue in sodium dodecyl sulfate-polyacrylamide gel electrophoresis , 2002 .

[55]  D. Jacobs,et al.  Protein flexibility predictions using graph theory , 2001, Proteins.

[56]  Eric Jones,et al.  SciPy: Open Source Scientific Tools for Python , 2001 .

[57]  N. Sreerama,et al.  Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. , 2000, Analytical biochemistry.

[58]  J. Ecker,et al.  Ethylene signaling: from mutants to molecules. , 2000, Current opinion in plant biology.

[59]  Liam J. McGuffin,et al.  The PSIPRED protein structure prediction server , 2000, Bioinform..

[60]  G. Klebe,et al.  Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.

[61]  A. Bleecker,et al.  Ethylene: a gaseous signal molecule in plants. , 2000, Annual review of cell and developmental biology.

[62]  N. Sreerama,et al.  Estimation of the number of α‐helical and β‐strand segments in proteins using circular dichroism spectroscopy , 2008, Protein science : a publication of the Protein Society.

[63]  J. Ecker,et al.  EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. , 1999, Science.

[64]  W. C. Johnson,et al.  Analyzing protein circular dichroism spectra for accurate secondary structures , 1999, Proteins.

[65]  J R Ecker,et al.  EIN4 and ERS2 Are Members of the Putative Ethylene Receptor Gene Family in Arabidopsis , 1998, Plant Cell.

[66]  Jian Hua,et al.  Ethylene Responses Are Negatively Regulated by a Receptor Gene Family in Arabidopsis thaliana , 1998, Cell.

[67]  S. L. Mayo,et al.  Automated design of the surface positions of protein helices , 1997, Protein science : a publication of the Protein Society.

[68]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[69]  E. Meyerowitz,et al.  Ethylene insensitivity conferred by Arabidopsis ERS gene. , 1995, Science.

[70]  E. Meyerowitz,et al.  Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators. , 1993, Science.

[71]  N. Sreerama,et al.  A self-consistent method for the analysis of protein secondary structure from circular dichroism. , 1993, Analytical biochemistry.

[72]  Joseph R. Ecker,et al.  CTR1, a negative regulator of the ethylene response pathway in arabidopsis, encodes a member of the Raf family of protein kinases , 1993, Cell.

[73]  Ali S. Hadi,et al.  Finding Groups in Data: An Introduction to Chster Analysis , 1991 .

[74]  M. Estelle,et al.  Insensitivity to Ethylene Conferred by a Dominant Mutation in Arabidopsis thaliana , 1988, Science.

[75]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[76]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[77]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[78]  S. Provencher,et al.  Estimation of globular protein secondary structure from circular dichroism. , 1981, Biochemistry.