Keyword search (4,164 papers available)

"interactions" Keyword-tagged Publications:

Title Authors PubMed ID
1 The temperate forest phyllosphere and rhizosphere microbiome: a case study of sugar maple Enea M; Beauregard J; De Bellis T; Faticov M; Laforest-Lapointe I; 39881993
BIOLOGY
2 Cortical-subcortical interactions underlie processing of auditory predictions measured with 7T fMRI Ara A; Provias V; Sitek K; Coffey EBJ; Zatorre RJ; 39087881
PSYCHOLOGY
3 Parental autonomy support in relation to preschool aged children's behavior: Examining positive guidance, negative control, and responsiveness Linkiewich D; Martinovich VV; Rinaldi CM; Howe N; Gokiert R; 33691509
EDUCATION
4 Exploring the effects of anthropogenic disturbance on predator inspection activity in Trinidadian guppies Brusseau AJP; Feyten LEA; Crane AL; Brown GE; 38476138
BIOLOGY
5 An intensive longitudinal investigation of maternal and infant touching patterns across context and throughout the first 9-months of life Mercuri M; Stack DM; De France K; Jean ADL; Fogel A; 37337452
CRDH
6 Respiratory sinus arrhythmia, negative social interactions, and fluctuations in unmet interpersonal needs: A daily diary study MacNeil S; Renaud J; Gouin JP; 37208985
PSYCHOLOGY
7 Maternal and infant touching behaviours during perturbed interactions: Associations with maternal depressive symptomatology and infant crying Mercuri M; Stack DM; Mantis I; Moszkowski R; Field TM; 36758294
CRDH
8 Mutualistic coevolution and community diversity favour persistence in metacommunities under environmental changes Cosmo LG; Sales LP; Guimarães PR; Pires MM; 36629106
BIOLOGY
9 Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses Cuesta S; Burdisso P; Segev A; Kourrich S; Sperandio V; 36323315
CSBN
10 Evidence of an intracellular interaction between the Escherichia coli enzymes EntC and EntB and identification of a potential electrostatic channeling surface Ouellette S; Pakarian P; Bin X; Pawelek PD; 35952947
CHEMBIOCHEM
11 Assessing effects of predator density and diversity on neophobia in Trinidadian guppies Feyten LEA; Demers EEM; Ramnarine IW; Brown GE; 35907447
BIOLOGY
12 On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review Martínez RF; Cuccia LA; Viedma C; Cintas P; 35796896
CHEMBIOCHEM
13 Regional variation drives differences in microbial communities associated with sugar maple across a latitudinal range De Bellis T; Laforest-Lapointe I; Solarik KA; Gravel D; Kembel SW; 35412652
BIOLOGY
14 Cryptic eco-evolutionary feedback in the city Carly D Ziter 35238028
BIOLOGY
15 Evaluation of Lanthanide-Doped Upconverting Nanoparticles for in Vitro and in Vivo Applications Samhadaneh DM; Mandl GA; Han Z; Mahjoob M; Weber SC; Tuznik M; Rudko DA; Capobianco JA; Stochaj U; 35025434
CNSR
16 Defensive Traits during White Spruce (Picea glauca) Leaf Ontogeny Antoine-Olivier Lirette 34357304
BIOLOGY
17 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2 Nguyen K; Chakraborty S; Mansbach RA; Korber B; Gnanakaran S; 34067878
PHYSICS
18 Improved Parent-Child Interactions Predict Reduced Internalizing Symptoms Among the Offspring of Parents with Bipolar Disorder Undergoing a Prevention Program: A Proof-of-Concept Study Serravalle L; Iacono V; Wilson AL; Orlando MA; Tsekova V; Ellenbogen MA; 33544277
CRDH
19 O6-Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron. Copp W, Wilds CJ 32543755
CHEMBIOCHEM
20 Sender and receiver experience alters the response of fish to disturbance cues. Goldman JA, Feyten LEA, Ramnarine IW, Brown GE 32440286
BIOLOGY
21 Eating Disorders, Heredity and Environmental Activation: Getting Epigenetic Concepts into Practice. Steiger H, Booij L 32375223
PSYCHOLOGY
22 Top-down and bottom-up controls on an herbivore on a native and introduced plant in a tropical agricultural landscape. Despland E, Santacruz PG 32206453
BIOLOGY
23 Diversity, evolution, and classification of virophages uncovered through global metagenomics. Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC 31823797
BIOLOGY
24 Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains Orabi EA; Davis RL; Lamoureux G; 31652004
CERMM
25 Subunit orientation in the Escherichia coli enterobactin biosynthetic EntA-EntE complex revealed by a two-hybrid approach. Pakarian P, Pawelek PD 27086082
CHEMBIOCHEM
26 Chemogenomic Profiling of the Fungal Pathogen Candida albicans. Chen Y, Mallick J, Maqnas A, Sun Y, Choudhury BI, Côte P, Yan L, Ni TJ, Li Y, Zhang D, Rodríguez-Ortiz R, Lv QZ, Jiang YY, Whiteway M 29203491
BIOLOGY
27 Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Muñoz G, Kissling WD, van Loon EE 30692868
BIOLOGY
28 The evolutionary rewiring of the ribosomal protein transcription pathway modifies the interaction of transcription factor heteromer Ifh1-Fhl1 (interacts with forkhead 1-forkhead-like 1) with the DNA-binding specificity element. Mallick J, Whiteway M 23625919
BIOLOGY

 

Title:Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains
Authors:Orabi EADavis RLLamoureux G
Link:https://pubmed.ncbi.nlm.nih.gov/31652004/
DOI:10.1002/jcc.26084
Publication:Journal of computational chemistry
Keywords:Cation-πinteractionsDrude polarizable force fieldab initio calculationsalkali metal ionsbinding free energyquaternary ammonium ions
PMID:31652004 Category:J Comput Chem Date Added:2019-10-28
Dept Affiliation: CERMM
1 Department of Chemistry, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
2 Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
3 Department of Chemistry and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, New Jersey, 08102.
4 Centre for Research in Molecular Modeling (CERMM), Concordia University, Montréal, Québec, H4B 1R6, Canada.

Description:

Cation-p interactions play important roles in molecular recognition and in the stability and function of proteins. However, accurate description of the structure and energetics of cation-p interactions presents a challenge to both additive and polarizable force fields, which are rarely designed to account for the complexation of charged groups with aromatic moieties. We calibrate the Drude polarizable force field for complexes of alkali metal ions (Li+ , Na+ , K+ , Rb+ , Cs+ ), ammonium (NH4+ ), tetramethylammonium (TMA+ ), and tetraethylammonium (TEA+ ) with aromatic amino acid side chain model compounds (benzene, toluene, 4-methylphenol, 3-methylindole) using high-level ab initio quantum chemical properties of these complexes. Molecular dynamics simulations reveal that cation-p complexes of the hard and tightly coordinated Li+ and Na+ ions are not stable in water but that larger ions form stable complexes, with binding free energies ranging between -0.8 and -2.9 kcal/mol. Like in gas phase, all complexes at equilibrium adopt an "en-face" complexation mode in water. The optimized Drude polarizable model provides an accurate description of the cation-p interactions involving small ions and proteins. © 2019 Wiley Periodicals, Inc.





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