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1. Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides

Author:
Bansal, Rachit; Care, Andrew; Lord, Megan S.; Walsh, Tiffany R.; Sunna, Anwar
Source:
New biotechnology 2019 v.52 pp. 9-18
ISSN:
1871-6784
Subject:
binding capacity,   etc   ; nanobiotechnology; peptides;     Show all 3 Subjects
Abstract:
... The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been ...
DOI:
10.1016/j.nbt.2019.04.001

2. Post-assembly Modification of Phosphine Cages Controls Host–Guest Behavior

Author:
McTernan, Charlie T.; Ronson, Tanya K.; Nitschke, Jonathan R.
Source:
Journal of the American Chemical Society 2019 v.141 no.17 pp. 6837-6842
ISSN:
1520-5126
Subject:
binding capacity,   etc   ; methylation; oxidation; phosphine;     Show all 4 Subjects
Abstract:
... We report the design, synthesis, and post-assembly modification of a new phosphine-paneled supramolecular cage framework, the anion binding ability of which can be modified rationally through selective post-assembly functionalization. The parent phosphine-paneled cage can be modified in situ through oxidation, methylation, or auration. These covalent and coordinative modifications to the exterior ...
DOI:
10.1021/jacs.9b02604

3. An Allosteric Switch Primes Sequence-Specific DNA Recognition

Author:
Walker, Matthew J.; Varani, Gabriele
Source:
Cell 2019 v.176 no.1-2 pp. 4-6
ISSN:
0092-8674
Subject:
binding capacity,   etc   ; DNA; DNA-binding proteins; enzymes;     Show all 4 Subjects
Abstract:
... Regulation of protein-DNA binding specificity occurs through myriad mechanisms. Boudet et al. discover yet a new form of specificity through allosteric regulation, an ATP-induced structural switch that mediates specific DNA recognition in an archaeoeukaryotic primase. ...
DOI:
10.1016/j.cell.2018.12.020

4. Donor–acceptor-type supramolecular polymers on the basis of preorganized molecular tweezers/guest complexation

Author:
Han, Yifei; Tian, Yukui; Li, Zijian; Wang, Feng
Source:
Chemical Society reviews 2018 v.47 no.14 pp. 5165-5176
ISSN:
1460-4744
Subject:
binding capacity,   etc   ; chemical interactions; polymers;     Show all 3 Subjects
Abstract:
... The bottom-up self-assembly of donor–acceptor (D–A) units has received tremendous attention in recent years. Charge-transfer interactions, which are inherently embedded in D–A pairs, have suffered from some disadvantages such as erratic arrangements and weak binding affinity, thus hampering the precise arrangement of D–A units into long-range-ordered supramolecular polymers. To address this issue, ...
DOI:
10.1039/c7cs00802c

5. The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus

Author:
Ren, Jingshan; Nettleship, Joanne E.; Harris, Gemma; Mwangi, William; Rhaman, Nahid; Grant, Clare; Kotecha, Abhay; Fry, Elizabeth; Charleston, Bryan; Stuart, David I.; Hammond, John; Owens, Raymond J.
Source:
Molecular immunology 2019 v.112 pp. 123-130
ISSN:
0161-5890
Subject:
binding capacity,   etc   ; Bovine orthopneumovirus; antibodies; antibody binding sites; antigens; cattle;     Show all 6 Subjects
Abstract:
... Cattle antibodies have unusually long CDR3 loops in their heavy chains (HCs), and limited light chain (LC) diversity, raising the question of whether these mask the effect of LC variation on antigen recognition. We have investigated the role of the LC in the structure and activity of two neutralizing cattle antibodies (B4 and B13) that bind the F protein of bovine respiratory syncytial virus (bRSV ...
DOI:
10.1016/j.molimm.2019.04.026

6. Monodisperse hollow-shell structured molecularly imprinted polymers for photocontrolled extraction α-cyclodextrin from complex samples

Author:
Fan, Haoran; Wang, Jinpeng; Meng, Qingran; Jin, Zhengyu
Source:
Food chemistry 2019 v.281 pp. 1-7
ISSN:
0308-8146
Subject:
binding capacity,   etc   ; adsorption; alpha-cyclodextrin; mass transfer; polymers;     Show all 5 Subjects
Abstract:
... In present study, monodisperse photoresponsive hollow-shell structured molecularly imprinted polymers (PHSMIPs) were fabricated based on surface imprinting technique and first proposed for selective recognition and adsorption of α-cyclodextrin (α-CD) from complex samples. The structure and the binding properties of PHSMIPs and photoresponsive surface molecularly imprinted polymers (PSMIPs) were co ...
DOI:
10.1016/j.foodchem.2018.12.084

7. Tunable regulatory activities of 1,10-phenanthroline derivatives towards acid sphingomyelinase and Zn(ii)–amyloid-β

Author:
YiThese authors contributed equally to this work., Yelim; Han, Jiyeon; Park, Min Hee; Park, Nahye; Nam, Eunju; Jin, Hee Kyung; Bae, Jae-sung; Lim, Mi Hee
Source:
Chemical communications 2019 v.55 no.42 pp. 5847-5850
ISSN:
1364-548X
Subject:
binding capacity,   etc   ; Alzheimer disease; brain; chemical reactions; enzymes; hydrophobicity; zinc;     Show all 7 Subjects
Abstract:
... We report a new series of small molecules able to achieve the tunability of modulatory activities against acid sphingomyelinase (ASM) and Zn(ii)-bound amyloid-β [Zn(ii)–Aβ], two pathological targets found in the brain affected by Alzheimer's disease. Rational tuning of the hydrophobicity and Zn(ii) binding affinity of the 1,10-phenanthroline (phen) framework successfully yielded compounds as chemi ...
DOI:
10.1039/c9cc01005j

8. Recognition and protection of glycosphingolipids by synthetic nanoparticle receptors

Author:
Gunasekara, Roshan W.; Zhao, Yan
Source:
Chemical communications 2019 v.55 no.33 pp. 4773-4776
ISSN:
1364-548X
Subject:
binding capacity,   etc   ; chemical compounds; glycosphingolipids; hydroxylation; nanoparticles; receptors;     Show all 6 Subjects
Abstract:
... Nanoparticle receptors were synthesized through micellar imprinting to bind glycosphingolipids with 20–140 μM binding affinities, meanwhile distinguishing glycan composition, the number of acyl chains, and hydroxylation of acyl chains in the lipids. The strong binding enabled the receptors to protect their target glycolipids dispersed in lipid membranes from enzymatic degradation. ...
DOI:
10.1039/c9cc01694e

9. The interaction of dietary flavonoids with xanthine oxidase in vitro: molecular property-binding affinity relationship aspects

Author:
Yuan, Mengmeng; Liu, Yi; Xiao, Aiping; Leng, Juan; Liao, Liping; Ma, Lei; Liu, Liangliang
Source:
RSC advances 2019 v.9 no.19 pp. 10781-10788
ISSN:
2046-2069
Subject:
binding capacity,   etc   ; chemical bonding; glycosylation; hydrogenation; hydroxylation; methylation; xanthine oxidase;     Show all 7 Subjects
Abstract:
... The molecular property–affinity relationships of dietary flavonoids binding to xanthine oxidase were investigated in vitro by comparing the binding constants obtained from a fluorescence-quenching method. The inhibitions of dietary flavonoids on xanthine oxidase were also investigated and analyzed, revealing that the binding process was influenced by the structural differences of the flavonoids un ...
DOI:
10.1039/c8ra09926j

10. Double strand DNA functionalized Au@Ag Nps for ultrasensitive detection of 17β-estradiol using surface-enhanced raman spectroscopy

Author:
Pu, Hongbin; Xie, Xiaohui; Sun, Da-Wen; Wei, Qingyi; Jiang, Yingfen
Source:
Talanta 2019 v.195 pp. 419-425
ISSN:
0039-9140
Subject:
binding capacity,   etc   ; DNA; Raman spectroscopy; estradiol; nanoparticles; oligonucleotides;     Show all 6 Subjects
Abstract:
... A detection method for 17β-estradiol (E2) using surface-enhanced Raman scattering (SERS)-based aptamer sensor was presented. Raman reporter molecule Cy3 labeled E2-aptamer and DNA functionalized gold-silver core-shell nanoparticles (Au@Ag CS NPs) offered SERS with high sensitivity and selectivity. Based on the fabricated double strand DNA-immobilized gold-silver core-shell nanoparticles (Au@Ag NPs ...
DOI:
10.1016/j.talanta.2018.10.021

11. Structures, photoresponse properties and DNA binding abilities of 4-(4-pyridinyl)-2-pyridone salts

Author:
Mandal, Tripti; Dey, Arka; Pathak, Sudipta; Islam, Md. Maidul; Konar, Saugata; Ortega-Castro, Joaquín; Seth, Saikat Kumar; Ray, Partha Pratim; Frontera, Antonio; Mukhopadhyay, Subrata
Source:
RSC advances 2019 v.9 no.17 pp. 9663-9677
ISSN:
2046-2069
Subject:
binding capacity,   etc   ; DNA; crystal structure; electrical conductivity; perchlorates; photosensitivity; spectroscopy;     Show all 7 Subjects
Abstract:
... Three salts [perchlorate (2), chloride (3) and tetrafluoroborate (4)] were synthesized from a 1-(2-aminoethyl)-6-hydroxy-2-oxo-1,2-dihydro-[4,4′-bipyridine]-3,5-dicarbonitrile compound (1) and characterized by spectroscopic and single crystal X-ray diffraction methods. Various noncovalent interactions (e.g., anion⋯π⁺, π⋯π, lp⋯π) are explored in the solid state crystal structure of the salts. Optic ...
DOI:
10.1039/c9ra00666d

12. Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations

Author:
Bekker, Gert-Jan; Araki, Mitsugu; Oshima, Kanji; Okuno, Yasushi; Kamiya, Narutoshi
Source:
TheJournal of physical chemistry 2019 v.123 no.11 pp. 2479-2490
ISSN:
1520-5207
Subject:
binding capacity,   etc   ; Gibbs free energy; amyloid; drugs; enzymes; molecular dynamics;     Show all 6 Subjects
Abstract:
... A medium-sized and highly flexible inhibitor to the enzyme β-secretase 1 (BACE), which produces the amyloid β-peptide by cleavage of its precursor protein, was dynamically docked into the large and wide catalytic cleft of BACE that binds to the amyloid-precursor by employing multicanonical molecular dynamics (McMD) simulations. We applied our method to predict the native binding configuration and ...
DOI:
10.1021/acs.jpcb.8b12419

13. ELTA: Enzymatic Labeling of Terminal ADP-Ribose

Author:
Ando, Yoshinari; Elkayam, Elad; McPherson, Robert Lyle; Dasovich, Morgan; Cheng, Shang-Jung; Voorneveld, Jim; Filippov, Dmitri V.; Ong, Shao-En; Joshua-Tor, Leemor; Leung, Anthony K.L.
Source:
Molecular cell 2019 v.73 no.4 pp. 845-856.e5
ISSN:
1097-2765
Subject:
binding capacity,   etc   ; DNA; RNA; fluorescence; peptides; polymers; proteins;     Show all 7 Subjects
Abstract:
... ADP-ribosylation refers to the addition of one or more ADP-ribose groups onto proteins. The attached ADP-ribose monomers or polymers, commonly known as poly(ADP-ribose) (PAR), modulate the activities of the modified substrates or their binding affinities to other proteins. However, progress in this area is hindered by a lack of tools to investigate this protein modification. Here, we describe a ne ...
DOI:
10.1016/j.molcel.2018.12.022

14. Synthesis of neuraminidase-resistant sialoside-modified three-way junction DNA and its binding ability to various influenza viruses

Author:
Yamabe, Miyuki; Fujita, Akira; Kaihatsu, Kunihiro; Ebara, Yasuhito
Source:
Carbohydrate research 2019 v.474 pp. 43-50
ISSN:
0008-6215
Subject:
binding capacity,   etc   ; DNA; Orthomyxoviridae; binding sites; glycosides; hemagglutinins; sialidase; viruses;     Show all 8 Subjects
Abstract:
... Natural sialic acid-modified compounds are capable of targeting influenza virus hemagglutinin (HA). However, these compounds have limited inhibitory effect because natural O-glycoside bond in these compounds are prone to be cleaved by neuraminidase (NA) on the surface of viruses. In this study, we synthesized NA-resistant sialoside that included unnatural S-glycoside bonds and modified this sialos ...
DOI:
10.1016/j.carres.2019.01.008

15. Dynamic Supramolecular Hydrogels Spanning an Unprecedented Range of Host–Guest Affinity

Author:
Zou, Lei; Braegelman, Adam S.; Webber, Matthew J.
Source:
ACS applied materials & interfaces 2019 v.11 no.6 pp. 5695-5700
ISSN:
1944-8252
Subject:
binding capacity,   etc   ; crosslinking; encapsulation; hydrogels; macrocyclic compounds; materials science;     Show all 6 Subjects
Abstract:
... Cucurbit[7]uril (CB[7]) macrocycles exhibit a broad range of host–guest binding affinity. Attaching pendant CB[7] and complementary guests on 8-arm PEG macromers affords supramolecular hydrogels with cross-link affinity spanning more than 5 orders of magnitude (1.5 × 10⁷ to 5.4 × 10¹² M–¹) without changing network topology. Cross-link affinity translates directly to bulk dynamic properties; hydrog ...
DOI:
10.1021/acsami.8b22151

16. New opportunities in synthetic macrocyclic arenes

Author:
Wu, Jia-Rui; Yang, Ying-Wei
Source:
Chemical communications 2019 v.55 no.11 pp. 1533-1543
ISSN:
1364-548X
Subject:
binding capacity,   etc   ; aromatic hydrocarbons; chemical communication; chemical reactions; geometry; receptors;     Show all 6 Subjects
Abstract:
... Synthetic macrocyclic receptors generally display unique geometries, preorganized cavities, and tunable binding affinities, which facilitate their application in numerous fields including molecular recognition and self-assembly. Calix[n]arenes and pillar[n]arenes are very prevalent synthetic macrocyclic arenes, whose syntheses, host–guest properties, and supramolecular functions have been intensiv ...
DOI:
10.1039/c8cc09374a

17. Multivalent Recognition at Fluid Surfaces: The Interplay of Receptor Clustering and Superselectivity

Author:
Dubacheva, Galina V.; Curk, Tine; Frenkel, Daan; Richter, Ralf P.
Source:
Journal of the American Chemical Society 2019 v.141 no.6 pp. 2577-2588
ISSN:
1520-5126
Subject:
binding capacity,   etc   ; ligands; mathematical models; physicochemical properties; prediction; receptors;     Show all 6 Subjects
Abstract:
... The interaction between a biological membrane and its environment is a complex process, as it involves multivalent binding between ligand/receptor pairs, which can self-organize in patches. Any description of the specific binding of biomolecules to membranes must account for the key characteristics of multivalent binding, namely, its unique ability to discriminate sharply between high and low rece ...
DOI:
10.1021/jacs.8b12553

18. Comparison of systematically functionalized heterogeneous and homogenous glycopolymers as toxin inhibitors

Author:
Martyn, Benjamin; Biggs, Caroline I.; Gibson, Matthew I.
Source:
Journal of polymer science 2019 v.57 no.1 pp. 40-47
ISSN:
0887-624X
Subject:
binding capacity,   etc   ; cholera toxin; glycosylation; lectins; monosaccharides; polymers; polysaccharides; therapeutics;     Show all 8 Subjects
Abstract:
... Multivalent glycosylated polymers and particles display enhanced binding affinity toward lectins compared to individual glycans. The design of glycopolymers with selectivity toward pathogen‐associated lectins (toxins) for sensing or in antiadhesion therapy is complicated due to lectins having promiscuous binding profiles and can be considered to be pattern recognition “readers,” with the capabilit ...
DOI:
10.1002/pola.29279

19. PKA-dependent phosphorylation of IP3K-A at Ser119 regulates a binding affinity with EB3

Author:
Mo, Seo Jung; Cho, Yongsang; Choi, Byung-il; Lee, Dongmin; Kim, Hyun
Source:
Biochemical and biophysical research communications 2019 v.508 no.1 pp. 52-59
ISSN:
0006-291X
Subject:
binding capacity,   etc   ; cAMP-dependent protein kinase; microtubules; neurons; phosphorylation;     Show all 5 Subjects
Abstract:
... Microtubule-associated end-binding protein 3 (EB3) accumulates asymmetrically at the tip-end of growing microtubules, providing a central platform for linking various cellular components. EB3 orchestrates microtubule dynamics and targeting, enabling diverse processes within neurons. Inositol 1, 4, 5-trisphosphate 3-kinase A (IP3K-A; also known as ITPKA) is a neuron-enriched protein that binds to m ...
DOI:
10.1016/j.bbrc.2018.11.042

20. Adsorption and recovery of phosphate from water by amine fiber, effects of co-existing ions and column filtration

Author:
Wei, Jinshan; Meng, Xiaoguang; Wen, Xianghua; Song, Yonghui
Source:
Journal of environmental sciences (China) 2020 v.87 pp. 123-132
ISSN:
1001-0742
Subject:
binding capacity,   etc   ; Fourier transform infrared spectroscopy; adsorption; calcium; carbonates; desorption; filtration; fluorides; hydrochloric acid; hydroxyapatite; ions; nitrates; pH; scanning electron microscopes; sulfates; tap water;     Show all 16 Subjects
Abstract:
... A weak-base adsorption fiber, acrylic amine fiber (AAF), was prepared for removal and recovery of phosphate from water. The adsorption properties of the AAF for phosphate and effects of co-existing ions were investigated using batch and column filtration experiments, scanning electron microscope, and Fourier transform infrared techniques. Experimental results showed that AAF had a high phosphate a ...
DOI:
10.1016/j.jes.2019.05.009