Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site

Giosia, Matteo Di; Marforio, Tainah Dorina; Cantelli, Andrea; Valle, Francesco; Zerbetto, Francesco; Su, Qianqian; Wang, Haifang; Calvaresi, Matteo

doi:10.1016/j.jcis.2020.03.034

Cited by 25 publications

(19 citation statements)

References 85 publications

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“…Concurrently, the larger the contact area between the amino acid side chain and the C 60 , the larger the stabilizing effect due to vdW interactions (dispersion forces). Shape complementarity represents a quick way to estimate both the stabilizing van der Waals and hydrophobic interactions between proteins and carbon nanomaterials [ 21 , 45 , 62 , 63 ].…”

Section: Resultsmentioning

confidence: 99%

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Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Marforio

Calza

Mattioli

et al. 2021

IJMS

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Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol−1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C60 was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C60 binding.

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Section: Resultsmentioning

confidence: 99%

“…The Ramachandran plots and FES were obtained using MDAnalysis software [ 63 , 64 ]. The analysis of distances and angles in the MD trajectories was carried out by CPPTRAJ [ 67 ], as implemented in AMBER 16.…”

Section: Methodsmentioning

confidence: 99%

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Marforio

Calza

Mattioli

et al. 2021

IJMS

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“…If CNTs bind to the catalytic site of the protein, the protein is inhibited. [62] If the active site of the protein is located away from the interaction area with the CNT, the protein remains active. [44] A docking procedures was used to determine the geometry of the complex formed by LZ and (6,5)CNT.…”

Section: Resultsmentioning

confidence: 99%

Green Fabrication of (6,5)Carbon Nanotube/Protein Transistor Endowed with Specific Recognition

Berto

Giosia

Giordani

et al. 2021

Adv Elect Materials

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will attenuate their invasiveness, yielding a reduced reaction of the living organism against a foreign object: the main visible effects are the enhancement of the signalto-noise ratio, and higher spatio-temporal resolution. The ultimate progress from bioelectronics to nano-bioelectronics [5,6] will exploit nanowires, low-dimensional materials, and nanostructured carbon allotropes such as carbon nanotubes (CNTs). These promising candidates for high performing transducers are characterized by outstanding electronic properties. [7][8][9][10][11][12][13][14][15][16][17] In particular, the interest for CNTs as biosensor components [18][19][20][21][22][23][24][25][26] is further supported by their exceptional electrical performances, even at small applied potentials (<1 V). CNT-field-effect transistor-based biosensors have shown great potential for ultrasensitive biomarker detection despite the presence of important challenges, which include difficulty in stable functionalization, incompatibility with scalable fabrication, and nonuniform performance. [27] A crucial challenge lies in the CNTs insolubility both in water and in organic solvents and in their high tendency to aggregate that hinder their wide applicability. Methods enabling their processability are strongly needed.A general single-step approach is introduced for the green fabrication of hybrid biosensors from water dispersion. The resulting device integrates the semiconducting properties of a carbon nanotube (CNT) and the functionality of a protein. In the initial aqueous phase, the protein (viz., lysozyme [LZ]) disperses the (6,5)CNT. Drop-casting of the dispersion on a test pattern (a silicon wafer with interdigitated Au source and drain electrodes) yields a fully operating, robust, electrolyte-gated transistor (EGT) in one step. The EGT response to biorecognition is then assessed using the LZ inhibitor N-acetyl glucosamine trisaccharide. Analysis of the output signal allows one to extract a protein-substrate binding constant in line with values reported for the free (without CNT) system. The methodology is robust, easy to optimize, redirectable toward different targets and sets the grounds for a new class of CNT-protein biosensors that overcome many limitations of the technology of fabrication of CNT biosensors.

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“…AFM imaging allows us to directly visually analyse labelling stoichiometry at the level of the individual molecules. Close contact with a hard substrate surface can severely affect protein viability and function (Giosia et al ., 2020). It is, therefore, essential to test the effects of the conjugation process on protein activity in order to be able to interpret protein interactions correctly (Andreeva et al ., 2020).…”

Section: Resultsmentioning

confidence: 99%

Atomic force microscopy as an imaging tool to study the bio/nonbio complexes

Bednarikova

Gažová

Valle

et al. 2020

Journal of Microscopy

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Atomic force microscopy (AFM) besides X-ray crystallography and electron microscopy is one of the most attractive methods to study bio/nonbio complexes. Information on how biomacromolecules interact with nanomaterials under different environmental conditions has important implications for the practice of nanomedicine and concerning the safety of nanomaterials. These complexes cover a broad range both in terms of stability and composition. AFM offers a wealth of structural and functional data about such assemblies. The variety of samples investigated using AFM in biology includes nanometre-sized proteins, lipids, DNA, amyloid fibrils, as well as larger objects such as cells. Herein we choose to review the significance of AFM to study various biological aspects of selected assemblies. We have focused on the exploitation of AFM operating in the air. The presented AFM research offers a unique and often unexpected insight into the structure and function of the bio/nonbio complexes.

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Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site

Cited by 25 publications

References 85 publications

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Green Fabrication of (6,5)Carbon Nanotube/Protein Transistor Endowed with Specific Recognition

Atomic force microscopy as an imaging tool to study the bio/nonbio complexes

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