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Analyzing nanomaterial bioconjugates: a review of current and emerging purification and characterization techniques.

The interaction of proteins in living cells is one of the key processes in the maintenance of their homeostasis Introduction of additional agents into the chain of these interactions may influence homeostatic processes Recent advances in nanotechnologies have led to a wide use of nanoparticles (NPs) in industrial and biomedical applications NPs are small enough to enter almost all compartments of the body, including cells and organelles, and to complicate the pattern of protein interactions In some cases, interaction of nanoscale objects with proteins leads to hazardous consequences, such as abnormal conformational changes leading to exposure of cryptic peptide epitopes or the appearance of abnormal functions caused by structural modifications In addition, the high local protein concentration resulting from protein adsorption on NPs may provoke avidity effects arising from close spatial repetition of the same protein Finally, the interaction of NPs with proteins is known to induce cooperative effect

Molecular Interaction of Proteins and Peptides with Nanoparticles

Antimicrobial peptides (AMPs) are crucial effectors of the innate immune system. They provide the first line of defense against a variety of pathogens. AMPs display synergistic effects with conventional antibiotics, and thus present the potential for combined therapies. Insects are extremely resistant to bacterial infections. Insect AMPs are cationic and comprise less than 100 amino acids. These insect peptides exhibit an antimicrobial effect by disrupting the microbial membrane and do not easily allow microbes to develop drug resistance. Currently, membrane mechanisms underlying the antimicrobial effects of AMPs are proposed by different modes: the barrel-stave mode, toroidal-pore, carpet, and disordered toroidal-pore are the typical modes. Positive charge quantity, hydrophobic property and the secondary structure of the peptide are important for the antibacterial activity of AMPs. At present, several structural families of AMPs from insects are known (defensins, cecropins, drosocins, attacins, diptericins, ponericins, metchnikowins, and melittin), but new AMPs are frequently discovered. We reviewed the biological effects of the major insect AMPs. This review will provide further information that facilitates the study of insect AMPs and shed some light on novel microbicides.

Insect Antimicrobial Peptides, a Mini Review.

Effect of gold nanoparticle morphology on adsorbed protein structure and function.

Effect of surface concentration on secondary and tertiary conformational changes of lysozyme adsorbed on silica nanoparticles.

Nanoparticles possess unique properties as a result of their large surface area per unit volume and therefore can be functionalized by the immobilization of enzymes for a variety of biosensing applications. Changes in the tertiary conformation of beta-lactoglobulin adsorbed on 90 nm silica nanoparticles with time were inferred using tryptophan fluorescence and Fourier transform infrared spectroscopy (FTIR) for different surface concentrations, temperature, pH, ionic strength, and 2,2,2-trifluoroethanol (TFE) and dithiothreitol (DTT) concentrations. Rapid initial unfolding followed by a much slower rate at longer times was observed, with the extent of unfolding being higher at lower surface concentrations, higher ionic strengths, higher temperature, higher TFE and DTT concentrations, and pI. The effect of temperature on the unfolding of adsorbed protein on the nanoparticle surface was similar to that in the bulk even though the extent of unfolding was higher for adsorbed protein molecules. The results of the extent of change in tertiary conformation using FTIR as indicated by the change in the ratio of amide II'/amide I were consistent with those obtained by tryptophan fluorescence whereas the rates of conformational changes given by FTIR were found to be much faster. Circular dichroism (CD) spectra showed that altering the surface concentration by itself did not change the secondary structure of beta-lactoglobulin on the surface. TFE was found to increase the alpha helix content at the expense of the fraction of the beta sheet, whereas the beta sheet was converted to an unordered conformation in the presence of DTT.

Characterization of secondary and tertiary conformational changes of beta-lactoglobulin adsorbed on silica nanoparticle surfaces.

Characterization of antimicrobial activity against Listeria and cytotoxicity of native melittin and its mutant variants.

A coarse-grain (CG) algorithm is developed for molecular dynamics (MD) simulation of proteins in which the polypeptide backbone as well as side chains were mapped into spherical interaction centres. The force field parameters for non-bonded interaction between these centres (beads) were evaluated from the interaction of all atoms corresponding to these beads using pairwise additivity. The validity of CG algorithm was demonstrated by comparing the potential energy, radius of gyration (RG), end-to-end distance and root-mean-square deviation with those obtained by all-atom (AA) simulation for a small protein molecule Trp-cage as well as for lysozyme in solution. The CG simulation for lysozyme in solution requires less than 1/50 CPU-time compared to that for the AA method. Also, the CG method converges to equilibrium potential energy much faster than AA simulation. CG simulation for lysozyme adsorbed on silica surface showed that the molecule is more unfolded with a less compact tertiary structure compared to...

Coarse grain molecular dynamics simulation for the prediction of tertiary conformation of lysozyme adsorbed on silica surface

Explicit solvent molecular dynamics (MD) simulation was carried out for the antimicrobial peptides (i) Cecropin P1 and C-terminus cysteine modified Cecropin P1 (Cecropin P1 C) in solution, (ii) Cecropin P1 and Cecropin P1 C adsorbed onto coesite −Si − O − and Si − O − H surfaces, and (iii) Cecropin P1 C tethered to coesite −Si − O − surface with either (PEO)3 or (PEO)6 linker. Low energy structures for Cecropin P1 and Cecropin P1 C in solution consists of two regions of high α helix probability with a sharp bend, consistent with the available structures of other antimicrobial peptides. The structure of Cecropin P1 C at low ionic strength of 0.02 M exhibits two regions of high α helix probability (residues AKKLEN and EGI) whereas at higher ionic strength of 0.12 M, the molecule was more compact and had three regions of higher α helix probability (residues TAKKLENSA, ISE, and AIQG) with an increase in α helical content from 15.6% to 18.7% as a result of shielding of electrostatic interactions. In the presence of Cecropin P1 C in the vicinity of −Si − O − surface, there is a shift in the location of two peaks in H − O − H density profile to larger distances (2.95 A and 7.38 A compared to 2.82 A and 4.88 A in the absence of peptide) with attenuated peak intensity. This attenuation is found to be more pronounced for the first peak. H-bond density profile in the vicinity of −Si − O − surface exhibited a single peak in the presence of Cecropin P1 C (at 2.9 A) which was only slightly different from the profile in the absence of polypeptide (2.82 A) thus indicating that Cecropin P1 C is not able to break the H-bond formed by the silica surface. The α helix probability for different residues of adsorbed Cecropin P1 C on −Si − O − surface is not significantly different from that of Cecropin P1 C in solution at low ionic strength of 0.02 M whereas there is a decrease in the probability in the second (residues ISE) and third (residues AIQG) α helical regions at higher ionic strength of 0.12 M. Though the total α helical content of adsorbed and tethered Cecropin P1 C was lower for hydrophilic Si − O − H surface compared to hydrophobic −Si − O −, hydrophobicity of the surface did not significantly affect the α helix probability of different residues. The conformation of Cecropin P1 C in solution is closer to that of tethered to −Si − O − with (PEO)6 than that tethered with (PEO)3 as a result of less surface interaction of tethered polypeptide with a longer linker. At low ionic strength of 0.02 M, tethered Cecropin P1 C to −Si − O − is found to exhibit lower α helix (13.0%) compared to adsorbed (15.6%) for (PEO)3 linker with this difference being insignificant for larger (PEO)6 linker molecule. Experimental values of % α helix inferred from circular dichroism spectra of Cecropin P1 in solution as well as in adsorbed state on silica surface compared well with the corresponding values obtained from MD simulation thereby validating the simulation procedure.

Xiaoyu Wu

Papers

Effect of surface concentration on secondary and tertiary conformational changes of lysozyme adsorbed on silica nanoparticles.

Characterization of secondary and tertiary conformational changes of beta-lactoglobulin adsorbed on silica nanoparticle surfaces.

Characterization of antimicrobial activity against Listeria and cytotoxicity of native melittin and its mutant variants.

Coarse grain molecular dynamics simulation for the prediction of tertiary conformation of lysozyme adsorbed on silica surface

Effect of interaction with coesite silica on the conformation of Cecropin P1 using explicit solvent molecular dynamics simulation