Comprehensive Density Functional Theory Study on the Mechanism of Activation of the Nonapeptide Hormone Oxytocin by Metal Ions

Bicyclopeptides: a new class of ligands for Cu(II) ions

There is growing interest in bicyclic peptides among scientists. This group of compounds has more advantageous properties than monocyclic ligands and their application in medicine and biological sciences is possible. It is known that sometimes the presence of metal ions is crucial for the activity of peptides in biological systems, like in the case of oxytocin or vasopressin. Therefore, in this study, we performed a series of experiments with the new bicyclic peptide c(PKKHP-c(CFWKTC)-PKKH) (BCL) that was designed and synthesized by a fully automated induction-assisted solid phase synthesizer. We analyzed the coordination abilities of BCL relative to copper(II) ions. The new bicyclic peptide contains two histidine moieties, separated by proline residues, with two distinct sites for metal ion coordination. The obtained results showed that in all analyzed systems both mono- and dinuclear complexes are formed.

Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure

To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

Analysis of argentinated peptide complexes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: Peptide = oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, neurotensin

RATIONALE

The increased use of silver nanoparticles (AgNPs) for various biological applications, and over-expression of various peptide receptors in different tumors/cancer cells, necessitate the need for dedicated investigations on the intrinsic binding ability of Ag with various biologically important peptides for better understanding of AgNPs-peptide interactions and for the future development of contrasting agents as well as drugs for imaging/biomedical applications.

METHODS

The [M+(Ag)n ](+) complexes are prepared and characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS).

RESULTS

Silver complexes of the peptides [M+(Ag)n ](+) , where M = oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, and neurotensin, have been investigated for their intrinsic Ag(+) -binding ability. Unusual binding of up to seven Ag(+) with these small peptides is observed. The mass spectra show n = 1-5 for bombesin and somatostatin, n = 1-6 for bradykinin and arg(8) -vasopressin, and n = 1-7 for oxytocin and neurotensin. In addition, oxytocin and arg(8) -vasopressin show the formation of dimers and their complexes [M2 +(Ag)n ](+) with n = 1-8 and n = 1-5, respectively. The possible amino acid residues responsible for Ag(+) binding in each peptide have been identified on the basis of density functional theory (DFT)-calculated binding energy values of Ag(+) towards individual amino acids.

CONCLUSIONS

Mass spectrometric evidence indicates that the peptides, viz., oxytocin, arg(8) -vasopressin, bradykinin, bombesin, somatostatin, and neurotensin, show greater affinity for Ag(+) . Hence, they may be used as carriers for AgNPs in targeted drug delivery as well as an alternative for iodinated contrasting agents in dual energy X-ray imaging techniques. Radio-labeled Ag with these peptides can also be used in radio-pharmaceuticals for diagnostic and therapeutic applications. Copyright © 2016 John Wiley & Sons, Ltd.

Colorimetric response of dithizone product and hexadecyl trimethyl ammonium bromide modified gold nanoparticle dispersion to 10 types of heavy metal ions: understanding the involved molecules from experiment to simulation

A new kind of analytical reagent, hexadecyl trimethyl ammonium bromide (CTAB), and dithizone product-modified gold nanoparticle dispersion, is developed for colorimetric response to 10 types of heavy metal ions (M(n+)), including Cr(VI), Cr(3+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+), and Pb(2+). The color change of the modified gold nanoparticle dispersion is instantaneous and distinct for Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+), and Pb(2+). The color change results from the multiple reasons, such as electronic transitions, cation-π interactions, formation of coordination bonds, and M(n+)-induced aggregation of gold nanoparticles (AuNPs). The different combining capacity of heavy metal ions to modifiers results in the different broadening and red-shifting of the plasmon peak of modified AuNPs. In addition, Cr(VI), Cu(2+), Co(2+), Ni(2+), and Mn(2+) cause the new UV-vis absorption peaks in the region of 360-460 nm. The interactions between the modifiers and AuNPs, and between the modifiers and M(n+), are investigated by using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. The results confirm that AuNPs are modified by CTAB and dithizone products through electrostatic interactions and Au-S bonds, respectively, and the M(n+)-N bonds form between M(n+) and dithizone products. Furthermore, the experimental and density functional theory calculated IR spectra prove that dithizone reacts with NaOH to produce C6H5O(-) and [SCH2N4](2-). The validation of this method is carried out by analysis of heavy metal ions in tap water.

Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid

On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.

A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion

The present study analyzed binding of Cu²⁺ to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches including electron correlation effects. In order to shed light on the character of interactions between Cu²⁺ and peptides, which are expected to be mainly electrostatic in nature, decomposition of interaction energy into physically meaningful components was applied.

A rapid and sensitive colorimetric assay method for Co2+ based on the modified Au nanoparticles (NPs): understanding the involved interactions from experiments and simulations

We previously reported a colorimetric assay method for Co(2+) based on the thioglycolic acid (TGA) functionalized hexadecyl trimethyl ammonium bromide (CTAB) modified Au NPs. However, the detection limit of 3×10(-7) M was still higher than that of the sanitary standard for drinking water (6.8×10(-8) M). In addition, the interactions between the modifier and Au NPs, and between the modifier-Au NPs and Co(2+) remain to be clarified and confirmed. Thus, in the present study, the modified Au NPs solution was dialyzed and its detection limit was optimized to be 5×10(-10) M. The interactions between the modifier and Au NPs, and between the modifier-Au NPs and Co(2+) were investigated in both experimental characterizations and theoretical calculations, consistently confirming that the Au NPs were modified by the negatively charged anions of [SCH(2)CO(2)](2-) through Au-S bonds and Co(2+) was recognized by the modifier-Au NPs through Co-O chelate bonds. The results of X-ray photoelectron spectroscopy (XPS) suggest that there were no chemical bonds formed between CTAB and Co(2+). Moreover, the colorimetric assay of Co(2+) using the modified Au NPs has been proved to be a rapid, very sensitive and highly selective method. The validation of the method was carried out by analysis of a certified reference material, GSBZ 50030-94.

Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures

Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides.